title: Rat iPS F65 cells' gene expression difference compared with that of the adult cells including rat BMC and PEF cells

summary: Rat iPS F65 cells had different gene expression level compared with that of the adult cells including rat bone marrow cells(BMC) and rat primary ear fibroblasts(PEF). This difference gave rat iPS F65 cells unique characteristics which could then be compared with other species' ES cells or iPS cells like human ES cells and mouse ES cells by the homologue genes comparison to show which species' ES cells or iPS cells were more competitive with the other.

overall_design: There were three replicates sample of the Rat iPS F65 cells named 1, 2, 3. And the adult cells were the mixture of rat bone marrow cells and rat primary ear fibroblasts named mix1. Rat iPS F65 cells samples were labled with Cy3 and the mix1 were labled with Cy5. The data was process to show the Rat iPS F65 cells' gene expression difference compared with that of mix1.


title: The Effects of Aging on the Molecular and Cellular Composition of the Prostate Microenvironment

status: Public on Sep 15 2010

city: Seattle

first: Ilsa

last: Coleman

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

country: USA

institute: Fred Hutchinson Cancer Center

summary: Advancing age is associated with substantial increases in the incidence rates of common diseases affecting the prostate including benign prostatic hyperplasia (BPH) and prostate carcinoma. However, to date, there is no established molecular explanation for the age-dependent increases in these pathologies. The prostate is comprised of a functional secretory epithelium supported by a spectrum of cell types and structural elements comprising the stroma. As reciprocal interactions between epithelium and stromal constituents are essential for normal organogenesis and serve to maintain normal functions, discordance within the stromal could permit or promote disease processes. In this study we sought to identify aging-associated alterations in the mouse prostate that could influence pathology. We quantitated transcript levels in microdissected periglandular stroma from young (4 month-old) and old (20-24 month-old) C57BL/6 mice, and identified a significant change in the expression of 1259 genes (p<0.05). These included increases in transcripts encoding genes associated with inflammation (e.g., Ccl8, Ccl12), genotoxic/ oxidative stress (e.g., Apod, Serpinb5) and paracrine-acting proteins (e.g., Cyr61). The expression of several collagen genes (e.g., Col1a1 and Col3a1) exhibited age associated declines. By immunofluorescence and electron microscopy we determined that the aged prostate contains an abundant disorganized collagen matrix and a significant increase in inflammatory infiltrates comprised of macrophages, T cells and, to a lesser extent, B cells. These findings demonstrated that during normal aging the prostate stroma exhibits phenotypic and molecular characteristics plausibly contributing to the striking age associated pathologies affecting the prostate through oxidative stress and inflammatory cell damage.

overall_design: Custom Agilent 44K whole mouse genome expression oligonucleotide microarrays as well as custom mouse cDNA microarrays were used to measure transcript levels in microdissected periglandular stroma from young (4 month-old) and old (20-24 month-old) C57BL/6 mice. All samples were laser-capture microdissected and total RNA isolated and amplified prior to hybridization against a reference pool of normal adult mouse tissues.

first: Daniella

last: Bianchi-Frias

first: Funda

last: Vakar-Lopez

middle: M

first: May

last: Reed

first: Stephen

middle: R

last: Plymate

first: Peter

middle: S

last: Nelson


title: Transcriptome analysis of mesothelioma induced by intraperitoneal injections of ferric saccharate in rats

status: Public on Dec 31 2009

city: Nagoya

first: Shinya

last: Toyokuni

state: Aichi

address: 65 Tsuruma-Cho, Showa-Ku

department: Pathology

country: Japan

institute: Nagoya University

summary: Iron plays an important role in oxidative tissue damage and subsequent carcinogenesis. Iron deposition in the peritoneum causes neoplastic changes. Here we used gene expression microarrays to find common genetic alterations in a rat model by repeated intraperitoneal injections of ferric saccharate. Gene expression microarray revealed the expression of uromodulin (Umod) is increased in mesothelioma approximately 250-fold.

overall_design:
Carcinogenesis protocol was performed using specific pathogen-free male and female F1 hybrid rats between Fischer344 and Brown-Norway strains. A total of 12 microarrays (Whole Rat Genome Oligo Microarrary) were used for the screening purpose;
The scraped pleural mesothelial cells of 8 week male rat untreated or peri-testicular tissue as control; Induced mesothelioma of epithelioid and sarcomatoid types.

first: Qian

last: Hu

last: Akatsuka


title: Colon mucosa of F344 rats: control treated with 5% DSS vs Resveratrol + 5% DSS

status: Public on Jan 28 2009

city: Florence

first: Maria del Mar

last: Larrosa Pérez

address: Viale G. Pieracinni 6

country: Italy

institute: Department of Pharmacology

summary:
Expression profile of colon mucosa of F344 rats treated with 5% DSS during five days vs colon mucosa of F344 rats pre-treated for 20 days with resveratrol 1mg/kg/day and during the five days of 5% DSS administration

