title: Larval Reference, biological rep 3

city: Nashville

first: David

last: Miller

state: TN

address: 465 21st Avenue South

department: Cell and Developmental Biology

institute: Vanderbilt University

description: Gene expression data from all wildtype mid-L2 nematode cells

hyb_protocol: affymetrix

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

data_processing:
Microarray data were processed as described [8, 33]. Briefly, intensity values from each hybridization were scaled vs a global average signal from the same array and normalized by Robust Multichip Average analysis (RMA) [34].  To identify differentially expressed transcripts, normalized intensity values from the Pan-neural data sets were compared to a Reference (from all larval cells) using Significance Analysis of Microarray software (SAM) [35].  A two-class unpaired analysis of the data was performed to identify neuron-enriched genes. Pan-neural enriched transcripts in the IVT and WT-Pico-derived data set were defined as 1.5X elevated vs the Reference at a False Discovery Rate (FDR) = 3%. An earlier report describing the IVT-amplified Pan-neural data set utilized a more stringent FDR of 1% and therefore identified a smaller number of Pan-neural enriched transcripts (1,562 vs 1,592 in this study) (Von Stetina et al. Watson et al. 2007).
Annotation was performed as previously described using WormBase Release 170 (WS170.wormbase.org).  Affymetrix GeneChip Operating Software (GCOS) was used to calculate the average number of present calls in for each probe set (Table 1) [25].  Present calls listed in Table 2 and used to calculate Fig. 6 were identified with a perl script (consensus.pl) (Additional Data File 10). For a given sample (e.g. IVT Pan-neural) a transcript was scored “present” if it was called present in all replicates. For Fig 6., RMA-normalized intensities for these present genes were averaged across all replicates.  Average Pan-neural/Reference intensities were calculated for WT-Pico and IVT data and log2 transformed.  The coefficient of determination (R2) for the resulting scatter plot was calculated in Microsoft Excel.  Mismatch (MM) intensities were compared against Perfect Match (PM) intensities for both Pan-neural and reference and samples using the Bioconductor [36] Affy package [36] for Fig 3 .   RMA normalized intensity values for all datasets were imported into GeneSpring GX 7.3 (http://www.chem.agilent.com/scripts/pds.asp?lpage=27881) to generate the line graphs shown in Fig 7.  Each Experimental dataset was normalized vs the average intensity value for each probe set in the corresponding Reference data set and plotted as log (Experimental/Reference). Each vertical line represents an individual replicate for each Experimental sample.    p-values for total yield, number of present genes, and perfect vs mismatch probes were calculated using a two-tailed t-test with unequal variance.  3’ bias analysis   IVT-only and WT-Pico only enriched transcripts were examined for 3’ bias.  C_elegans_target.fa was downloaded from Affymetrix.  This file contains the reference sequence for each probeset on the array.  The file Caenorhabditis_elegans.WB170.45.dna.seqlevel.fa was downloaded from Ensembl (Ensembl 45, based on Wormbase 170).  Probesets were aligned to chromosomes using BLAT [31].  Where multiple alignments were found, the alignment that covered the longest portion of the probeset sequence was chosen.  The genes and chromosomal locations of those genes were downloaded using Ensembl 45.  The probeset distance from the 3’ end of the gene was calculated.  For genes on the (+) strand, the distance is given as (Gene End) – (Probeset End).  For genes on the (-) strand, the distance is given as (Probeset Start) – (Gene Start).  For probesets that correspond to multiple genes, the gene with the smallest absolute value of 3’ distance was chosen.  p value was calculated using a 2-tailed t-test with equal variance.

organism: Caenorhabditis elegans

source_name: WT-Pico amplified RNA obtained from all cells by performing a control IP

label_protocol: A 2-round IVT protocol (modified from the Affymetrix small-sample protocol) was used to convert 25ng of RNA into biotinylated aRNA (described in Von Stetina, Watson, et al 2007).  For WT-Pico, 2 ng of these RNAs was amplified using version 1 of the WT-Ovation Pico System, which combines WT-Ovation™ Pico RNA Amplification System and target preparation according to fragmentation and labeling section of Ovation™ Biotin RNA Amplification and Labeling System as described in the respective User Guides (http://www.nugeninc.com/html/04_technical_resources1.html)

growth_protocol: A synchronized population of larvae was obtained by the following method.  Gravid adults expressing either F25B3.3::FLAG::PAB-1 (pan-neural) or unc-4::FLAG::PAB-1 (A-class) transgenes were subjected to bleach/NaOH treatment to release embryos. Embryos were harvested and allowed to hatch o/n in M9 liquid. Hatched L1 larvae were harvested and placed on plates containing food to restart development. After 22-24hr, when >80% of larvae had reached the mid-L2 stage, larvae were harvested for RNA extraction.

extract_protocol: For mRNA-tagging samples, following elution/crosslink, RNAs were isolated by TriZOL extraction and isopropanol precipitation (following manufacturer's protocol).

treatment_protocol: For mRNA-tagging samples, synchronized L2 larvae were fixed in 0.5% formaldehyde, homogenized by passing through a French press (6000 psi on minicell) and using a Dounce homogenizer, and the cell-free extract isolated after a low-speed and high-speed spin. The FLAG-PAB bound RNA was isolated by immunoprecipitating with anti-FLAG antibodies, reversing the crosslink in a Tris buffer at 65 degrees Celcius, and TriZOL extracted.

tag: Wildtype (N2 isolate) nematodes


title: Recovery from freezing (60 min) 2nd

status: Public on Nov 01 2007

type: RNA

city: Tsukuba

first: Emiko

last: Kitagawa

state: Ibaraki

address: Onogawa 16-1

country: Japan

institute: National Institute of Advanced Industrial Science and Technology

description: Data with flag value 0 were used for LOWESS normalization processing.

hyb_protocol: Hybridized for 16-18 h at 65 C

scan_protocol: Scan Array 4000 (PerkinElmer Japan Co., Ltd) was used for scanning. Array images were analyzed with Gene Pix Pro 4.0 (Axon Instrument).

data_processing: GeneSpring ver 7.3.1 (Agilent Technologies Inc.)

molecule: polyA RNA

organism: Saccharomyces cerevisiae

source_name: Recovery from freezing (60 min), Cy5

label_protocol: At least 4 µg of mRNA and a 0.4 µM oligo dT12-17 primer (GIBCO BRL; Life Technologies) were denatured at 70 ºC for 5 min, and the labeled cDNA was synthesized.  The reaction mixture contained 0.5 mM each of dATP, dGTP, and dCTP; 0.2 mM dTTP (GIBCO BRL; Life Technologies); 15 mM Cy5-labeled dUTP (PE Applied Biosystems); 200 units of PowerScript Reverse Transcriptase (CLONTEC, Palo Alto, CA); and an appropriate buffer and RNase inhibiter (GIBCO BRL; Life Technologies).  The reactions were performed at 42 ºC for 1h and 30 min.  Another 200 units of transcriptase was added in the tubes 40 min after the beginning of reverse transcription.  The template mRNA was dissolved by the addition of 0.5 N NaOH for 1 h at 65 ºC.  After neutralization with 1 M Tris-HCl, Cy3- and Cy5-labeled cDNA solution was mixed and filtered on Microcon 30 (AMICON).

growth_protocol: Yeast strain S288C was grown until the exponential phase (A660, 1.0) in 600 ml YPD medium in a 3 L Erlenmeyer flask at 30 °C. An aliquot of 400 ml in a 3 L Erlenmeyer flask was frozen at −80 C without the addition of a cryoprotectant, and stored for 1 week. The frozen cell culture was then thawed at 30 °C in a water-bath for 25 min. The thawed cells were further incubated and an aliquot of 100 ml was sampled from the culture at 60 min after complete thawing.

extract_protocol: Hot-phenol and oligotex dt mRNA purification kit (TaKaRa)

treatment_protocol: Recovery from freezing (60 min)

tag: strain S288C

source_name: control (before freezing treatment), Cy3

label_protocol: At least 4 µg of mRNA and a 0.4 µM oligo dT12-17 primer (GIBCO BRL; Life Technologies) were denatured at 70 ºC for 5 min, and the labeled cDNA was synthesized.  The reaction mixture contained 0.5 mM each of dATP, dGTP, and dCTP; 0.2 mM dTTP (GIBCO BRL; Life Technologies); 15 mM Cy3-labeled dUTP (PE Applied Biosystems); 200 units of PowerScript Reverse Transcriptase (CLONTEC, Palo Alto, CA); and an appropriate buffer and RNase inhibiter (GIBCO BRL; Life Technologies).  The reactions were performed at 42 ºC for 1h and 30 min.  Another 200 units of transcriptase was added in the tubes 40 min after the beginning of reverse transcription.  The template mRNA was dissolved by the addition of 0.5 N NaOH for 1 h at 65 ºC.  After neutralization with 1 M Tris-HCl, Cy3- and Cy5-labeled cDNA solution was mixed and filtered on Microcon 30 (AMICON).

growth_protocol: Yeast strain S288C was grown until the exponential phase (A660, 1.0) in 600 ml YPD medium in a 3 L Erlenmeyer flask at 30 °C. An aliquot of 200 ml was taken from the cell culture and used as the control without freezing.

treatment_protocol: before freezing treatment


title: Recovery from freezing (30 min) 2nd

source_name: Recovery from freezing (30 min), Cy5

growth_protocol: Yeast strain S288C was grown until the exponential phase (A660, 1.0) in 600 ml YPD medium in a 3 L Erlenmeyer flask at 30 °C. An aliquot of 400 ml in a 3 L Erlenmeyer flask was frozen at −80 C without the addition of a cryoprotectant, and stored for 1 week. The frozen cell culture was then thawed at 30 °C in a water-bath for 25 min. The thawed cells were further incubated and an aliquot of 100 ml was sampled from the culture at 30 min after complete thawing.

treatment_protocol: Recovery from freezing (30 min)


title: Recovery from freezing (30 min) 3rd


title: Larval Reference, biological rep 2

country: USA

label: biotin

molecule: total RNA


title: Recovery from freezing (15 min) 2nd

source_name: Recovery from freezing (15 min), Cy5

growth_protocol: Yeast strain S288C was grown until the exponential phase (A660, 1.0) in 600 ml YPD medium in a 3 L Erlenmeyer flask at 30 °C. An aliquot of 400 ml in a 3 L Erlenmeyer flask was frozen at −80 C without the addition of a cryoprotectant, and stored for 1 week. The frozen cell culture was then thawed at 30 °C in a water-bath for 25 min. The thawed cells were further incubated and an aliquot of 100 ml was sampled from the culture at 15 min after complete thawing.

treatment_protocol: Recovery from freezing (15 min)


title: 67-68-5 Dimethylsulfoxide 4th

source_name: DMSO treated for 2 h, Cy5

growth_protocol: Saccharomyces cerevisiae strain S288C was grown in YPD medium (2% polypeptone, 1% yeast extract, 2% glucose) at 25 C with shaking. Chemical solution was added into OD=1 (exponential growing) culture (final concentration; 10 %=1.41 M) then the yeast cells were exposed for 2 h.

treatment_protocol: dimethylsulfoxide (Wako, 043-07216)

source_name: control (without treatment), Cy3

growth_protocol: Saccharomyces cerevisiae strain S288C was grown in YPD medium (2% polypeptone, 1% yeast extract, 2% glucose) at 25 C with shaking until OD=1, then grown for 2 h without any treatment.

treatment_protocol: without treatment


title: Larval Reference, biological rep 1


title: Larval Pan-neural, biological rep 4

description: Gene expression data from all wildtype mid-L2 nematode neurons

source_name: WT-Pico amplified RNA obtained from all neurons after co-IP from F25B3.3::FLAG::PAB-1 transgenic

tag: F25B3.3::FLAG::PAB-1 transgenic


title: Recovery from freezing (15 min) 3rd


title: 7553-56-2 Iodine, 0.5 mM 2 h (dose-response) 2nd L

description: In order to rescue data that had a higher intensity than the scanning range, the array were scanned twice with different laser power. This data were result from low power scanning. Data with flag value 0 were used for LOWESS normalization processing, although original raw data were remaining in this table. Merging high and low scanned data were done on the GeneSpring and represented as “AVG_VALUE”.

source_name: Iodine treated with 0.5 mM for 2 h, Cy5

growth_protocol: Saccharomyces cerevisiae strain S288C was grown in YPD medium (2% polypeptone, 1% yeast extract, 2% glucose) at 25 C with shaking. Chemical solution were added into OD=1 (exponential growing) culture with 0.5 mM (final concentration) then the yeast cells were exposed for 2 h.

treatment_protocol: Iodine (Wako 095-00392). An iodine solution (0.5 M) was prepared just before use as 12.7 g iodine and 25 g iodide in 100 ml solution


title: GM08729-U133B, biological rep1

city: Gainesville

first: bilian

last: jin

state: FL

address: 1601 SW Archer Road

institute: University of Florida

description: Gene expression data from GM08729 LCL

hyb_protocol: Following fragmentation, 10 ug of cRNA was hybridized for 16 hr at 45C on GeneChip Human Genome U133A and U133B Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

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

organism: Homo sapiens

source_name: Homo Sapiens GM08729

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

growth_protocol: ICF LCLs were grown in RPMI1640 media supplemented with 2 mM L-glutamine  and 20% heat-inactivated fetal bovine serum;Normal LCLs were grown in the same media except 10% fetal bovine serum was used.

