title: JH003_ATH1_A11-Hammond-KR2

status: Public on Jan 08 2007

city: Loughborough

last: Nottingham Arabidopsis Stock Centre (NASC)

address: Sutton Bonington Campus

department: School of Biosciences, University of Nottingham

country: United Kingdom

description:
Rows (integer) = 712
Cols (integer) = 712
Number of Probe Sets (integer) = 22810
Background Avg (float) = 60.97
Background Stdev (float) = 1.90
Background Max (float) = 64.7
Background Min (float) = 56.3
Noise Avg (float) = 2.81
Noise Stdev (float) = 0.16
Noise Max (float) = 3.2
Noise Min (float) = 2.5
RawQ (float) = 2.26
Number Cells Masked (integer) = 0
Number Outlier Cells (integer) = 350
Number Cells Modified (integer) = 0
Rows (integer) = 712
Cols (integer) = 712
Number of Cells (integer) = 506944
Image: JH003_ATH1_A11-Hammond-KR2.DAT

hyb_protocol: EukGE-WS2v4; Protocol Type = Hybridization; Parameter Wash A1 Recovery Mixes = 0 (type integer); Parameter Wash A1 Temperature (C) = 25 (type integer); Parameter Number of Wash A1 Cycles = 10 (type integer); Parameter Mixes per Wash A1 Cycle = 2 (type integer); Parameter Wash B Recovery Mixes = 0 (type integer); Parameter Wash B Temperature (C) = 50 (type integer); Parameter Number of Wash B Cycles = 4 (type integer); Parameter Mixes per Wash B Cycle = 15 (type integer); Parameter Stain Temperature (C) = 25 (type integer); Parameter First Stain Time (seconds) = 600 (type integer); Parameter Wash A2 Recovery Mixes = 0 (type integer); Parameter Wash A2 Temperature (C) = 25 (type integer); Parameter Number of Wash A2 Cycles = 10 (type integer); Parameter Mixes per Wash A2 Cycle = 4 (type integer); Parameter Second Stain Time (seconds) = 600 (type integer); Parameter Third Stain Time (seconds) = 600 (type integer); Parameter Wash A3 Recovery Mixes = 0 (type integer); Parameter Wash A3 Temperature (C) = 30 (type integer); Parameter Number of Wash A3 Cycles = 15 (type integer); Parameter Mixes per Wash A3 Cycle = 4 (type integer); Parameter Holding Temperature (C) = 25 (type integer); Software: type: Acquisition and analysis software; Hardware: type: Fluidics Station, Parameter: Parameter Station Number = 1 (type integer), Parameter: Parameter Position = 3 (type integer); Performers: John,Y,Okyere, , Janet,,Higgins

scan_protocol: Protocol Type = CEL Analysis; Parameter Algorithm name = Percentile (type string); Parameter Upper left corner x coordinate = 230 (type integer); Parameter Upper left corner y coordinate = 232 (type integer); Parameter Upper right corner x coordinate = 4501 (type integer); Parameter Upper right corner y coordinate = 246 (type integer); Parameter Lower right corner x coordinate = 4488 (type integer); Parameter Lower right corner y coordinate = 4516 (type integer); Parameter Lower left corner x coordinate = 217 (type integer); Parameter Lower left corner y coordinate = 4502 (type integer); Parameter Percentile = 75 (type integer); Parameter Cell margin = 2 (type integer); Parameter Outlier high = 1.500 (type float); Parameter Outlier low = 1.004 (type float); Software: type: Acquisition and analysis software; Protocol Type = Scan; Parameter Pixel Size = 3 (type integer); Parameter Number of Scans = 2 (type integer); Software: type: Acquisition and analysis software; Hardware: type: Scanner, Parameter: Parameter Scanner ID = not specified (type string), Parameter: Parameter Scanner Type = HP (type string); Performers: John,Y,Okyere, , Janet,,Higgins

data_processing: Protocol Type = CHP Analysis; Parameter Algorithm name = ExpressionStat (type string); Parameter Algorithm version = 5.0 (type string); Parameter Baseline file = not specified (type string); Parameter Alpha1 = 0.04 (type float); Parameter Alpha2 = 0.06 (type float); Parameter Tau = 0.015 (type float); Parameter Gamma1H = 0.0025 (type float); Parameter Gamma1L = 0.0025 (type float); Parameter Gamma2H = 0.003 (type float); Parameter Gamma2L = 0.003 (type float); Parameter Perturbation = 1.1 (type float); Parameter Normalization factor = 1.000000 (type float); Parameter Scale factor = 0.567670 (type float); Parameter Mask file = not specified (type string); Software: type: Acquisition and analysis software;

organism: Arabidopsis thaliana

label_protocol: Preparation of biotin-labeled cRNA; RNA samples were quality controlled using the Agilent 2100 Bioanalyzer. 100 pmol T7-(dT)24 primer (5'-GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGG-(dT)24-3')  was hybridized with the Total RNA ( 8 - 12ug) at 70°C for 10 minutes. First strand cDNA was synthesized by reverse transcription using 400 units SuperScript II Reverse Transcriptase in a reaction containing 50 mM Tris-HCl (pH 8.3), 75 mM KCl, 3 mM MgCl2, 10 mM dithiothreitol (DTT) and 0.5 mM dNTPs at 42C for 1 hour.  The reaction was then put on ice for 2 mins, followed by second strand cDNA synthesis.  130ul of the second strand reaction mix was added to the 20ul  first strand synthesis reaction. The second strand reaction mix  contained 40 units E. coli DNA polymerase I, 10 units E. coli DNA ligase, 2 units  E. coli RNase H and 0.2 mM dNTPs in a buffer containing 20 mMTris-HCl (pH 6.9), 90 mM KCl, 4.6 mM MgCl2, 10mM (NH4)SO4 and 0.15 mM ß-NAD+. The reaction was incubated at 16 C for 2 hours.  10 units T4 DNA Polymerase was added and the reaction incubated for a further 5 minutes at 16 C, then the reaction was terminated using EDTA.  The double-stranded cDNA was cleaned up using the cDNA Cleanup Spin Column supplied in the Affymetrix GeneChip Sample Cleanup Module.  The double-stranded cDNA was used as a template for in Vitro transcription of biotin-labeled cRNA using the ENZO BioArray RNA Transcript Labeling Kit supplied by Affymetrix.  The Transcript Labeling kit produces large amounts of hybridizable biotin-labeled RNA targets by in Vitro transcription from bacteriophage T7 RNA polymerase promoters.  The reaction mixture containing Biotin-Labeled ribonucleotides (ATP, GTP, CTP, UTP with Bio-UTP and Bio-CTP), DTT, RNase inhibitor mix and T7 RNA polymerase was incubated at 37 C for 5 hrs, gently mixing every 30 minutes during the incubation. This produced an average of 40ug biotin-labeled cRNA . The biotin-labeled cRNA  was cleaned up using the cRNA Cleanup Spin Column supplied in the Affymetrix GeneChip Sample Cleanup Module.  The quantity and quality of the cRNA was measured using the Agilent 2100 Bioanalyzer. The total amount of cRNA was calculated, the starting quantity of RNA subtracted to give the quantity of adjusted cRNA.  The cRNA was fragmented by metal-induced hydrolysis to break down full-length cRNA to 35-200 base fragments.  15ug of adjusted cRNA was used to prepare 300ul of hybridization cocktail of which 200ul was hybridized with the GeneChip.   ; Protocol Type = labeling; Performers: John,Y,Okyere, Janet,,Higgins

growth_protocol: unknown; Parameter location = Growth Room; Parameter Atmosphere = Normal; Parameter Humidity = 80 %; Parameter Temperature = imbibed for 3-5 days at 4 ; Performer: John,,Hammond

extract_protocol: Qiagen / Trizol; Protocol: Qiagen RNAeasy kit protocol ; Protocol Type = nucleic_acid_extraction; Performer: John,,Hammond

treatment_protocol: 1/10 MS nutrient solution without any potassium ; Performer: John,,Hammond

tag: OrganismPart

value: all root material

tag: Ecotype

tag: NASC:Growth Stage


title: Whole Genome array hippocampus_cocaine1

status: Public on Jan 09 2007

type: RNA

city: Baltimore

first: Svetlana

middle: I

last: Novikova

state: MD

address: 666 W. Baltimore st

department: Biomedical Sciences

country: USA

institute: University of Maryland

description:
These data were used as preliminary results for paper:
Maternal Cocaine Administration Alters DNA Methylation in Hippocampal Neurons of Neonatal and Prepubertal Mice
Svetlana I. Novikova, Fang He, Jie Bai, Nicholas J. Cutrufello, Ashiwel S. Undie and Michael S. Lidow

hyb_protocol: Hybridizations and washing were carried out as required by “3DNA Array 350: Alexa Fluor 546, Alexa Fluor 647” (Genisphere Inc.) kit protocol “Hybridization of Agilent Oligo Array” with using 2x Agilent Hybridization Buffer. The cDNAs containing the capture sequences are first hybridized to the array overnight (16 hours) in Agilent Hybridization Buffer at 60°C. On the following morning the arrays were washed for 10 minutes with 6X SSC, 0.005% Triton, then for 5 minutes in chilled (+4°C) 0.1X SSC, 0.005% Triton at room temperature and 1 minute in chilled (+4°C) 0.1X SSC. The arrays were dried and incubated at 65°C in dry incubator for 5 minutes to prewarm the array. The 3DNA capture reagents hybridization mixture was added to each array and hybridized complementary to cDNA capture sequence for 3 hours at 65°C. The arrays were washed for 10 minutes with 2X SSC, 0.005% Triton at room temperature and 10 minutes in 0.2X SSC at room temperature. The slides were dried and ready to scan.

scan_protocol: Processed slides were scanned at a GenePix 4100A personal microarray scanner (Axon Instruments) with the lasers excitation to 635 nm (emission filter 670DF40, PMT voltage 695) for Alexa 647   and 532 nm (emission filter 575DF35, PMT voltage 550) for Alexa 546 according manufacturer’s protocol. The scan resolution was 10 microns. The intensity of each spot and ratios of Alexa 647/Alexa 546 were analyzed and finally the differentially expressed genes were selected by GenePix Pro 4.1 software (Axon Instruments). Background was subtracted using “Local background correction” method in GenePix Pro 4.1 software. For quality control we utilized house-keeping genes and special Agilent’s “QC-spots” on array.

data_processing: Data of each slide were further normalized in Acuity 3.1 (Axon Instruments) software by way of locally weighted scatterplot smoothing (LOWESS) method. Normalized data were analyzed via the significant analyses for microarray (SAM) algorithm. Two-class unpaired analysis was applied to compare cocaine samples to the control. SAM calculates a false discovery rate (FDR), which is the median percentage of genes from a list that are likely to be mistakenly identified as differentially expressed. According to the SAM algorithm, genes are identified as differentially expressed based on the difference in expression among the sample groups and the consistency of this expression difference.

label: Alexa 647

molecule: total RNA

organism: Mus musculus

source_name: P3 hippocampus, cocaine

label_protocol: For each assay 2 mkg of RNA from control tissue and 2 mg from experimental tissue were reverse transcribed using SuperScript™ II Reverse Transcriptase (Invitrogen) and 3DNA Array Detection Array 350™ Kit (Genisphere) with primers containing different ‘capture’ sequences for control and experimental samples. The obtained cDNA were  hybridized to microarray slides overnight at 60C in hybridization buffer (Agilent Technologie). For fluorescent labeling of microarray-bound cDNA, the slides will be further incubated for 3 h at 65C with Capture Reagent Hybridization Mixture from a 3DNA Array Detection Array 900™ Kit (Genisphere). In this mixture, Alexa 546 fluorochrome-incorporating dendrimers will contain single-stranded arms complimentary to the ‘capture’ sequence used in the reverse transcription of RNA from the control tissue, while Alexa 647 fluorochrome-incorporating dendrimers will contain single-stranded arms complimentary to the ‘capture’ sequence used in the reverse transcription of RNA from experimental tissue.

