title: 50% hydrogen used as sole electron donor in defined minimal media

status: Public on Jul 02 2007

type: mixed

city: Calgary

first: Sean

middle: Michael

last: Caffrey

state: Alberta

address: 2500 University Dr NW

department: Biological Scineces

institute: University of Calgary

description: Normalized data obtained from 4 arrays.

hyb_protocol: Dried probes from the treatment condition (cDNA) and universal reference (gDNA) were mixed and diluted to 40 µl using a hybridization solution containing 50% (vol/vol) formamide, 5x SSC, 0.1% (wt/vol) SDS and 0.1 mg/ml herring sperm DNA. This solution was then incubated at 98 °C for 5 minutes and then kept at 60 °C. 16 ul of 3x SSC solution was added to the wells at the ends of the microarray slides to maintain proper chamber humidity, and then the hybridization solution was applied to the Corning UltraGAPS microarray slide which had been pre-washed according to manufacturer specification (Corning, New York). The slides were incubated for 17 hours in Corning hybridization chambers and then washed according the manufacturer’s specifications and dried in a centrifuge.

scan_protocol: The hybridized slides were scanned on a PerkinElmer Scanarray 5000 scanner (PerkinElmer, Massachusetts).

data_processing: Spot and background intensities were quantified using TIGR’s Spotfinder software. The gDNA channel was used as the control for spot uniformity and labeling efficiency. Spots were flagged and rejected if the spot was saturated, of irregular size, missing in one channel or had a poor signal to noise ratio (lower than 2 times the median local background). Data was normalized with a lowpass filter and with total intensity normalization. These normalized data columns were then analyzed with Stanford Tools SAM (Significance Analysis of Microarrays) which median centered the data averaged the duplicate spots and replicate arrays and generated a q-value to represent the probability that the if the spot is included as differentially expressed that it is a false positive.

label: Alexa Fluor 647

organism: Nitratidesulfovibrio vulgaris str. Hildenborough

source_name: 50% hydrogen fed Culture

label_protocol: Amino modified cDNA was generated from 10 ug of total RNA using indirect cDNA labeling and random hexamers utilizing the Indirect SuperScript labeling kit from invitrogen. Amino-modified gDNA was generated using 1 µg of gDNA using indirect labeling with random hexamers utilizing the Bioprime indirect labeling kit from Invitrogen. The amino-modified cDNA was then coupled with Alexa fluor 647 and the amino-modified gDNA with Alexa fluor 555.

growth_protocol: D. vulgaris was cultured at 30 °C in 1 L Erlenmeyer flasks containing 500 ml of defined Widdel-Pfenning (WP) medium containing 3 mM acetate and 28 mM sulfate. The medium was bubbled with oxygen-free mixed gas consisting of either 0.5% (vol/vol), 5% or 50% hydrogen, 10% CO2 and the balance made up by N2. Alternatively, 65 mM lactate was the sole electron donor in cultures gassed with 10% CO2 and 90% N2. Gas was delivered at 100 ml/min after passing through a heated (325 °C) copper reduction tube for oxygen removal.

extract_protocol: Total RNA was extracted from mid-log phase cells using Invitrogen Trizol and Bacterial Max reagents. The RNA was purified with the Qiagen RNA Easy kit with on column DNase digestion. RNA quality and quantity were assessed using the absorbance ratio at 260 and 280 nm (A260/A280), denaturing agarose gel electrophoresis with ethidium bromide staining and with a Qubit fluorometer. To extract genomic DNA (gDNA) cell pellets were resuspended in NaCl-EDTA with lysozime, SDS, NaCL04, and chloroform:isoamylalcohol. This solution was centrifuged for 3 minutes at 10xg and the supernatant was added to 2 volumes of 95% EtOH to precipitate the DNA. Once the ethanol was removed the DNA is dissolved in TE and DNAse-Free RNAase and Proteinase K are used to remove contaminates. A phenol extraction and ethanol precipitation is then used to isolate the purified DNA. Quantification of DNA was conducted using absorbance ratio at 260 and 280 nm (A260/A280), agrose gel electrophoresis and with a Qubit fluorometer.

tag: 50% hydrogen condition

label: Alexa Fluor 555

tag: universal reference


title: lactate used as sole electron donor in defined minimal media

country: Canada

description: Normalized data obtained from 4 arrays.

molecule: total RNA

source_name: Lactate fed Culture

tag: lactate condition

molecule: genomic DNA


title: T98G 2 hr PDGF+CHX vs T98G 2 hr PDGF Cy5-Cy3 rep 3

status: Public on Jul 03 2007

type: RNA

city: Boston

first: Geoffrey

middle: M

last: Cooper

state: MA

address: 5 Cummington St

department: Biology

country: USA

institute: Boston University

description: For each treated sample, three independent replicate microarray experiments were performed.

hyb_protocol: For each slide, 4 micrograms of both treated and untreated cyanine-labeled aRNA samples were combined with a hybridization buffer (2.3X SSC, 18 mM HEPES, 0.2 mg/ml BSA, 0.6 mg/ml poly(A), 0.2% SDS), heat denatured for 3 minutes at 95 degrees C, and applied to microarrays under a LifterSlip coverslip (Erie Scientific).  The slides were placed in a hybridization chamber (Dietech) and incubated in a 63 degree C water bath for 16 hr.  Following hybridization, the slides were successively washed in 0.6X SSC with 0.025% SDS, 0.05X SSC, and water, then dried by centrifugation at 1000 rpm for 3 min.

scan_protocol: The microarrays were scanned with an Axon 4000B scanner and adaptive spot segmentation performed with GenePix Pro software (version 5.0) (Axon Instruments).

data_processing: Triplicate dye-swap, background-subtracted median intensity values were used as input to the LIMMA analysis package (Smyth, 2005) in Bioconductor (Gentleman et al., 2004), and average LOESS-corrected log2 ratios were used to estimate differential gene expression.  For the PDGF-treated samples, genes with positive log2 ratios greater than or equal to 1 (2-fold) relative to untreated samples and FDR-corrected (Benjamini et al., 1995) moderated t-test p-values less than 0.01 were considered differentially expressed.  Additional microarray dye-swap experiments were performed to identify genes with PDGF-stimulated inductions that were independent of new protein synthesis.  RNA was extracted from cells treated with the translation inhibitor, cycloheximide (CHX), for 30 min followed by 2 or 4 hr PDGF treatments.  For each of three replicates, two microarray experiments were performed with different reference samples.  The first compared CHX and PDGF-treated samples to untreated samples, while the other compared CHX and PDGF-treated samples to PDGF-treated samples.  Based on this data and a linear model of the experimental design, the LIMMA program was used to calculate PDGF inductions in the presence of cycloheximide at 2 and 4 hrs as log2 ratios relative to untreated cells.  The effect of cycloheximide prior to PDGF stimulation was calculated as the percent inhibition of inductions by PDGF alone at 2 or 4 hrs.

molecule: polyA RNA

organism: Homo sapiens

source_name: 72 hr serum-deprived T98G cells with 2 hr PDGF treatment and cycloheximide added 0.5 hr prior to PDGF

label_protocol: Starting with 100 ng of poly(A)+ RNA, one round of RNA amplification was performed with the MessageAmp aRNA Amplification Kit (Ambion) using a 4:1 amino-allyl UTP:UTP ratio for aRNA incorporation.  For each sample, 8 micrograms of aRNA was coupled to N-hydroxysuccinimidyl esters of cyanine-3 or cyanine-5 (Amersham).  Following clean-up, treated and untreated aRNA samples with opposing cyanine labels were combined, concentrated, and treated with a fragmentation reagent (Ambion) according to the manufacturer's protocol.

extract_protocol: RNA was extracted with TRIzol reagent (Invitrogen) followed by poly(A)+ RNA isolation with an Oligotex mRNA Midi Kit (Qiagen) according to each manufacturer's protocol.

treatment_protocol: T98G human glioblastoma cells were grown in Minimal Essential Medium (Invitrogen) supplemented with fetal calf serum (10%).  Cells were rendered quiescent by incubation in serum-free medium for 72 h, and either left unstimulated, or stimulated for 0.5, 2, or 4 hr with human PDGF-BB (50 ng/ml) (Sigma).  When called for, cycloheximide (10 micrograms/ml) was added 30 min prior to PDGF addition.

tag: T98G human glioblastoma cells


title: T98G 2 hr PDGF+CHX vs Untreated Cy5-Cy3 rep 3

source_name: 72 hr serum-deprived T98G cells (untreated)


title: T98G 0.5 hr PDGF vs Untreated Cy3-Cy5 rep 1

source_name: 72 hr serum-deprived T98G cells with 0.5 hr PDGF treatment


title: T98G 2 hr PDGF+CHX vs Untreated Cy3-Cy5 rep 3


title: 5% hydrogen used as sole electron donor in defined minimal media

description: Normalized data obtained from 5 arrays.

source_name: 5% hydrogen fed Culture

tag: 5% condition


title: T98G 0.5 hr PDGF vs Untreated Cy5-Cy3 rep 3


title: T98G 4 hr PDGF+CHX vs Untreated Cy3-Cy5 rep 3

source_name: 72 hr serum-deprived T98G cells with 4 hr PDGF treatment and cycloheximide added 0.5 hr prior to PDGF


title: Hypothalamus RYGB-Success Repl3

status: Public on Jun 30 2007

city: Syracuse

first: Frank

middle: A

last: Middleton

state: NY

address: 505 Irving Avenue

department: Neuroscience and Physiology

institute: SUNY Upstate Medical Univ

description: 1 of 3 replicates in treatment group

hyb_protocol: Affymetrix FS450_0004

scan_protocol: Affymetrix GeneChip Scanner 3000 7G Default

label: Biotin

organism: Rattus norvegicus

source_name: Hypothalamus

label_protocol: Nugen WT Ovation

extract_protocol: Qiagen RNeasy

treatment_protocol: RYGB-Success

tag: Adult Male Sprague-Dawley


title: T98G 2 hr PDGF vs Untreated Cy5-Cy3 rep 1

source_name: 72 hr serum-deprived T98G cells with 2 hr PDGF treatment


title: T98G 0.5 hr PDGF vs Untreated Cy3-Cy5 rep 2


title: T98G 0.5 hr PDGF vs Untreated Cy3-Cy5 rep 3


title: T98G 2 hr PDGF vs Untreated Cy3-Cy5 rep 1


title: Non-meristematic root, biological rep 3

status: Public on Jul 01 2007

city: Canberra

first: Peta

last: Holmes

state: Australian Capital Territory

address: Building 46, Australian National University

department: Reseach School of Biological Sciences

country: Australia

institute: Genomic Interactions Group

description: Gene expression data from non-meristematic Medicago truncatula roots

hyb_protocol: Fifteen to 20 µg of each biotin-labeled fragmented cRNA sample was used to prepare 300 µL of hybridization mixture. Aliquots of each sample (100 µL) were hybridized for 16 hours at 45 degrees celcius onto Test3 arrays to check the quality of the samples prior to hybridization (200 µL) onto the Medicago GeneChip arrays

scan_protocol: GeneChips were scanned with the Agilent GeneArray Scanner (Affymetrix)

data_processing: To remove certain systematic biases from microarray, the raw Affymetrix data (.cel files) were normalized with the GCRMA (GC content – Robust Multi-Array Average) algorithm (ver. 2.2.0) including quantile normalization and variance stabilisation, using the affy package of the bioconductor software. The normalized average of the replicates was then log transformed in base 2 to reduce the proportional relationship between random error and signal intensity. Differentially expressed genes were identified by evaluating the log2 ratio between the two conditions

organism: Medicago truncatula

source_name: Non-meristematic root tissue, 1cm section adjacent to the meristematic tissue

label_protocol: Biotinylated cRNA was generated using the Enzo BioArray kit (Affymetrix), purified using RNeasy spin columns (Qiagen), according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Root sections were harvested from 3 day old plants grown on vertical plates incubated in a growth chamber at 20°C over a 16 hour photoperiod and a photon flux density of 100 mmol m-2 s-1 and 86% relative humidity.

extract_protocol: Total RNA was extracted and purified from plant tissues using the Qiagen RNeasy plant mini kit (Qiagen).