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

treatment_protocol: Cells were harvested when 70-80% confluency.

tag: Genotype

value: DNMT 3B wild type and mutation

tag: normal


title: Larval Pan-neural, biological rep 5


title: Supress under 40 MPa 25 C 4th L

source_name: Supress under 40 MPa 25 C, Cy5

growth_protocol: For the pressure shock treatment, 200 ml of yeast culture, at an exponential growth phase (A660=1.0), was transferred into a 30 or 50 ml syringe. These syringes were pressed with 40 MPa in the 30-11HF4 (High Pressure Equipment Co.) at 25 C for 2 h. After decompression, the cells were harvested by centrifugation.

treatment_protocol: Growing cell under 40 MPa 25 C

source_name: control (before pressure treatment), Cy3

growth_protocol: 200 ml of yeast culture, at an exponential growth phase (A660=1.0), was harvested by centrifugation.

treatment_protocol: before pressure treatment


title: Human Ntera2, me3K27 Promoter 2 Array, 99684

type: genomic

city: Davis

first: Kimberly

middle: Rose

last: Blahnik

state: CA

address: GBSF 1 Shields Ave

department: Genome and Biomedical Sciences

institute: University of California Davis

description: Human Ntera2 cells

hyb_protocol: The hybridization of DNA samples for ChIP-ChIP analysis was performed by NimbleGen Systems, Inc. Briefly, 13ug of the Cy5-labeled ChIP sample and 13ug of the Cy3-labeled total sample were mixed, dried down, and resuspended in 40 ul of NimbleGen Hybridization Buffer (NimbleGen Systems) plus 1.5 ug of human COT1 DNA. After denaturation, hybridization was carried out in a MAUI Hybridization System (BioMicro Systems) for 18 h at 42°C. The arrays were washed using NimbleGen Wash Buffer System (NimbleGen Systems), dried by centrifugation.

scan_protocol: The arrays were scanned at 5-um resolution using the GenePix 4000B scanner (Axon Instruments).

data_processing: log base 2 ratios

molecule: genomic DNA

source_name: Ntera2 cells

label_protocol: The labeling of DNA samples for ChIP-ChIP analysis was performed by NimbleGen Systems, Inc. Briefly, each DNA sample (1 ug) was denatured in the presence of 5'-Cy3- or Cy5-labeled random nonamers (TriLink Biotechnologies) and incubated with 100 units (exo-) Klenow fragment (NEB) and dNTP mix [6 mM each in TE buffer (10 mM Tris/1 mM EDTA, pH 7.4; Invitrogen)] for 2 h at 37°C. Reactions were terminated by addition of 0.5 M EDTA (pH 8.0), precipitated with isopropanol, and resuspended in water.

extract_protocol: Performed following the 'Chromatin Immunoprecipitation Assay (ChIPs)' protocol provided at http://genomics.ucdavis.edu/farnham

label_protocol: see labeling protocol for channel 1

extract_protocol: see extract protocol for channel 1

tag: control total input


title: Larval Pan-neural, biological rep 3


title: Supress under 40 MPa 25 C 4th H

description: In order to rescue data that had a higher intensity than the scanning range, the array were scanned twice with different laser power. This data were result from high power scanning. Data with flag value 0 were used for LOWESS normalization processing, although original raw data were remaining in this table. Merging high and low scanned data were done on the GeneSpring and represented as “AVG_VALUE”.


title: Human Ntera2, SUZ12 Promoter 2 Array, 97985

description: Human Ntera2 cells


title: Human Ntera2, SUZ12 Promoter 2 Array, 97983

description: Human Ntera2 cells


title: Larval Pan-neural, biological rep 2


title: Supress under 40 MPa 25 C 3rd


title: Recovery from 180 MPa 4C 5th H

source_name: Recovery from 180 MPa 4C, Cy5

growth_protocol: For the pressure shock treatment, 200 ml of yeast culture, at an exponential growth phase (A660=1.0), was centrifuged and resuspended in 10 ml YPD medium in a 10 ml syringe. These syringes were pressed with 180 MPa. To achieve pressurization, we used the wp3000 (High Pressure Equipment Co., USA). During the treatment, the temperature was maintained by an ice-water bath. After decompression, the cells were resuspended in 200 ml fresh YPD medium and incubated for 1 h at 25°C. The yeast cells were then centrifuged and washed in distilled water before storage at −80°C.

treatment_protocol: Recovery from 180 MPa 4C

source_name: control (without pressure treatment), Cy3

growth_protocol: For the control cells, 200 ml of yeast culture, at an exponential growth phase (A660=1.0), was centrifuged and resuspended in 10 ml YPD medium in a 10 ml syringe. These syringes were kept under 0.1 MPa in ice-water bath. The cells were resuspended in 200 ml fresh YPD medium and incubated for 1 h at 25°C. The yeast cells were then centrifuged and washed in distilled water before storage at −80°C.

treatment_protocol: without pressure treatment


title: 3-day-old TJ1090 worms with skn-1 RNAi & oxidative stress (SO2)

city: Boulder

first: Sang-Kyu

last: Park

state: CO

department: IBG

institute: University of Colorado at Boulder

description: Gene chip hybridization and scanning were done at Genome Explorations (Memphis, MN) and the University of Colorado at Boulder Gene Chip Core Facility (Boulder, CO).

hyb_protocol: Following fragmentation, 15 microg of cRNA were hybridized to the Affymetrix GeneChip C. elegans Genome Array according to the protocols provided by the manufacturer.

scan_protocol: GeneChips were scanned using the Affymetrix GCS3000 7G high resolution laser scanner.

data_processing: The data were background corrected and summarized with MAS 5.0 using Affymetrix GCOS v1.4 software (Affymetrix, Santa Clara, CA). The normalization target (TGT) was set to 250.

label: Biotin

source_name: skn-1 RNAi worms with oxidative stress (SO2)

label_protocol: Biotinylated cRNA were prepared by the RT-IVT method from 10 microg total RNA using the BioArray-High-Yield-RNA-Transcript-Labeling-Kit (Enzo, Farmingdale, NY).

extract_protocol: Worms were harvested by washing off plates with S-basal and quick frozen in liquid nitrogen.  Total RNA was prepared using TRIZOL reagent and standard protocols and cleaned up on Qiagen RNeasy columns.

tag: Strain

tag: Gender

value: hermaphrodite

tag: Age

value: 3 days old


title: 3-day-old TJ1090 worms with skn-1 RNAi & oxidative stress (SO3)

source_name: skn-1 RNAi worms with oxidative stress (SO3)


title: Recovery from 180 MPa 4C 5th L


title: Human Ntera2, me3K27 Promoter 2 Array, 99685

description: Human Ntera2 cells


title: 3-day-old TJ1090 worms with skn-1 RNAi & oxidative stress (SO1)

source_name: skn-1 RNAi worms with oxidative stress (SO1)


title: Recovery from 180 MPa 4C 3rd


title: Larval Pan-neural, biological rep 1


title: 3-day-old TJ1090 worms with oxidative stress (O4)

source_name: control worms with oxidative stress (O4)


title: 40465-66-5 Round up hi-load herbicide 1st

source_name: Round up treated for 2 h, Cy5

growth_protocol: Saccharomyces cerevisiae strain S288C was grown in YPD medium (2% polypeptone, 1% yeast extract, 2% glucose) at 25 C with shaking. Chemical solution was added into OD=1 (exponential growing) culture with 1500 times dilution then the yeast cells were exposed for 2 h.

treatment_protocol: Round up hi-loadTM herbicide (Monsanto company, MON77692)


title: 3-day-old TJ1090 worms with oxidative stress (O3)

source_name: control worms with oxidative stress (O3)


title: 3-day-old TJ1090 worms without any stress (C4)

source_name: control worms without any stress (C4)


title: 3-day-old TJ1090 worms with oxidative stress (O1)

source_name: control worms with oxidative stress (O1)


title: Human Ntera2, KAP1 Promoter 2 Array, 94916

description: Human Ntera2 cells


title: 3-day-old TJ1090 worms with oxidative stress (O2)

source_name: control worms with oxidative stress (O2)


title: Human Ntera2, me3K9 Promoter 2 Array, 94567

description: Human Ntera2 cells


title: 1897-45-6 TPN 3rd

source_name: TPN treated for 2 h, Cy5

growth_protocol: Saccharomyces cerevisiae strain S288C was grown in YPD medium (2% polypeptone, 1% yeast extract, 2% glucose) at 25 C with shaking. 40 ul of 50 mM chemical stock solution were added into 200 ml OD=1 (exponential growing) culture (final concentration; 10 uM) then the yeast cells were exposed for 2 h.

treatment_protocol: TPN Standard (Wako 200-06581)

source_name: control (without treatment), Cy3


title: Recovery from freezing (60 min) 1st

source_name: Recovery from freezing (60 min), Cy5

source_name: control (before freezing treatment), Cy3


title: 23513-14-6 Gingerol 2nd

source_name: Gingerol treated for 2 h, Cy5

growth_protocol: Saccharomyces cerevisiae strain S288C was grown in YPD medium (2% polypeptone, 1% yeast extract, 2% glucose) at 25 C with shaking. Chemical solution was added into OD=1 (exponential growing) culture (final concentration; 400 ppm) then the yeast cells were exposed for 2 h.

treatment_protocol: Gingerol (Nacalai tesque, 16739-86)


title: Recovery from freezing (15 min) 1st

source_name: Recovery from freezing (15 min), Cy5


title: Recovery from freezing (30 min) 1st

source_name: Recovery from freezing (30 min), Cy5


title: Human Ntera2, KAP1 Promoter 2 Array, 94918

description: Human Ntera2 cells

source_name: Ntera2 cells


title: 12122-67-7 Zineb 1st

source_name: Zineb treated for 2 h, Cy5

growth_protocol: Saccharomyces cerevisiae strain S288C was grown in YPD medium (2% polypeptone, 1% yeast extract, 2% glucose) at 25 C with shaking. 20 ul of 2 % chemical stock solution were added into 200 ml OD=1 (exponential growing) culture (final concentration; 2 ppm) then the yeast cells were exposed for 2 h.