growth_protocol:
Laser microdissection.
Upon collection, the brains were cut into left and right hemispheres, which were subjected to freezing for 5 min on aluminium foil placed on top of dry ice. The frozen tissue was transferred to -80oC freezer for storage not exceeding 2 months after collection. For each brain hemisphere selected for the study, the initial serial coronal 12-µm-thick sections were generated on a Zeiss Cryostat (Carl Zeiss, Thornwood, NY). All sections containing hippocampus were mounted on sterile PEN foil-covered slides (Leica Microsystems, Wetzlar, Germany). Slides with sections were boxed without taking out of the cryostat. The boxed slides were transferred to -80oC freezer until use within 2 weeks from sectioning. No more than 20 slides were processed for staining and microdissection at a time. The staining was conducted in RNAs-free environment in laminar flow hood. It included the following 30-sec-long steps: 57% ethanol - distilled water - Histo-Gene stain (Arcturus, Mountain View, CA) - distilled water - 75%,  - 95%, and - 100% ethanol. After that, the sections were air-dried for 0.5-1.0 h. The laser microdissection was performed on an AS LMD Microscope System (Leica Microsystems, Wetzlar, Germany). All dissections were executed by a single investigator without knowledge of the group assignment of the samples. On every section, the pyramidal layer, encompassing the C1, C2 and C3 hippocampal regions was carefully cut out. The pieces of tissue cut out from the left hemisphere of the brains from the two 3-day-old males taken from each litter were combined and used for investigating CGI methylation. The tissue cut out from the right hemisphere of one of these brains was used for analyzing gene expression. The tissue cut out from every 5th section from the right hemisphere of the second brain was used for measuring the total DNA content, while the remaining cut out tissue was used for evaluating the global DNA methylation.

extract_protocol: Total RNA was extracted from the designated tissue by RNeasy Micro kit (Qiagen, Valencia CA). The quantity and quality of the obtained RNA was determined by NANOChip on an 2100 Bioanalyzer (Agilent, Palo Alto, CA). All samples showed the 28S to 18S ratio >1.5 and the absence of low molecular weight smears indicating the appropriateness of the RNA.

treatment_protocol: Timed pregnant CD1 dams were maintained in individual cages in a climate-controlled room on a 12/12-h light/dark cycle. They were divided into two groups. The first (COC-injected) group received subcutaneous (at the dorsum of the neck) injections of 20 mg/kg cocaine hydrochloride (Research Technology Branch, National Institute of Drug Abuse, Rockville, MD) dissolved in 200 µl of 0.9% saline, twice a day (at 8:00 AM and 8:00 PM) from 8th through 19th day of pregnancy (E8 – E19). The second (saline-control) group was subjected to the same schedule of 0.9% saline only injections. The selected period of treatment started prior to hippocampal neurogenesis and ended after all hippocampal pyramidal neurons should have been generated and began to assemble into pyramidal layer. Throughout the treatment, all mice were weighed daily, and from E8, the control and experimental animals were pair-fed, with the daily amount of food (Mouse Chow; Ralston Purina Co. Saint Louis, MO) provided to each control dam being matched to that consumed by the paired experimental dam. Water was available ad libitum. We found that this feeding regiment resulted in similar weight gains from E8 to E19 in both experimental and control animal groups. The animals were allowed to deliver at term (~gestational day 20; P0). From the time of birth, all the litters were fostered by inhalation-procedure-naive surrogate dams that had given birth within the preceding 24-72 h. Ten litters from each group were used in this study. On P3, two male pups from every litter were identified based on the anogenital distance. The selected pups were deeply anesthetized with halothane and their brains were collected. In addition, pieces of liver were dissected out to verify the sex of the animals by TaqMan Gene Expression Mm01339632-s1 Assay Kit for Sry gene-sex determining region of Y chromosome (Applied Biosystems, Foster City, CA). The assay confirmed that all the sacrificed pups were males. The anesthetized pups were used for brain collection. All experiments conducted in this study were approved by the University of Maryland Animal Care and Use Committee.

tag: P3, hippocampus, male, from cocaine-treated mother

label: Alexa 546

source_name: P3 hippocampus, saline

extract_protocol: same as channel 1

tag: P3, hippocampus, male, from saline-control mother


title: E9_Embryo_Wild Type_2

city: Tel Aviv

first: Illana

last: Gozes

address: Einstein

country: Israel

institute: Tel Aviv University

description: Embryo dissections: All procedures involving animals have been approved previously by the Animal Care and Use Committee Tel Aviv University. ADNP heterozygous mice were housed in a 12-h light and 12-h dark cycle facility and free access to rodent chow and water was available. Mice were checked for plug every three hours. Plug day was assigned as day 0 (E0). A definitive determination of the developmental stage of each embryo at the time of harvesting was also based on anatomical analysis. E9 whole embryos were separated from the extra embryonic tissue (yolk sac and amnion), immersed in ice-cold magnesium- and calcium-free phosphate-buffered saline, snap-frozen in liquid nitrogen, and stored at -80°C until analysis. The extra embryonic tissue was stored separately and used for genotyping. Genotyping: Genomic DNA was extracted from embryonic yolk sacs. Lysis buffer (100 mM Tris HCl pH 8.5, 5mM EDTA, 0.2% SDS, 200 mM NaCl, proteinase K 0.35 mg/ml) was added to each sample (0.5ml) followed by a 16hr incubation period at 37°C with gentle shaking. Isopropanol (0.5 ml) was then added and samples were mixed. Precipitated DNA was then transferred to a new tube containing 1ml ethanol, subjected to centrifugation at 20,000g and the resulting DNA pellet was air-dried and dissolved in 50 microLl 10 mM Tris-HCl, pH 8, 1 mM EDTA (TE) buffer. The resulting DNA was then subjected to polymerase chain reaction (PCR) amplification to check for the existence of ADNP and/or neomycin resistance gene in the embryonic genome. The PCR mixtures contained 0.5μg genomic DNA, 0.25 μM of each primer (sense and antisense), 1.5 mM MgCl2 and 3 units Taq polymerase in a final volume of 50 μl. (Buffers and enzyme were obtained from Life Technology Gibco BRL, Paisley, Scotland). PCR was performed using the following cycle parameters: 94 °C for 4 min, followed by 30 cycles, each including 94 °C for 30 s, specific annealing temperature for 40 s and elongation at 72 °C for 40 s. Reactions were terminated at 72 °C for 10 min. Control reactions containing water instead of DNA template for each primer used (PCR-) were included. RNA extraction: Two embryos from the same genotype and gestational time were pooled and RNA was isolated using Qiagene RNeasy mini kit (Quiagene, Hilden, Germany). Because of the small amounts of RNA extracted from one embryo at age E9 (~1.5μg) a two embryo pool comprised of littermates possessing the same genotype was used. For comparative experiments all embryos were at approximately the same age. Gene array: All experiments were performed using Affymetrix MOE430A oligonucleotide arrays, as described at http://www.affymetrix.com/products/arrays/specific/mouse430a_2.affx. Total RNA from each sample was used to prepare biotinylated target RNA, with minor modifications from the manufacturer's recommendations (http://www.affymetrix.com/support/technical/manual/expression_manual.affx). Briefly, 3-5 µg of mRNA was used to generate first-strand cDNA by using a T7-linked oligo(dT) primer. After second-strand synthesis, in vitro transcription was performed with biotinylated UTP and CTP (Enzo Diagnostics), resulting in approximately 100-fold amplification of RNA. A complete description of procedures is available at: http://bioinf.picr.man.ac.uk/mbcf/downloads/GeneChip_Target_Prep_Protocol_CRUK_v_2.pdf. The target cDNA generated from each sample was processed according to manufacturer's recommendation using an Affymetrix GeneChip Instrument System (http://www.affymetrix.com/support/technical/manual/expression_manual.affx). Briefly, spike controls were added to 10 µg fragmented cDNA before overnight hybridization. Arrays were then washed and stained with streptavidin-phycoerythrin, before being scanned on an Affymetrix Gene Chip scanner. A complete description of these procedures is available at http://bioinf.picr.man.ac.uk/mbcf/downloads/GeneChip_Hyb_Wash_Scan_Protocol_v_2_web.pdf Additionally, quality and amount of starting RNA was confirmed using an agarose gel. After scanning, array images were assessed by eye to confirm scanner alignment and the absence of significant bubbles or scratches on the chip surface. 3'/5' ratios for GAPDH and beta-actin were confirmed to be within acceptable limits (0.8-0.88), and BioB spike controls were found to be present on all the arrays, with BioC, BioD and CreX also present in increasing intensity.

data_processing: When scaled to a target intensity of 100 (using Affymetrix MAS 5.0 array analysis software), scaling factors for all arrays were within acceptable limits (0.607-0.982), as were background, Q values and mean intensities.

label: Biotin

source_name: Whole body

tag: Strain

value: C57BL/6 Gender:mixed Age:E9 Tissue:whole embryonic body


title: E9_Embryo_Heterozygous_1

value: C57BL/6, ADNP+/- Gender:mixed Age:E9 Tissue:whole embryonic body

tag: Please refer to

value: Activity-dependent neuroprotective protein:a novel gene essential for brain formation.

tag: Brain Res Dev Brain Res. 2003 Aug 12;144(1):83-90. PMID

value: 12888219 [PubMed - indexed for MEDLINE]


title: St.Clair_1-85_286b_Mt-0_0.30mM-SA-in-0.02%-silwet_Rep1_ATH1

institute: Nottingham Arabidopsis Stock Centre (NASC)

description: Treatment: 0.30 mM SA in 0.02% silwet

data_processing: The data were analysed using Affymetrix Microarray Suite 5.0 (MAS5)

label: biotin


title: JH003_ATH1_A10-Hammond-FR2

description:
Rows (integer) = 712
Cols (integer) = 712
Number of Probe Sets (integer) = 22810
Background Avg (float) = 75.72
Background Stdev (float) = 1.38
Background Max (float) = 79.6
Background Min (float) = 71.8
Noise Avg (float) = 3.59
Noise Stdev (float) = 0.19
Noise Max (float) = 4.3
Noise Min (float) = 3.0
RawQ (float) = 2.71
Number Cells Masked (integer) = 0
Number Outlier Cells (integer) = 211
Number Cells Modified (integer) = 0
Rows (integer) = 712
Cols (integer) = 712
Number of Cells (integer) = 506944
Image: JH003_ATH1_A10-Hammond-FR2.DAT

hyb_protocol: EukGE-WS2v4; Protocol Type = Hybridization; Parameter Wash A1 Recovery Mixes = 0 (type integer); Parameter Wash A1 Temperature (C) = 25 (type integer); Parameter Number of Wash A1 Cycles = 10 (type integer); Parameter Mixes per Wash A1 Cycle = 2 (type integer); Parameter Wash B Recovery Mixes = 0 (type integer); Parameter Wash B Temperature (C) = 50 (type integer); Parameter Number of Wash B Cycles = 4 (type integer); Parameter Mixes per Wash B Cycle = 15 (type integer); Parameter Stain Temperature (C) = 25 (type integer); Parameter First Stain Time (seconds) = 600 (type integer); Parameter Wash A2 Recovery Mixes = 0 (type integer); Parameter Wash A2 Temperature (C) = 25 (type integer); Parameter Number of Wash A2 Cycles = 10 (type integer); Parameter Mixes per Wash A2 Cycle = 4 (type integer); Parameter Second Stain Time (seconds) = 600 (type integer); Parameter Third Stain Time (seconds) = 600 (type integer); Parameter Wash A3 Recovery Mixes = 0 (type integer); Parameter Wash A3 Temperature (C) = 30 (type integer); Parameter Number of Wash A3 Cycles = 15 (type integer); Parameter Mixes per Wash A3 Cycle = 4 (type integer); Parameter Holding Temperature (C) = 25 (type integer); Software: type: Acquisition and analysis software; Hardware: type: Fluidics Station, Parameter: Parameter Station Number = 1 (type integer), Parameter: Parameter Position = 2 (type integer); Performers: John,Y,Okyere, , Janet,,Higgins