treatment_protocol: Tissue 3 mm from the root tip which contains meristematic cells and a further 1 cm section from the root containing non-meristematic cells were collected

tag: Accession A17


title: Hypothalamus RYGB-Success Repl1

description: 1 of 3 replicates in treatment group


title: Hypothalamus RYGB-Success Repl2

description: 1 of 3 replicates in treatment group


title: Root meristem, biological rep 2

description: Gene expression data from root meristems of Medicago truncatula

source_name: Meristematic root tissue, sectioned 3mm from the root tip


title: Root meristem, biological rep 1


title: Fat RYGB-Success Repl3

description: 1 of 3 replicates in treatment group

source_name: Subcutaneous Fat


title: Fat RYGB-Success Repl1

description: 1 of 3 replicates in treatment group


title: Fat RYGB-Success Repl2

description: 1 of 3 replicates in treatment group


title: Non-meristematic root, biological rep 1


title: Non-meristematic root, biological rep 2


title: Fat RYGB-Fail Repl3

description: 1 of 3 replicates in treatment group

treatment_protocol: RYGB-Fail


title: NB_tum_1310

type: genomic

first: Rani

middle: E.

last: George

address: Dana 322, 44 Binney St

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

hyb_protocol: Affymetrix SNP array protocol

scan_protocol: Hewlett-Packard scanner

data_processing: Affymetrix Gene chip 5.0 and www.dchipSNP.org (Cheng Li)

label: biotin

source_name: neuroblastoma tumor

label_protocol: Affymetrix SNP array protocol

extract_protocol: Quiagen DNA extraction protocol

tag: Stage 4, MYCN nonamplified, UH, hyperdiploid


title: Root meristem, biological rep 3


title: Hypothalamus RYGB-Fail Repl2

description: 1 of 3 replicates in treatment group


title: Hypothalamus Pair-Fed Repl3

description: 1 of 3 replicates in treatment group

treatment_protocol: Pair-Fed


title: Hypothalamus Pair-Fed Repl2

description: 1 of 3 replicates in treatment group

hyb_protocol: Affymetrix  FS450_0004


title: Hypothalamus RYGB-Fail Repl1

description: 1 of 3 replicates in treatment group


title: NB_bld_1310

source_name: matched blood

tag: matched blood


title: NB_tum_1266

tag: Stage 4, MYCN amplified UH, hyperdiploid


title: Fat RYGB-Fail Repl2

description: 1 of 3 replicates in treatment group


title: Fat Pair-Fed Repl2

description: 1 of 3 replicates in treatment group


title: Fat Pair-Fed Repl3

description: 1 of 3 replicates in treatment group


title: Fat RYGB-Fail Repl1

description: 1 of 3 replicates in treatment group


title: Fat Pair-Fed Repl1

description: 1 of 3 replicates in treatment group


title: Hypothalamus RYGB-Fail Repl3

description: 1 of 3 replicates in treatment group


title: NB_tum_1258

tag: Stage 3, MYCN nonamplified, UH, hyperdiploid


title: NB_bld_1266


title: NB_tum_1204

tag: Stage 4, MYCN nonamplified, UH, Hyperdiploid


title: NB_bld_1213


title: NB_tum_1218


title: NB_bld_1167


title: NB_tum_1167

tag: Stage 4, MYCN nonamplified, UH, diploid


title: NB_tum_1213


title: NB_bld_1258


title: NB_bld_1066


title: NB_bld_1218


title: NB_tum_1066

tag: Stage 4, MYCN amplified, diploid


title: NB_tum_495


title: NB_tum_969

description: CHOP 969T

tag: Stage 4, MYCN amplified, UH, diploid


title: T98G 0.5 hr PDGF vs Untreated Cy5-Cy3 rep 1


title: NB_bld_205


title: NB_bld_982


title: NB_bld_974


title: NB_tum_974

tag: Stage 4, MYCN nonamplified, UH, hyperdiploidy


title: NB_bld_969

description: CHOP 969B


title: NB_bld_396


title: NB_tum_1246

description: CHOP 1246T

tag: Stage 4, MYCN amplified, UH, hyperdiploid


title: NB_tum_1092

description: CHOP 1092T


title: NB_tum_205


title: NB_bld_1092

description: CHOP 1092B


title: NB_bld_1246

description: CHOP 1246B


title: NB_tum_396

tag: Stage 4, MYCN nonamplified, FH, hyperdiploid


title: Hypothalamus Pair-Fed Repl1

description: 1 of 3 replicates in treatment group


title: NB_bld_495


title: NB_tum_427

description: CHOP 427T


title: NB_tum_260


title: NB_bld_427

description: CHOP 427B


title: NB_bld_260


title: NB_tum_982


title: T98G 2 hr PDGF vs Untreated Cy5-Cy3 rep 3


title: NB_bld_1220

description: CHOP 1220B


title: NB_tum_1194

description: CHOP 1194T


title: NB_tum_1100

description: CHOP 1100T


title: NB_bld_1100

description: CHOP 1100B


title: NB_tum_1220

description: CHOP 1220T


title: NB_bld_1194

description: CHOP 1194B


title: NB_bld_158

description: CHOP 158B


title: Rainbow trout prespawn ovary Replicate 1 microarray GB032_035

status: Public on Jun 29 2007

city: Victoria

first: Ben

middle: F

last: Koop

state: BC

address: PO Box 3020 STN CSC

institute: The University of Victoria

description: Oncorhynchus mykiss prespawn gonad Replicate 1 dye flip

hyb_protocol: Microarray was prepared for hybridization by washing 2 x 5 min with 0.2% SDS, 5 x 1 min with MilliQ water followed by drying using centrifugation (5 min, 514 x g in 50 mL tube).  Array was pre-hybridized in 5X SSC, 0.1% SDS, 3% BSA for 1.5 h at 49C, briefly washed 3 X 20 sec in MilliQ water and dried by centrifugation. Labeled cDNAs were hybridized to pre-warmed microarray in a formamide based buffer (25% formamide, 4X SSC, 0.5% SDS, 2X Denhardt's solution, and 4 ul of Genisphere LNA dT blocker) for 16 h at 49C. Coverslips were removed in 2X SSC, 0.1% SDS at 49C.  The arrays were washed 1 x 10 min at 49C (2X SSC, 0.1% SDS). All subsequent washes were at room temperature;  2 x 5 min in 2X SSC, 0.1% SDS, 2 x 5 min in 1X SSC and 4 x 5 min in 0.1X SSC and dried by centrifugation.

scan_protocol: Fluorescent array images were collected immediately for both Cy3 and Cy5 using ScanArray Express (PerkinElmer). Scanning resolution 10 microns.  Image intensity data were extracted using Imagene 5.5 software (Biodiscovery).

data_processing: Only elements deemed present by Imagene software in 3 of 6 replicates were used. Expression ratios were generated using background corrected lowess normalized data using GeneSpringGX 7 software (Agilent Technologies, Palo Alto, Ca, USA).

organism: Oncorhynchus mykiss

source_name: Fish 1 Ovary

label_protocol: Labeled cDNA was generated using a SuperScript Indirect cDNA Labeling System kit (Invitrogen) according to the manufacturer's instructions. For each sample 5.0 ug of total RNA was used to generate modified cDNAs.

extract_protocol: Trizol and Ambion megaclear column purification

tag: 3 year old normal

tag: 2 year old precocious


title: NB_tum_158

description: CHOP 158T


title: Pdr1-Sin3 fusion, biological rep3

city: Memphis

last: Neale

state: TN

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

description: Gene expression data from yeast expressing Pdr1-Sin3 fusion protein

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Yeast Genome Array YG-s98. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with GeneChip Operating Software version 1.4 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

organism: Saccharomyces cerevisiae

source_name: Yeast expressing Pdr1-Sin3 fusion protein

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, revision 4, Affymetrix).

growth_protocol: Yeast were grown in synthetic dextrose media, logarithmically growing, 30 degrees centigrade

extract_protocol: Extraction of total RNA using Ambion RiboPure-Yeast protocol according to the manufacturer's instructions.

tag: Yeast strain BY4741


title: Pdr1-Sin3 fusion, biological rep2


title: Pdr1-Cyc8 fusion Dpdr1, biological rep3

description: Gene expression data from yeast containing deletion of endogenous Pdr1 gene and expressing Pdr1-Cyc8 fusion protein

source_name: Yeast with deletion of endogenous Pdr1 gene and expressing Pdr1-Cyc8 fusion protein


title: Pdr1-Sin3 fusion, biological rep1


title: NB_bld_1204


title: Rainbow trout maturing testis Replicate 1 microarray GB032_019

description: Oncorhynchus mykiss maturing gonad Replicate 1 dye flip

source_name: Fish 1 Testis

tag: 2 year old normal


title: Rainbow trout prespawn testis Replicate 2 microarray GB032_038

description: Oncorhynchus mykiss prespawn gonad Replicate 2

source_name: Fish 2 Testis


title: Rainbow trout maturing testis Replicate 2 microarray GB032_020

description: Oncorhynchus mykiss maturing gonad Replicate 2 dye flip


title: Rainbow trout prespawn testis Replicate 1 microarray GB032_030

description: Oncorhynchus mykiss prespawn gonad Replicate 1


title: Rainbow trout maturing testis Replicate 3 microarray GB032_018

description: Oncorhynchus mykiss maturing gonad Replicate 3

source_name: Fish 3 Testis


title: Rainbow trout prespawn ovary Replicate 3 microarray GB032_034

description: Oncorhynchus mykiss prespawn gonad Replicate 3

source_name: Fish 3 Ovary


title: Rainbow trout maturing testis Replicate 1 microarray GB032_006

description: Oncorhynchus mykiss maturing gonad Replicate 1


title: Rainbow trout maturing ovary Replicate 1 microarray GB032_009


title: Rainbow trout prespawn ovary Replicate 1 microarray GB032_037


title: Rainbow trout prespawn testis Replicate 3 microarray GB032_032

description: Oncorhynchus mykiss prespawn gonad Replicate 3 dye flip


title: Rainbow trout prespawn testis Replicate 2 microarray GB032_028

description: Oncorhynchus mykiss prespawn gonad Replicate 2 dye flip


title: Pdr1-Cyc8 fusion Dpdr1, biological rep2


title: Rainbow trout maturing ovary Replicate 3 microarray GB032_025


title: Rainbow trout prespawn testis Replicate 3 microarray GB032_027


title: Rainbow trout prespawn ovary Replicate 2 microarray GB032_029

source_name: Fish 2 Ovary


title: Rainbow trout prespawn ovary Replicate 2 microarray GB032_036


title: Rainbow trout maturing ovary Replicate 2 microarray GB032_013


title: Rainbow trout maturing testis Replicate 3 microarray GB032_015

description: Oncorhynchus mykiss maturing gonad Replicate 3 dye flip


title: Dpdr1, biological rep3

description: Gene expression data from yeast containing deletion of endogenous Pdr1 gene

source_name: Yeast with deletion of endogenous Pdr1 gene


title: Pdr1-Cyc8 fusion, biological rep2

description: Gene expression data from yeast expressing Pdr1-Cyc8 fusion protein

source_name: Yeast expressing Pdr1-Cyc8 fusion protein


title: Rainbow trout maturing ovary Replicate 1 microarray GB032_023


title: Pdr1-Cyc8 fusion, biological rep3


title: Rainbow trout prespawn ovary Replicate 3 microarray GB032_033


title: Rainbow trout maturing ovary Replicate 2 microarray GB032_014

description: Oncorhynchus mykiss maturing gonad Replicate 2


title: Rainbow trout prespawn testis Replicate 1 microarray GB032_031


title: Rainbow trout maturing ovary Replicate 3 microarray GB032_008


title: Dpdr1, biological rep1


title: Rainbow trout maturing testis Replicate 2 microarray GB032_004


title: Empty vector, biological rep2

description: Gene expression data from yeast containing empty vector

source_name: Yeast harboring empty vector


title: Pdr1-Cyc8 fusion, biological rep1


title: S. mansoni_wt mice_25d_rep1

status: Public on Jun 28 2007

city: San Francisco

first: Steve

last: Miller

state: CA

address: 1600 Divisadero St, Room B-232, Box 1613

department: Laboratory Medicine

institute: University of California, San Francisco

description: Included.

hyb_protocol: Arrays were pretreated with 3xSSC, 0.2% SDS at 65 degrees C for 5 minutes and washed in water.  Probes consisting of mixed dye-coupled sample and reference RNA were prepared in 3.3xSSC, 0.0275M HEPES, 0.3 mg/ml polyA, 0.05% SDS and 20 U RNase Inhibitor.  Probe solutions were heated 100 degress C for 3 minutes and applied to array, which was incubated 63 degrees C for 18-22 hours.  Arrays were washed with 0.6xSSC, 0.3% SDS and then 0.3% SDS at room temperature.  Immersion solution (6xSSPE, 5% trehalose, 2.5% polyvinylpyrollidone) was overlaid onto the array, which was covered with a coverslip.