treatment_protocol: Zineb Standard (Wako, 266-00783)


title: 3-day-old TJ1090 worms without any stress (C1)

source_name: control worms without any stress (C1)


title: Recovery from 180 MPa 4C 2nd

source_name: Recovery from 180 MPa 4C, Cy5

source_name: control (without pressure treatment), Cy3


title: 3-day-old TJ1090 worms without any stress (C2)

source_name: control worms without any stress (C2)


title: 87-86-5 Pentachlorophenol 1st

source_name: PCP treated for 2 h, Cy5

growth_protocol: Saccharomyces cerevisiae strain S288C was grown in YPD medium (2% polypeptone, 1% yeast extract, 2% glucose) at 25 C with shaking. 200 ul of 50 mM chemical stock solution were added into 200 ml OD=1 (exponential growing) culture (final concentration; 50 uM) then the yeast cells were exposed for 2 h.

treatment_protocol: Pentachlorophenol (Nacalai tesque, 262-28)


title: ventral marginal zone explant

city: Bethesda

first: Hui

last: Zhao

state: MD

address: 9000 Rockville Pike

department: NICHD

institute: NIH

description: gene expression in ventral marginal zone of stage 10 Xenopus embryo

hyb_protocol: 2.2 micrograms of labeled cDNA in a volume of 200 microliters was hybridized to the Affymetrix Xenopus Genecip in a standard Affymetrix Probe Array Cartridge at 45 degrees , using the fluidics protocol EukGE-WS2v4_450 of a Fluidics Station 450 (Affymetrix) for 18hrs.

scan_protocol: the hybridized chip was scanned by Affymetrix GeneChip Scanner 3000 and then processed with Genechip Operating Software.

data_processing: Hybridiation controls (bioB, bioC, BioD) and oligo B2 were examined to check the quality of the assay. GAPDH and B-actin were used as the internal control to check 3' to 5' ratios. Global scaling was employed for analysis and the target Intensity value (TGT) was set as 500 following the manual form Affymetrix. Genechip Operating Software (Affymetrix) was used to create CEL files from each experiment and further generate Chip file.

organism: Xenopus laevis

source_name: ventral marginal zone explant from stage 10 Xenopus embryo

label_protocol: Biotinylated probe was prepared from 100 ng total RNA using the OVATION RNA amplification system (Nugen Technologies, Inc)

extract_protocol: The dissected explants were homogenized in Stat 60 (TEL TEST), RNA was precipitated by isopropanol, treated with DNase I, and purified using the RNeasy kit (Qiagen).

tag: the ventral marginal zone explant contained ventral marginal zone and a ventral portion of the yolk plug.


title: Recovery from 180 MPa 4C 1st


title: Human Ntera2, me3K9 Promoter 2 Array, 94568

description: Human Ntera2 cells


title: 137-26-8 Thiuram, 75 uM 2 h 2nd

source_name: Thiuram treatment with 75 uM for 2 h, Cy5

growth_protocol: Saccharomyces cerevisiae strain S288C was grown in YPD medium (2% polypeptone, 1% yeast extract, 2% glucose) at 25 C with shaking. 300 ul of 50 mM chemical stock solution were added into 200 ml OD=1 (exponential growing) culture (final concentration; 75 uM) then the yeast cells were exposed for 2 h.

treatment_protocol: Thiuram Standard (Wako 204-11371)


title: 66-81-9 Cycloheximide 1st

source_name: Cycloheximide treated for 2 h, Cy5

growth_protocol: Saccharomyces cerevisiae strain S288C was grown in YPD medium (2% polypeptone, 1% yeast extract, 2% glucose) at 25 C with shaking. 60 ul of 50 mM chemical stock solution were added into 200 ml OD=1 (exponential growing) culture (final concentration; 15 uM) then the yeast cells were exposed for 2 h.

treatment_protocol: Cycloheximide, 95% (Wako, 038-11131)


title: 137-26-8 Thiuram, 75 uM 2 h 1st

source_name: Thiuram treated for 2 h with 75 uM, Cy5


title: dorsal marginal zone explant

description: gene expression in dorsal marginal zone

source_name: dorsal marginal zone from stage 10 Xenopus embryo

tag: the dorsal marginal zone including the blastopore and some ectoderm and dorsal yolk plug composed mostly of endomesoderm


title: 251318510270_K27LNCaP

city: Chicago

first: Jindan

last: Yu

state: IL

address: 303 E. Superior St.

department: Medicine - Hem/Onc

institute: Northwestern University

description:
H3K27me3 binding in LNCaP, Replicate 2
Biological replicate 2 of 2. H3K27me3 antibody

hyb_protocol: human Cot DNA was added to labelled cDNA and hybridized in Agilent blocking and hybridization buffer to arrays in Agilent hybridization chamber and Oven at 65C for 72hrs.

scan_protocol: Scanned on an Agilent scanner Images were quantified using Agilent Feature Extraction Software

data_processing: median normalized, background subtracted data obtained

source_name: ChIP-enriched, H3K27me3  antibody; labeled with Cyanine-5 (red).

label_protocol: 30ul of ChIP product was LM-PCR amplified, labeled using Invitrogen BioPrimer Array CGH genomic labeling system.

extract_protocol: ChIP performed using corresponding antibodies against SUZ12 and H3K27me3 respectively.

tag: H3K27me3 antibody

tag: LNCaP prostate cancer cell line

tag: Grown in RPMI with 10%FBS

tag: ChIP-enriched genomic DNA

source_name: whole cell extract DNA

tag: sheared genomic DNA


title: Environmental DNA + Prochloro Mixed, MED4 dominant

status: Public on Oct 31 2007

city: Tucson

first: Virginia

middle: Isabel

last: Rich

state: AZ

address: 1041 E. Lowell St.

institute: University of Arizona

description: Environmental DNA with added Prochlorococcus strains, mixed, strain MED4 dominant

hyb_protocol: 17.33μl of labeled DNA was added to hybridization buffer for final concentrations of 3X SSC, 0.2% SDS, 0.4 mg/ml poly A, 0.02M HEPES, pH7, in a final volume of 25μl. Samples were denatured 4 minutes at 100 deg C, then pipetted onto the arrays. Arrays were hybridized overnight in a heating oven (Model 2000 Micro Hybridization Incubator, Robbins Scientific, Sunnyvale, California), then washed, first vigorously for 30 seconds in 0.6X SSC, 0.03% SDS, and second in 0.06X SSC vigorously for 30 seconds then gently for five minutes. For the data shown in this paper, hybridizations were done at 65 deg C and washes were done at room temperature.

scan_protocol: Hybridized arrays were scanned using an Axon Instruments 4000B scanner (Foster City, CA) and the data was normalized and filtered using perl scripts written for the purpose, by the steps described below.

data_processing: (1) Signal intensities for each spot were calculated by subtracting the local background (mean F532 – median B532, as calculated by GenePix Pro 5.1 software, Axon Instruments). (2) The median value across replicates was calculated for each probe. (3) For each probe set, the number of probes greater than twice the mean negative control signal was calculated, before further processing. (4) Filter I: Arrays with less than half their positive control probes exceeding twice the mean negative control signal were considered poor quality, low dynamic range, arrays and were excluded from further analysis. (5) Each probe signal was corrected for non-specific binding by subtracting the mean negative control spot signal. (6) The data was then normalized for array-to-array variations in brightness by dividing each probe signal by the mean positive control signal. This positive control signal was the mean signal across the Halobacterium salinarum probes in each hybridization, with identical amounts of H. salinarum DNA having been added to each reaction prior to amplification and labeling. (7) Filter II: In order for a genotype to be considered “present”, at least 45% of its probes had to exceed twice the mean negative control signal. (8) Finally, each genotype signal was calculated as either the MEAN or TUKEY BIWEIGHT across its probe set. Finally, outlier arrays were identified as having normalized mean positive control signal less than 25% of the average across the experimental series, and were excluded from further analyses. Pre-processed data was imported into Excel for visualization.

organism:
Prochlorococcus marinus subsp. pastoris str. CCMP1986
Prochlorococcus marinus str. MIT 9312
Prochlorococcus marinus str. MIT 9313
Prochlorococcus marinus str. MIT 9515
marine metagenome

source_name: Environmental DNA with added Prochlorococcus strains, mixed: 10^5 cell/ml MED4, and 10^3 cells/ml each strains 9515, 9312 and 9313

label_protocol: Target DNA was amplified and labeled using A/B/C random-amplification (Wang et al., 2003), with the modification that the initial reverse transcription step was omitted.  Briefly, random-primed amplification was carried out in three reactions: Round A used Sequenase to extend Primer A (GTT TCC CAG TCA CGA TCN NNN NNN NN); Round B used 20 rounds of PCR to amplify the resulting fragments, using Primer B (GTT TCC CAG TCA CGA TC); and Round C used 10 rounds of PCR to incorporate amino-allyl-deoxyuridine triphosphates (aa-dUTP). For the environmental samples, the amount of DNA into each reaction was normalized to represent 70ml of filtered seawater. All A/B/C reactions were performed in triplicate and pooled. Amplification products were cleaned using a Microcon YM-30 and concentrated to 9μl in nuclease-free water, and labeled with Cy3 by combining 8μl aa-DNA, 2μl 0.5M NaHCO3 and 5μl Cy3 dye (33μg in DMSO), and incubating at room temperature in the dark for one hour. Samples were cleaned in a Microcon YM-30, and concentrated to 19μl in TE.

extract_protocol: Extractions were a modification of a filter extraction protocol described previously (Suzuki et al, 2001). Filters were transferred to 2.0ml screw-top microcentrifuge tubes and 242μl of lysis buffer was added to each (lysis buffer: 40mM EDTA, 50mM Tris ph8.3, 0.73M sucrose, 1.15mg/ml lysozyme (Sigma, #L-6876), 200μg/ml RNase (Qiagen, Valencia, California, #1018048), 0.2μm-filter-sterilized). Samples were incubated at 37 deg C for 30 minutes, rotating. 13.5μl of a Proteinase K solution (10mg/ml (EMD, #24568-2) in 40mM EDTA, 50mM Tris ph8.3, 0.73M sucrose) was added, and SDS was added to a final concentration of 1%. Each sample was incubated at 55 deg C, rotating, overnight. The samples were then extracted with the DNeasy 96 Tissue kit (Qiagen, Valencia, CA), by a modification of the manufacturer’s protocol. Each tube received 300μl of Buffer AL (buffer AL/E without ethanol added), was vortexed, and incubated for 70 deg C for 10 minutes. Then 300μl of 99% ethanol was added to each, they were vortexed, and pipetted onto the 96-well spin plate. The plate was sealed with the Airpore sheets (supplied with kit) and spun. All spins were carried out at 40 deg C, 4612 x g in a Sorvall Legend RT centrifuge (Kendro Laboratory Products, Newtown, Connecticut). The plate was spun 10 minutes, 500μl Buffer AW1 was added to each well, the plate re-sealed and spun 5 minutes. 500μl Buffer AW2 was then added to each well, the plate resealed and spun 5 minutes. To dry the plate, the column portion was then transferred to a new rack of elution microtubes RS (supplied with kit) and incubated for 15 minutes at 70 deg C. To elute, 200μl Buffer AE pre-heated to 70 deg C was then added to each well, the plate was re-sealed, incubated 1 minute and spun for 2 minutes. The elution was repeated with an additional 200μl. The eluted DNA was then concentrated using Excela-Pure 96-well PCR purification kits (Edge BioSystems, Gaithersburg, Maryland), following the manufacturer’s protocol. Each well was rinsed once with 100μl nuclease-free water (#9937, Ambion, Austin, Texas), then resuspended in 20μl dilute TE (1mM Tris pH 8, 0.1mM EDTA pH 8), transferred to a clean 96-well plate, and stored at -20 deg C. Concentrations were measured by Nanodrop.