scan_protocol: Protocol Type = CEL Analysis; Parameter Algorithm name = Percentile (type string); Parameter Upper left corner x coordinate = 229 (type integer); Parameter Upper left corner y coordinate = 232 (type integer); Parameter Upper right corner x coordinate = 4500 (type integer); Parameter Upper right corner y coordinate = 257 (type integer); Parameter Lower right corner x coordinate = 4476 (type integer); Parameter Lower right corner y coordinate = 4527 (type integer); Parameter Lower left corner x coordinate = 205 (type integer); Parameter Lower left corner y coordinate = 4502 (type integer); Parameter Percentile = 75 (type integer); Parameter Cell margin = 2 (type integer); Parameter Outlier high = 1.500 (type float); Parameter Outlier low = 1.004 (type float); Software: type: Acquisition and analysis software; Protocol Type = Scan; Parameter Pixel Size = 3 (type integer); Parameter Number of Scans = 2 (type integer); Software: type: Acquisition and analysis software; Hardware: type: Scanner, Parameter: Parameter Scanner ID = not specified (type string), Parameter: Parameter Scanner Type = HP (type string); Performers: John,Y,Okyere, , Janet,,Higgins

data_processing: Protocol Type = CHP Analysis; Parameter Algorithm name = ExpressionStat (type string); Parameter Algorithm version = 5.0 (type string); Parameter Baseline file = not specified (type string); Parameter Alpha1 = 0.04 (type float); Parameter Alpha2 = 0.06 (type float); Parameter Tau = 0.015 (type float); Parameter Gamma1H = 0.0025 (type float); Parameter Gamma1L = 0.0025 (type float); Parameter Gamma2H = 0.003 (type float); Parameter Gamma2L = 0.003 (type float); Parameter Perturbation = 1.1 (type float); Parameter Normalization factor = 1.000000 (type float); Parameter Scale factor = 0.433860 (type float); Parameter Mask file = not specified (type string); Software: type: Acquisition and analysis software;


title: St.Clair_1-86_305_Mt-0_0.30mM-SA-in-0.02%-silwet_Rep2_ATH1

description: Treatment: 0.30 mM SA in 0.02% silwet


title: St.Clair_1-78_366_Mt-0_0.02%-silwet_Rep3_ATH1

description: Treatment: 0.02% silwet


title: St.Clair_1-17_317_Col-0_0.30mM-SA-in-0.02%-silwet_Rep2_ATH1

description: Treatment: 0.30 mM SA in 0.02% silwet


title: St.Clair_1-29_362_Cvi-1_0.30mM-SA-in-0.02%-silwet_Rep2_ATH1

description: Treatment: 0.30 mM SA in 0.02% silwet


title: Raghavan_1-3_1MM-1HR-B_Rep2_ATH1

description:
Sample: hormone - 2,4-D, 1 mM, duration: 1 hour
growth media substrate: phytagel  -  1 %  for 14 days
light regime:  darkness  - 48 hours
photoperiod:  16 hr  - 14 day
nutrients:  MS medium  for 14 days
sugar :  sucrose, 1.5 %, 14 days
average daily temperature:  14 days
temperature: 4 C  for 48 hours

treatment_protocol: The chemical 2,4-D was dissolved in water and the pH was adjusted to 7.0. Plates were flooded with 1 mL of stock solutions of 2,4-D.

tag: Stock Code

tag: Developmental stage

value: At this stage the plants had developed four rosette leaves 1.04

tag: Tissue

value: whole plant


title: St.Clair_1-117_450_Van-0_0.02%-silwet_Rep3_ATH1

description: Treatment: 0.02% silwet


title: St.Clair_1-104_304_Tsu-1_0.30mM-SA-in-0.02%-silwet_Rep2_ATH1

description: Treatment: 0.30 mM SA in 0.02% silwet


title: St.Clair_1-54_391_Est_0.30mM-SA-in-0.02%-silwet_Rep3_ATH1

description: Treatment: 0.30 mM SA in 0.02% silwet

source_name: Est


title: Fukuda_1-1_0A_Rep1_ATH1

description:
harvesting: collection after treatment -  0 days
growth media type: liquid culture media
nutrients: MS1  MS salts, 1 ug /ml 2,4-dichlorphenoxyacetic acid and 3% sucrose
nutrients: MS2  MS salts, 3% sucrose, 1 uM brassinolide and 10 mM H3BO3
average daily temperature: 22C

treatment_protocol: no treatment

value: Col-0 suspension cells


title: Weigel_2-9_CHIP-205-C_Rep3_ATH1

description:
germplasm: FRI-Sf-2 in Col
light regime1: short day
light regime2: long day
growth media type: soil
average daily humidity:
average daily temperature: 23C

source_name: FRI-Sf-2 in Col

treatment_protocol: LD 5 days

value: vegetative plant, 10-18 leaves

value: apical region


title: St.Clair_1-33_443_Cvi-1_0.30mM-SA-in-0.02%-silwet_Rep3_ATH1

description: Treatment: 0.30 mM SA in 0.02% silwet


title: Newbury_2-1_non-acc-bulk-control-root(NRO)_Rep1_ATH1

description:
location: Growth Room
Humidity: 80
Temperature: 25
Lighting: 10hrs
Medium: Full mineral medium
Water: weekly

organism: Arabidopsis halleri

source_name: halleri

value: whole root system


title: 11-26 12h v. 16h RNA

city: Stanford

first: Ryan

middle: C

last: Fong

state: CA

address: 318 Campus Dr. W-300 Clark Center

department: Chemical Engineering

institute: Stanford University

description:
Simple annotation: RNA processing, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32047.gif
Strain Name: Low copy number strain CH999/pKOS011-26
Measurement: time(absolute) 16 h

hyb_protocol: not provided

scan_protocol: not provided

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

organism: Streptomyces coelicolor

label_protocol: not provided

extract_protocol: not provided


title: Newbury_2-22_acc-bulk-highZn-leaf(ALH)_Rep1_ATH1

source_name: accumulating bulk

treatment_protocol: 25um Zinc

value: Rosette leaves


title: 11-26* 12h v. 64h RNA

description:
Simple annotation: RNA processing, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32071.gif
Strain Name: High copy number strain CH999/pKOS011-26*
Measurement: time(absolute) 64 h


title: 11-26 12h v. 24h RNA

description:
Simple annotation: RNA processing, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32043.gif
Strain Name: Low copy number strain CH999/pKOS011-26
Measurement: time(absolute) 24 h


title: Raghavan_1-1_CONTROL_Rep1_ATH1

description:
Sample: water   - 1 hours
growth media substrate: phytagel  -  1 %  for 14 days
light regime:  darkness  - 48 hours
photoperiod:  16 hr  - 14 day
nutrients:  MS medium  for 14 days
sugar :  sucrose, 1.5 %, 14 days
average daily temperature:  14 days
temperature: 4 C  for 48 hours

treatment_protocol: Plants were flooded with 1 mL distilled water.


title: Newbury_2-9_non-acc-bulk-control-leaf(NLO)_Rep3_ATH1

source_name: non-accumulating bulk


title: 11-26 12h v. 40h RNA

description:
Simple annotation: RNA processing, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32044.gif
Strain Name: Low copy number strain CH999/pKOS011-26
Measurement: time(absolute) 40 h


title: 11-26* 12h v. 88h RNA

description:
Simple annotation: RNA processing, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32072.gif
Strain Name: High copy number strain CH999/pKOS011-26*
Measurement: time(absolute) 88 h


title: 11-26 12h v. 20h RNA

description:
Simple annotation: RNA processing, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32042.gif
Strain Name: Low copy number strain CH999/pKOS011-26
Measurement: time(absolute) 20 h


title: 11-26* 12h v. 40h RNA

description:
Simple annotation: RNA processing, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32070.gif
Strain Name: High copy number strain CH999/pKOS011-26*
Measurement: time(absolute) 40 h


title: 11-26 12h v. 64h RNA

description:
Simple annotation: RNA processing, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32045.gif
Strain Name: Low copy number strain CH999/pKOS011-26
Measurement: time(absolute) 64 h


title: 11-26 12h v. 88h RNA

description:
Simple annotation: RNA processing, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32046.gif
Strain Name: Low copy number strain CH999/pKOS011-26
Measurement: time(absolute) 88 h


title: 11-26* 12h v. 24h RNA

description:
Simple annotation: RNA processing, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32069.gif
Strain Name: High copy number strain CH999/pKOS011-26*
Measurement: time(absolute) 24 h


title: 11-26* 12h v. 16h RNA

description:
Simple annotation: RNA processing, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32067.gif
Strain Name: High copy number strain CH999/pKOS011-26*
Measurement: time(absolute) 16 h


title: PJ001_AG_75-IV

description:
Rows (integer) = 534
Cols (integer) = 534
Number of Probe Sets (integer) = 8297
Background Avg (float) = 56.59
Background Stdev (float) = 2.44
Background Max (float) = 65.0
Background Min (float) = 52.5
Noise Avg (float) = 1.94
Noise Stdev (float) = 0.26
Noise Max (float) = 2.8
Noise Min (float) = 1.6
RawQ (float) = 1.78
Number Cells Masked (integer) = 0
Number Outlier Cells (integer) = 20
Number Cells Modified (integer) = 0
Rows (integer) = 534
Cols (integer) = 534
Number of Cells (integer) = 285156
Image: PJ001_AG_75-IV.DAT

scan_protocol: Protocol Type = CEL Analysis; Parameter Algorithm name = Percentile (type string); Parameter Upper left corner x coordinate = 233 (type integer); Parameter Upper left corner y coordinate = 235 (type integer); Parameter Upper right corner x coordinate = 4499 (type integer); Parameter Upper right corner y coordinate = 256 (type integer); Parameter Lower right corner x coordinate = 4478 (type integer); Parameter Lower right corner y coordinate = 4521 (type integer); Parameter Lower left corner x coordinate = 213 (type integer); Parameter Lower left corner y coordinate = 4500 (type integer); Parameter Percentile = 75 (type integer); Parameter Cell margin = 2 (type integer); Parameter Outlier high = 1.500 (type float); Parameter Outlier low = 1.004 (type float); Software: type: Acquisition and analysis software; Protocol Type = Scan; Parameter Pixel Size = 3 (type integer); Parameter Number of Scans = 2 (type integer); Software: type: Acquisition and analysis software; Hardware: type: Scanner, Parameter: Parameter Scanner ID = not specified (type string), Parameter: Parameter Scanner Type = HP (type string); Performers: John,Y,Okyere, , Janet,,Higgins

data_processing: Protocol Type = CHP Analysis; Parameter Algorithm name = ExpressionStat (type string); Parameter Algorithm version = 5.0 (type string); Parameter Baseline file = not specified (type string); Parameter Alpha1 = 0.04 (type float); Parameter Alpha2 = 0.06 (type float); Parameter Tau = 0.015 (type float); Parameter Gamma1H = 0.0025 (type float); Parameter Gamma1L = 0.0025 (type float); Parameter Gamma2H = 0.003 (type float); Parameter Gamma2L = 0.003 (type float); Parameter Perturbation = 1.1 (type float); Parameter Normalization factor = 1.000000 (type float); Parameter Scale factor = 0.774768 (type float); Parameter Mask file = not specified (type string); Software: type: Acquisition and analysis software;

growth_protocol: unknown; Parameter Light = 16 hours light/8 hours dark; Parameter Medium = MS; Parameter Nutrients = 0.5% sucrose; Performer: Paul,,Jarvis

extract_protocol: Unknown; Protocol Type = nucleic_acid_extraction; Performer: Paul,,Jarvis

value: Whole Seedlings

tag: GeneticModification

value: T-DNA insertion in Toc75 (At4g09070) gene

tag: StrainOrLine


title: 11-26* 12h v. 20h RNA

description:
Simple annotation: RNA processing, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32068.gif
Strain Name: High copy number strain CH999/pKOS011-26*
Measurement: time(absolute) 20 h


title: SEKH0840_EM

city: Cleveland

first: Peter

middle: A

last: Wilkinson

state: Ohio

address: 2103 Cornell Road

department: Pathology / Systems Biology & Bioinformatics

institute: Case Western Reserve University

description: Peripheral blood mononuclear cells (PBMCs) from healthy adult individuals were isolated by Ficoll-HyPaque (Pharmacia) density gradient. We first enriched for CD4+ T cells using negative immunomagnetic beads selection (Automacs, Myltenii), cells were then labeled with anti-CD4-APCcy7, anti-CD45RA-ECD, anti-CD27-FITC and anti-CCR7-PEcy7 and sorted into Na�ve cells described as CD4+, CD45RA+, CD27+ and CCR7+, Central Memory cells (TCM) described as CD4+, CD45RA-, CD27+ and CCR7+ cells and Effector Memory cells (TEM) described as CD4+, CD45RA-, CD27- and CCR7- cells. Sorting was performed using a BDAria (BD Pharmingen).  Purity of the TCM and TEM sub-populations was ranging from 96 to 99%. All procedures were done at 4C to avoid any changes in cell phenotype or gene expression.