scan_protocol: Arrays were scanned with Axon 400B scanned at 100% laser power with 5 micrometer resolution and images analyzed with GenePix Pro 4 software.

data_processing: Microarray data were stored in the NOMAD database (http://derisilab.ucsf.edu) and normalized glabally using unflagged features with a regression correlation coefficient greater than or equal to 0.75 and median intensity > 0.

organism: Schistosoma mansoni

source_name: S.mansoni, wt mice, 25d

label_protocol: During RNA amplification IVT step, amino-allyl dUTP was incorporated into RNA. 4 micrograms amplified RNA containing aa-dUTP was coupled to mono-reactive Cy5 dye (GE Healthcare) in 0.75% sodium bicarbonate at room temperature in the dark for one hour

growth_protocol: Growth in C57BL/6 mice host for 25 days post-infection.

treatment_protocol:
S. mansoni cerceriae were injected IP into C57BL/6 mice and allowed to grow to 25 days post-infection.
Worms were isolated by liver perfusion of infected mice, washed with RPMI medium and resuspended in small volume of RPMI.

tag: S. mansoni C57BL/6 mice

source_name: S. mansoni, reference pooled RNA (RAG-/- and wt), 21-27d_rep1

label_protocol: During RNA amplification IVT step, amino-allyl dUTP was incorporated into RNA. 4 micrograms of amplified RNA containing aa-dUTP was coupled to mono-reactive Cy3 in 0.75% sodium bicarbonate for one hour.

growth_protocol: Growth in C57BL/6 or RAG-/- mice host for 21-27 days post-infection.

extract_protocol:
RNA purified with Trizol (InVitrogen) following manufacturer's instructions and resuspended in 20 microliters DEPC-water.
RNA was amplified using Ambion MessageAmp II kit following manufacturer's instructions.
Equal amounts of RNA for each of 8 conditions (C57BL/6 and RAG-/- mice at 21, 23, 25 and 27 days post-infection) were pooled and aliquoted into 4 microgram aliquots.

treatment_protocol:
S. mansoni cerceriae were injected IP into 4 C57BL/6 mice and 4 RAG-/- mice.  Worms were isolated at 21, 23, 25 and 27 days post-infection for each mouse pair.
Worms were isolated by liver perfusion of infected mice, washed with RPMI medium and resuspended in small volume of RPMI.

tag: S. mansoni C57BL/6 mice RAG-/- mice


title: S. mansoni_RAG mice_27d_rep1

description: Included.

source_name: S.mansoni, RAG mice, 27d

growth_protocol: Growth in RAG-/- mice host for 27 days post-infection.

extract_protocol:
RNA purified with Trizol (InVitrogen) following manufacturer's instructions and resuspended in 20 microliters DEPC-water.
RNA was amplified using Ambion MessageAmp II kit following manufacturer's instructions.

treatment_protocol:
S. mansoni cerceriae were injected IP into RAG-/- mice and allowed to grow to 27 days post-infection.
Worms were isolated by liver perfusion of infected mice, washed with RPMI medium and resuspended in small volume of RPMI.

tag: S. mansoni RAG-/- mice


title: S. mansoni_wt mice_27d_rep1

description: Included.

source_name: S.mansoni, wt mice, 27d

growth_protocol: Growth in C57BL/6 mice host for 27 days post-infection.

treatment_protocol:
S. mansoni cerceriae were injected IP into C57BL/6 mice and allowed to grow to 27 days post-infection.
Worms were isolated by liver perfusion of infected mice, washed with RPMI medium and resuspended in small volume of RPMI.


title: S. mansoni_wt mice_21d_rep1

description: Included.

source_name: S.mansoni, wt mice, 21d

growth_protocol: Growth in C57BL/6 mice host for 21 days post-infection.

treatment_protocol:
S. mansoni cerceriae were injected IP into C57BL/6 mice and allowed to grow to 21 days post-infection.
Worms were isolated by liver perfusion of infected mice, washed with RPMI medium and resuspended in small volume of RPMI.


title: S. mansoni_wt mice_23d_rep1

description: Included.

source_name: S.mansoni, wt mice, 23d

growth_protocol: Growth in C57BL/6 mice host for 23 days post-infection.

treatment_protocol:
S. mansoni cerceriae were injected IP into C57BL/6 mice and allowed to grow to 23 days post-infection.
Worms were isolated by liver perfusion of infected mice, washed with RPMI medium and resuspended in small volume of RPMI.


title: S. mansoni_RAG mice_21d_rep1

description: Included.

source_name: S.mansoni, RAG mice, 21d

growth_protocol: Growth in RAG-/- mice host for 21 days post-infection.

treatment_protocol:
S. mansoni cerceriae were injected IP into RAG-/- mice and allowed to grow to 21 days post-infection.
Worms were isolated by liver perfusion of infected mice, washed with RPMI medium and resuspended in small volume of RPMI.

tag: S. mansoni

tag: RAG-/- mice

tag: C57BL/6 mice


title: MONOB11-4, Monocytes 0h-sample 3

status: Public on Jun 27 2007

city: Chicago

first: Bo

last: Shi

state: IL

address: 240 E. Huran

department: Medicine

institute: Northwestern University

description: MONOB11-4, monocytes 0h-sample 3

hyb_protocol: 20ug of fragmented labeled cRNA was hybridized to Human U133A GeneChip at 45C for 18 hours

scan_protocol: labeled cRNA were assessed by 2100 Bioanalyzer (Agilent Technologies)

data_processing: dChip normalization

source_name: Monocytes 0 hour

label_protocol: cRNA was labeled by Biotin acccording to affymatrix's protocol

extract_protocol: Trizol extraction kit

tag: Normal human blood sample


title: hypothalamus of late pubertal (LP) rat_LP14

city: Beaverton

first: Alejandro

last: Lomniczi

state: OR

address: 505 NW 185th Ave

department: Neuroscience

institute: Oregon National Primate Research Center - OHSU

description: gene expression data derived from a hypothalamus of a normal late pubertal female rat. This sample is considered as an experimental sample.

hyb_protocol: For array hybridization and processing, the labelled target was fragmented at 95°C in the presence of high magnesium concentration.  The fragmented material was combined with biotinylated hybridization control oligomer and biotinylated control cRNAs for BioB, BioC, BioD and cre (Affymetrix) in hybridization buffer.  Ten mg of target was hybridized with the GeneChip (Rat Genome 230 2.0) array (Affymetrix) overnight, followed by washing, staining, signal amplification with biotinylated anti-streptavidin antibody, and a final staining step on the Fluidics Station (Affymetrix). The distribution of fluorescent material on the processed array was determined using the GeneArray laser scanner (Affymetrix).  Image inspection was performed manually immediately following each scan.

scan_protocol: The array image scan was processed with Affymetrix Microarray Suite software, version 5.0 (MAS 5.0). The GeneChip expression arrays contained control probe sets for both spiked and endogenous RNA transcripts (e.g., BioB, BioC, BioD, cre and species-specific actin and GAPDH).

data_processing: Image processing and expression analysis were performed using Affymetrix Microarray Suite (MAS) 5.0 software. An absolute (single assay) expression analysis was performed for each GeneChip genome array hybridization. The GeneChip expression arrays contain control probe sets for both spiked and endogenous RNA transcripts (e.g., BioB, BioC, BioD, CreX and species-specific actin and GAPDH). Following image processing and absolute analysis of the array pattern with MAS 5.0, six parameters were examined to assess the overall assay performance: background, noise, average signal, % present, ratio of signal values for probe sets representing the 5’ and 3’ ends of actin and GAPDH transcripts, and total signal for BioC, BioD and CreX probe sets. Prior to further analysis, array data were globally scaled to a uniform, average target intensity for all assays prior to further analysis. Initial filters removed all absent genes and genes with no change across all data sets.

source_name: Hypothalamus of 31 day old late pubertal female rat

label_protocol: For target labelling, messenger RNA was amplified and labeled from 2 mg of total RNA in two steps. In the first step, mRNA was converted to double-stranded cDNA using Superscript Reverse Transcriptase (Invitrogen) and an oligo-dT primer linked to a T7 RNA polymerase binding site sequence (IDT).  In the second step, amplified and labeled cRNA (the target) was produced in an in vitro transcription reaction using T7 RNA polymerase and biotin-UTP (Affymetrix, Santa Clara, CA). Following removal of free nucleotides, target yield was measured by UV260 absorbance. For target quality assessment, approximately 200 ng of each sample cRNA target along with a control cRNA target was analyzed on the RNA 6000 LabChip using the 2100 Bioanalyzer (Agilent).  The target quality was determined based on yield and cRNA size distribution produced in the in vitro synthesis reaction. Samples that fail quality control were discarded or relabeled.

extract_protocol: Total RNA was isolated and purified using RNeasy Mini Columns according to the manufacturer’s specifications. RNA quality was assessed by OD reading and was subjected to electrophoretic trace using an Agilent Bioanalyzer (Agilent Technologies, Palo Alto, CA).

treatment_protocol: Tissue was rapidly extracted and stored in RNAlater solution (Ambion) according to the manufacturers instructions.

tag: Hypothalamus of 31 day old female late pubertal rat


title: Pdr1-Cyc8 fusion Dpdr1, biological rep1

source_name: Yeast with deletion of endogenous Pdr1 gene and expressing Pdr1-Cyc8 fusion protein


title: Mono16h4-21, Monocytes 16h-sample 3

description: Mono16h4-21, monocytes 16h-sample 3

source_name: Monocytes 16 hour


title: hypothalamus of early pubertal (EP) rat_EP7

description: gene expression data derived from a hypothalamus of a normal early pubertal female rat. This sample is considered as an experimental sample.

source_name: Hypothalamus of 29 day old early pubertal female rat

tag: Hypothalamus of 29 day old female early pubertal rat


title: S. mansoni_RAG mice_25d_rep1

description: Included.

source_name: S.mansoni, RAG mice, 25d

growth_protocol: Growth in RAG-/- mice host for 25 days post-infection.

treatment_protocol:
S. mansoni cerceriae were injected IP into RAG-/- mice and allowed to grow to 25 days post-infection.
Worms were isolated by liver perfusion of infected mice, washed with RPMI medium and resuspended in small volume of RPMI.


title: hypothalamus of late pubertal (LP) rat_LP12


title: MONO7-9, Monocytes 0h-sample 1

description: MONO7-9, monocytes sample 1, 0h


title: Low-level MMS treatment, YPD medium, 0.0125% MMS, 30 min

status: Public on Jun 26 2007

city: Heidelberg

first: Ana

last: Kitanovic

address: Im Neuenheimer Feld 364

country: Germany

institute: Institute for Pharmacy and Molecular Biotechnology

description: Filters were stripped washing twice with boiled stripping buffer (5mM sodium phosphate, pH 7.2, 0.1% SDS), rinsing membranes in 200 mM KOH for 1h and repeated washing for three times with boiled stripping buffer. Samples from the same medium and the same time point, but different treatments (mock-treated; 0.00125%; 0.0125% MMS) were hybridized on the same membrane (membranes were stripped in between two hybridizations).

hyb_protocol: Arrays were pre-hybridised for 2h at 68° in hybridisation buffer (7% SDS, 1mM EDTA, 0.5 M sodium phosphate pH 7.2, 1% BSA, 500 µg Herring Sperm DNA and 250 µg yeast t-RNA). Probe hybridisation was done in the same buffer, at 68° for 16-20 h in 5 ml. Subsequently, filters were washed 5 times at 68° with Wash buffer I (1% SDS, 1mM EDTA, 40mM sodium phosphate pH 7.2) and 3 times at room temperature with Wash buffer II (100 mM sodium phosphate pH 7.2).

scan_protocol: Signals were detected by exposition to Image Plates (Fuji) and scanning on Storm 860 Phosphor Imager (Molecular Dynamics, USA). All images were analyzed with the AIDA Image Analyser Software (Raytest, version 3.22).

data_processing: Data analysis was performed for each set of results from one filter separately. Datasets from one experiment were ranked and compared in a rank intensity plot (Kroll and Wölfl, 2002). The curves varied as expected not only in scaling but as well in an additional offset. The real offset cannot be determined, so we calculated the average intensity of each rank. To this curve, all pooled experiments were mapped rank wise (Kroll and Wölfl, 2002; Bolstad et al., 2003).