tag: Coastal seawater was collected from the Woods Hole, MA, town pier using a rinsed bucket and transported to MIT in a 50L carbuoy; Prochlorococcus was undetected in this water by flow cytometry (per Moore et al., 1998), and total cell density was 4.15 x 10^6 by Sybr-stained flow cytometric counts. Prochlorococcus strains MED4, MIT9515, MIT9312 and MIT9313 were separately spiked into the natural samples, each to final cell concentrations ranging from ~10^1 to 10^6 cells/ml. Culture cell concentrations were measured using flow cytometry and necessary dilutions of cultures were made with 0.2μm-filtered Sargasso Sea water. Each aliquot of Woods Hole water with its spiked-in Prochlorococcus was filtered through a GF-A prefilter, then collected on a Supor-200 (#60300, Pall Corporation, Ann Arbor, Michigan) 25mm 0.2μm filter, using a MasterFlex peristaltic pump system (Cole-Parmer Instrument Company, Vernon Hills, Illinois).  Filtered volumes ranged from 250ml to 1L. Filters were immediately frozen. All additions and filtrations were made within 24 hours of water collection.


title: 404-86-4 Capsaicin 1st

source_name: Capsaicin treated for 2 h, Cy5

growth_protocol: Saccharomyces cerevisiae strain S288C was grown in YPD medium (2% polypeptone, 1% yeast extract, 2% glucose) at 25 C with shaking. Chemical solution was added into OD=1 (exponential growing) culture (final concentration; 250 ppm) then the yeast cells were exposed for 2 h.

treatment_protocol: Capsaicin (Wako, 033-15961)

source_name: control (without treatment), Cy3


title: Environmental DNA + Prochloro Mixed, all strains equal

description: Environmental DNA with added Prochlorococcus strains, mixed, all strains equal

source_name: Environmental DNA with added Prochlorococcus strains MED4, 9515, 9312, and 9313


title: 251318510271_SUZ12LNCaP

description:
SUZ12 binding in LNCaP
SUZ12 antibody, no replicate

source_name: ChIP-enriched, SUZ12 antibody; labeled with Cyanine-5 (red).

tag: SUZ12 antibody


title: Environmental DNA + Prochloro MED4, 10^5 cells/ml

description: Environmental DNA with added Prochlorococcus strain MED4, 10^5 cells/ml.

organism:
Prochlorococcus marinus subsp. pastoris str. CCMP1986
marine metagenome


title: Environmental DNA + Prochloro Mixed, 9515 dominant

description: Environmental DNA with added Prochlorococcus strains, mixed, strain 9515 dominant

source_name: Environmental DNA with added Prochlorococcus strains, mixed: 10^5 cell/ml 9515, and 10^3 cells/ml each strains MED4, 9312 and 9313


title: Environmental DNA + Prochloro MED4, 10^3 cells/ml

description: Environmental DNA with added Prochlorococcus strain MED4, 10^3 cells/ml.


title: Environmental DNA + Prochloro Mixed, 9312 dominant

description: Environmental DNA with added Prochlorococcus strains, mixed, strain 9312 dominant

source_name: Environmental DNA with added Prochlorococcus strains, mixed: 10^5 cell/ml 9312, and 10^3 cells/ml each strains MED4, 9515 and 9313


title: vegetal explant

description: gene expression in vegetal pole of stage 10 Xenopus embryo

source_name: vegetal explant from stage 10 Xenopus embryo

tag: the vegetal explant composed of the central part of the yolk plug.


title: Recovery from 40 MPa 4C 1st

source_name: Recovery from 40 MPa 4C, Cy5

growth_protocol: For the pressure shock treatment, 200 ml of yeast culture, at an exponential growth phase (A660=1.0), was centrifuged and resuspended in 10 ml YPD medium in a 10 ml syringe. These syringes were pressed with 40 MPa for 16 h. To achieve pressurization, we used the 30-11HF4 (High Pressure Equipment Co.). During the treatment, the temperature was maintained by an ice-water bath. After decompression, the cells were resuspended in 200 ml fresh YPD medium and incubated for 1 h at 25°C. The yeast cells were then centrifuged and washed in distilled water before storage at −80°C.

treatment_protocol: Recovery from 40 MPa 4C

tag: strain S288C

source_name: control (without pressure treatment), Cy3

growth_protocol: For the control cells, 200 ml of yeast culture, at an exponential growth phase (A660=1.0), was centrifuged and resuspended in 10 ml YPD medium in a 10 ml syringe. These syringes were kept under 0.1 MPa in ice-water bath for 16 h. The cells were resuspended in 200 ml fresh YPD medium and incubated for 1 h at 25°C. The yeast cells were then centrifuged and washed in distilled water before storage at −80°C.


title: Environmental DNA + Prochloro MED4, 10^4 cells/ml

description: Environmental DNA with added Prochlorococcus strain MED4, 10^4 cells/ml.


title: 251318610277_K27LNCaP

description:
H3K27me3 binding in LNCaP
H3K27me3 antibody, no replicate


title: 251318510269_K27LNCaP

description:
H3K27me3 binding in LNCaP, Replicate 1
Biological replicate 1 of 2. H3K27me3 antibody


title: Environmental DNA + Prochloro 9515, 10^6 cells/ml

description: Environmental DNA with added Prochlorococcus strain 9515, 10^6 cells/ml

organism:
Prochlorococcus marinus str. MIT 9515
marine metagenome


title: Environmental DNA + Prochloro MED4, 10^2 cells/ml

description: Environmental DNA with added Prochlorococcus strain MED4, 10^2 cells/ml.


title: Environmental DNA + Prochloro 9515, 10^5 cells/ml

description: Environmental DNA with added Prochlorococcus strain 9515, 10^5 cells/ml


title: Environmental DNA + Prochloro 9515, 10^3 cells/ml

description: Environmental DNA with added Prochlorococcus strain 9515, 10^3 cells/ml.


title: 87-86-5 Pentachlorophenol 2nd

description: Data with flag value 0 were used for LOWESS normalization processing.

source_name: PCP treated for 2 h, Cy5

growth_protocol: Saccharomyces cerevisiae strain S288C was grown in YPD medium (2% polypeptone, 1% yeast extract, 2% glucose) at 25 C with shaking until OD=1, then grown for 2 h without any treatment.


title: Environmental DNA + Prochloro 9515, 10^4 cells/ml

description: Environmental DNA with added Prochlorococcus strain 9515, 10^4 cells/ml


title: Environmental DNA + Prochloro 9515, 10^2 cells/ml

description: Environmental DNA with added Prochlorococcus strain 9515, 10^2 cells/ml.


title: Environmental DNA + Prochloro MED4, 10^6 cells/ml

description: Environmental DNA with added Prochlorococcus strain MED4, 10^6 cells/ml.


title: Environmental DNA + Prochloro 9515, 10^1 cells/ml

description: Environmental DNA with added Prochlorococcus strain 9515, 10^1 cells/ml.


title: 3-day-old TJ1090 worms without any stress (C3)

description: Gene chip hybridization and scanning were done at Genome Explorations (Memphis, MN) and the University of Colorado at Boulder Gene Chip Core Facility (Boulder, CO).

source_name: control worms without any stress (C3)


title: Recovery from 180 MPa 4C 4th

source_name: Recovery from 180 MPa 4C, Cy5


title: Environmental DNA + Prochloro 9313, 10^6 cells/ml

description: Environmental DNA with added Prochlorococcus strain 9313, 10^6 cells/ml

organism:
Prochlorococcus marinus str. MIT 9313
marine metagenome


title: Environmental DNA + Prochloro 9313, 10^2 cells/ml

description: Environmental DNA with added Prochlorococcus strain 9313, 10^2 cells/ml


title: Environmental DNA + Prochloro 9313, 10^5 cells/ml

description: Environmental DNA with added Prochlorococcus strain 9313, 10^5 cells/ml


title: Environmental DNA + Prochloro 9312, 10^5 cells/ml

description: Environmental DNA with added Prochlorococcus strain 9312, 10^5 cells/ml.

organism:
Prochlorococcus marinus str. MIT 9312
marine metagenome


title: Environmental DNA + Prochloro 9312, 10^2 cells/ml

description: Environmental DNA with added Prochlorococcus strain 9312, 10^2 cells/ml


title: Environmental DNA + Prochloro 9313, 10^1 cells/ml

description: Environmental DNA with added Prochlorococcus strain 9313, 10^1 cells/ml.


title: Environmental DNA + Prochloro 9313, 10^4 cells/ml

description: Environmental DNA with added Prochlorococcus strain 9313, 10^4 cells/ml


title: Environmental DNA + Prochloro 9312, 10^4 cells/ml

description: Environmental DNA with added Prochlorococcus strain 9312, 10^4 cells/ml.


title: Environmental DNA + Prochloro 9313, 10^3 cells/ml

description: Environmental DNA with added Prochlorococcus strain 9313, 10^3 cells/ml


title: Environmental DNA + Prochloro 9312, 10^1 cells/ml

description: Environmental DNA with added Prochlorococcus strain 9312, 10^1 cells/ml.


title: Environmental DNA + Prochloro MED4, 10^1 cells/ml

description: Environmental DNA with added Prochlorococcus strain MED4, 10^1 cells/ml.


title: Environmental DNA + Prochloro 9312, 10^3 cells/ml

source_name: Environmental DNA with added Prochlorococcus strain 9312, 10^3 cells/ml.


title: Environmental DNA + Prochloro 9312, 10^6 cells/ml

description: Environmental DNA with added Prochlorococcus strain 9312, 10^6 cells/ml.


title: Right STG, Biological Rep3

city: Los Angeles

first: Brett

middle: S

last: Abrahams

address: 695 Charles Young Drive

institute: UCLA

description: Gene expression data from STG

hyb_protocol: Manufacturer Protocols via UCLA Microarray Core (http://microarray.genetics.ucla.edu/)

data_processing: The data were analyzed with R affy package, part of the Bioconductor Suite.  They were normalized by Robust Multi-Array expression measure using sequence information (gcrma method).

source_name: NICHD Brain and Tissue Bank for Developmental Disorders (University of Maryland, Baltimore, MD)

label_protocol: Biotinylated cRNA were prepared according to manufacturer Protocols via UCLA Microarray Core (http://microarray.genetics.ucla.edu/)

extract_protocol: Total RNA was prepared from fresh-frozen brains using Trizol

value: 19 weeks gestation

tag: Sex

value: Male


title: Left Cortex, Biological Rep9

description: Gene expression data from CTX

scan_protocol: Manufacturer Protocols via UCLA Microarray Core (http://microarray.genetics.ucla.edu/)

value: 18 weeks gestation


title: Right Cortex, Biological Rep5

description: Gene expression data from CTX

value: 17 weeks gestation

value: Female


title: Right STG, Biological Rep7

description: Gene expression data from STG


title: Left STG, Biological Rep2

description: Gene expression data from STG

value: 22 weeks gestation


title: Right Cortex, Biological Rep8

description: Gene expression data from CTX

value: Unknown


title: Left STG, Biological Rep6

description: Gene expression data from STG


title: 13372783 - NT vs Man

city: Evry

first: Frederique

last: Bitton

address: 2 rue Gaston Cremieux

country: France

institute: INRA

description: Role of PLDzeta to abiotic stress adaptation

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

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

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

organism: Arabidopsis thaliana

source_name: Man

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

growth_protocol: whole plant - Media:MS/2			 Temperature:22degreeC	 Light:60 uE

extract_protocol: Pool of extract, Man-1:1.5ug, Man-2:1.5ug, Man-3:1.5ug. Total RNA Isolation - Guanidinium thiocyanate method Reagents All the solutions should be treated with DEPc 2 ml/L Guanidinium solution 4M stock (3 months on bench) 250.0 g Guanidinium (Fluka) 293.0 ml H2O 17.6 ml 0.75 M sodium citrate pH7 26.4 ml 10% sarcosyl 200 ml total Denaturing Guanidinium solution 0.36 ml 2-mercaptoethanol for 50 ml of the stock solution CsCl buffer For 100 ml Weigh 95.97 g CsCl, dissolved it in 0.1 M EDTA to 100 ml, add 200 µl DEPc Weigh the bottle and autoclave 20', check the weigh Protocol Grind 1g of frozen tissue in a mortar under liquid nitrogen to a fine powder. Transfer the powder with a cold spatula in a homogenizer containing 7 ml of the denaturing solution. Mix well by vortexing. Put the mixture to a centrifuge tube to spin down the membranes and debris 10 000 rpm for 10' Load the supernatant onto a 5.7M CsCl cushion (3ml) equilibrated with EDTA. Centrifuge for at least 15 h at 35 000 rpm at 19°C. Remove most of the solution, invert quickly the tube and let it dry for 10'. Cut off the bottom of the tube and dissolve the RNA pellet with100 µl H2O. Add the same volume of phenol-chloroforme, mix well and centrifuge for 3'. Collect the aqueous phase and re-extract the organic phase with 100 µl H2O. Collect the two fractions and re-extract twice with chloroform. Precipitate the RNA with 0.3 M NaAcetate final concentration and 2.5 volume of ethanol for at least 1 h. Spin down the precipitate at 13 000 rpm, 4 °C, 20' and wash the pellet twice with 70% ethanol. Dry the pellet and dissolve it in 100 µl H2O in order to measure the concentration. Keep the RNA at -70°C.