hyb_protocol: similar to direct labelling protocol lists at UHN Microarray facility web site.

scan_protocol: Scanned at 16 bits using the ScanArray Express Scanner (Packard Bioscience) at 10micro-meter resolution at 635 nm (Cy5) and 532 nm (Cy3) using Genepix Pro 6.0 analysis software (Molecular Divices Corporation)

data_processing: Each quantified output file was run though the following pre-processing steps using R (URL: www.r-project.org)and the Limma package. For Minimum Intensity filtering, R and G values were treated with a surrogate replacement policy for estimating sub-threshold values. For normalization within Arrays, the raw merged R and G channels were lowess-normalized (grouped by print-tip) and transformed to log2 ratios (70).

organism: Homo sapiens

source_name: Universal RNA

tag: Tissue:Universal RNA

source_name: PBMC from healthy donors

extract_protocol: Total RNA was isolated from beads purified CD4+T cell populations using an RNA extraction kit (Quiagen) then amplified using the MessageAmp RNA kit (Ambion) as per the manufacturer's instructions.


title: LM001_AG_A1_MUR_NOT

description:
Rows (integer) = 534
Cols (integer) = 534
Number of Probe Sets (integer) = 8297
Background Avg (float) = 75.02
Background Stdev (float) = 2.74
Background Max (float) = 83.9
Background Min (float) = 70.5
Noise Avg (float) = 2.38
Noise Stdev (float) = 0.27
Noise Max (float) = 3.1
Noise Min (float) = 1.7
RawQ (float) = 2.16
Number Cells Masked (integer) = 0
Number Outlier Cells (integer) = 67
Number Cells Modified (integer) = 0
Rows (integer) = 534
Cols (integer) = 534
Number of Cells (integer) = 285156
Image: LM001_AG_A1_MUR_NOT.DAT

hyb_protocol: EukGE-WS2v4; Protocol Type = Hybridization; Parameter Wash A1 Recovery Mixes = 0 (type integer); Parameter Wash A1 Temperature (C) = 25 (type integer); Parameter Number of Wash A1 Cycles = 10 (type integer); Parameter Mixes per Wash A1 Cycle = 2 (type integer); Parameter Wash B Recovery Mixes = 0 (type integer); Parameter Wash B Temperature (C) = 50 (type integer); Parameter Number of Wash B Cycles = 4 (type integer); Parameter Mixes per Wash B Cycle = 15 (type integer); Parameter Stain Temperature (C) = 25 (type integer); Parameter First Stain Time (seconds) = 600 (type integer); Parameter Wash A2 Recovery Mixes = 0 (type integer); Parameter Wash A2 Temperature (C) = 25 (type integer); Parameter Number of Wash A2 Cycles = 10 (type integer); Parameter Mixes per Wash A2 Cycle = 4 (type integer); Parameter Second Stain Time (seconds) = 600 (type integer); Parameter Third Stain Time (seconds) = 600 (type integer); Parameter Wash A3 Recovery Mixes = 0 (type integer); Parameter Wash A3 Temperature (C) = 30 (type integer); Parameter Number of Wash A3 Cycles = 15 (type integer); Parameter Mixes per Wash A3 Cycle = 4 (type integer); Parameter Holding Temperature (C) = 25 (type integer); Software: type: Acquisition and analysis software; Hardware: type: Fluidics Station, Parameter: Parameter Station Number = 1 (type integer), Parameter: Parameter Position = 1 (type integer); Performers: John,Y,Okyere, , Janet,,Higgins

scan_protocol: Protocol Type = CEL Analysis; Parameter Algorithm name = Percentile (type string); Parameter Upper left corner x coordinate = 236 (type integer); Parameter Upper left corner y coordinate = 232 (type integer); Parameter Upper right corner x coordinate = 4501 (type integer); Parameter Upper right corner y coordinate = 215 (type integer); Parameter Lower right corner x coordinate = 4520 (type integer); Parameter Lower right corner y coordinate = 4479 (type integer); Parameter Lower left corner x coordinate = 255 (type integer); Parameter Lower left corner y coordinate = 4497 (type integer); Parameter Percentile = 75 (type integer); Parameter Cell margin = 2 (type integer); Parameter Outlier high = 1.500 (type float); Parameter Outlier low = 1.004 (type float); Software: type: Acquisition and analysis software; Protocol Type = Scan; Parameter Pixel Size = 3 (type integer); Parameter Number of Scans = 2 (type integer); Software: type: Acquisition and analysis software; Hardware: type: Scanner, Parameter: Parameter Scanner ID = not specified (type string), Parameter: Parameter Scanner Type = HP (type string); Performers: John,Y,Okyere, , Janet,,Higgins

data_processing: Protocol Type = CHP Analysis; Parameter Algorithm name = ExpressionStat (type string); Parameter Algorithm version = 5.0 (type string); Parameter Baseline file = not specified (type string); Parameter Alpha1 = 0.04 (type float); Parameter Alpha2 = 0.06 (type float); Parameter Tau = 0.015 (type float); Parameter Gamma1H = 0.0025 (type float); Parameter Gamma1L = 0.0025 (type float); Parameter Gamma2H = 0.003 (type float); Parameter Gamma2L = 0.003 (type float); Parameter Perturbation = 1.1 (type float); Parameter Normalization factor = 1.000000 (type float); Parameter Scale factor = 0.382152 (type float); Parameter Mask file = not specified (type string); Software: type: Acquisition and analysis software;

growth_protocol: unknown; Parameter location = Growth Room; Parameter Humidity = not specified; Parameter Temperature = 22oC; Parameter Lighting = 24h; Parameter Medium = compost; Parameter Water = every other day.; Parameter Stratification = 1 week at 4oC in a domestic fridge ; Performer: Luis,,Mur

extract_protocol: Qiagen Plant RNAeasy kit; Protocol: Seedlings harvested and snap-frozen in liquid nitrogen and RNA extracted as described in the Qiagen RNAeasy kit. ; Protocol Type = nucleic_acid_extraction; Performer: Luis,,Mur

treatment_protocol: Each sample, NO-11/02 - control and NO-12/02 represent four pooled experiments. In each experiment, RNA was extracred from ~8 leaves. ; Performer: Luis,,Mur


title: LM001_AG_A2_MUR_WDC

description:
Rows (integer) = 534
Cols (integer) = 534
Number of Probe Sets (integer) = 8297
Background Avg (float) = 76.78
Background Stdev (float) = 3.04
Background Max (float) = 86.3
Background Min (float) = 71.2
Noise Avg (float) = 2.67
Noise Stdev (float) = 0.43
Noise Max (float) = 4.1
Noise Min (float) = 2.0
RawQ (float) = 2.19
Number Cells Masked (integer) = 0
Number Outlier Cells (integer) = 46
Number Cells Modified (integer) = 0
Rows (integer) = 534
Cols (integer) = 534
Number of Cells (integer) = 285156
Image: LM001_AG_A2_MUR_WDC.DAT

scan_protocol: Protocol Type = CEL Analysis; Parameter Algorithm name = Percentile (type string); Parameter Upper left corner x coordinate = 236 (type integer); Parameter Upper left corner y coordinate = 232 (type integer); Parameter Upper right corner x coordinate = 4500 (type integer); Parameter Upper right corner y coordinate = 221 (type integer); Parameter Lower right corner x coordinate = 4512 (type integer); Parameter Lower right corner y coordinate = 4486 (type integer); Parameter Lower left corner x coordinate = 248 (type integer); Parameter Lower left corner y coordinate = 4497 (type integer); Parameter Percentile = 75 (type integer); Parameter Cell margin = 2 (type integer); Parameter Outlier high = 1.500 (type float); Parameter Outlier low = 1.004 (type float); Software: type: Acquisition and analysis software; Protocol Type = Scan; Parameter Pixel Size = 3 (type integer); Parameter Number of Scans = 2 (type integer); Software: type: Acquisition and analysis software; Hardware: type: Scanner, Parameter: Parameter Scanner ID = not specified (type string), Parameter: Parameter Scanner Type = HP (type string); Performers: John,Y,Okyere, , Janet,,Higgins

data_processing: Protocol Type = CHP Analysis; Parameter Algorithm name = ExpressionStat (type string); Parameter Algorithm version = 5.0 (type string); Parameter Baseline file = not specified (type string); Parameter Alpha1 = 0.04 (type float); Parameter Alpha2 = 0.06 (type float); Parameter Tau = 0.015 (type float); Parameter Gamma1H = 0.0025 (type float); Parameter Gamma1L = 0.0025 (type float); Parameter Gamma2H = 0.003 (type float); Parameter Gamma2L = 0.003 (type float); Parameter Perturbation = 1.1 (type float); Parameter Normalization factor = 1.000000 (type float); Parameter Scale factor = 0.379374 (type float); Parameter Mask file = not specified (type string); Software: type: Acquisition and analysis software;

growth_protocol: unknown; Parameter location = Growth Room; Parameter Temperature = 22oC; Parameter Lighting = 24h; Parameter Medium = compost; Parameter Water = every other day.; Parameter Stratification = 1 week at 4oC in a domestic fridge ; Performer: Luis,,Mur


title: Expression analysis of primary mouse megakaryocyte differentiation-MK4 replicate

city: Boston

first: Ramesh

last: Shivdasani

state: MA

address: 44 Binney St.

department: Medical Oncology

institute: Dana-Farber Cancer Institute

hyb_protocol: The purified cRNA is fragmented in order to facilitate the subsequent hybridization step. The cRNA is purified from the fragmentation reaction using phenol/chloroform extraction and ethanol precipitation. The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. The chips are then transferred to a fluidics instrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE.

scan_protocol: Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured. These measures provide the basis of subsequent biostatistical analysis.

data_processing: Affymetrix MAS 5.0

source_name: Mouse primary Megakaryocytes stage MK4

label_protocol:
RNA is converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis is then carried out.
The double-stranded cDNA is used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates.
The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using the RNeasy system (Qiagen). The cRNA is quantified spectrophotometrically and purity of the cRNA is also assessed by spectrophometric measurements. Those cRNA.s that fall outside of an acceptable range will not be carried forward in the analysis. Should this occur, investigators would be notified and asked to provide a new RNA sample

extract_protocol: Trizol reagents

tag: mouse CD1 day 14.5 fetal liver cultured megakaryocytes collected at day 4


title: Expression analysis of primary mouse megakaryocyte differentiation-MK6 replicate1

source_name: Mouse primary Megakaryocytes stage MK6

tag: mouse CD1 day 14.5 fetal liver cultured megakaryocytes collected at day 6


title: JH001_AG_A3-Hammo-P24_2

description:
Rows (integer) = 534
Cols (integer) = 534
Number of Probe Sets (integer) = 8297
Background Avg (float) = 55.21
Background Stdev (float) = 1.81
Background Max (float) = 60.9
Background Min (float) = 52.8
Noise Avg (float) = 1.64
Noise Stdev (float) = 0.15
Noise Max (float) = 2.1
Noise Min (float) = 1.3
RawQ (float) = 1.66
Number Cells Masked (integer) = 0
Number Outlier Cells (integer) = 36
Number Cells Modified (integer) = 0
Rows (integer) = 534
Cols (integer) = 534
Number of Cells (integer) = 285156
Image: JH001_AG_A3-Hammo-P24_2.DAT