source_name: FF18984 strain, YPD medium, 0.0125% MMS, 30 min

label_protocol: Probes were generated by a first-strand cDNA synthesis. 4 µg of total RNA was mixed with 100 pmol (dT)18 and p(dN6) random primer and heated at 70°C 5 min. Reverse transcription was performed in a total volume of 20 µl using Super ScriptTMII (Invitrogen) and 25 µCi of [alpha-33P]dATP (2500 Ci/mmol; Amersham, UK) and incubated at 42° for 1.5 h. Subsequently, probes were denatured with 1/10 volume denaturing solution (1M NaOH, 10 mM EDTA) at 68°C for 20 min and afterwards neutralized with 1M NaH2PO4, pH 7.0 at 68°C for 10 min The unincorporated nucleotides were removed using Atlas NucleoSpin Extraction Columns (Clontech).

growth_protocol: YPD or F1 media were inoculated with overnight pre-cultures and grown at 30°C to mid log-phase (OD600 0.6 to 0.8). Cultures were split into three parts: the first aliquot was mock-treated and used as control; the second and third aliquots were treated with low concentration of MMS (0.00125% and 0.0125%). All cultures were incubated at 30° C. Samples were collected after 30 min and 1h incubation.

extract_protocol: Cells were pelleted, frozen in liquid nitrogen and stored at -80°C until RNA preparation. Total RNA was isolated with the hot-phenol method described by Schmitt et al. (1990). RNA was treated with DNAse and precipitated by ethanol.

treatment_protocol: Cells were either mock-treated or treated with low concentration of MMS (0.00125% and 0.0125%) for 30 min and 1h.


title: Dpdr1, biological rep2

source_name: Yeast with deletion of endogenous Pdr1 gene


title: Low-level MMS treatment, YPD medium, 0.0125% MMS, 1h

source_name: FF18984 strain, YPD medium, 0.0125% MMS, 1h


title: hypothalamus of early pubertal (EP) rat_EP8


title: Low-level MMS treatment, YPD medium, mock-treated, 1h

source_name: FF18984 strain, YPD medium, mock-treated, 1h


title: hypothalamus of juvenile (JUV) rat_JUV2

description: gene expression data derived from a hypothalamus of a normal juvenile female rat. This sample is considered as a control sample.

source_name: Hypothalamus of 26 day old juvenile female rat

tag: Hypothalamus of 26 day old female juvenile rat


title: Mono16h3-31, Monocytes 16h-sample 1

description: Mono16h3-31, monocytes 16h-sample 1


title: Low-level MMS treatment, YPD medium, 0.00125% MMS, 1h

source_name: FF18984 strain, YPD medium, 0.00125% MMS, 1h


title: Mono16h4-14, Monocytes 16h-sample 2

description: Mono16h4-14, monocytes 16h-sample 2


title: Low-level MMS treatment, BY4742 strain, YPD medium, mock-treated, 1h

tag: BY4742 (leu2Δ0,  ura3Δ0, lys2Δ0, hisΔ1)


title: MONOB10-22, Monocytes 0h-sample 2

description: MONOB10-22, monocytes 0h-sample 2


title: Empty vector, biological rep3

source_name: Yeast harboring empty vector


title: hypothalamus of late pubertal (LP) rat_LP20


title: MOB11-4, Macrophage sample 3

description: MOB-11-4, macrophage sample 3, monocytes 168h

source_name: Monocytes 168h


title: hypothalamus of early pubertal (EP) rat_EP10


title: Empty vector, biological rep1


title: Low-level MMS treatment, BY4742 strain, YPD medium, 0.0125% MMS, 1h


title: Low-level MMS treatment, YPD medium, 0.00125% MMS, 30 min

source_name: FF18984 strain, YPD medium, 0.00125% MMS, 30 min


title: Low-level MMS treatment, F1 medium, 0.0125% MMS, 1h

source_name: FF18984 strain, F1 medium, 0.0125% MMS, 1h


title: S. mansoni_RAG mice_23d_rep1

description: Included.

source_name: S.mansoni, RAG mice, 23d

growth_protocol: Growth in RAG-/- mice host for 23 days post-infection.

treatment_protocol:
S. mansoni cerceriae were injected IP into RAG-/- mice and allowed to grow to 23 days post-infection.
Worms were isolated by liver perfusion of infected mice, washed with RPMI medium and resuspended in small volume of RPMI.

source_name: S. mansoni, reference pooled RNA (RAG-/- and wt), 21-27d_rep1


title: hypothalamus of juvenile (JUV) rat_JUV3


title: Low-level MMS treatment, YPD medium, mock-treated, 30 min

source_name: FF18984 strain, YPD medium, mock-treated, 30 min


title: Low-level MMS treatment, F1 medium, 0.0125% MMS, 30 min

source_name: FF18984 strain, F1 medium, 0.0125% MMS, 30 min


title: IRTGFBd8_11

status: Public on Jun 25 2007

city: Berkeley

first: Mary

middle: Helen

last: Barcellos-Hoff

address: 1 Cyclotron Rd MS977R225A

department: Life Sciences Division

institute: Lawrence Berkeley National Laboratory

description: X-ray irradiation (2 Gy) and TGFB added.

hyb_protocol: Standard Affymetrix High Throughput Array protocol.

data_processing: CEL files were processed in a single batch with RMA 2, as implemented in Bioconductor for R version 2.3.0, with default parameters.

extract_protocol: RNeasy for cultured cells.


title: TGFBd8_22

description: TGFbeta harvest d8 022106

scan_protocol: Standard Affymetrix High Throughput Array protocol.


title: sham_23

description: Untreated cells.

label_protocol: Standard Affymetrix High Throughput Array protocol.


title: sham_21

description: Untreated cells.


title: Low-level MMS treatment, F1 medium, 0.00125% MMS, 1h

source_name: FF18984 strain, F1 medium, 0.00125% MMS, 1h


title: Low-level MMS treatment, F1 medium, mock-treated, 1h

source_name: FF18984 strain, F1 medium, mock-treated, 1h


title: E_098_048_03_DS7226_W F

status: Public on Jun 23 2007

city: SEATTLE

first: John

last: Stamatoyannopoulos

state: WA

address: 2211 Elliott Avenue, 6th Floor

department: Genome Sciences

institute: Altius Institute / University of Washington

description: DnaseI enriched

hyb_protocol: Labeled samples were hybridized for 16 hr at 45C on Affymetrix whole Genome Tiling Arrays.  Arrays were washed and post stained using the Affymetrix 450 Fluidics Station.

scan_protocol: Arrays were scanned using an Affymetrix GeneChip Scanner 3000.

data_processing: Cel files were generated using Affymetrix's GCOS software and Analyzed using the Affymetrix TAS analysis software.

source_name: HL60 ATCC; DnaseI enriched

label_protocol: Fragments were cleaned using Qiagen PCR columns.  Samples were amplified using the Sigma WGA amplification kit.  Cleaned and fragmented to an avg size of 75 bp using DNaseI and labeled with Biotin 16-ddUTP and Terminal Transferase.  (See Affymetrix Chip Chip protocol)

growth_protocol: (follow vendor recommendations for medium) with 2 mM L-glutamine adjusted to contain 1.5 g-L sodium bicarbonate. 4.5 g-L glucose. 10 mM HEPES and 1.0 mM sodium pyruvate and supplemented with 0.5 mg-ml G418 and 10percent  fetal bovine serum

extract_protocol: Samples were extracted with an equal volume of Phenol and Chloroform and small fragments separated out by running the sample through a 10% sucrose cushion for 24 hrs at 25000 rpm on a Beckman Ultracentrfuge using a SW41 rotor.

treatment_protocol: Cells were lysed and Intact nuclei were isolated using NP40 and treated for 3 minutes with varying concentrations of DNaseI

tag: HL60 ATCC


title: Low-level MMS treatment,  F1 medium, mock-treated, 30 min

source_name: FF18984 strain, F1 medium, mock-treated, 30 min


title: hypothalamus of juvenile (JUV) rat_JUV1


title: IR2Gyd8_12

description: X-ray irradiation (2 Gy).


title: Low-level MMS treatment, F1 medium, 0.00125% MMS, 30 min

source_name: FF18984 strain, F1 medium, 0.00125% MMS, 30 min


title: IRTGFBd8_21


title: MOA10-22, Macrophage sample 2

description: MOA10-22, macrophage sample 2, monocytes 168h


title: sham_22

description: Untreated cells.


title: IR2Gyd8_21

description: X-ray irradiation (2 Gy).


title: IR2Gyd8_11

description: X-ray irradiation (2 Gy).


title: TGFBd8_13

description: TGFbeta added.


title: IR2Gyd8_22

description: X-ray irradiation (2 Gy).


title: MO7-9, Macropage sample 1

description: MO7-9, macrophage sample 1, monocytes 168h


title: TGFBd8_23

description: TGFbeta added.


title: S. coelicolor YSK4425 45h Replicate 2

city: Minneapolis

first: Salim

last: Charaniya

state: MN

address: 421 Washington Ave SE., 151 Amundson Hall

department: Chemical Engineering and Materials Science

institute: University of Minnesota

description: No additional description

hyb_protocol: The labeled cDNA and gDNA were then mixed and co-hybridized to microarray slides in the presence of 50% formamide.  After 16 hours incubation at 50°C, slides were washed and scanned.

scan_protocol: Arrays were scanned using ScanArray5000 (Perkin Elmer, Wellesley, MA). Images were analyzed using GenePix (Axon Instruments, Union City, CA) to obtain raw intensity data for each spot.  The median fluorescence intensity from each spot was used for all subsequent analysis.

data_processing: A quantile normalization method was employed to normalize these log2 ratios from each hybridization (S Mehra, W Lian, KP Jayapal, SP Charaniya, DH Sherman, WS Hu: A framework to analyze multiple time series data: a case study with Streptomyces coelicolor. J Ind Microbiol Biotechnol 2006, 33:159-72).  The resulting log2 ratios were not only used to compare transcript levels of the same mRNA species in different biological samples, but also used as an estimate of the relative abundance of each mRNA species.

label: Alexa 647

organism: Streptomyces coelicolor

source_name: S. coelicolor RNA R5- medium 45h

label_protocol: The cDNA was then incubated with Alexa 647 (Invitrogen, Carlsbad, CA) for labeling as per manufacturer's instructions.

growth_protocol: S. coelicolor A3(2) strain YSK4425 was maintained on R5 solid agar (Kieser, T., M. J. Bibb, M. J. Buttner, K. F. Chater, and D. A. Hopwood. 2000. Practical Streptomyces Genetics. The John Innes Foundation, Norwich, UK) for high density spores.  For liquid culture, spores were pre-germinated in 2xYT medium (Kieser, T., M. J. Bibb, M. J. Buttner, K. F. Chater, and D. A. Hopwood. 2000. Practical Streptomyces Genetics. The John Innes Foundation, Norwich, UK) and inoculated into R5- liquid medium (Huang, J., C. J. Lih, K. H. Pan, and S. N. Cohen. 2001. Global analysis of growth phase responsive gene expression and regulation of antibiotic biosynthetic pathways in Streptomyces coelicolor using DNA microarrays. Genes Dev 15:3183-92) at a density of ~10exp7 spores/ml.  Baffled 2L flasks containing stainless steel coils with 350 ml working volume were used for liquid cultures.  Cultures were incubated at 30°C in an orbital shaker at 300 rpm.  For measuring cell growth, samples were collected at regular intervals and mixed with one-eighth volume of 2.5 M HCl and then subjected to sonication to break mycelial pellets (Brana, A. F., S. Wolfe, and A. L. Demain. 1986. Relationship between nitrogen assimilation and cephalosporin synthesis in Streptomyces clavuligerus. Arch Microbiol 146:46-51).  Absorbance of the resulting solution at 450 nm was then taken as a measure of growth.  Proper dilution was made to ensure an OD450 measurement below 1, which is in the linear range of detection.

extract_protocol: Immediately after culture samples were collected, one-fifth volume of an ice-cold stop solution (5% phenol in ethanol) (Bernstein, J. A., A. B. Khodursky, P. H. Lin, S. Lin-Chao, and S. N. Cohen. 2002. Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays. Proc Natl Acad Sci U S A 99:9697-702) was added to the sample volume to prevent RNA degradation.  The sample was quickly centrifuged at 4°C and the supernatant was discarded.  The remaining sample was then stored at -80°C.  To isolate RNA, the frozen pellets were transferred to a mortar and pestle and ground to fine powder in the presence of liquid nitrogen.  RLT solution from RNeasy Mini Kit (Qiagen Inc., Valencia, CA) was added before the ground pellets thawed.  The remaining steps for RNA isolation were carried out as per manufacturer's instructions.  RNA integrity was determined by gel electrophoresis while its quantity and purity were estimated by UV absorbance at OD260 and OD260/OD280, respectively.Total RNA was reverse transcribed to cDNA by SuperscriptII (Invitrogen, Carlsbad, CA) with random hexamers (IDT, Coralville, IA) incorporating aminoallyl-dUTP (Ambion, Austin, TX).