treatment_protocol: Name:Man - abiotic stress - abiotic stress,mannitol:quantity 400mM time 3hour . 12-day-old seedlings were removed from 0.5 x MS agar plates and transferred onto 0.5xMS liquid medium containing 400 mM mannitol. After 3 h treatment at 22degre Celsius, seedlings were collected and frozen immediately.

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

source_name: NT

extract_protocol: Pool of extract, NT-1:1.5ug, NT-2:1.5ug, NT-3:1.5ug. Total RNA Isolation - Guanidinium thiocyanate method Reagents All the solutions should be treated with DEPc 2 ml/L Guanidinium solution 4M stock (3 months on bench) 250.0 g Guanidinium (Fluka) 293.0 ml H2O 17.6 ml 0.75 M sodium citrate pH7 26.4 ml 10% sarcosyl 200 ml total Denaturing Guanidinium solution 0.36 ml 2-mercaptoethanol for 50 ml of the stock solution CsCl buffer For 100 ml Weigh 95.97 g CsCl, dissolved it in 0.1 M EDTA to 100 ml, add 200 µl DEPc Weigh the bottle and autoclave 20', check the weigh Protocol Grind 1g of frozen tissue in a mortar under liquid nitrogen to a fine powder. Transfer the powder with a cold spatula in a homogenizer containing 7 ml of the denaturing solution. Mix well by vortexing. Put the mixture to a centrifuge tube to spin down the membranes and debris 10 000 rpm for 10' Load the supernatant onto a 5.7M CsCl cushion (3ml) equilibrated with EDTA. Centrifuge for at least 15 h at 35 000 rpm at 19°C. Remove most of the solution, invert quickly the tube and let it dry for 10'. Cut off the bottom of the tube and dissolve the RNA pellet with100 µl H2O. Add the same volume of phenol-chloroforme, mix well and centrifuge for 3'. Collect the aqueous phase and re-extract the organic phase with 100 µl H2O. Collect the two fractions and re-extract twice with chloroform. Precipitate the RNA with 0.3 M NaAcetate final concentration and 2.5 volume of ethanol for at least 1 h. Spin down the precipitate at 13 000 rpm, 4 °C, 20' and wash the pellet twice with 70% ethanol. Dry the pellet and dissolve it in 100 µl H2O in order to measure the concentration. Keep the RNA at -70°C.

treatment_protocol: no treatment


title: Superior Temporal Gyrus vs. Remaining Cortex (Replicate8)

scan_protocol: Agilent Scanner via UCLA Microarray Core (http://microarray.genetics.ucla.edu/)

data_processing: Agilent Feature Extraction software (Ver. 7.5.1)

source_name: Total RNA from 867.L.STG

label_protocol: Samples from Superior Temporal Gyrus (STG) and Remaining Cortex (CTX) were labelled with Cy5 and Cy3, respectively.

growth_protocol: Human Fetal Brains were obtained from NICHD Brain and Tissue Bank for Developmental Disorders (University of Maryland, Baltimore, MD)

extract_protocol: Total RNA was prepared from fresh-frozen brain using Trizol

source_name: Total RNA from 1007.L.CTX


title: 13372789 - Cold vs NT

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

source_name: Cold

extract_protocol: Pool of extract, Cold-1:1.5ug, Cold-2:1.5ug, Cold-3:1.5ug. Total RNA Isolation - Guanidinium thiocyanate method Reagents All the solutions should be treated with DEPc 2 ml/L Guanidinium solution 4M stock (3 months on bench) 250.0 g Guanidinium (Fluka) 293.0 ml H2O 17.6 ml 0.75 M sodium citrate pH7 26.4 ml 10% sarcosyl 200 ml total Denaturing Guanidinium solution 0.36 ml 2-mercaptoethanol for 50 ml of the stock solution CsCl buffer For 100 ml Weigh 95.97 g CsCl, dissolved it in 0.1 M EDTA to 100 ml, add 200 µl DEPc Weigh the bottle and autoclave 20', check the weigh Protocol Grind 1g of frozen tissue in a mortar under liquid nitrogen to a fine powder. Transfer the powder with a cold spatula in a homogenizer containing 7 ml of the denaturing solution. Mix well by vortexing. Put the mixture to a centrifuge tube to spin down the membranes and debris 10 000 rpm for 10' Load the supernatant onto a 5.7M CsCl cushion (3ml) equilibrated with EDTA. Centrifuge for at least 15 h at 35 000 rpm at 19°C. Remove most of the solution, invert quickly the tube and let it dry for 10'. Cut off the bottom of the tube and dissolve the RNA pellet with100 µl H2O. Add the same volume of phenol-chloroforme, mix well and centrifuge for 3'. Collect the aqueous phase and re-extract the organic phase with 100 µl H2O. Collect the two fractions and re-extract twice with chloroform. Precipitate the RNA with 0.3 M NaAcetate final concentration and 2.5 volume of ethanol for at least 1 h. Spin down the precipitate at 13 000 rpm, 4 °C, 20' and wash the pellet twice with 70% ethanol. Dry the pellet and dissolve it in 100 µl H2O in order to measure the concentration. Keep the RNA at -70°C.

treatment_protocol: Name:Cold - abiotic stress - temperature,temperature:quantity 4degree time 3hour . 12-day-old seedlings were removed from 0.5 x MS agar plates and transferred onto 0.5xMS liquid medium. After 3 h treatment at 4degre Celsius, seedlings were collected and frozen immediately.


title: 13372782 - NaCl vs NT

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

source_name: NaCl

extract_protocol: Pool of extract, NaCl-1:1.5ug, NaCl-2:1.5ug, NaCl-3:1.5ug. Total RNA Isolation - Guanidinium thiocyanate method Reagents All the solutions should be treated with DEPc 2 ml/L Guanidinium solution 4M stock (3 months on bench) 250.0 g Guanidinium (Fluka) 293.0 ml H2O 17.6 ml 0.75 M sodium citrate pH7 26.4 ml 10% sarcosyl 200 ml total Denaturing Guanidinium solution 0.36 ml 2-mercaptoethanol for 50 ml of the stock solution CsCl buffer For 100 ml Weigh 95.97 g CsCl, dissolved it in 0.1 M EDTA to 100 ml, add 200 µl DEPc Weigh the bottle and autoclave 20', check the weigh Protocol Grind 1g of frozen tissue in a mortar under liquid nitrogen to a fine powder. Transfer the powder with a cold spatula in a homogenizer containing 7 ml of the denaturing solution. Mix well by vortexing. Put the mixture to a centrifuge tube to spin down the membranes and debris 10 000 rpm for 10' Load the supernatant onto a 5.7M CsCl cushion (3ml) equilibrated with EDTA. Centrifuge for at least 15 h at 35 000 rpm at 19°C. Remove most of the solution, invert quickly the tube and let it dry for 10'. Cut off the bottom of the tube and dissolve the RNA pellet with100 µl H2O. Add the same volume of phenol-chloroforme, mix well and centrifuge for 3'. Collect the aqueous phase and re-extract the organic phase with 100 µl H2O. Collect the two fractions and re-extract twice with chloroform. Precipitate the RNA with 0.3 M NaAcetate final concentration and 2.5 volume of ethanol for at least 1 h. Spin down the precipitate at 13 000 rpm, 4 °C, 20' and wash the pellet twice with 70% ethanol. Dry the pellet and dissolve it in 100 µl H2O in order to measure the concentration. Keep the RNA at -70°C.

treatment_protocol: Name:NaCl - abiotic stress - abiotic stress,sodium chloride:quantity 200mM time 3hour . 12-day-old seedlings were removed from 0.5 x MS agar plates and transferred onto 0.5xMS liquid medium containing 200 mM NaCl. After 3 h treatment at 22degre Celsius, seedlings were collected and frozen immediately.


title: Left Cortex, Biological Rep7

description: Gene expression data from CTX


title: Right STG, Biological Rep5

description: Gene expression data from STG


title: 13372784 - Man vs NT

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


title: Left STG, Biological Rep1

description: Gene expression data from STG


title: Superior Temporal Gyrus vs. Remaining Cortex (Replicate7)

source_name: Total RNA from 867.R.STG

source_name: Total RNA from 1007.R.CTX


title: Left Cortex, Biological Rep1

description: Gene expression data from CTX


title: Right Cortex, Biological Rep10

description: Gene expression data from CTX


title: Left Cortex, Biological Rep3

description: Gene expression data from CTX


title: Right STG, Biological Rep4

description: Gene expression data from STG


title: Left Cortex, Biological Rep2

description: Gene expression data from CTX


title: Right Cortex, Biological Rep6

description: Gene expression data from CTX


title: 13372787 - NT vs Cold

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


title: Superior Temporal Gyrus vs. Remaining Cortex (Replicate4)

source_name: Total RNA from 490.R.STG

source_name: Total RNA from 183.R.CTX

value: 19.5 weeks gestation


title: Superior Temporal Gyrus vs. Remaining Cortex (Replicate3)

source_name: Total RNA from 532.L.STG

source_name: Total RNA from 183.L.CTX


title: Superior Temporal Gyrus vs. Remaining Cortex (Replicate6)

source_name: Total RNA from 488.L.STG

source_name: Total RNA from 532.L.CTX


title: Superior Temporal Gyrus vs. Remaining Cortex (Replicate5)

source_name: Total RNA from 488.R.STG

source_name: Total RNA from 532.R.CTX


title: 13372781 - NT vs NaCl

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


title: Right Cortex, Biological Rep4

description: Gene expression data from CTX

source_name: NICHD Brain and Tissue Bank for Developmental Disorders (University of Maryland, Baltimore, MD)


title: Superior Temporal Gyrus vs. Remaining Cortex (Replicate2)

source_name: Total RNA from 532.R.STG


title: Superior Temporal Gyrus vs. Remaining Cortex (Replicate1)


title: bc-ZT9-3

status: Public on Oct 30 2007

city: Philadelphia

first: Maja

last: Bucan

state: PA

address: 415 Curie Blvd

institute: UPENN

description: Analysis of prefrontal cortex from 3 biological replicates of C57BL/6J mice at four Zeitgeber Times (ZT 3, 9, 15, and 21).