hyb_protocol: EukGE-WS2v4; Protocol Type = Hybridization; Parameter Wash A1 Recovery Mixes = 0 (type integer); Parameter Wash A1 Temperature (C) = 25 (type integer); Parameter Number of Wash A1 Cycles = 10 (type integer); Parameter Mixes per Wash A1 Cycle = 2 (type integer); Parameter Wash B Recovery Mixes = 0 (type integer); Parameter Wash B Temperature (C) = 50 (type integer); Parameter Number of Wash B Cycles = 4 (type integer); Parameter Mixes per Wash B Cycle = 15 (type integer); Parameter Stain Temperature (C) = 25 (type integer); Parameter First Stain Time (seconds) = 600 (type integer); Parameter Wash A2 Recovery Mixes = 0 (type integer); Parameter Wash A2 Temperature (C) = 25 (type integer); Parameter Number of Wash A2 Cycles = 10 (type integer); Parameter Mixes per Wash A2 Cycle = 4 (type integer); Parameter Second Stain Time (seconds) = 600 (type integer); Parameter Third Stain Time (seconds) = 600 (type integer); Parameter Wash A3 Recovery Mixes = 0 (type integer); Parameter Wash A3 Temperature (C) = 30 (type integer); Parameter Number of Wash A3 Cycles = 15 (type integer); Parameter Mixes per Wash A3 Cycle = 4 (type integer); Parameter Holding Temperature (C) = 25 (type integer); Software: type: Acquisition and analysis software; Hardware: type: Fluidics Station, Parameter: Parameter Station Number = 1 (type integer), Parameter: Parameter Position = 4 (type integer); Performers: John,Y,Okyere, , Janet,,Higgins

scan_protocol: Protocol Type = CEL Analysis; Parameter Algorithm name = Percentile (type string); Parameter Upper left corner x coordinate = 234 (type integer); Parameter Upper left corner y coordinate = 235 (type integer); Parameter Upper right corner x coordinate = 4499 (type integer); Parameter Upper right corner y coordinate = 255 (type integer); Parameter Lower right corner x coordinate = 4481 (type integer); Parameter Lower right corner y coordinate = 4519 (type integer); Parameter Lower left corner x coordinate = 215 (type integer); Parameter Lower left corner y coordinate = 4499 (type integer); Parameter Percentile = 75 (type integer); Parameter Cell margin = 2 (type integer); Parameter Outlier high = 1.500 (type float); Parameter Outlier low = 1.004 (type float); Software: type: Acquisition and analysis software; Protocol Type = Scan; Parameter Pixel Size = 3 (type integer); Parameter Number of Scans = 2 (type integer); Software: type: Acquisition and analysis software; Hardware: type: Scanner, Parameter: Parameter Scanner ID = not specified (type string), Parameter: Parameter Scanner Type = HP (type string); Performers: John,Y,Okyere, , Janet,,Higgins

data_processing: Protocol Type = CHP Analysis; Parameter Algorithm name = ExpressionStat (type string); Parameter Algorithm version = 5.0 (type string); Parameter Baseline file = not specified (type string); Parameter Alpha1 = 0.04 (type float); Parameter Alpha2 = 0.06 (type float); Parameter Tau = 0.015 (type float); Parameter Gamma1H = 0.0025 (type float); Parameter Gamma1L = 0.0025 (type float); Parameter Gamma2H = 0.003 (type float); Parameter Gamma2L = 0.003 (type float); Parameter Perturbation = 1.1 (type float); Parameter Normalization factor = 1.000000 (type float); Parameter Scale factor = 1.436632 (type float); Parameter Mask file = not specified (type string); Software: type: Acquisition and analysis software;

growth_protocol: unknown; Parameter Atmosphere = Normal; Parameter Humidity = 80% in growth cabinet; Parameter Light = 16h day length until hydroponics, then constant light in growth cabinet; Parameter Medium = MS in polycarbonate discs until 21 days, then hydroponics in growth cabinet; Parameter Temperature = 24 C; Parameter Water = Hydropoincs; Parameter Nutrients = 1% sucrose in agar, then see in-vivo treatment; Parameter Treatment = None; Parameter Location = Growth room until 21 days, then hydroponics in Saxcil growth cabinet; Performer: John,,Hammond

treatment_protocol: Full nutrient solution: KH2PO4 0.25mM, KOH 0.5mM, MgSO4.7H2O 0.75mM, CaCl2.2H2O 0.025 FeNaEDTA 0.1mM, H3BO3 0.03 mM, MnSO4.4H2O 0.01mM, ZnSO4.7H2O 0.001mM, CuSO4.5H2O 0.003 mM, Na2MoO4.2H2O 0.0005mM ; Performer: John,,Hammond

tag: Age time point

value: 100 hours after nutrient removal


title: Expression analysis of primary mouse megakaryocyte differentiation-MKP replicate

source_name: Mouse primary Megakaryocytes stage MKP


title: JH001_AG_A2-Hammo-PO6_2

description:
Rows (integer) = 534
Cols (integer) = 534
Number of Probe Sets (integer) = 8297
Background Avg (float) = 56.94
Background Stdev (float) = 1.79
Background Max (float) = 61.4
Background Min (float) = 53.6
Noise Avg (float) = 1.62
Noise Stdev (float) = 0.14
Noise Max (float) = 1.9
Noise Min (float) = 1.4
RawQ (float) = 1.61
Number Cells Masked (integer) = 0
Number Outlier Cells (integer) = 38
Number Cells Modified (integer) = 0
Rows (integer) = 534
Cols (integer) = 534
Number of Cells (integer) = 285156
Image: JH001_AG_A2-Hammo-PO6_2.DAT

scan_protocol: Protocol Type = CEL Analysis; Parameter Algorithm name = Percentile (type string); Parameter Upper left corner x coordinate = 233 (type integer); Parameter Upper left corner y coordinate = 235 (type integer); Parameter Upper right corner x coordinate = 4498 (type integer); Parameter Upper right corner y coordinate = 265 (type integer); Parameter Lower right corner x coordinate = 4470 (type integer); Parameter Lower right corner y coordinate = 4529 (type integer); Parameter Lower left corner x coordinate = 205 (type integer); Parameter Lower left corner y coordinate = 4500 (type integer); Parameter Percentile = 75 (type integer); Parameter Cell margin = 2 (type integer); Parameter Outlier high = 1.500 (type float); Parameter Outlier low = 1.004 (type float); Software: type: Acquisition and analysis software; Protocol Type = Scan; Parameter Pixel Size = 3 (type integer); Parameter Number of Scans = 2 (type integer); Software: type: Acquisition and analysis software; Hardware: type: Scanner, Parameter: Parameter Scanner ID = not specified (type string), Parameter: Parameter Scanner Type = HP (type string); Performers: John,Y,Okyere, , Janet,,Higgins

data_processing: Protocol Type = CHP Analysis; Parameter Algorithm name = ExpressionStat (type string); Parameter Algorithm version = 5.0 (type string); Parameter Baseline file = not specified (type string); Parameter Alpha1 = 0.04 (type float); Parameter Alpha2 = 0.06 (type float); Parameter Tau = 0.015 (type float); Parameter Gamma1H = 0.0025 (type float); Parameter Gamma1L = 0.0025 (type float); Parameter Gamma2H = 0.003 (type float); Parameter Gamma2L = 0.003 (type float); Parameter Perturbation = 1.1 (type float); Parameter Normalization factor = 1.000000 (type float); Parameter Scale factor = 1.218438 (type float); Parameter Mask file = not specified (type string); Software: type: Acquisition and analysis software;

treatment_protocol: This source has no KH2PO4 (No Phosphate!). It has 0.125mM additional K2SO4. ; Performer: John,,Hammond

tag: OrganismPart

value: 4 hours after nutrient removal


title: Expression analysis of primary mouse megakaryocyte differentiation-MK3

source_name: Mouse primary Megakaryocytes stage MK3

tag: mouse CD1 day 14.5 fetal liver cultured megakaryocytes collected at day 3


title: Expression analysis of primary mouse megakaryocyte differentiation-MK6


title: Expression analysis of primary mouse megakaryocyte differentiation-MK3 replicate


title: Expression analysis of primary mouse megakaryocyte differentiation-MK6 replicate2


title: JH001_AG_A1-Hammo-NPK_2

description:
Rows (integer) = 534
Cols (integer) = 534
Number of Probe Sets (integer) = 8297
Background Avg (float) = 49.74
Background Stdev (float) = 0.82
Background Max (float) = 52.7
Background Min (float) = 48.1
Noise Avg (float) = 1.40
Noise Stdev (float) = 0.09
Noise Max (float) = 1.6
Noise Min (float) = 1.2
RawQ (float) = 1.49
Number Cells Masked (integer) = 0
Number Outlier Cells (integer) = 17
Number Cells Modified (integer) = 0
Rows (integer) = 534
Cols (integer) = 534
Number of Cells (integer) = 285156
Image: JH001_AG_A1-Hammo-NPK_2.DAT

scan_protocol: Protocol Type = CEL Analysis; Parameter Algorithm name = Percentile (type string); Parameter Upper left corner x coordinate = 233 (type integer); Parameter Upper left corner y coordinate = 236 (type integer); Parameter Upper right corner x coordinate = 4498 (type integer); Parameter Upper right corner y coordinate = 277 (type integer); Parameter Lower right corner x coordinate = 4458 (type integer); Parameter Lower right corner y coordinate = 4541 (type integer); Parameter Lower left corner x coordinate = 193 (type integer); Parameter Lower left corner y coordinate = 4501 (type integer); Parameter Percentile = 75 (type integer); Parameter Cell margin = 2 (type integer); Parameter Outlier high = 1.500 (type float); Parameter Outlier low = 1.004 (type float); Software: type: Acquisition and analysis software; Protocol Type = Scan; Parameter Pixel Size = 3 (type integer); Parameter Number of Scans = 2 (type integer); Software: type: Acquisition and analysis software; Hardware: type: Scanner, Parameter: Parameter Scanner ID = not specified (type string), Parameter: Parameter Scanner Type = HP (type string); Performers: John,Y,Okyere, , Janet,,Higgins

data_processing: Protocol Type = CHP Analysis; Parameter Algorithm name = ExpressionStat (type string); Parameter Algorithm version = 5.0 (type string); Parameter Baseline file = not specified (type string); Parameter Alpha1 = 0.04 (type float); Parameter Alpha2 = 0.06 (type float); Parameter Tau = 0.015 (type float); Parameter Gamma1H = 0.0025 (type float); Parameter Gamma1L = 0.0025 (type float); Parameter Gamma2H = 0.003 (type float); Parameter Gamma2L = 0.003 (type float); Parameter Perturbation = 1.1 (type float); Parameter Normalization factor = 1.000000 (type float); Parameter Scale factor = 1.501865 (type float); Parameter Mask file = not specified (type string); Software: type: Acquisition and analysis software;

tag: Ecotype

tag: NASC:Growth Stage


title: JH001_AG_A4-Hammo-P72_2

description:
Rows (integer) = 534
Cols (integer) = 534
Number of Probe Sets (integer) = 8297
Background Avg (float) = 69.92
Background Stdev (float) = 2.46
Background Max (float) = 77.7
Background Min (float) = 64.7
Noise Avg (float) = 2.12
Noise Stdev (float) = 0.25
Noise Max (float) = 2.9
Noise Min (float) = 1.7
RawQ (float) = 2.00
Number Cells Masked (integer) = 0
Number Outlier Cells (integer) = 22
Number Cells Modified (integer) = 0
Rows (integer) = 534
Cols (integer) = 534
Number of Cells (integer) = 285156
Image: JH001_AG_A4-Hammo-P72_2.DAT

scan_protocol: Protocol Type = CEL Analysis; Parameter Algorithm name = Percentile (type string); Parameter Upper left corner x coordinate = 234 (type integer); Parameter Upper left corner y coordinate = 234 (type integer); Parameter Upper right corner x coordinate = 4499 (type integer); Parameter Upper right corner y coordinate = 256 (type integer); Parameter Lower right corner x coordinate = 4479 (type integer); Parameter Lower right corner y coordinate = 4521 (type integer); Parameter Lower left corner x coordinate = 213 (type integer); Parameter Lower left corner y coordinate = 4499 (type integer); Parameter Percentile = 75 (type integer); Parameter Cell margin = 2 (type integer); Parameter Outlier high = 1.500 (type float); Parameter Outlier low = 1.004 (type float); Software: type: Acquisition and analysis software; Protocol Type = Scan; Parameter Pixel Size = 3 (type integer); Parameter Number of Scans = 2 (type integer); Software: type: Acquisition and analysis software; Hardware: type: Scanner, Parameter: Parameter Scanner ID = not specified (type string), Parameter: Parameter Scanner Type = HP (type string); Performers: John,Y,Okyere, , Janet,,Higgins

data_processing: Protocol Type = CHP Analysis; Parameter Algorithm name = ExpressionStat (type string); Parameter Algorithm version = 5.0 (type string); Parameter Baseline file = not specified (type string); Parameter Alpha1 = 0.04 (type float); Parameter Alpha2 = 0.06 (type float); Parameter Tau = 0.015 (type float); Parameter Gamma1H = 0.0025 (type float); Parameter Gamma1L = 0.0025 (type float); Parameter Gamma2H = 0.003 (type float); Parameter Gamma2L = 0.003 (type float); Parameter Perturbation = 1.1 (type float); Parameter Normalization factor = 1.000000 (type float); Parameter Scale factor = 1.009822 (type float); Parameter Mask file = not specified (type string); Software: type: Acquisition and analysis software;


title: GM12264

status: Public on Jan 07 2007

city: Philadelphia

first: Michael

middle: Patrick

last: Morley

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

institute: Perelman School of Medicine at the University of Pennsylvania

description: The cells were grown at a density of 5 x 105 cells/ ml in RPMI 1640 with 15% FBS, 100 U penicillin/ml, 100 ugm streptomycin sulfate/ml, 1% L-glutamine at 37°C in a humidified 5% CO2 chamber. RNA was extracted using the Qiagen mini-kits