tag: Strain

tag: Sample

value: 45h Replicate 2

source_name: S. coelicolor genomic DNA

label_protocol: The DNA was labeled with Label IT® Cy3 Labeling Kit (Mirus Bio Corp., Madison, WI) according to suppliers instructions.

growth_protocol: Spores for S. coelicolor M145 were generated on Mannitol-Soy flour or R5 agar  Cultures for genomic DNA preparation were performed in YEME medium with 0.5% glycine supplement at 30°C until early stationary phase (refer to T Kieser, MJ Bibb, MJ Buttner, KF Chater, DA Hopwood: Practical Streptomyces Genetics: The John Innes Foundation, Norwich, UK; 2000).

extract_protocol: Genomic DNA (gDNA) extraction was carried out using Kirby mix procedure as described elsewhere (T Kieser, MJ Bibb, MJ Buttner, KF Chater, DA Hopwood: Practical Streptomyces Genetics: The John Innes Foundation, Norwich, UK; 2000). About 500 µl of 20 µg/µl gDNA was sonicated briefly for 30-40 sec for shearing them to ~500 bp average size (confirmed by gel electrophoresis).


title: 99-048-05_DS7147_gp_5ug D

description: DnaseI enriched

source_name: HepG2 ATCC; DnaseI enriched

tag: HepG2 ATCC


title: S. coelicolor YSK4425 41h Replicate 2

description: No additional description

source_name: S. coelicolor RNA R5- medium 41h

value: 41h Replicate 2


title: S. coelicolor YSK4425 32h Replicate 1

description: No additional description

source_name: S. coelicolor RNA R5- medium 32h

value: 32h Replicate 1


title: E_098_048_03_DS7226_W D

description: DnaseI enriched


title: S. coelicolor YSK4425 45h Replicate 1

description: No additional description

value: 45h Replicate 1


title: S. coelicolor YSK4425 41h Replicate 1

description: No additional description

value: 41h Replicate 1


title: IRTGFBd8_13


title: E_099_086_04_DS6883_W D

description: DnaseI enriched

source_name: HCD4 Wilson; DnaseI enriched

tag: HCD4 Wilson


title: S. coelicolor YSK4425 31h

description: No additional description

source_name: S. coelicolor RNA R5- medium 31h


title: S. coelicolor YSK4425 37h

description: No additional description

source_name: S. coelicolor RNA R5- medium 37h


title: TGFBd8_12

description: TGFbeta added.


title: S. coelicolor YSK4425 23h Replicate 1

description: No additional description

source_name: S. coelicolor RNA R5- medium 23h

value: 23h Replicate 1


title: S. coelicolor YSK4425 35h

description: No additional description

source_name: S. coelicolor RNA R5- medium 35h


title: S. coelicolor YSK4425 28h

description: No additional description

source_name: S. coelicolor RNA R5- medium 28h


title: S. coelicolor YSK4425 19h Replicate 1

description: No additional description

source_name: S. coelicolor RNA R5- medium 19h

value: 19h Replicate 1


title: S. coelicolor YSK4425 32h Replicate 2

description: No additional description

value: 32h Replicate 2


title: S. coelicolor YSK4425 19h Replicate 2

description: No additional description

value: 19h Replicate 2


title: S. coelicolor YSK4425 21h Replicate 2

description: No additional description

source_name: S. coelicolor RNA R5- medium 21h

value: 21h Replicate 2


title: Backskin_DN-CLIM_P23_rep2

city: Irvine

first: Kevin

middle: K

last: Lin

address: 250 Sprague Hall

department: Biological Chemistry & Medicine

institute: University of California, Irvine

description: Performed by UCI Microarray Facility.

hyb_protocol: Labeled RNA was hybridized with the Affymetrix chips (MG-U74Av2) and washed according to manufacturer's recommendations.

scan_protocol: The hybridized probe array was then stained with streptavidin pycoerythrin conjugate, and each GeneChip scanned twice in a HP GeneArray Confocal Laser Scanner at 570 nm with a laser resolution of 3 mm.

data_processing: MAS 5.0

organism: Mus musculus

source_name: DN-CLIM mouse backskin, Postnatal day 23

label_protocol: Double stranded cDNA was synthesized from the total RNA, and an in vitro transcription reaction was then performed to biotin label RNA made from the cDNA.

extract_protocol:
Extraction: TRIzol method (Invitrogen)
Clean up: RNeasy columns (Qiagen)

tag: Tissue

value: backskin

tag: Age

value: Postnatal day 23


title: Backskin_WT_P14_rep3

description: Performed by UCI Microarray Facility.

source_name: Wild-type mouse backskin, Postnatal day 14

value: Postnatal day 14


title: Backskin_DN-CLIM_P14_rep1

description: Performed by UCI Microarray Facility.

source_name: DN-CLIM mouse backskin, Postnatal day 14


title: S. coelicolor YSK4425 15h Replicate 2

description: No additional description

source_name: S. coelicolor RNA R5- medium 15h

value: 15h Replicate 2


title: S. coelicolor YSK4425 23h Replicate 2

description: No additional description

value: 23h Replicate 2


title: S. coelicolor YSK4425 17h Replicate 2

description: No additional description

source_name: S. coelicolor RNA R5- medium 17h

value: 17h Replicate 2


title: Backskin_WT_P23_rep3

description: Performed by UCI Microarray Facility.

source_name: Wild-type mouse backskin, Postnatal day 23


title: S. coelicolor YSK4425 25h Replicate 2

description: No additional description

source_name: S. coelicolor RNA R5- medium 25h

value: 25h Replicate 2

source_name: S. coelicolor genomic DNA


title: S. coelicolor YSK4425 21h Replicate 1

description: No additional description

value: 21h Replicate 1


title: S. coelicolor YSK4425 38h

description: No additional description

source_name: S. coelicolor RNA R5- medium 38h


title: Backskin_WT_P23_rep2

description: Performed by UCI Microarray Facility.


title: S. coelicolor YSK4425 25h Replicate 1

description: No additional description

value: 25h Replicate 1


title: E_098_048_03_DS7226_W E

description: DnaseI enriched

source_name: HL60 ATCC; DnaseI enriched


title: 99-007-02_DS7135_wga A

description: DnaseI enriched

source_name: HESC G.Stam; DnaseI enriched

tag: HESC G.Stam


title: Backskin_WT_P23_rep1

description: Performed by UCI Microarray Facility.


title: 99-007-03_DS7136_wga A

description: DnaseI enriched


title: Backskin_DN-CLIM_P14_rep2

description: Performed by UCI Microarray Facility.


title: Backskin_DN-CLIM_P14_rep3

description: Performed by UCI Microarray Facility.


title: C_094_065_03_PDS273_D G

description: Control genomic dna (untreated)

source_name: CACO2 ATCC; Control genomic dna (untreated)

extract_protocol: Samples were extracted/cleaned using Qiagen Midi Preps according to manufacturer

treatment_protocol: Cells were lysed and Intact nuclei were isolated using NP40.  Nuclei were lysed using SDS and treated overnight with Proteinase K

tag: CACO2 ATCC


title: S. coelicolor YSK4425 15h Replicate 1

description: No additional description

value: 15h Replicate 1


title: Backskin_DN-CLIM_P6_rep5

description: Performed by UCI Microarray Facility.

source_name: DN-CLIM mouse backskin, Postnatal day 6

value: Postnatal day 6


title: E_098_048_02_DS7213_W G

description: DnaseI enriched


title: S. coelicolor YSK4425 17h Replicate 1

description: No additional description

value: 17h Replicate 1


title: E_098_048_03_DS7226_W G

description: DnaseI enriched


title: Backskin_WT_P14_rep1

description: Performed by UCI Microarray Facility.


title: Backskin_WT_P14_rep2

description: Performed by UCI Microarray Facility.


title: Backskin_DN-CLIM_P23_rep1

description: Performed by UCI Microarray Facility.


title: Backskin_DN-CLIM_P6_rep4

description: Performed by UCI Microarray Facility.


title: Backskin_DN-CLIM_P6_rep3

description: Performed by UCI Microarray Facility.


title: Backskin_DN-CLIM_P6_rep1

description: Performed by UCI Microarray Facility.


title: Backskin_WT_P6_rep1

description: Performed by UCI Microarray Facility.

source_name: Wild-type mouse backskin, Postnatal day 6


title: Backskin_DN-CLIM_P6_rep2

description: Performed by UCI Microarray Facility.


title: U937 cells treated with anisomycin (3 h)

city: Toyama

first: Yoshiaki

last: Tabuchi

state: Toyama

address: 2630 Sugitani

department: Life Science Research Center

country: Japan

institute: University of Toyama

description: Human lymphoma U937 cells were treated with anisomysin (1 μM) for 3 h.

hyb_protocol: After fragmentation, the biotinylated cRNA was hybridized to arrays at 45°C for 16 h.

scan_protocol: The arrays were washed, stained with streptavidin-phycoerythrin and scanned with a probe array scanner (Affymetrix).

data_processing: GeneChip Analysis Suite

label: phycoerythrin

source_name: Human lymphoma U937 cells

label_protocol: 5 μg of total RNA was used to synthesize double-strand cDNA with a GeneChip® Expression 3’-Amplification Reagents One-Cycle cDNA Synthesis Kit (Affymetrix). Biotin-labeled cRNA was then synthesized from the cDNA using GeneChip® Expression 3’-Amplification Reagents for IVT Labeling (Affymetrix).

extract_protocol: Total RNA was extracted from the cells using an RNeasy Total RNA Extraction Kit (Qiagen K.K., Tokyo, Japan). Then, RNA samples were treated with RNase-free DNase.

tag: Human lymphoma U937 cells


title: U937 cells treated with anisomycin (0 h)

description: Human lymphoma U937 cells were treated with anisomysin for 0 h (control).


title: U937 cells treated with paeoniflorin (6 h)

description: U937 cells, a human lymphoma cell line, were treated with paeoniflorin (0.16 mg/ml; 30 min) and followed by incubation for 6 h at 37°C.


title: Backskin_WT_P6_rep4

description: Performed by UCI Microarray Facility.


title: U937 cells treated with paeoniflorin (0 h)

description: U937 cells, a human lymphoma cell line, were treated with paeoniflorin (0.16 mg/ml; 30 min) and followed by incubation for 0 h at 37°C.


title: U937 cells treated with anisomycin (6 h)

description: Human lymphoma U937 cells were treated with anisomysin (1 μM) for 6 h.


title: Backskin_WT_P6_rep2

description: Performed by UCI Microarray Facility.


title: U937 cells treated with paeoniflorin (control)

description: Human lymphoma U937 cells were cultured at 37°C (non-treatment; control).


title: IRTGFBd8_23


title: high salt, 45 minutes B

status: Public on Jun 22 2007

city: Laramie

first: Mark

last: Gomelsky

state: WY

department: Molecular Biology

institute: University of Wyoming

description: Rhodobacter sphaeroides 2.4.1, Laramie

hyb_protocol: according to Affymetrix protocol

scan_protocol: according to Affymetrix protocol

data_processing: RMA (context-dependent) processing for corresponding experimental series was used for data analysis and mentioned in the papers; MAS 5.0 values are also depositied here for consistensy with other submissions

organism: Cereibacter sphaeroides 2.4.1

source_name: photosynthetic conditions (10W/m2 white light illumination, no oxygen); high salt stress (1.5% NaCl) during 45 min

label_protocol: according to Affymetrix protocol

growth_protocol: Cells were grown at anoxic photosynthetic (10 W/m2 illumination) conditions; salt stress was induced by the addition of NaCl to the exponentially grown (A600 = 0.4 ± 0.03) cultures to the final concentration of 1.5 %; Cultures were collected at 45 min after addition of NaCl

extract_protocol: RNA isolated with bead beater + RNeasy kits

tag: strain


title: SD Rat Control 24 hour rep1

city: Toronto

first: Paul

middle: C

last: Boutros

state: Ontario

address: 101 College Street, Suite 800

institute: Ontario Institute for Cancer Research

description: Control animals at 24 hours

hyb_protocol: The microarray facility at the University of Toronto at The Centre for Applied Genomics, Hospital for Sick Children (Toronto, ON) processed the gene chips as per the manufacturer’s instructions.

data_processing: Array data was loaded into R (v2.0.1) using the Affy package (v1.5.8) of the BioConductor open-source project.  Data were investigated for spatial and distributional homogeneity, then pre-processed with a sequence-specific version of the RMA algorithm termed GCRMA, as implemented in BioConductor (v1.1.3).