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix Microarray Suite version 5.0 followed by GCRMA normalization by GeneSpring 7.2

organism: Mus musculus

source_name: prefrontal cortex

label_protocol: Approximately 5 µg of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: The prefrontal cortex tissue was homogenized in 1 ml TriZol reagent and total RNA was extracted according to manufacture's protocol. Total RNA was cleaned up using an RNeasy kit (Qiagen).

tag: prefrontal cortex


title: OV01-9_pre-treatment

city: Cambridge

first: Ahmed

middle: Ashour

last: Ahmed

address: Robinson Way

department: Oncology, University of Cambridge

country: United Kingdom

institute: Cancer Research UK Cambridge Research Institute

description: Responder

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: All statistical analysis was conducted using the R environment and the R packages affy and   affy-PLM. All the raw data tables are included in the accompanying CD in the folder (OV01).   We first started by reading the data files into R.   > library(affy)   > library(affyPLM)   > Data <- ReadAffy()   > sampleNames(Data) <- c('12a', '14a', '15a', '16a', '19a', '24a2', '27a2',   + '28a2', '2a', '33a2', '34a', '38a2', '39a',   + '41a', '43a', '44a', '5a2', '7a', '8a', '9a')                                 Normalization   Background subtraction and normalization was performed using the method of Li and Wong.   This method finds a rank-invariant set of probes across the arrays and uses this for between array   normalization.   > Data.norm <- expresso(Data, normalize.method='invariantset',   + bg.correct=FALSE, pmcorrect.method='pmonly', summary.method='liwong')   > Data.norm.values <- exprs(Data.norm)                                                                                Present and absent calls   Affy probes are arranged as 11 pairs of perfect matches and mismatches for each affymetrix ID  present on the array. Ideally, a mismatch should yield minimum intensity values. Thus, for a   specific hybridization to have occurred, the intensity from the perfect match probes should be  “significantly” higher than that from the mismatched probes. Probe level data were used to  categorize genes to either present ( p < 0.04), absent ( p > 0.06) or marginal (0.04   ≤ p ≤ 0.06).   The mean percentage present calls across all arrays was 51.1% (sd = 8.9%). All the arrays had a percentage present calls of more than 33% of the total number of probe pair sets on an array.   > Calls <- mas5calls(Data)   > Calls.data <- exprs(Calls)   > Data filtering   Data filtering was performed in two stages. First, genes that were either absent or marginal in  more than 6 arrays (30% of the arrays) were filtered out. After applying this filtering method only 10,161 genes (out of 22,227) remained for downstream analysis.   > Calls.data.AP <- Calls.data==A| Calls.data==M   > Calls.data.AP.sum <- apply(Calls.data.AP, 1, sum)   > Calls.data.AP.filter <- which(Calls.data.AP.sum > 6)   > Calls.data.AP.retain <- which(Calls.data.AP.sum <= 6)   > eset.AP.retained <- Data.norm.values[Calls.data.AP.retain,]   > length(Calls.data.AP.retain)   Second, genes that showed non significant variation in gene expression across arrays were removed   according to the method adopted by Simon et al in which only genes that were significantly more variable across arrays than the median variance of all genes were included. This was done by computing the quantity (n − 1) ∗ (Var.i/Var.med ) and comparing it against the chi-square distribution at n − 1 degrees of freedom. After performing this step only 3426 genes were retained for further downstream analysis.   > eset.AP.retained.var <- apply(log2(eset.AP.retained), 1, var)   > eset.AP.retained.var.quant <-   + (ncol(eset.AP.retained)-1)*(eset.AP.retained.var/median(eset.AP.retained.var))                             > eset.AP.retained.var.quant.centile <- pchisq(eset.AP.retained.var.quant,   + df=ncol(eset.AP.retained)-1)   # Genes above the 95th centile (p<0.05) were retained   > Var.retain <- which(eset.AP.retained.var.quant.centile > 0.95)   > eset.AP.var.retained <- eset.AP.retained[Var.retain,]   > dim(eset.AP.var.retained)

source_name: biopsy from patient with suspected ovarian cancer

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix). Samples with less than 1 ug quantities were amplified using 10 ng of total RNA.

extract_protocol: RNA was extracted using RNA-Easy kit from Qiagen according to manufacturer's instructions.

tag: Responder


title: bc-ZT9-1


title: OV01-39_pre-treatment

description: Responder


title: OV01-8_pre-treatment

description: Responder


title: OV01-7_pre-treatment

description: Responder


title: bc-ZT3-3


title: bc-ZT3-1


title: OV01-43_pre-treatment

description: Responder


title: bc-ZT3-2


title: bc-ZT21-1


title: bc-ZT15-3


title: OV01-34_pre-treatment

description: Responder


title: bc-ZT21-2


title: bc-ZT9-2


title: bc-ZT15-1


title: bc-ZT21-3


title: bc-ZT15-2


title: OV01-41_pre-treatment

description: Responder


title: OV01-2_pre-treatment

description: Responder


title: OV01-28_pre-treatment

description: Non-responder

tag: Non-responder


title: OV01-38_pre-treatment

description: Non-responder


title: OV01-44_pre-treatment

description: Responder


title: OV01-5_pre-treatment

description: Responder


title: 40 minutes_RepB

city: Buffalo

first: M

middle: M

last: Vickerman

state: NY

address: 3435 Main St.

department: Oral Biology

institute: University at Buffalo

description: Biological replicate 2 of 2.  Bacterial culture exposed to 100 ng/ml competence signaling peptide (CSP) for 40 minutes.

hyb_protocol: Before hybridization, slides were pre-treated in a 5X SSC, 0.1% SDS, and 1% BSA solution for 1 hr at 42C.  Slides were then washed twice in H20 followed by one wash in isopropanol and dried.  Fifty ul of hybridization solution (50% formamide, 5X SSC, 0.1% SDS) filtered through a Nalgene 0.45uM filter and containing 0.5mg of salmon sperm DNA was used to resuspend each dried probe.  Resuspended probes were denatured at 95C, chilled on ice to 4C and added between slides and lifterslips (Erie Scientific, Portsmouth, NH) and sealed in hybridization chambers (Corning Life Sciences, Lowell, MA) containing 40ul of H20 to maintain humidity.  Slides were incubated in the dark in a 42C water bath overnight.  Slides were washed once in 1X SSC/0.2% SDS for 5 min at ~45C, once in 1X SSC/0.1% SDS for 5 min at room temperature, and three times in 0.1X SSC for 5 min each at room temperature.  Slides were dried and scanned immediately or the same day after storage in the dark.

scan_protocol: Microarrays were scanned using GenePix Pro v5.0 with a Axon 4000B GenePix scanner (Molecular Devices, Sunnyvale, CA).  The intensities of the two dyes at each spot were quantified using TIGR spotfinder (http://www.tigr.org).

data_processing: The TIGR TM4 Microarray Software Suite (http://www.tigr.org) was used for all analyses, including analysis of TIF files using TIGR Spotfinder and normalization using Microarray Data Analysis System (MIDAS).  Normalization included LocFit, a low intensity filter of 10,000, and in-slide replicate analysis which calculated geometric means for in-slide replicates.  Geometric means were then calculated for flip dye pairs using flip dye pair consistency checking in MIDAS.  Statistical analyses were conducted using Multiexperiment Viewer (MEV).

organism: Streptococcus gordonii str. Challis

source_name: untreated

label_protocol: Streptococcus gordonii RNA was first converted to amino-allyl cDNA (aa-cDNA) by reverse transcription with Superscript III reverse transcriptase (Invitrogen) in a deoxynucleotide triphosphate mixture containing amino-allyl dUTP (Ambion, Austin, TX).  The RNA template was removed by alkaline hydrolysis and aa-cDNA recovered by purification on Qiagen QIAquick PCR columns (Qiagen).  The cDNA was dried in a SpeedVacTM, labeled by coupling to either Cy3 or Cy5 NHS-Cy dye (GE Healthcare Bio-Sciences Corp., Piscataway, NJ) and purified on Qiagen QIAquick PCR columns (Qiagen).  The quality of the probes and their specific activity were confirmed by a spectrophotometric scan from 200 to 700 nm.  Typical yields from this synthesis were 3 ug of cDNA with 150-200 pmol of dye molecule incorporated per microgram of cDNA produced.  Only targets with > 200 pmol of dye incorporation per sample and a ratio of less than 50 nucleotides/dye molecules were used for hybridizations.  Arabidopsis control oligonucleotides for array quality were printed onto each slide.

growth_protocol: Cells were grown at 36C in Todd Hewitt broth with 8mM HCl to OD600 of 0.4.  The cells were grown for an additional 40 min. at 36C as the control for cells incubated with competence signaling peptide (CSP).  A 10 ml aliquot of cells was removed and mixed with hot acid phenol to extract RNA.

extract_protocol:
Ten milliliters of cells were mixed with hot acid phenol (95C), incubated for 10 minutes at 95C, chilled on ice.  A total of 0.2 volumes of chloroform was added, mixed well and centrifuged to separate the aqueous and organic layers.  The aqueous layer (containing the RNA) was re-extracted with 1 volume of acid phenol-chloroform and centrifuged.  The supernatant was adjusted to 0.3 M sodium acetate, mixed with one volume of isopropanol and centrifuged to precipitate the RNA.  The RNA pellet was resuspended in DEPC treated water containing 150 U of RNase inhibitor (RNaseOUT, Invitrogen, Carlsbad, CA) per ml and purified on a Qiagen RNeasy midi-column (Qiagen, Valencia, CA) according to manufacturer’s recommendations.  After elution from the Qiagen RNeasy column, 50 U of RNase inhibitor was added to the RNA prior to storage at
-80C.

treatment_protocol:
Total RNA from cell cultures was extracted with hot acid phenol and purified on
Qiagen RNeasy columns.

tag: Streptococcus gordonii str. Challis CH1

source_name: 100 ng/ml CSP; 40 minutes.

growth_protocol: Cells were grown at 36C in Todd Hewitt broth with 8mM HCl to OD600 of 0.4. Synthetic competence signaling peptide (CSP) was added to cell cultures to achieve a concentration of 100 ng/ml.  After 40 minutes, a 10 ml aliquot of cells was removed and mixed with hot acid phenol to extract RNA.


title: OV01-33_pre-treatment

description: Non-responder


title: 15 minutes_RepB

description: Biological replicate 1 of 2.  Bacterial culture exposed to 100 ng/ml competence signaling peptide (CSP) for 15 minutes.

hyb_protocol: Before hybridization, slides were pre-treated in a 5X SSC, 0.1% SDS, and 1% BSA solution for 1 hr at 42C.  Slides were then washed twice in H20 followed by one wash in isopropanol and dried.  Fifty ul of hybridization solution (50% formamide, 5X SSC, 0.1% SDS) filtered through a Nalgene 0.45uM filter and containing 0.5mg of salmon sperm DNA was used to resuspend each dried probe.  Resuspended probes were denatured at 95C, chilled on ice to 4C and added between slides and lifterslips (Erie Scientific, Portsmouth, NH) and sealed in hybridization chambers (Corning Life Sciences, Lowell, MA) containing 40ul of H20 to maintain humidity.  Slides were incubated in the dark in a 42C water bath overnight.  Slides were washed once in 1X SSC/0.2% SDS for 5 min at ~45ºC, once in 1X SSC/0.1% SDS for 5 min at room temperature, and three times in 0.1X SSC for 5 min each at room temperature.  Slides were dried and scanned immediately or the same day after storage in the dark.

growth_protocol: Cells were grown at 36C in Todd Hewitt broth with 8mM HCl to OD600 of 0.4.  The cells were grown for an additional 15 min. at 360C as the control for cells incubated with competence signaling peptide (CSP).  A 10 ml aliquot of cells was removed and mixed with hot acid phenol to extract RNA.

source_name: 100 ng/ml CSP; 15 minutes.

growth_protocol: Cells were grown at 36C in Todd Hewitt broth with 8mM HCl to OD600 of 0.4. Synthetic competence signaling peptide (CSP) was added to cell cultures to achieve a concentration of 100 ng/ml.  After 15 minutes, a 10 ml aliquot of cells was removed and mixed with hot acid phenol to extract RNA.