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix Microarray Suite version 5.0

source_name: lymphoblastoid cell lines from the CEU, CHB and JPT samples in the International HapMap Collection.

label_protocol: standard Affymetrix procedures

tag: lymphoblastoid cell line


title: GM17761


title: PJ001_AG_Ppil

description:
Rows (integer) = 534
Cols (integer) = 534
Number of Probe Sets (integer) = 8297
Background Avg (float) = 61.98
Background Stdev (float) = 1.56
Background Max (float) = 65.9
Background Min (float) = 59.1
Noise Avg (float) = 2.49
Noise Stdev (float) = 0.25
Noise Max (float) = 3.1
Noise Min (float) = 2.0
RawQ (float) = 2.50
Number Cells Masked (integer) = 0
Number Outlier Cells (integer) = 504
Number Cells Modified (integer) = 0
Rows (integer) = 534
Cols (integer) = 534
Number of Cells (integer) = 285156
Image: PJ001_AG_Ppil.DAT

scan_protocol: Protocol Type = CEL Analysis; Parameter Algorithm name = Percentile (type string); Parameter Upper left corner x coordinate = 236 (type integer); Parameter Upper left corner y coordinate = 235 (type integer); Parameter Upper right corner x coordinate = 4501 (type integer); Parameter Upper right corner y coordinate = 242 (type integer); Parameter Lower right corner x coordinate = 4495 (type integer); Parameter Lower right corner y coordinate = 4507 (type integer); Parameter Lower left corner x coordinate = 229 (type integer); Parameter Lower left corner y coordinate = 4500 (type integer); Parameter Percentile = 75 (type integer); Parameter Cell margin = 2 (type integer); Parameter Outlier high = 1.500 (type float); Parameter Outlier low = 1.004 (type float); Software: type: Acquisition and analysis software; Protocol Type = Scan; Parameter Pixel Size = 3 (type integer); Parameter Number of Scans = 2 (type integer); Software: type: Acquisition and analysis software; Hardware: type: Scanner, Parameter: Parameter Scanner ID = not specified (type string), Parameter: Parameter Scanner Type = HP (type string); Performers: John,Y,Okyere, , Janet,,Higgins

data_processing: Protocol Type = CHP Analysis; Parameter Algorithm name = ExpressionStat (type string); Parameter Algorithm version = 5.0 (type string); Parameter Baseline file = not specified (type string); Parameter Alpha1 = 0.04 (type float); Parameter Alpha2 = 0.06 (type float); Parameter Tau = 0.015 (type float); Parameter Gamma1H = 0.0025 (type float); Parameter Gamma1L = 0.0025 (type float); Parameter Gamma2H = 0.003 (type float); Parameter Gamma2L = 0.003 (type float); Parameter Perturbation = 1.1 (type float); Parameter Normalization factor = 1.000000 (type float); Parameter Scale factor = 0.922912 (type float); Parameter Mask file = not specified (type string); Software: type: Acquisition and analysis software;

growth_protocol: unknown; Parameter Light = 16 hours light/8 hours dark; Parameter Medium = MS; Parameter Temperature = Normal; Parameter Nutrients = 0.5% sucrose; Performer: Paul,,Jarvis

value: T-DNA insertion in Toc33 gene


title: GM11840


title: GM18940


title: Expression analysis of primary mouse megakaryocyte differentiation-MK4


title: GM17759


title: GM12056


title: Expression analysis of primary mouse megakaryocyte differentiation-MKP


title: GM17757


title: PJ001_AG_A1-SK-Col

description:
Rows (integer) = 534
Cols (integer) = 534
Number of Probe Sets (integer) = 8297
Background Avg (float) = 50.47
Background Stdev (float) = 2.12
Background Max (float) = 57.8
Background Min (float) = 47.2
Noise Avg (float) = 1.65
Noise Stdev (float) = 0.20
Noise Max (float) = 2.2
Noise Min (float) = 1.3
RawQ (float) = 1.57
Number Cells Masked (integer) = 0
Number Outlier Cells (integer) = 11
Number Cells Modified (integer) = 0
Rows (integer) = 534
Cols (integer) = 534
Number of Cells (integer) = 285156
Image: PJ001_AG_A1-SK-Col.DAT

scan_protocol: Protocol Type = CEL Analysis; Parameter Algorithm name = Percentile (type string); Parameter Upper left corner x coordinate = 235 (type integer); Parameter Upper left corner y coordinate = 234 (type integer); Parameter Upper right corner x coordinate = 4500 (type integer); Parameter Upper right corner y coordinate = 248 (type integer); Parameter Lower right corner x coordinate = 4487 (type integer); Parameter Lower right corner y coordinate = 4513 (type integer); Parameter Lower left corner x coordinate = 222 (type integer); Parameter Lower left corner y coordinate = 4499 (type integer); Parameter Percentile = 75 (type integer); Parameter Cell margin = 2 (type integer); Parameter Outlier high = 1.500 (type float); Parameter Outlier low = 1.004 (type float); Software: type: Acquisition and analysis software; Protocol Type = Scan; Parameter Pixel Size = 3 (type integer); Parameter Number of Scans = 2 (type integer); Software: type: Acquisition and analysis software; Hardware: type: Scanner, Parameter: Parameter Scanner ID = not specified (type string), Parameter: Parameter Scanner Type = HP (type string); Performers: John,Y,Okyere, , Janet,,Higgins

data_processing: Protocol Type = CHP Analysis; Parameter Algorithm name = ExpressionStat (type string); Parameter Algorithm version = 5.0 (type string); Parameter Baseline file = not specified (type string); Parameter Alpha1 = 0.04 (type float); Parameter Alpha2 = 0.06 (type float); Parameter Tau = 0.015 (type float); Parameter Gamma1H = 0.0025 (type float); Parameter Gamma1L = 0.0025 (type float); Parameter Gamma2H = 0.003 (type float); Parameter Gamma2L = 0.003 (type float); Parameter Perturbation = 1.1 (type float); Parameter Normalization factor = 1.000000 (type float); Parameter Scale factor = 0.998392 (type float); Parameter Mask file = not specified (type string); Software: type: Acquisition and analysis software;


title: GM17755


title: GM17756


title: GM17753


title: GM17754


title: GM17746


title: GM17752


title: GM17737


title: GM17738


title: GM17744


title: GM17740


title: GM17734


title: GM17739


title: GM17733


title: GM17747


title: GM17742


title: GM17741


title: GM17736


title: GM17735


title: GM17745


title: GM18608


title: GM18637


title: GM18570


title: GM17743


title: GM18620


title: GM18562


title: GM18636


title: GM18624


title: GM18612


title: GM18635


title: GM18632


title: GM18564


title: GM18621


title: GM18611


title: GM18623


title: GM18622


title: GM18576


title: GM19007


title: GM18999


title: GM18981


title: GM19003


title: GM18566


title: GM18579


title: GM18964


title: GM18592


title: GM18577


title: GM19000


title: GM18594


title: GM18582


title: GM18573


title: GM18563


title: GM18545


title: GM18593


title: GM18558


title: GM18991


title: GM18605


title: GM18537


title: GM18526


title: GM18524


title: GM18990


title: GM18561


title: GM18995


title: GM18532


title: GM18547


title: GM18603


title: GM18992


title: GM18529


title: GM18987


title: GM18994


title: GM19005


title: GM18969


title: GM18974


title: GM18978


title: GM18972


title: GM18971


title: GM18976


title: GM18980


title: GM18959


title: GM18970


title: GM18968


title: GM18960


title: GM18540


title: GM18975


title: GM18943


title: GM18948


title: GM18966


title: GM18552


title: GM18953


title: GM18967


title: GM18973


title: GM18555


title: GM18952


title: GM18965


title: GM18947


title: GM18542


title: GM18949


title: GM18942


title: GM18961


title: G-WT, biological replicate 5

status: Public on Jan 06 2007

city: Worcester

first: Feng

last: He

address: 368 Plantation Street

department: Microbiology and Physiological Systems

institute: University of Massachusetts Medical School

description: Wild-type yeast strain HFY114

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Yeast YG-S98 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: 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 250.

organism: Saccharomyces cerevisiae

source_name: Wild-type yeast strain HFY114

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: Cells were grown in YEPD at 30°C

extract_protocol: Hot phenol

tag: Genotype, WT


title: GM18550


title: GM18956


title: E-WT, biological replicate 4

description: Wild-type yeast strain HFY114


title: G-edc3D, biological replicate 5

description: edc3 deletion strain CFY25

source_name: edc3 deletion strain CFY25

tag: Genotype, edc3::URA3


title: E-edc3D, biological replicate 4

description: edc3 deletion strain CFY25


title: C-WT, biological replicate 3

description: Wild-type yeast strain HFY114


title: GM18944


title: C-edc3D, biological replicate 3

description: edc3 deletion strain CFY25


title: GM18945


title: A-edc3D, biological replicate 1

description: edc3 deletion strain CFY25


title: B-edc3D, biological replicate 2

description: edc3 deletion strain CFY25


title: B-WT, biological replicate 2

description: Wild-type yeast strain HFY114


title: Kainate-hippocampus, biological rep2

status: Public on Jan 04 2007

city: Maebashi

first: Noriyuki

last: Akahoshi

state: Gunma

address: 3-39-22 Showa-machi

department: Molecular and Cellular Neurobiology

country: Japan

institute: Gunma University Graduate School of Medicine

description: Gene expression data from a hippocampus from mouse injected 15 mg/kg kainate

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

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 1000.

source_name: hippocampus

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 12 microgram total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

treatment_protocol: Kainate (15 mg/kg x 3) ip injected at postnatal day 23

tag: C57BL/6N, postnatal day 30


title: Kainate-hippocampus, biological rep1


title: Kainate-hippocampus, biological rep4


title: Kainate-hippocampus, biological rep3


title: A-WT, biological replicate 1

description: Wild-type yeast strain HFY114


title: Kainate-hippocampus, biological rep5


title: Saline control-hippocampus, biological rep6

description: Gene expression data from a hippocampus of saline-injected mouse

treatment_protocol: saline ip injection at postnatal day 23


title: L7 vs sensory cluster 3 (DAA array)

status: Public on Jan 05 2007

city: St Augustine

first: Andrea

middle: B

last: Kohn

state: FL

address: 9505 Ocean Shore Blvd

department: Whitney lab

institute: University of Florida

description: L7 neuron vs sensory cluster

hyb_protocol: The recommended amount of 750 ng of labeled cRNA was fragmented and hybridized to the arrays using recommended procedures described in the In situ Hybridization Kit PlusTM (Agilent Technologies). Controls provided in the In situ Hybridization Kit were spiked in at the time of hybridization. The arrays were washed according to the manufactures recommended protocol.

scan_protocol: The arrays were scanned on an Agilent Technologies G2565AA Microarray ScannerTM. Data were extracted after scanning using Agilent’s Feature Extraction 5.1.1TM software

data_processing: The balancing between the Cy3 and Cy5 signals within each array was performed by the RANK order method using LOWESS smoothing procedure as implemented in the Agilent feature extraction software version 7.0 (http://chem.agilent.com/scripts/LiteraturePDF.asp?iWHID=30997). The background on all arrays analyzed for the Cy3 and Cy5 channels was observed to be nearly identical (41.8  1.1) over all 44,000 features. No local background subtraction was performed; instead the data was filtered by P-values obtained from fitting the signal and background values and spatial detrending algorithm.  Only data that had P-values of less than or equal to 0.01 (meaning feature signal is significantly and positively higher than background signal) on both Cy3 and Cy5 channels from each array was used for further analysis (“floor”). A suite of algorithms are also included in the processing of the final TIFF image involving an error-model proprietary to Agilent that has been pre-determined to give the best corrected data for downstream analysis.  All experiments were performed in triplicates from three independent samples from 3 different animals.