source_name: control liver, 24 hours

growth_protocol: Male Sprague Dawley rats (Charles River, Montreal, QC) weighing 210-230 g were housed in plastic cages (2 per cage) with wooden chip bedding in a 12:12 h light:dark cycle at 22 °C.  Rats were given unrestricted access to standard rat chow (Agribrands, Purina Canada, Strathroy, ON) and tap water, and allowed to acclimatize for one week prior to the start of experimentation.

extract_protocol: Immediately following RNA stabilization in RNAlater, livers were kept at –20 °C, and at -80 °C for long-term storage.  Small samples (10-30 mg) of liver were homogenized using a rotor-stator homogenizer (IKA Ultra-Turrax T25 S1, Janke & Kunkel, Staufen, Germany), and total RNA was extracted as per the manufacturer’s instructions.   RNA concentration and purity were determined via UV spectrophotometry, and the quality of RNA was further assessed by capillary electrophoresis using the Agilent Bioanalyzer

treatment_protocol: Rats were orally dosed with TA (100 mg/kg) by gavage in a total volume of 1 mL dissolved in an equal molar amount of sodium bicarbonate.  Control animals were orally dosed with 1 mL of sodium bicarbonate.  Eight animals were divided into two groups: Group 1 consisted of two animals that received a single dose of TA, and the two control animals received only sodium bicarbonate.  Group 1 was sacrificed 6 h after drug/vehicle administration.  Group 2 also comprised of two animals, and they were given two doses of TA (given at t=0 and t=16 h) and sacrificed at 24 h.  Control rats in group 2 received two oral doses of sodium bicarbonate.  Animals were sacrificed by CO2 asphyxiation and liver RNA was stabilized by immediate tissue submersion in RNAlater RNA Stabilization Reagent (Qiagen).

value: Sprague Dawley, Gender:male, Weight:210-230g, Tissue:liver


title: U937 cells treated with anisomycin (2 h)

description: Human lymphoma U937 cells were treated with anisomysin (1 μM) for 2 h.


title: high salt, 45 minutes A

description: Rhodobacter sphaeroides 2.4.1, Laramie

data_processing: RMA (context-dependent) processing for corresponding experimental series was used for data analysis and mentioned in the papers; MAS 5.0 values are depositied here for consistensy with other submissions

growth_protocol: Cells are grown at anoxic photosynthetic (10 W/m2 illumination) conditions; salt stress was induced by the addition of NaCl to the exponentially grown (A600 = 0.4 ± 0.03) cultures to the final concentration of 1.5 %; Cultures were collected at 45 min after addition of NaCl


title: U937 cells treated with paeoniflorin (3 h)

description: U937 cells, a human lymphoma cell line, were treated with paeoniflorin (0.16 mg/ml; 30 min) and followed by incubation for 3 h at 37°C.


title: Backskin_DN-CLIM_P23_rep3

description: Performed by UCI Microarray Facility.

source_name: DN-CLIM mouse backskin, Postnatal day 23


title: Backskin_WT_P6_rep5

description: Performed by UCI Microarray Facility.


title: U937 cells treated with anisomycin (1 h)

description: Human lymphoma U937 cells were treated with anisomysin (1 μM) for 1 h.


title: Backskin_WT_P6_rep3

description: Performed by UCI Microarray Facility.


title: SD Rat Tienilic 24 hour rep1

description: Treated animal #1 at 24 hours

scan_protocol: The microarray facility at the University of Toronto at The Centre for Applied Genomics, Hospital for Sick Children (Toronto, ON) processed the gene chips as per the manufacturer’s instructions.

source_name: Tienilic acid treated liver, 24 hours


title: high salt, 7 minutes A

description: Rhodobacter sphaeroides 2.4.1, Laramie

source_name: photosynthetic conditions (10W/m2 white light illumination, no oxygen); high salt stress (1.5% NaCl) during 7 min

growth_protocol: Cells are grown at anoxic photosynthetic (10 W/m2 illumination) conditions; salt stress was induced by the addition of NaCl to the exponentially grown (A600 = 0.4 ± 0.03) cultures to the final concentration of 1.5 %; Cultures were collected at 7 min after addition of NaCl


title: SD Rat Control 6 hour rep1

description: Control animals at six hours

source_name: control liver, 6 hours

label_protocol: The microarray facility at the University of Toronto at The Centre for Applied Genomics, Hospital for Sick Children (Toronto, ON) processed the gene chips as per the manufacturer’s instructions.


title: low salt, 45 minutes A

description: Rhodobacter sphaeroides 2.4.1, Laramie

source_name: photosynthetic conditions (10W/m2 white light illumination, no oxygen); low salt stress (0.25% NaCl) during 45 min

growth_protocol: Cells are grown at anoxic photosynthetic (10 W/m2 illumination) conditions; salt stress was induced by the addition of NaCl to the exponentially grown (A600 = 0.4 ± 0.03) cultures to the final concentration of 0.25 %; Cultures were collected at 45 min after addition of NaCl


title: high salt, 7 minutes B

description: Rhodobacter sphaeroides 2.4.1, Laramie


title: SD Rat Tienilic 24 hour rep2

description: Treated animal #2 at 24 hours


title: SD Rat Tienilic 6 hour rep1

description: Treated animal #1 at six hours

source_name: Tienilic acid treated liver, 6 hours


title: low salt, 45 minutes B

description: Rhodobacter sphaeroides 2.4.1, Laramie


title: SD Rat Tienilic 6 hour rep2

description: Treated animal #2 at six hours


title: low salt, 7 minutes A

description: Rhodobacter sphaeroides 2.4.1, Laramie

hyb_protocol: according Affymetrix protocol

scan_protocol: according Affymetrix protocol

source_name: photosynthetic conditions (10W/m2 white light illumination, no oxygen); low salt stress (0.25% NaCl) during 7 min

label_protocol: according Affymetrix protocol

growth_protocol: Cells are grown at anoxic photosynthetic (10 W/m2 illumination) conditions; salt stress was induced by the addition of NaCl to the exponentially grown (A600 = 0.4 ± 0.03) cultures to the final concentration of 0.25 %; Cultures were collected at 7 min after addition of NaCl


title: 10-4, photosynthetic, 10 W/m2

description: Rhodobacter sphaeroides 2.4.1, Laramie

source_name: photosynthetic conditions (10W/m2 white light illumination, no oxygen); no salt stress

growth_protocol: Cells are grown at anoxic photosynthetic (10 W/m2 illumination) conditions without salt stress


title: low salt, 7 minutes B

description: Rhodobacter sphaeroides 2.4.1, Laramie


title: ovary_cultured_progesterone_rep2

city: Pullman

first: Michael

last: Skinner

address: Abelson 507

department: SBS

institute: WSU

description: Chip ID=EricBK1P35-P4-2-071905.  RNA from zero-day old rat ovaries cultured two days with progesterone treatment.

hyb_protocol: standard Affymetrix procedure

scan_protocol: chips were scanned using Agilent GeneArray Scanner G2500A

data_processing: Auto-scale ON (1-1000).  Scaling = all probe sets.  The microarray image data were converted to numerical data with GeneChip Operating Software using a scaling factor of 125, and then imported into the GeneSpring program (Agilent Technologies, Palo Alto, CA) where raw data were filtered for flags (present/absent calls), expression level, fold change and confidence (t-test p-value) with no multiple testing correction.

source_name: 0-day rat ovary cultured 2 days

label_protocol: standard Affymetrix procedures

extract_protocol: Ovaries with the same treatment were pooled to make each RNA sample.  RNA was extracted using the Trizol reagent according to manufacturers instructions (Sigma, St. Louis, MO).  Two pooled independent RNA samples were analysed for each treatment group (control or P4-treated ovaries cultured for two days).

treatment_protocol: Female rat pups less than eight hours old were euthanized and rat ovaries were removed according to IACUC-approved animal use protocols.  Newborn rat ovaries were dissected from freshly euthanized rat pups.  Whole ovaries were cultured as previously described (Nilsson, Parrott et al. 2001) on floating filters (0.4 um Millicell-CM, Millipore, Bedford, MD) in 0.5 ml Dulbecco's Modified Eagle's Medium (DMEM)-Ham's F-12 medium (1:1, vol/vol) containing 0.1 % bovine serum albumin (BSA, Sigma, St. Louis, MO), 0.1% Albumax (Gibco BRL, Gaithersburg, MD), 27.5 ug/ml transferrin, 200 ng/ml insulin (human recombinant, Sigma), and 0.05 mg/ml L-ascorbic acid (Sigma) in a 4-well culture plate (Nunc plate, Applied Scientific, South San Francisco, CA).  Ovaries were randomly assigned to treatment groups with 2-3 ovaries per floating filter in each well.   Ovaries were treated with progesterone (P4) (Sigma Chemical Co., St. Louis, MO) at 10-6M.  Medium was supplemented with penicillin and streptomycin to prevent bacterial contamination.

tag: ovaries dissected from 0-day old Sprague-Dawley rats and cleaned of ovarian bursa.


title: ovary_cultured_control_rep1

description: Chip ID=EricBK1P47-C-1-071905.  RNA from zero-day old rat ovaries cultured two days as controls with no treatment.

treatment_protocol: Female rat pups less than eight hours old were euthanized and rat ovaries were removed according to IACUC-approved animal use protocols.  Newborn rat ovaries were dissected from freshly euthanized rat pups.  Whole ovaries were cultured as previously described (Nilsson, Parrott et al. 2001) on floating filters (0.4 um Millicell-CM, Millipore, Bedford, MD) in 0.5 ml Dulbecco's Modified Eagle's Medium (DMEM)-Ham's F-12 medium (1:1, vol/vol) containing 0.1 % bovine serum albumin (BSA, Sigma, St. Louis, MO), 0.1% Albumax (Gibco BRL, Gaithersburg, MD), 27.5 ug/ml transferrin, 200 ng/ml insulin (human recombinant, Sigma), and 0.05 mg/ml L-ascorbic acid (Sigma) in a 4-well culture plate (Nunc plate, Applied Scientific, South San Francisco, CA).  Ovaries were randomly assigned to treatment groups with 2-3 ovaries per floating filter in each well.   Ovaries were un-treated and used as controls.  Medium was supplemented with penicillin and streptomycin to prevent bacterial contamination.


title: R724P00901

city: San Diego

first: Yipeng

last: Wang

institute: Vaccine Research Institute of San Diego

description: prostate

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

scan_protocol: GeneChips were scanned using the Affymetrix Scanner.

data_processing: The data were analyzed and normalized with RMA.

source_name: prostate cancer sample

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

tag: Percentage of Tumor

tag: Percentage of Stroma

tag: Percentage of BPH

tag: Percentage of Atrophic Gland


title: R743P00701

description: prostate

tag: Percentage of Tumor:not Known

tag: Percentage of Stroma:not Known

tag: Percentage of BPH:not Known

tag: Percentage of Atrophic Gland:not Known


title: R727P01204

description: prostate


title: R744P00748

description: prostate


title: R723P00881

description: prostate


title: R705P01282

description: prostate


title: R725P00941

description: prostate


title: R746P00821

description: prostate


title: R721P00481

description: prostate


title: R707P01302

description: prostate


title: R748P01234

description: prostate


title: R741P00668

description: prostate


title: R722P00829

description: prostate


title: R742P00670

description: prostate


title: R703P01230

description: prostate


title: R726P01003

description: prostate


title: R708P01308

description: prostate


title: R745P00782

description: prostate


title: R702P01103

description: prostate


title: R749P01262

description: prostate


title: ovary_cultured_progesterone_rep1

description: Chip ID=EricBK1P47-P4-1-071905.  RNA from zero-day old rat ovaries cultured two days with progesterone treatment.


title: R706P01301

description: prostate


title: R685P01201

description: prostate


title: R683P01102

description: prostate


title: R704P01242

description: prostate


title: R684P01106

description: prostate


title: R686P01236

description: prostate


title: R701P01101

description: prostate


title: R681P00686

description: prostate


title: R653P01205

description: prostate


title: R651P01105

description: prostate


title: R650P01104

description: prostate


title: R663P00904

description: prostate


title: R668P01211

description: prostate


title: R682P00687

description: prostate


title: R662P00808

description: prostate


title: R649P01087

description: prostate


title: R664P01207

description: prostate


title: R652P01186

description: prostate


title: R626P01184

description: prostate


title: R644P00804

description: prostate


title: R648P01085

description: prostate


title: R643P00803

description: prostate


title: R661P00807

description: prostate


title: R624P00744

description: prostate


title: R647P01068

description: prostate


title: R641P00801

description: prostate


title: R646P00806

description: prostate


title: R625P00906

description: prostate


title: R645P00805

description: prostate


title: ovary_cultured_control_rep2

description: Chip ID=EricBK1P-C-2-071905.  RNA from zero-day old rat ovaries cultured two days as controls with no treatment.