treatment_protocol:
Total RNA from cell cultures was extracted with hot acid phenol and purified on Qiagen
RNeasy columns.


title: 40 minutes_RepA

description: Biological replicate 1 of 2.  Bacterial culture exposed to 100 ng/ml competence signaling peptide (CSP) for 40 minutes.


title: 15 minutes_RepA


title: OV01-24_pre-treatment

description: Responder


title: OV01-16_pre-treatment

description: Responder


title: OV01-15_pre-treatment

description: Responder


title: OV01-19_pre-treatment

description: Non-responder


title: HepG2_100uM_Trovafloxacin_24hr_prep3

city: Abbott Park

first: Michael

middle: J

last: Liguori

address: 100 Abbott Park Rd

department: Cellular and Molecular Toxicology

institute: Abbott Laboratories

description:
HepG2 cells treated in vitro with fluoroquinolones
Growth Media: Minimal Essential Media with 10%FBS

hyb_protocol: Standard Eukaryotic Affymetrix Preparation 16-20hr 45C

scan_protocol: Scanner: Affymetrix GeneChip Scanner (Part No. 900154)

data_processing: Rosetta resolver

growth_protocol: Grown on tissue culture treated 6-well plated

extract_protocol: Trizol extraction

treatment_protocol:
Treated with 100uM Trovafloxacin for 24 hrs
Treatment on a different day than original treatments

tag: Tissue

value: HepG2 Cells

tag: Gender

tag: Source

value: ATCC


title: OV01-12_pre-treatment

description: Non-responder


title: HepG2_100uM_Grepafloxacin_24hr_prep1

label_protocol: Standard Eukaryotic Affymetrix Preparation

treatment_protocol: Treated with 100uM grepafloxacin for 24 hrs

value: HepG2 cells

tag: 1st technical replicate


title: HepG2_VehicleB_24hr

description:
HepG2 cells treated in vitro with fluoroquinolones
Growth Media: Minimal Essential Media with 10%FBS
This vehicle is associated with accession No. GSM231519-GSM231525

treatment_protocol: Treated with vehicle for 24 hrs

tag: Vehicle Treated 0.1N KOH (equivalent volume to treated) in cell culture media


title: HepG2_100uM_Trovafloxacin_24hr_Prep2

treatment_protocol: Treated with 100uM trovafloxacin for 24 hrs

tag: 2nd technical replicate


title: HepG2_Vehicle_24hr_prep4

description:
HepG2 cells treated in vitro with fluoroquinolones
Growth Media: Minimal Essential Media with 10%FBS
This vehicle is associated with GSM231528 and GSM231529

treatment_protocol:
Treated with vehicle for 24 hrs
Treatment on a different day than original treatments-associated with high dose quinolones

value: male


title: HepG2_100uM_Clinafloxacin_24hr_prep1

treatment_protocol: Treated with 100uM clinafloxacin for 24 hrs


title: OV01-27_pre-treatment

description: Non-responder


title: HepG2_100uM_Ciprofloxacin_24hr_prep1

treatment_protocol: Treated with 100uM ciprofloxacin for 24 hrs


title: HepG2_100uM_Gatifloxacin_24hr_prep1

treatment_protocol: Treated with 100uM gatifloxacin for 24 hrs


title: HepG2_800uM_Levofloxacin_24hr_prep1

treatment_protocol: Treated with 800uM levofloxacin for 24 hrs


title: HepG2_Vehicle_24hr_prep3

description:
HepG2 cells treated in vitro with fluoroquinolones
Growth Media: Minimal Essential Media with 10%FBS
This vehicle is associated with GSM231517 and GSM231518.


title: 5 minutes_RepB

description: Biological replicate 2 of 2.  Bacterial culture exposed to 100 ng/ml competence signaling peptide (CSP) for 5 minutes.

growth_protocol: Cells were grown at 36C in Todd Hewitt broth with 8mM HCl to OD600 of 0.4.  The cells were grown for an additional 5 min. at 36C as the control for cells incubated with competence signaling peptide (CSP).  A 10 ml aliquot of cells was removed and mixed with hot acid phenol to extract RNA.

source_name: 100 ng/ml CSP; 5 minutes.

growth_protocol: Cells were grown at 360C in Todd Hewitt broth with 8mM HCl to OD600 of 0.4. Synthetic competence signaling peptide (CSP) was added to cell cultures to achieve a concentration of 100 ng/ml.  After 5 minutes, a 10 ml aliquot of cells was removed and mixed with hot acid phenol to extract RNA.

tag: Streptococcus gordonii str. Challis


title: 5 minutes_RepA

description: Biological replicate 1 of 2.  Bacterial culture exposed to 100 ng/ml competence stimulating peptide (CSP) for 5 minutes.

growth_protocol: Cells were grown at 36C in Todd Hewitt broth with 8mM HCl to OD600 of 0.4. Synthetic competence signaling peptide (CSP) was added to cell cultures to achieve a concentration of 100 ng/ml.  After 5 minutes, a 10 ml aliquot of cells was removed and mixed with hot acid phenol to extract RNA.

treatment_protocol: Total RNA from cell cultures was extracted with hot acid phenol and purified on Qiagen RNeasy columns.


title: HepG2_100uM_Trovafloxacin_24hr_prep1


title: HepG2_VehicleA_24hr

tag: Vehicle Treated 0.1N KOH (at equivalent volume as treated) in media


title: OV01-14_pre-treatment

description: Non-responder


title: HepG2_500uM_Ciprofloxacin_24hr_prep1

description:
HepG2 incubated in vitro with quinolones
Growth Media:  Mimimal Essential Media with 10% FBS

hyb_protocol: Standard Affymetrix Eukaryotic Preparation Hyb 16-20hr at 45C

scan_protocol: Scanner: Affymetrix Gene Chip Scanner (Part No. 900154)

growth_protocol: Grown on 6-well cell culture treated plates

extract_protocol: Trizol Extraction

treatment_protocol: Treated with 500uM ciprofloxacin for 24hrs in vitro


title: human_hepatocyte_400uM_Trovafloxacin_donorB_24hr_prep2

description:
Primary human hepatocytes incubated in vitro with quinolones
Growth Media:  In Vitro Technologies Hepatocyte Incubation Media (Cat No. Z90009

label_protocol: Standard Affymetrix Eukaryotic Preparation

growth_protocol: Grown on 6-well collagren type I coated plates

treatment_protocol: Treated with 400uM trovafloxacin for 24hrs in vitro

value: Primary Human Hepatocyte

value: In Vitro Technologies

tag: Cause of Death

value: Anoxia

tag: Tobacco Use

value: No


title: human_hepatocyte_400uM_Trovafloxacin_donorB_24hr_prep1


title: HepG2_100uM_Levofloxacin_24hr_prep1

treatment_protocol: Treated with 100uM levofloxacin for 24 hrs


title: animal cap explant

description: gene expression in animal cap

hyb_protocol: 2.2 micrograms of labeled cDNA in a volume of 200 microliters was hybridized to the Affymetrix Xenopus Genecip in a standard a standard Affymetrix Probe Array Cartridge at 45 degrees , using the fluidics protocol EukGE-WS2v4_450 of a Fluidics Station 450 (Affymetrix) for 18hrs.

scan_protocol: the hybridized chip was scanned by Affymetrix GeneChip Scanner 3000 and then processed with Genechip Operating Software

source_name: animal cap from stage 10 Xenopus embryo

tag: Animal caps were dissected from stage 10 Xenopus embryos.


title: HepG2_800uM_Gatifloxacin_24hr_Prep1

treatment_protocol: Treated with 800uM gatifloxacin for 24 hrs

tag: 1st Technical replicate


title: human_hepatocyte_400uM_Trovafloxacin_donorA_24hr_prep1

value: Celebral Vascular Accident

value: Yes


title: human_hepatocyte_400uM_Trovafloxacin_donorA_24hr_prep2


title: human_hepatocyte_400uM_clinafloxacin_donorA_24hr_prep1

description:
Primary Human Hepatocytes Incubated In Vitro with quinolones
Growth Media:  In Vitro Technologies Hepatocyte Incubation Media (cat # Z90009

hyb_protocol: Standard Affymetrix Eukaryotic Preparation 16-20 hr at 45C

scan_protocol: Scanner:  Affymetrix Gene Chip Scanner (Part No.900154)

growth_protocol:
Grown on 6-well collagen type I coated plates
Treatment period: 24 hrs

treatment_protocol: Treated with 400uM clinafloxacin at 37C for 24 hrs

value: primary human hepatocyte


title: human_hepatocyte_400uM_levofloxacin_donorA_24hr_prep1

treatment_protocol: Treated with 400uM levofloxacin for 24hrs in vitro


title: human_hepatocyte_vehicle_donorA_24hr_prep2

description: Vehicle treament for human hepatocyte donor A.  Growth media:  In vitro technologies hepatocyte incubation media (cat no. Z90009)

hyb_protocol: Standard Affymetrix Eukaryotic Procedure

scan_protocol: Scanner:  Affymetrix Gene-Chip scanner (Part No. 900154)

growth_protocol:
Grown on 6-well collagen type I coated plates.
Treatment period: 24 hr

treatment_protocol: Vehicle:  0.1N KOH added at an equivalent volume as treatment groups

value: Primary human hepatocyte

value: CVA


title: human_hepatocyte_400uM_grepafloxacin_donorA_24hr_prep2

treatment_protocol: Treated with 400uM grepafloxacin for 24hrs in vitro

value: Female


title: human_hepatocyte_400uM_clinafloxacin_donorA_24hr_prep2

treatment_protocol: Treated with 400uM clinafloxacin for 24hrs in vitro


title: human_hepatocyte_400uM_Ciprofloxacin_donorA_24hr_prep1

description: 400uM Ciprofloxacin treament for human hepatocyte donor A.  Growth media:  In vitro technologies hepatocyte incubation media (cat no. Z90009)

hyb_protocol: Standard Affymetrix Eukaryotic Procedure 16-20hrs at 45C

treatment_protocol: Treated with 400uM Ciprofloxacin for 24 hrs

value: female


title: human_hepatocyte_vehicle_donorB_24hr_prep1

description: Vehicle treament for human hepatocyte donor B.  Growth media:  In vitro technologies hepatocyte incubation media (cat no. Z90009)

label_protocol: Standard Affymetrix Eukaryotic Procedure

value: Male

value: In Vitro technologies

value: Hypoxia


title: human_hepatocyte_400uM_levofloxacin_donorA_24hr_prep2


title: human_hepatocyte_400uM_gatifloxacin_donorA_24hr_prep2

treatment_protocol: Treated with 400uM gatifloxacin for 24hrs in vitro

tag: Tissue:Primary Human Hepatocyte


title: human_hepatocyte_gatifloxacin_donorA_24hr_prep1


title: human_hepatocyte_vehicle_donorB_24hr_prep2


title: MLN treated L363 (12 hours) - sample 2 - mAdbID:71650

status: Public on Oct 29 2007

first: Christina

last: Annunziata

address: 10 Center Drive

department: Metabolism Branch

institute: Center for Cancer Research

description: mAdb experiment ID: 71650

hyb_protocol: Sample Hybridization Protocol Other: For hybridization to the array, the Cy3 reaction was added to the Cy5 reaction for each array and placed onto a Microcom YM30 column (Amicon). The column was centrifuged at 14K for approximately 7 minutes, so that 20-40 microliters of probe remained. Flow-through from column was discarded, and an additional 400 microliters TE was applied to the column. Also added to the column was: 20 microliters cot-1 DNA (10 µg/µl, Roche), 2 microliters yeast tRNA (2µg/µl, Sigma), 2 microliters poly d(A) (8µg/µl, Amersham). The column was centrifuged for approximately 7 minutes until there was approximately 20 microliters left. The column was inverted into a fresh tube and centrifuged for 30 seconds to elute probe. TE was added to bring up volume to 25 µl. SDS (0.75 µl of 10% SDS) 20x SSC (4.25 µl) were added to the sample. The sample was incubated at 100oC for 2 minutes and then centrifuged for 30 sec at 13,000 RPM. The probe (30 µl) was applied to the microarray and covered with a coverslip (Fisher #02-671-35), being careful to avoid bubbles. Water (40 µl) was added in small droplets to each side of the slide to maintain humidity after which the hybridization chamber was closed and and place at 65oC overnight. The hybridized slide was washed as follows: 2xSSC + 0.1% SDS for 1 min, 1xSSC for 1 min x 2 washess, 0.5xSSC for 1 min, 0.2xSSC for 1 min. The slide was centrifuged immediately in slide holder in swinging bucket rotor at 550 rpm for 5 min, and then scanned.