organism: Aplysia californica

source_name: L7 Neuron

label_protocol: cRNA production was preformed using Agilent’s Low RNA Input Linear Amplification kitTM (Agilent Technologies). All amplification reactions involved only one round of amplification. Concentration of the cRNA was determined by GeneSpec IIITM and the 2100 Bioanalyzer both described above. The cRNA was labeled either using the direct method in Agilent’s Low RNA Input Linear Amplification kit or with an indirect technique using the MicroMax ASAP RNA labeling kitTM (PerkinElmer).

growth_protocol: Aplysia californica were obtained from the NIH/University of Miami National Resource for Aplysia and held in 40-400 liter aquaria with circulating fresh seawater at 15-17º C.

extract_protocol: Total RNA was extracted using RNAqueousTM or RNAqueous-MicroTM (Ambion, Austin, TX) kits depending on sample size. Before further processing of the RNA, quality was checked using a 2100 BioanalyzerTM (Agilent Technologies). Small aliquots of extracted RNA were loaded on a 6000 Nano Lab chip that produces an electropherogram image along with a gel-like image of the sample representing peak ratios of the 28s/18s RNA contained in the sample. Moreover it provides information about potential DNA contamination and the approximate RNA concentration. Additionally RNA concentration was measured spectrophotometrically by using the GeneSpec III systemTM (Mirai Bio).

treatment_protocol: Aplysia californica weighing 100-160g were used. Animals were anesthetized by injection of 60% (volume/body weight) isotonic MgCl2 (337mM) prior to removal of the CNS. Ganglia were mechanical removed with fine forceps and scissors and cell were isolated as described above. Neurons were then fixed in 75% ethanol for several minutes and RNA isolated immediately.

tag: Aplysia californica weighing 100-160g

tag: L7 was identified electorphysiologically

source_name: Sensory cluster

tag: Sensory cluster was identified and isolated


title: Nicotine-hippocampus, biological rep3

description: Gene expression data from a hippocampus from mouse injected 10 mg/kg nicotine

treatment_protocol: Nicotine (10 mg/kg x 3) ip injected at postnatal day 23


title: Nicotine-hippocampus, biological rep1


title: L7 vs sensory cluster 1 (DAA array)

description: L7 neuron vs sensory cluster

tag: sensory cluster was identified and isolated


title: Saline control-hippocampus, biological rep5


title: L7 vs sensory cluster 3 (AAA array)

description: L7 neuron vs sensory cluster


title: Nicotine-hippocampus, biological rep4


title: L7 vs sensory cluster 2 (DAA array)

description: L7 neuron vs sensory cluster


title: Saline control-hippocampus, biological rep4


title: Saline control-hippocampus, biological rep3


title: Nicotine-hippocampus, biological rep2


title: Nicotine-hippocampus, biological rep5


title: Saline control-hippocampus, biological rep2


title: Nicotine-hippocampus, biological rep6


title: L7 vs sensory cluster 2 (AAA array)

description: L7 neuron vs sensory cluster

source_name: Sensory Cluster


title: Nicotine-neocortex, biological rep5

description: Gene expression data from a neocortex from mouse injected 10 mg/kg nicotine

source_name: neocortex


title: Nicotine-neocortex, biological rep6


title: Saline control-hippocampus, biological rep1


title: Sir4-regulated gene expression in Candida glabrata (Exp 2-1)

first: Brendan

last: Cormack

address: Hunterian Building 617, 725 N. Wolfe St.

department: Molecular Biology & Genetics

institute: Johns Hopkins Univ. School of Medicine

description: This is experiment 1 of a dye-swap experiment. Experiment 2 is deposited in GSM153754.

hyb_protocol: Both Cy5- and Cy3- cDNA probes were resuspened into hybridization buffer (35% formamide, 5*SSC, 0.1%SDS, 0.1 mg/ml denatured salmon sperm DNA) and combined to a total volume of 40 ul. The probe mix was denatured at 100 C for 10 s and quickly cooled on ice, then it was added on a microarray slides. The slides was covered with a cover glass and incubated in a chamber (Corning) at 42 C for 16-18 hrs. The washing protocol follows the manual for UltraGAPS coated slides (Corning).

scan_protocol: Hybridized slides was scaned by Axon 4000B microarray scanner with 100% power and PMT ranging 600-800. Data were acquired by Axon GenePix 5.0 software.

data_processing: The median signal captured from Cy5-channel (F635) and from Cy3-channel (F532) was used to calculate C. glabrata gene expression ratio in SIR4 null versus in wild type cells.

organism: Nakaseomyces glabratus

source_name: C. glabrata SIR4 null strain

label_protocol: 20 ug of total RNA was used to synthesize Cy5-cDNA probes with an anchor primer [(dT)18(dA/dG/dC)] in the presence of Cy5-dCTP (PerkinElmer) using SuperscriptTM III reverse transcriptase (Invitrogen). The probe was purified using MinElute TM reaction Cleanup kit (Qiagen) and vaccum dried.

growth_protocol: C. glabrata SIR4 null strain grown in 100 ml YPD medium for 5 hrs at 30 C with agitation of 150 rpm (Start O.D. 0.02, final O.D. 0.5).

extract_protocol: The cell pellet was disrupted using 0.5 mm glass beads in a fast bead-beater. Total RNA was extracted using acid phenol. The RNA was further purified by RNeasy Mini kit (Qiagen).

tag: C. glabrata SIR4 null strain (Bg1217) derived from wild type clinical isolate Bg2.

source_name: C. glabrata wild type strain Bg2

label_protocol: same as above

growth_protocol: C. glabrata wild type strain Bg2 was grown in 100 ml YPD medium for 5 hrs at 30 C with agitation of 150 rpm (Start O.D. 0.02, final O.D. 0.4).

extract_protocol: same as above

tag: C. glabrata wild type strain Bg2


title: Sir4-regulated gene expression in Candida glabrata (Exp 1-1)

description: This is experiment 1 of a dye-swap experiment. Experiment 2 is deposited in GSM153752.


title: L7 vs sensory cluster 1 (AAA array)

description: L7 neuron vs sensory cluster

source_name: Neuron L7

tag: Sensory cluster neurons were identified and isloated


title: Sir4-regulated gene expression in Candida glabrata (Exp 1-2)

description: This is experiment 2 of a dye-swap experiment. Experiment 1 is deposited in GSM153750.


title: Sir4-regulated gene expression in Candida glabrata (Exp 2-2)

description: This is experiment 2 of a dye-swap experiment. Experiment 1 is deposited in GSM153753.


title: Nicotine-neocortex, biological rep3


title: Nicotine-neocortex, biological rep4


title: Sir2-regulated gene expression in Candida glabrata (Exp 2-2)

description: This is experiment 2 of a dye-swap experiment. Experiment 1 is deposited in GSM153744.

data_processing: The median signal captured from Cy5-channel (F635) and from Cy3-channel (F532) was used to calculate C. glabrata gene expression ratio in SIR2 null versus in wild type cells.

source_name: C. glabrata SIR2 null strain

growth_protocol: C. glabrata SIR2 null strain grown in 100 ml YPD medium for 5 hrs at 30 C with agitation of 150 rpm (Start O.D. 0.02, final O.D. 0.4).

tag: C. glabrata SIR2 null strain (Bg1216) derived from wild type clinical isolate Bg2


title: Sir2-regulated gene expression in Candida glabrata (Exp 2-1)

description: This is experiment 1 of a dye-swap experiment. Experiment 2 is deposited in GSM153749.

tag: C. glabrata SIR2 null strain (Bg1216) derived from wild type clinical isolate Bg2.


title: Nicotine-neocortex, biological rep1


title: Nicotine-neocortex, biological rep2


title: Sir2-regulated gene expression in Candida glabrata (Exp 1-2)

description: This is experiment 2 of a dye-swap experiment. Experiment 1 is deposited in GSM153742.


title: Sir2-regulated gene expression in Candida glabrata (Exp 1-1)

description: This is experiment 1 of a dye-swap experiment. Experiment 2 is deposited in GSM153743.


title: Hst2-regulated gene expression in Candida glabrata (Exp 2-2)

description: This is experiment 2 of a dye-swap experiment. Experiment 1 is deposited in GSM153713.

data_processing: The median signal captured from Cy5-channel (F635) and from Cy3-channel (F532) was used to calculate C. glabrata gene expression ratio in HST2 null versus in wild type cells.

source_name: C. glabrata HST2 null strain

growth_protocol: C. glabrata HST2 null strain grown in 100 ml YPD medium for 5 hrs at 30 C with agitation of 150 rpm (Start O.D. 0.02, final O.D. 0.4).

tag: C. glabrata HST2 null strain (Bg1219) derived from wild type clinical isolate Bg2


title: Kainate-neocortex, biological rep3

description: Gene expression data from a neocortex from mouse injected 15 mg/kg kainate


title: Kainate-neocortex, biological rep2


title: Kainate-neocortex, biological rep1


title: Adult occipital cortex cocaine4

description:
Pregnant Swiss Webster mice were used as a model
because cocaine treatment in these animals has been shown
to result in offspring with reduced cerebral cortical mass.

hyb_protocol: The resultant cDNAs were hybridized to microarray slides for 16 h in Agilent Hybridization Buffer (Agilent Technol) at 60C. Upon completion of the hybridization, the slides were washed for 10 min with 0.005% Triton in 6xsodium chloride/sodium citrate buffer (pH 7; SSC) at room temperature and then for five more min with 0.005% Triton in 0.1xSSC and 1 more minute in 0.1xSSC (pH 7), both at 4C. Washed slides were air-dried for 30 s. For fluorescent labeling of microarray-bound cDNA, the slides were incubated for 3 h at 65C with Capture Reagent Hybridization Mixture from 3DNA Array Detection Kit (Genesphere). In this mixture, Alexa 546 fluorochromei ncorporating dendrimers contained single-stranded arms complimentary to the dcaptureT sequences used in the reverse transcription of RNA from control tissue, while Alexa 647 fluorochrome-incorporating dendrimers contained arms complimentary to the capture sequences used in reverse transcription of RNA from experimental tissue. The labeling reaction was terminated by washing of the microarray slides at room temperature for 10 min with 0.005% Triton in 2xSSC and for another 10 min with in 0.2xSSC. After that, the slides were air-dried for 30 s.

scan_protocol: The processed microarray slides were scanned at 10 mkm resolution on a GenePix 4100A scanner (Axon Instr., Union City, CA) with the laser excitation at 532 nm [emission filter 575DF35 (green); photomultiplier voltage 550] for Alexa 546 (control samples) and the laser excitation at 635 nm [emission filter 670DF40 (red); photomultiplier voltage 695] for Alexa 647 (experimental samples). The signals were converted into 16-bits-per pixel resolution images, providing color depth of 65,536 levels. The densitometry was performed with GenePix Pro 4.1 software (Axon Instr.). Background was subtracted using the dlocal background correctionT procedure available in the software. Quality control utilized 255 positive controls, 161 negative controls and 646 QC-spots present on Agilent’s arrays.

data_processing:
For replicates within a slide, median signal values were
calculated. For each array, the data were normalized in
Acuity 3.1 software (Axon Instr.) by applying locally
weighted scatterplot smoothing (LOWESS) transformation.
The between array scale normalization
was done  using intensity log10 ratio distribution box plots (GeneSight
software, BioDiscovery, El Segundo, CA) for verification.
The box plots of the fully normalized data showed fairly
similar spread for all microarray slides used in this study.
Statistical analysis of the normalized data was conducted
by the Significant Analyses for Microarray Algorithm
(SAM) using Excel macros available at Stanford
SAM website. In the analyses of
both frontal and occipital regions of the fetal cerebral wall,
the cut-off thresholds were set to identify the maximum
number of cocaine exposure-regulated genes at the minimal
false discovery rate (FDR) allowed by SAM for a given set
of microarray data. For both regions, the FDR rates were
<0.5%.