title: R623P01188

description: prostate


title: R591P01072

description: prostate


title: R592P01081

description: prostate

source_name: normal prostate sample


title: R601P01083

description: prostate


title: R621P01206

description: prostate


title: R642P00802

description: prostate


title: R589P01070

description: prostate


title: R590P01071

description: prostate


title: R585P01065

description: prostate


title: R583P01063

description: prostate


title: R588P01069

description: prostate


title: R586P01066

description: prostate


title: R569P00764

description: prostate


title: R622P01005

description: prostate


title: R567P00147

description: prostate


title: R570P00762

description: prostate


title: R581P01061

description: prostate


title: R587P01067

description: prostate


title: R565P00156

description: prostate


title: R568P00766

description: prostate


title: R540P00550

description: prostate


title: R539P00546

description: prostate


title: R564P00721

description: prostate


title: R534P00429

description: prostate


title: R566P00154

description: prostate


title: R582P01062

description: prostate


title: R561P00761

description: prostate


title: R541P00728

description: prostate


title: R535P00441

description: prostate


title: R533P00403

description: prostate


title: R563P00723

description: prostate


title: R562P00726

description: prostate


title: R537P00446

description: prostate


title: R536P00445

description: prostate


title: R538P00541

description: prostate


title: R531P00647

description: prostate


title: R524P00603

description: prostate


title: R527P00606

description: prostate


title: R529P00609

description: prostate


title: R525P00604

description: prostate


title: R523P00585

description: prostate


title: R495P00447

description: prostate


title: R530P00643

description: prostate


title: R496P00521

description: prostate


title: R526P00605

description: prostate


title: R532P00648

description: prostate


title: R490P00325

description: prostate


title: R489P00323

description: prostate


title: R481P00302

description: prostate


title: R521P00428

description: prostate


title: R491P00345

description: prostate


title: R483P00305

description: prostate


title: R494P00442

description: prostate


title: R488P00312

description: prostate


title: R487P00311

description: prostate


title: R493P00433

description: prostate


title: R484P00306

description: prostate


title: R469P00501

description: prostate


title: R482P00304

description: prostate


title: R528P00607

description: prostate


title: R492P00424

description: prostate


title: R522P00584

description: prostate


title: R485P00308

description: prostate


title: R468P00438

description: prostate


title: R464P00422

description: prostate


title: R461P00322

description: prostate


title: R463P00344

description: prostate


title: R458P00307

description: prostate


title: R467P00436

description: prostate


title: R457P00303

description: prostate


title: R460P00321

description: prostate


title: R462P00324

description: prostate


title: R438P00060

description: prostate


title: R432P00185

description: prostate


title: R442P00227

description: prostate


title: R426P00145

description: prostate


title: R436P00056

description: prostate


title: R430P00182

description: prostate


title: R456P00301

description: prostate


title: R431P00183

description: prostate


title: R459P00309

description: prostate


title: R440P00121

description: prostate


title: R437P00057

description: prostate


title: R434P00230

description: prostate


title: R465P00426

description: prostate


title: R424P00100

description: prostate


title: R466P00431

description: prostate


title: R428P00155

description: prostate


title: R441P00225

description: prostate


title: R435P00262

description: prostate


title: R422P00092

description: prostate


title: R439P00089

description: prostate


title: R425P00102

description: prostate


title: R433P00224

description: prostate


title: R429P00163

description: prostate


title: R427P00146

description: prostate


title: Mo17xB73 19 day after pollination embryo tissue, biological replicate 3

status: Public on Jun 21 2007

city: Saint Paul

first: Nathan

last: Springer

address: 1445 Gortner Ave

department: Plant Biology

description: refer to PMID: 16702414

hyb_protocol: Hybridization was performed according to the recommended Affymetrix protocols at the University of Minnesota Microarray facility.

scan_protocol: The Genechip 3000 scanner was used to scan each array

data_processing: MAS5.0 values are reported; the .cel file is also available

organism: Zea mays

source_name: Zea mays 19 day after pollination embryo tissue, genotype Mo17xB73

label_protocol: Eight ug of total RNA was labeled for each hybridization using the One-Cycle cDNA Synthesis Kit, according to the manufacturer’s instructions (Affymetrix, Santa Clara CA).

growth_protocol: Embryos were collected from kernels of inbreds Mo17 and B73 and hybrids Mo17xB73 and B73xMo17 for gene expression analysis. Samples were collected during August 2005 from field-grown maize plants grown on the St. Paul campus Agricultural Experiment Station. Inbred and hybrid crosses were performed at three different time intervals within the same week. Embryos were collected at 19 days after pollination (DAP) for the three bioreplicates. All tissues were flash frozen in a dry ice-cooled ethanol bath and subsequently stored at -80C. We collected the plant materials for each biological replicate on the same date between 9 am and 10 am. The three biological replicates represent collections performed on three different dates.

extract_protocol: Embryo RNAs were isolated using the plant RNeasy kit, according to the manufacturer’s instructions (QIAGEN).

tag: Stage

value: 19 day after pollination embryo; Genotype:Mo17xB73


title: R421P00048

description: prostate


title: R584P01064

description: prostate


title: B73 19 day after pollination embryo tissue, biological replicate 3

description: refer to PMID: 16702414

source_name: Zea mays 19 day after pollination embryo tissue, genotype B73

value: 19 day after pollination embryo; Genotype:B73


title: B73x Mo17 19 day after pollination embryo tissue, biological replicate 3

description: refer to PMID: 16702414

source_name: Zea mays 19 day after pollination embryo tissue, genotype B73xMo17

value: 19 day after pollination embryo; Genotype:B73xMo17


title: B73xMo17 19 day after pollination embryo tissue, biological replicate 1

description: refer to PMID: 16702414


title: B73 19 day after pollination embryo tissue, biological replicate 2

description: refer to PMID: 16702414


title: B73 immature ear tissue, biological replicate 2

description: refer to PMID: 16702414

source_name: Zea mays immature ear tissue, genotype B73

growth_protocol:
Immature ears from inbreds Mo17 and B73
and hybrids Mo17xB73 and B73xMo17 were collected from
field-grown maize plants during July 2005 for gene expression
analysis. The maize plants were grown on the St. Paul campus
Agricultural Experiment Station. Ears were collected for each
genotype between 9 am and 11 am on each of three consecutive
days from various positions in the field. Ears ranging
from 3.7 to 5.4 mm in length were sampled. Ears were flash
frozen in liquid nitrogen following the manual removal of
husks and silks.

extract_protocol: For immature ear RNA isolation, tissues from 6 ears/genotype/biological replicate were pooled and ground in liquid nitrogen. RNAs were extracted using Trizol reagent according to the manufacturer’s instructions (Invitrogen, Carlsbad, CA). All RNAs were subsequently subjected to DNAse treatment and phenol:chloroform extraction. RNAs were precipitated with 0.13 volume sodium acetate (pH 5.5) and 2.53 volume ethanol. Resuspended RNAs were purified further using the RNeasy system, according to the manufacturer’s instructions (QIAGEN, Valencia, CA).

value: immature ear (3.7-5.4mm); Genotype:B73


title: Mo17 19 day after pollination embryo tissue, biological replicate 2

description: refer to PMID: 16702414

source_name: Zea mays 19 day after pollination embryo tissue, genotype Mo17

value: 19 day after pollination embryo; Genotype:Mo17


title: B73xMo17 immature ear tissue, biological replicate 2

description: refer to PMID: 16702414

source_name: Zea mays immature ear tissue, genotype B73xMo17

value: immature ear (3.7-5.4mm); Genotype:B73xMo17


title: B73xMo17 19 day after pollination embryo tissue, biological replicate 2

description: refer to PMID: 16702414


title: Mo17 immature ear tissue, biological replicate 2

description: refer to PMID: 16702414

source_name: Zea mays immature ear tissue, genotype Mo17

value: immature ear (3.7-5.4mm); Genotype:Mo17


title: B73xMo17 immature ear tissue, biological replicate 3

description: refer to PMID: 16702414


title: Mo17xB73 19 day after pollination embryo tissue, biological replicate 2

description: refer to PMID: 16702414


title: Mo17xB73 immature ear tissue, biological replicate 2

description: refer to PMID: 16702414

source_name: Zea mays immature ear tissue, genotype Mo17xB73

value: immature ear (3.7-5.4mm); Genotype:Mo17xB73


title: B73 19 day after pollination embryo tissue, biological replicate 1

description: refer to PMID: 16702414


title: Mo17xB73 immature ear tissue, biological replicate 1

description: refer to PMID: 16702414


title: Mo17 immature ear tissue, biological replicate 3

description: refer to PMID: 16702414


title: Mo17 immature ear tissue, biological replicate 1

description: refer to PMID: 16702414


title: Mo17xB73 immature ear tissue, biological replicate 3

description: refer to PMID: 16702414


title: B73xMo17 immature ear tissue, biological replicate 1

description: refer to PMID: 16702414


title: B73 11-day seedling aerial tissue biological replicate 3

description: refer to PMID: 16702414

source_name: Zea mays 11-day seedling aerial tissue genotype B73

label_protocol: For seedling RNA isolation, tissues from 12 seedlings/genotype/biological replicate were pooled and ground in liquid nitrogen. RNAs were extracted using Trizol reagent according to the manufacturer’s instructions (Invitrogen, Carlsbad, CA). All RNAs were subsequently subjected to DNAse treatment and phenol:chloroform extraction. RNAs were precipitated with 0.13 volume sodium acetate (pH 5.5) and 2.53 volume ethanol. Resuspended RNAs were purified further using the RNeasy system, according to the manufacturer’s instructions (QIAGEN, Valencia, CA).

extract_protocol: Seeds for inbreds Mo17 and B73 and hybrids Mo17 x B73 and B73 x Mo17 were sown and grown under greenhouse conditions for 11 days and then sampled for gene expression analysis. Three biological replicates were planted and grown sequentially over an 5-week period during May 2005. Seeds were planted such that one seed of each genotype was present in every pot. Twelve pots were selected for tissue collection; thus 12 plants were sampled per genotype. All plants were sampled between 9 am and 10 am and plants were cut immediately above the highest root; thus all aboveground tissues and meristems were sampled. The sampled tissues were flash frozen in liquid nitrogen and stored at  -80 C prior to RNA isolation.

tag: Genotype

value: B73 Stage:11-day old seedling, all aerial tissue


title: Mo17 19 day after pollination embryo tissue, biological replicate 3

description: refer to PMID: 16702414


title: B73 immature ear tissue, biological replicate 3

description: refer to PMID: 16702414


title: Mo17 11-day seedling aerial tissue biological replicate 3

description: refer to PMID: 16702414

source_name: Zea mays 11-day seedling aerial tissue genotype Mo17

value: Mo17 Stage:11-day old seedling, all aerial tissue


title: Mo17 19 day after pollination embryo tissue, biological replicate 1

description: refer to PMID: 16702414


title: Mo17xB73 19 day after pollination embryo tissue, biological replicate 1

description: refer to PMID: 16702414


title: B73xMo17 11-day seedling aerial tissue biological replicate 3

description: refer to PMID: 16702414

source_name: Zea mays 11-day seedling aerial tissue genotype B73xMo17

value: B73xMo17 Stage:11-day old seedling, all aerial tissue


title: Mo17xB73 11-day seedling aerial tissue biological replicate 3

description: refer to PMID: 16702414

source_name: Zea mays 11-day seedling aerial tissue genotype Mo17xB73

value: Mo17xB73 Stage:11-day old seedling, all aerial tissue


title: Mo17xB73 11-day seedling aerial tissue biological replicate 2

description: refer to PMID: 16702414


title: B73 immature ear tissue, biological replicate 1

description: refer to PMID: 16702414


title: B73 11-day seedling aerial tissue biological replicate 2

description: refer to PMID: 16702414


title: B73xMo17 11-day seedling aerial tissue biological replicate 1

description: refer to PMID: 16702414


title: B73xMo17 11-day seedling aerial tissue biological replicate 2

description: refer to PMID: 16702414


title: Mo17 11-day seedling aerial tissue biological replicate 2

description: refer to PMID: 16702414


title: Cultured_cortical_astrocyte_Cx43_siRNA_rep3

status: Public on Jun 20 2007

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

state: TX

address: Ann Preston St

department: Undergraduate Medical Academy

institute: Prairie View A&M University

description: Compare the transcriptomes of Cx43 null and Cx43 siRNA treated cortical astrocytes with the transcriptome of the wildtype cortical astrocytes

hyb_protocol: 20ug total RNA extracted from each culture dish were reverse transcribed into cDNA incorporating fluorescent Cy3-dUTP. The labeled cDNA was co-hybridized with a distinct Cy5-dUTP labeled biological replica overnight at 50°C on 10 aminosilane-coated Corning glass slides, spotted with 32K selected mouse oligonucleotide sequences (70-mer Operon mouse 3.0 series) printed by the Microarray Core Facility of the AECOM. After washing (0.1% SDS and 1% SSC) to remove the non-hybridized cDNAs, each array was scanned at 750V (635nm) and 670V (532nm). Hybridization design ("multiple yellow" strategy) described in Iacobas DA, Fan C, Iacobas S et al., Transcriptomic changes in developing kidney exposed to chronic hypoxia. Biochem Biophys Res Commun. 2006 349(1):329-38.