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000A [47890] PMTVolts: 700;; 700 ScanPower: 100;; 100 LaserPower: 1.25;; 2 Temperature: 38.53

data_processing:
mAdb Data Processing Protocol (v. 2)
Calculation Method: After background correction, ratios were median centered based on signals greater than 100 in both channels and linear transformed to obtain the log and linear values given in the data table.

source_name: DMSO (Control for L363)

label_protocol:
Cy3 Label Protocol
Other: For the preparation of fluorescence-labeled cDNA targets, 50 micrograms total RNA were reverse-transcribed according to the following reaction conditions. The reaction contained 50 micrograms of total RNA, 5x first strand buffer (8 microliters, Invitrogen), Oligo dT 25-mer (2 microliters of 2µg/µl, Invitrogen), Low dT-dNTPs (2 microliters, Amersham), 0.1 M DTT (4 microliters, Invitrogen), RNase Inhibitor, (1 microliters, Invitrogen), Cy3 dye (4 microliters, Amersham #PA53022), and ddH2O to a final volume of 40 microliters. The reaction was incubated at 65oC for 5 minutes and then cooled to 42oC for 2 minutes. Superscript II (1.5 microliters, Invitrogen) was added, and the reaction was incubated at 42oC for 30 minutes. An additional 1 microliter of Superscript II was added and the reaction was incubated at 42oC for an additional 30 minutes. The reaction was terminated by adding 5 microliters of 500 mM EDTA and 10 microliters of 1M NaOH, and was and incubated at 65oC for 20 minutes. Tris-HCl (1 molar, pH7.5) was then added. TE (450 microliters was added to the Cy3 reaction.

extract_protocol:
RNA extraction with TRIZOL
Other: Cells were lysed with TRIzol reagent (Invitrogen, Carlsbad, CA) and total RNA was isolated according to the manufacturers instructions.

value: bone marrow

tag: Cell line

tag: Cell type

value: multiple myeloma

tag: Disease state

source_name: MLN treated L363 (12 hours) - sample 2

label_protocol:
Cy5 Label Protocol
Other: For the preparation of fluorescence-labeled cDNA targets, 50 micrograms total RNA were reverse-transcribed according to the following reaction conditions. The reaction contained 50 micrograms of total RNA, 5x first strand buffer (8 microliters, Invitrogen), Oligo dT 25-mer (2 microliters of 2µg/µl, Invitrogen), Low dT-dNTPs (2 microliters, Amersham), 0.1 M DTT (4 microliters, Invitrogen), RNase Inhibitor, (1 microliters, Invitrogen), Cy5 dye (4 microliters, Amersham #PA55022), and ddH2O to a final volume of 40 microliters. The reaction was incubated at 65oC for 5 minutes and then cooled to 42oC for 2 minutes. Superscript II (1.5 microliters, Invitrogen) was added, and the reaction was incubated at 42oC for 30 minutes. An additional 1 microliter of Superscript II was added and the reaction was incubated at 42oC for an additional 30 minutes. The reaction was terminated by adding 5 microliters of 500 mM EDTA and 10 microliters of 1M NaOH, and was and incubated at 65oC for 20 minutes. Tris-HCl (1 molar, pH7.5) was then added.

treatment_protocol:
Treatment type: small molecule
Agent: MLN120b
Treatment dose: 12.5 microM
Treatment time: 12 hours
Treatment temperature: 37 C


title: IkB-SR induced EJM - 2 days - mAdbID:79134

description: mAdb experiment ID: 79134

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 840;; 720 ScanPower: 100;; 100 LaserPower: 2.93;; 3.03 Temperature: 29.93

source_name: Uninduced (Control for EJM)

value: EJM

tag: genotype/variation gene knock in

tag: genotype/variation

value: expresses IkappaBalpha super-repressor under control of tetracycline repressor

source_name: IkB-SR induced EJM - 2 days

treatment_protocol:
Treatment type: compound
Agent: doxycycline
Treatment dose: 20 ug/ml
Treatment time: 2 days
Treatment temperature: 37 C


title: IkB-SR induced EJM - 3 days - mAdbID:79135

description: mAdb experiment ID: 79135

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 820;; 660 ScanPower: 100;; 100 LaserPower: 2.9;; 3.07 Temperature: 30.11

tag: Tissue

source_name: IkB-SR induced EJM - 3 days

treatment_protocol:
Treatment type: compound
Agent: doxycycline
Treatment dose: 20 ug/ml
Treatment time: 3 days
Treatment temperature: 37 C


title: MLN treated L363 (12 hours) - sample 1 - mAdbID:70052

description: mAdb experiment ID: 70052

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000A [47890] PMTVolts: 940;; 750 ScanPower: 100;; 100 LaserPower: 1.13163;; 1.89917 Temperature: 36.8603

source_name: MLN treated L363 (12 hours) - sample 1


title: MLN treated L363 (8 hours) - sample 2 - mAdbID:70050

description: mAdb experiment ID: 70050

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000A [47890] PMTVolts: 850;; 750 ScanPower: 100;; 100 LaserPower: 1.14933;; 1.91046 Temperature: 35.8647

source_name: MLN treated L363 (8 hours) - sample 2

treatment_protocol:
Treatment type: small molecule
Agent: MLN120b
Treatment dose: 12.5 microM
Treatment time: 8 hours
Treatment temperature: 37 C


title: MLN treated L363 (8 hours) - sample 1 - mAdbID:71649

description: mAdb experiment ID: 71649

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000A [47890] PMTVolts: 700;; 700 ScanPower: 100;; 100 LaserPower: 1.16;; 1.99 Temperature: 38.43

source_name: MLN treated L363 (8 hours) - sample 1


title: human_hepatocyte_400uM_grepafloxacin_donorA_24hr_prep1

value: Primary Human Hepatocyte

tag: Gender

tag: Source

value: In Vitro Technologies


title: MLN treated L363 (24 hours) - sample 2 - mAdbID:71651

description: mAdb experiment ID: 71651

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000A [47890] PMTVolts: 700;; 700 ScanPower: 100;; 100 LaserPower: 1.25;; 2 Temperature: 38.61

source_name: MLN treated L363 (24 hours) - sample 2

treatment_protocol:
Treatment type: small molecule
Agent: MLN120b
Treatment dose: 12.5 microM
Treatment time: 24 hours
Treatment temperature: 37 C


title: IkB-SR induced EJM - 1 day - mAdbID:79133

description: mAdb experiment ID: 79133

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 840;; 720 ScanPower: 100;; 100 LaserPower: 3.02;; 3.04 Temperature: 29.62

source_name: IkB-SR induced EJM - 1 day

treatment_protocol:
Treatment type: compound
Agent: doxycycline
Treatment dose: 20 ug/ml
Treatment time: 1 day
Treatment temperature: 37 C


title: human_hepatocyte_vehicle_donorA_24hr_prep1


title: MLN treated L363 (24 hours) - sample 3 - mAdbID:67143

description: mAdb experiment ID: 67143

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 720;; 650 ScanPower: 100;; 100 LaserPower: 3.36;; 3.46 Temperature: 31.36

source_name: MLN treated L363 (24 hours) - sample 3


title: human_hepatocyte_400uM_Ciprofloxacin_donorA_24hr_prep2

treatment_protocol: Treated with 400uM ciprofloxacin for 24 hrs.


title: MLN treated L363 (12 hours) - sample 3 - mAdbID:67142

description: mAdb experiment ID: 67142

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 740;; 650 ScanPower: 100;; 100 LaserPower: 3.3;; 3.45 Temperature: 31.15

source_name: MLN treated L363 (12 hours) - sample 3


title: IkB-SR induced EJM - 4 days - mAdbID:79136

description: mAdb experiment ID: 79136

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 820;; 660 ScanPower: 100;; 100 LaserPower: 2.92;; 3.15 Temperature: 30.23

source_name: IkB-SR induced EJM - 4 days

treatment_protocol:
Treatment type: compound
Agent: doxycycline
Treatment dose: 20 ug/ml
Treatment time: 4 days
Treatment temperature: 37 C


title: MLN treated L363 (24 hours) - sample 1 - mAdbID:70054

description: mAdb experiment ID: 70054

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000A [47890] PMTVolts: 940;; 790 ScanPower: 100;; 100 LaserPower: 1.22379;; 1.94739 Temperature: 37.6292

source_name: MLN treated L363 (24 hours) - sample 1


title: B6J12-4.vs.B6J-1_rep1_hyb2

status: Public on Oct 28 2007

city: Cold Spring Harbor

first: Ira

last: Hall

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

hyb_protocol: Hybs were performed in 25 uL of solution consisting of 37.5% formamide, 4x SSC, and O.1% SDS.  Samples were denatured at 95° for 5 min, pre-annealed for 30 min at 37° with 1 µg of mouse COT1 DNA, applied to the microarray, and hybridized under a coverslip at 42°C for 14-18 h.  Slides were washed for 1 min in 0.2% SDS/0.2x SSC, 30 sec in 0.2x SSC,  30 sec in 0.05x SSC, and dried by centrifugation.

scan_protocol: Microarrays were scanned with an Axon GenePix 4000B scanner with pixel size set to 5um. GenePix Pro 4.0 software was used for gridding and quantitation of intensities.

data_processing: Measured intensities without background subtraction were used to calculate ratios.  Data were normalized using an intensity-based lowess curve fitting algorithm similar to that described in Yang et al (Nucleic Acids Research, 30 e15, Feb 15, 2002).

source_name: Bgl II genomic representation of DNA isolated from the liver of a C57BL/6J inbred mouse

label_protocol: 1.5 µg of DNA from genomic representations were differentially labeled with Cy5-dCTP or Cy3-dCTP dyes using the Amersham-Pharmacia Megaprime kit. Labeled DNA was purified with Microcon columns (Millipore) with lowTE.

extract_protocol:
DNA was isolated using the Puregene Kit (Gentra Systems), with the following modifications: livers were flash frozen in liquid nitrogen, ground with mortar and pestle, and dounce-homogenized in 20 ml cell lysis solution. Two additional extrections were performed with phenol/chloroform/isoamyl alcohol, and chloroform/isoamyl alcohol, and DNA was precipitated with 2 volumes isopropanol and 1/10 volume sodium acetate.
1.5 µg of DNA was digested with the Bgl II restriction enzyme for 8-12 hrs at 37°C.  Fragments were column-purified (Qiagen Minielute kit), and universal adaptors were added to fragments by overnight ligation with T4 ligase at 16º C.  After 22 cycles of PCR amplification with the universal primer, resulting genomic representations were predominantly composed of fragments 100-1200 bp in length.  Representations were then column-purified (Qiagen PCR purification kit).

tag: DNA prep ID

tag: Strain

value: liver

tag: Age

value: 4-8 weeks

source_name: Bgl II genomic representation of DNA isolated from the tail of a C57BL/6J inbred mouse

value: tail