source_name: adult occipital cortex, cocaine

label_protocol:
For each assay, 5 mkg of RNA from
control tissue and 5 mkg of RNA from experimental tissue
were reverse transcribed using 3DNA Array Detection Kit
(Genesphere, Hatfield, PA) with primers containing different
dcaptureT sequences for control and experimental
samples. SuperScript II Reverse Transcriptase for these
reactions was purchased from Gibco BRL (Gaithersburg,
MD).
 For fluorescent labeling of microarray-bound cDNA, the slides
were incubated for 3 h at 65 8C with Capture Reagent
Hybridization Mixture from 3DNA Array Detection Kit
(Genesphere).

extract_protocol:
Tissue from control and  experimental animals
were used in the processing of a single microarray slide
(Part G4121A, Agilent Technol). Five slides were processed
per region. For a given region, the
tissue for each microarray slide was obtained from a
separate set of control and experimental litters. Total RNA
was isolated using TRIzol Reagent (Invitrogen, Carlsbad,
CA). The yield of total RNA was determined by absorbance
at 260 nm on a DU 640 Spectrophotometer (Beckman
Coulter, Fullerton, CA). The 260/280 nm ratios of the
samples were >1.8.

treatment_protocol:
Timed pregnant Swiss Webster (CFW; Charles River
Lab. Wilmington, MA) dams were maintained in individual
cages in a climate-controlled room on a 12/12-h light/
dark cycle. They were divided into two groups. The first
(experimental) group received subcutaneous (at the dorsum
of the neck) injections of 20 mg/kg cocaine hydrochloride
(Research Technology Branch, National Institute
of Drug Abuse, Rockville, MD) dissolved in 200 mkl of
0.9% saline, twice a day (at 8:00 AM and 8:00 PM) from
8th through 18th day of pregnancy (E8–E18).  The cocaine treatment was designed to replicate the one capable of reducing cerebral
cortical mass in mouse offspring. Also, the
relatively protracted period the chronic treatment was
chosen to maximize the changes in the tissue expression
of cocaine-regulated genes of interest. Throughout the
treatment, all mice were weighed daily, and, from E8, the
control and experimental animals were pair-fed, with the
daily amount of food (Mouse Chow; Ralston Purina Saint
Louis, MO) provided to each control dam being matched
to that consumed by the paired experimental dam. Water
was available ad libitum. We found that this feeding
regiment resulted in similar weight gains from E8 to E18
in both experimental and control animal groups
(46.41F0.45% and 44.99F0.59% respectively). After delivery animals were grown one month. On P30 the animals were
anesthetized by peritoneal injection of 50 mg/kg sodium
pentobarbital (Abbott Lab., Abbott Park, IL). The frontal cerebral wall (containing cerebral cortex and underlying transient cortical zones
anterior to the striatal level) and the occipital cerebral wall
(containing cerebral cortex and underlying transient
cortical zones posterior to the level of the hippocampus)
were dissected and stored in liquid
nitrogen prior to analysis. The animal experimentations
used in this study were approved by the University of
Maryland Animal Care and Use Committee.

tag: P30 occipital cortex, mothers were cocaine-treated

source_name: adult occipital cortex, saline

label_protocol: The same as Channel 1, but with Alexa 546

extract_protocol: the same as Channel 1

treatment_protocol:
The second (control) group was subjected to the same schedule of
0.9% saline only injections.

tag: P30 occipital cortex, mothers were saline-control


title: Kainate-neocortex, biological rep4


title: Hst2-regulated gene expression in Candida glabrata (Exp 2-1)

description: This is experiment 1 of a dye-swap experiment. Experiment 2 is deposited in GSM153715.


title: Kainate-neocortex, biological rep5


title: Adult occipital cortex cocaine5


title: Adult frontal cortex cocaine5

source_name: adult frontal cortex, cocaine

tag: P30 frontal cortex, mothers were cocaine-treated

source_name: adult frontal cortex, saline

tag: P30 frontal cortex, mothers were saline-control


title: Adult occipital cortex cocaine3


title: Adult frontal cortex cocaine4


title: Hst2-regulated gene expression in Candida glabrata (Exp 1-1)

description: This is experiment 1 of a dye-swap experiment. Experiment 2 is deposited in GSM153708.


title: Adult occipital cortex cocaine2


title: Fetal frontal cortex cocaine5

source_name: fetal frontal cortex, cocaine

extract_protocol:
Tissue from two control and two experimental fetuses
were used in the processing of a single microarray slide
(Part G4121A, Agilent Technol). Five slides were processed
per region of the fetal cerebral wall. For a given region, the
tissue for each microarray slide was obtained from a
separate set of control and experimental litters. Total RNA
was isolated using TRIzol Reagent (Invitrogen, Carlsbad,
CA). The yield of total RNA was determined by absorbance
at 260 nm on a DU 640 Spectrophotometer (Beckman
Coulter, Fullerton, CA). The 260/280 nm ratios of the
samples were >1.8.

treatment_protocol:
Timed pregnant Swiss Webster (CFW; Charles River
Lab. Wilmington, MA) dams were maintained in individual
cages in a climate-controlled room on a 12/12-h light/
dark cycle. They were divided into two groups. The first
(experimental) group received subcutaneous (at the dorsum
of the neck) injections of 20 mg/kg cocaine hydrochloride
(Research Technology Branch, National Institute
of Drug Abuse, Rockville, MD) dissolved in 200 mkl of
0.9% saline, twice a day (at 8:00 AM and 8:00 PM) from
8th through 18th day of pregnancy (E8–E18).  The cocaine treatment was designed to replicate the one capable of reducing cerebral
cortical mass in mouse offspring. Also, the
relatively protracted period the chronic treatment was
chosen to maximize the changes in the tissue expression
of cocaine-regulated genes of interest. Throughout the
treatment, all mice were weighed daily, and, from E8, the
control and experimental animals were pair-fed, with the
daily amount of food (Mouse Chow; Ralston Purina Saint
Louis, MO) provided to each control dam being matched
to that consumed by the paired experimental dam. Water
was available ad libitum. We found that this feeding
regiment resulted in similar weight gains from E8 to E18
in both experimental and control animal groups
(46.41F0.45% and 44.99F0.59% respectively). On E18,
1 h after the morning treatment, the animals were
anesthetized by peritoneal injection of 50 mg/kg sodium
pentobarbital (Abbott Lab., Abbott Park, IL) and their
uteri were removed. The frontal cerebral wall (containing
cerebral cortex and underlying transient cortical zones
anterior to the striatal level) and the occipital cerebral wall
(containing cerebral cortex and underlying transient
cortical zones posterior to the level of the hippocampus)
were dissected from the fetuses and stored in liquid
nitrogen prior to analysis. The animal experimentations
used in this study were approved by the University of
Maryland Animal Care and Use Committee.

tag: E18 fetal frontal cortex from cocaine-treated mothers

source_name: fetal frontal cortex, saline

tag: E18 fetal frontal cortex from saline-control mothers


title: Hst1-regulated gene expression in Candida glabrata (Exp 3-2)

description: This is experiment 2 of a dye-swap experiment. Experiment 1 is deposited in GSM153704.

data_processing: The median signal captured from Cy5-channel (F635) and from Cy3-channel (F532) was used to calculate C. glabrata gene expression ratio in HST1 null versus in wild type cells.

source_name: C. glabrata HST1 null strain

growth_protocol: C. glabrata HST1 null strain grown in 100 ml YPD medium for 5 hrs at 30 C with agitation of 150 rpm (Start O.D. 0.02, final O.D. 0.2).

tag: C. glabrata HST1 null strain (Bg1218) derived from wild type clinical isolate Bg2


title: Adult occipital cortex cocaine1


title: Adult frontal cortex cocaine2


title: Adult frontal cortex cocaine3


title: Hst1-regulated gene expression in Candida glabrata (Exp 3-1)

description: This is experiment 1 of a dye-swap experiment. Experiment 2 is deposited in GSM153705.


title: Hst2-regulated gene expression in Candida glabrata (Exp 1-2)

description: This is experiment 2 of a dye-swap experiment. Experiment 1 is deposited in GSM153706.


title: Adult frontal cortex cocaine1

source_name: Adult frontal cortex, cocaine

source_name: Adult frontal cortex, saline


title: Saline control-neocortex, biological rep6

description: Gene expression data from a neocortex of saline-injected mouse

tag: C57BL/6N, postnatal day 30


title: Saline control-neocortex, biological rep5


title: Fetal frontal cortex cocaine4


title: Saline control-neocortex, biological rep4


title: Hst1-regulated gene expression in Candida glabrata (Exp 2-2)

description: This is experiment 2 of a dye-swap experiment. Experiment 1 is deposited in GSM153702.


title: Fetal frontal cortex cocaine2

source_name: Fetal frontal cortex, cocaine


title: Fetal frontal cortex cocaine3


title: Fetal occipital cortex cocaine5

source_name: Fetal occipital cortex, cocaine

tag: E18 fetal occipital cortex from cocaine-treated mothers

source_name: Fetal occipital cortex, saline

tag: E18 fetal occipital cortex from saline-control mothers


title: Saline control-neocortex, biological rep3

source_name: neocortex


title: Saline control-neocortex, biological rep2


title: Hst1-regulated gene expression in Candida glabrata (Exp 2-1)

description: This is experiment 1 of a dye-swap experiment. Experiment 2 is deposited in GSM153703.

source_name: C. glabrata wild type strain Bg2


title: Fetal occipital cortex cocaine4


title: rpoH mt vs wt_heat shock (15-37ºC) Exp2.1

status: Public on Jan 03 2007

first: Leyla

last: Slamti

address: 136 Harrison Ave

department: Molecular biology and microbiology

institute: Tufts University/HHMI

description: Vibrio cholerae El Tor N16961 total mRNA, heat shock for 20 min from 15ºC to 37ºC

data_processing: Intensity dependent normalization per spot and per chip, Lowess algorithm

organism: Vibrio cholerae

source_name: wild-type 37ºC

tag: Vibrio cholerae El Tor N16961, heat shock 20 min, 15ºC to 37ºC

source_name: rpoH 37ºC


title: Fetal occipital cortex cocaine1

source_name: fetal occipital cortex, cocaine

tag: Fetal (E18) occipital cortex from cocaine-treated mothers

tag: Fetal (E18) occipital cortex from saline-control mothers


title: Fetal occipital cortex cocaine3


title: Hst1-regulated gene expression in Candida glabrata

description: This is experiment 1 of a dye-swap experiment. Experiment 2 is deposited in GSM.

tag: C. glabrata wild type strain Bg2


title: rpoH mt vs wt_heat shock (15-37ºC) Exp3.2

description: Vibrio cholerae El Tor N16961, heat shock for 20 min from 15ºC to 37ºC


title: rpoH mt vs wt_heat shock (15-37ºC) Exp2.2


title: rpoH mt vs wt_heat shock (15-37ºC) Exp1.2


title: rpoH mt vs wt_heat shock (15-37ºC) Exp3.1


title: rpoH mt vs wt_heat shock (15-37ºC) Exp1.1


title: Hst1-regulated gene expression in Candida glabrata (Exp 1-2)

description: This is experiment 2 of a dye-swap experiment. Experiment 1 is deposited in GSM152133.


title: Fetal Occipital cortex cocaine1

data_processing:
For replicates within a slide, median signal values were
calculated. For each array, the data were normalized in
Acuity 3.1 software (Axon Instr.) by applying locally
weighted scatterplot smoothing (LOWESS) transformation.
The between array scale normalization
was done  using intensity log10 ratio distribution box plots (GeneSight
software, BioDiscovery, El Segundo, CA) for verification.
The box plots of the fully normalized data showed fairly
similar spread for all microarray slides used in this study.
Statistical analysis of the normalized data was conducted
by the Significant Analyses for Microarray Algorithm
(SAM [74]) using Excel macros available at Stanford
SAM website. In the analyses of
both frontal and occipital regions of the fetal cerebral wall,
the cut-off thresholds were set to identify the maximum
number of cocaine exposure-regulated genes at the minimal
false discovery rate (FDR) allowed by SAM for a given set
of microarray data. For both regions, the FDR rates were
<0.5%.