scan_protocol: Slides were scanned with GenePix 4100A scanner (Axon Instruments, CA) and images were primarily analyzed with GenePixPro 6.0 (Axon Instruments, CA)

data_processing: Data were normalized and analyzed with in house developed algorithms described in Iacobas DA, Iacobas S, Li WEI, et al. Physiol Genomics 20: 211-223, 2005.

label_protocol: 20 ug total RNA was used to synthesize fluorescent labeled cDNA probe by direct incorporation with Cy3 fluorescent dye (Amersham Biosciences, NJ)

growth_protocol: Cells were maintained in 5% CO2, 95% air atmosphere at 37°C and 100% relative humidity. After 1 week in culture, primary confluent cell cultures (referred to as passage P0) were trypsinized (0.05% tryspin) (passage P1) and plated on 1 cm round glass coverslips 1 or 2 days prior to experimentation.

extract_protocol: RNA samples were extracted in Trizol (Invitrogen, CA)

treatment_protocol: Within 15 min to 1 h after birth, brains were removed from each littermate and cultured separately. Briefly, whole brain tissue was dissected from neonatal mice and then minced and incubated for 15 min in 0.1% tyrpsin in PBS at 37°C. Cells were dissociated from minced tissue by trituration with an blue Eppendorf pipette tip, spun at 1000 RPM for 4 min and re-suspended in Dulbecco’s Modified Eagle medium (DMEM) supplemented with 5% (vol/vol) fetal bovine serum, penicillin (50 μg/ml), streptomycin (50 μg/ml) (Gibco BRL, Gaithersburg, MD). Cells were plated in a 100mm. After reaching confluency, cells were tranfected with 20ug of Cx43 siRNA construct diluted in 1.5ml of Opti-memI (Invitrogen, CA). Next day transfecting medium was replaced by regular growth medium and 48hrs post transfection protein from these cells was collect to be tested for gene silencing efficiency using Western blot technique.

tag: Astrocytes isolated from the brain of a neonatal C57Bl/6 mouse were treated with Cx43 siRNA construct


title: R423P00094

description: prostate


title: Cultured_cortical_astrocyte_Cx43_siRNA_rep2

label_protocol: 20 ug total RNA was used to synthesize fluorescent labeled cDNA probe by direct incorporation with Cy5 fluorescent dye (Amersham Biosciences, NJ)


title: Cultured_cortical_astrocyte_Cx43_siRNA_rep4

hyb_protocol: 20ug total RNA extracted from each culture dish were reverse transcribed into cDNA incorporating fluorescent Cy5-dUTP. The labeled cDNA was co-hybridized with a distinct Cy3-dUTP labeled biological replica overnight at 50°C on 10 aminosilane-coated Corning glass slides, spotted with 32K selected mouse oligonucleotide sequences (70-mer Operon mouse 3.0 series) printed by the Microarray Core Facility of the AECOM. After washing (0.1% SDS and 1% SSC) to remove the non-hybridized cDNAs, each array was scanned at 750V (635nm) and 670V (532nm). Hybridization design ("multiple yellow" strategy) described in Iacobas DA, Fan C, Iacobas S et al., Transcriptomic changes in developing kidney exposed to chronic hypoxia. Biochem Biophys Res Commun. 2006 349(1):329-38.

scan_protocol: Slides were scanned with GenePix 4100A scanner (Axon Instruments, CA) and images were primarily analyzed with GenePixPro 6.0 (Axon Instruments, CA).


title: Cultured_cortical_astrocyte_wild_type_rep6

treatment_protocol: Within 15 min to 1 h after birth, brains were removed from each littermate and cultured separately. Briefly, whole brain tissue was dissected from neonatal mice and then minced and incubated for 15 min in 0.1% tyrpsin in PBS at 37°C. Cells were dissociated from minced tissue by trituration with an blue Eppendorf pipette tip, spun at 1000 RPM for 4 min and re-suspended in Dulbecco’s Modified Eagle medium (DMEM) supplemented with 5% (vol/vol) fetal bovine serum, penicillin (50 μg/ml), streptomycin (50 μg/ml) (Gibco BRL, Gaithersburg, MD).

tag: Astrocytes isolated from the brain of a neonatal wildtype C57Bl/6 mouse


title: Scoelicolor_M145 29h

status: Public on Jun 19 2007

description: Comparison of wild type and mutant regulatory genes in a time course study with S. coelicolor

source_name: S. coelicolor RNA R5- medium 29h

growth_protocol: S. coelicolor A3(2) strain M145 was maintained on R5 solid agar (Kieser, T., M. J. Bibb, M. J. Buttner, K. F. Chater, and D. A. Hopwood. 2000. Practical Streptomyces Genetics. The John Innes Foundation, Norwich, UK) for high density spores.  For liquid culture, spores were pre-germinated in 2xYT medium (Kieser, T., M. J. Bibb, M. J. Buttner, K. F. Chater, and D. A. Hopwood. 2000. Practical Streptomyces Genetics. The John Innes Foundation, Norwich, UK) and inoculated into R5- liquid medium (Huang, J., C. J. Lih, K. H. Pan, and S. N. Cohen. 2001. Global analysis of growth phase responsive gene expression and regulation of antibiotic biosynthetic pathways in Streptomyces coelicolor using DNA microarrays. Genes Dev 15:3183-92) at a density of ~10exp7 spores/ml.  Baffled 2L flasks containing stainless steel coils with 350 ml working volume were used for liquid cultures.  Cultures were incubated at 30°C in an orbital shaker at 300 rpm.  For measuring cell growth, samples were collected at regular intervals and mixed with one-eighth volume of 2.5 M HCl and then subjected to sonication to break mycelial pellets (Brana, A. F., S. Wolfe, and A. L. Demain. 1986. Relationship between nitrogen assimilation and cephalosporin synthesis in Streptomyces clavuligerus. Arch Microbiol 146:46-51).  Absorbance of the resulting solution at 450 nm was then taken as a measure of growth.  Proper dilution was made to ensure an OD450 measurement below 1, which is in the linear range of detection.

tag: Strain

tag: Sample

source_name: S. coelicolor genomic DNA


title: Scoelicolor_M145 37h Replicate 2

source_name: S. coelicolor RNA R5- medium 37h

value: 37h Replicate 2


title: Scoelicolor_M145 34h

source_name: S. coelicolor RNA R5- medium 34h


title: Cultured_cortical_astrocyte_Cx43_siRNA_rep1


title: Cultured_cortical_astrocyte_wild_type_rep5


title: Scoelicolor_M145 27h

source_name: S. coelicolor RNA R5- medium 27h


title: Scoelicolor_M145 37h Replicate 1

value: 37h Replicate 1


title: Scoelicolor_M145 32h Replicate 1

source_name: S. coelicolor RNA R5- medium 32h

value: 32h Replicate 1


title: Cultured_cortical_astrocyte_wild_type_rep4


title: Cultured_cortical_astrocyte_Cx43_null_rep2

tag: Astrocytes isolated from the brain of a neonatal Cx43 null C57Bl/6 mouse


title: Cultured_cortical_astrocyte_wild_type_rep2


title: Cultured_cortical_astrocyte_Cx43_null_rep1


title: Scoelicolor_M145 24h Replicate 2

source_name: S. coelicolor RNA R5- medium 24h

value: 24h Replicate 2


title: Scoelicolor_M145 32h Replicate 2

value: 32h Replicate 2


title: Scoelicolor_M145 24h Replicate 1

value: 24h Replicate 1


title: Cultured_cortical_astrocyte_Cx43_null_rep3


title: Cultured_cortical_astrocyte_wild_type_rep3


title: Scoelicolor_M145 22h Replicate 2

source_name: S. coelicolor RNA R5- medium 22h

value: 22h Replicate 2


title: Scoelicolor_M145 20h Replicate 2

source_name: S. coelicolor RNA R5- medium 20h

value: 20h Replicate 2


title: Scoelicolor_M145 18h Replicate 2

source_name: S. coelicolor RNA R5- medium 18h

value: 18h Replicate 2


title: Cultured_cortical_astrocyte_Cx43_null_rep4


title: Cultured_cortical_astrocyte_wild_type_rep1


title: Scoelicolor_M145 22h Replicate 1

value: 22h Replicate 1


title: Scoelicolor_M145 16h Replicate 2

source_name: S. coelicolor RNA R5- medium 16h

value: 16h Replicate 2


title: Scoelicolor_M145 20h Replicate 1

value: 20h Replicate 1


title: Scoelicolor_M145 16h Replicate 1

value: 16h Replicate 1


title: Scoelicolor_M145 14h Replicate 2

source_name: S. coelicolor RNA R5- medium 14h

value: 14h Replicate 2


title: Laser capture microdissected (LCM) endosperm at the heart stage, biological replicate 3

city: Los Angeles

first: Bob

last: Goldberg

address: 610 Charles E Young Drive East

department: Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

description: Endosperm regions from heart stage seeds were microdissected using the LEICA LMD6000 system.

hyb_protocol: Following fragmentation, ten micrograms of cRNA were hybridized for 16 hr at 45°C with the GeneChip Soybean Genome Array. GeneChips were washed and stained using the EukGE-WS2V4_450 protocol in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with the Affymetrix GeneChip Operating System 1.3 (GCOS 1.3) using default analysis settings and global scaling as a normalization method. The trimmed mean target intensity of each array was set to 500.

organism: Glycine max

source_name: Soybean heart stage endosperm captured by LCM

label_protocol: Two nanograms of total RNA was amplified using the RiboAmp OA Amplification Kit (Molecular Devices, Sunnyvale, CA).  Biotinylated cRNAs were synthesized with the ENZO BioArray High Yield RNA Transcript Labeling Kit using all of the amplified RNA from the RiboAmp OA Kit.

growth_protocol: Soybean cv. Asgrow A3237 was grown in the UCLA Plant Growth Center using a 16:8 light-dark cycle at 22°C.

extract_protocol: Total RNA was extracted using the PicoPure RNA Extraction Kit (Molecular Devices, Sunnyvale, CA).

treatment_protocol: Pods with lengths between 1.3 and 2.0 cm containing seeds with heart-stage embryos were fixed in 3:1(v/v) ethanol:acetic acid and embedded in paraffin (Kerk et al.,  Plant Physiol.132. 27-35 (2003)).  Seed compartment was captured from eight-micron sections using a Leica LMD6000 System.

tag: Soybean cv. Asgrow A3237


title: Scoelicolor_M145 14h Replicate 1

value: 14h Replicate 1


title: Scoelicolor_M145_10h

source_name: S. coelicolor RNA R5- medium 10h


title: Laser capture microdissected (LCM) seed coat palisade at the early maturation stage, biological replicate 2

description: Seed coat palisade regions from early maturation-stage seeds were microdissected using the LEICA LMD6000 system.

hyb_protocol: Following fragmentation, ten micrograms of cRNA were hybridized for 16 hr at 45?C with the GeneChip Soybean Genome Array. GeneChips were washed and stained using the EukGE-WS2V4_450 protocol in the Affymetrix Fluidics Station 450.

source_name: Soybean early maturation-stage seed coat palisade captured by LCM

growth_protocol: Soybean cv. Asgrow A3237 was grown in the UCLA Plant Growth Center using a 16:8 light-dark cycle at 22?C.

treatment_protocol: Seeds with length between 6.0 and 7.0 mm containing early maturation-stage embryos were fixed in 3:1(v/v) ethanol:acetic acid and embedded in paraffin (Kerk et al.,  Plant Physiol.132. 27-35 (2003)).  Seed compartment was captured from eight-micron sections using a Leica LMD6000 system.


title: Scoelicolor_M145 13h Replicate 2

source_name: S. coelicolor RNA R5- medium 13h

value: 13h Replicate 2