Keywords: Inflammation experiment

overall_design: Two conditions experiment, colon mucosa of F344 rats treated 5% DSS for 5d vs colon mucosa of F344 rats pretreated with 1mg/kg/day resv +  5% DSS for 5d. 8 Biological samples for each group

first: Mar

last: Larrosa

first: Simona

last: Toti

first: Juan

middle: C

last: Espin


title: Evidence for a major role of antisense RNAs in cyanobacterial gene regulation

status: Public on Jan 14 2009

city: Freiburg

first: Jan

last: Mitschke

address: Schaenzlestr. 1

department: Biologie III

country: Germany

institute: University of Freiburg

type: Expression profiling by genome tiling array

type: Non-coding RNA profiling by genome tiling array

summary:
The model cyanobacterium Synechocystis sp. PCC 6803 was used for a systematic survey on the number and types of antisense (as)RNAs. A tiled microarray was constructed with probes for both strands of the genes or intergenic spacers with candidate transcripts predicted by an algorithm and an equally sized and distributed control set. The resulting 102,739 individual probes cover an accumulated length of 1,441,146 nt or about 40% of the total chromosome sequence of Synechocystis 6803. Hybridization of this array with total RNA isolated from cultures raised under different growth conditions identified a high number of transcripts from intergenic spacers and in antisense orientation to known genes (natural cis-asRNAs). Extrapolated to the whole genome, around 10% of all open reading frames in Synechocystis 6803 may have a corresponding asRNA, suggesting a much more important role of chromosomally encoded asRNAs in bacteria then anticipated so far.

Keywords: stress response

overall_design:
4 RNA hybridizations, 2 DNA controls.
The raw data from the DNA hybridizations are in the GSE14410_DNA_1.txt and GSE14410_DNA_2.txt files.

first: Jens

last: Georg

first: Björn

last: Voss

first: Ingeborg

last: Scholz

first: Annegret

last: Wilde


title: M1 MGAS5005 TrxR+ vs. TrxR- mutant

status: Public on Sep 01 2008

city: College Park

first: Kevin

last: McIver

state: MD

address: 3124 Biociences Research Bldg. (413)

department: Cell Biology and Molecular Genetics

institute: University of Maryland, College Park

summary:
The aim of this study was to determine the extent of the trxR regulon in the M1 serotype MGAS5005.  Gold, Leday, McIver 2008
Keywords: Wild-type vs trxR-

overall_design: series contains MGAS5005 and MGAS5005.trxR (trxR-) from three independent isolations.  cDNA ratios from these isolations as well as their dye swap included

first: Kathryn

last: Gold

first: Temekka

middle: V

last: Leday


title: Cane Toad Metamorphis

status: Public on Nov 27 2008

city: Canberra

first: Andrew

last: Spriggs

state: ACT

address: GPO Box 1600

department: Bioinformatics Group

country: Australia

institute: CSIRO Plant Industry

summary:
Comparison of pre and post metamorphis phases of cane toad
Keywords: Developmental Stages

overall_design: Samples were harvested at 9, 18, 28 (pre-metamorph), 30 and 53 (post-metamorph) days of age and RNA extracted using Trizol Reagent (Invitrogen). Total RNA (100 mg) was reverse transcribed (Qiagen) and labelled cDNA probes were generated using the fluorophores, Cy3 and Cy5 (Amersham Pharmacia Biotech). Prehybridization of slides, application of the probe to the microarray slides, hybridisation, and subsequent washing steps were performed according to manufacturer's instructions (Corning Microarray Technology). Slides were scanned and analysed with a GenePix 4000B laser scanner and GenePix 3.0 and 4.0 software (Axon Instruments).

first: Damien

last: Halliday

first: Gavin

last: Kennedy


title: mRNA profiles after experimental ischemia

status: Public on Dec 01 2012

city: Madrid

first: Jaime

middle: Ramos

last: Cejudo

address: Paseo de la Castellana, 261

department: Neuroscience

country: Spain

institute: La Paz University Hospital

summary: To analyze gene expression we isolated total mRNA from the core, periinfarct and contralateral cortex of 60 sprague-dawley rats after 24 hours or 3 days of permanent middle cerebral artery occlusion (pMCAo). Also ipsilateral and contralateral cortex was obtained from sham-operated and healthy animals. A total of 44 microarrays were performed with RNA pooled from 3 independent animals. For each experimental condition the total n number is of 12.

overall_design: Microarray analysis of different areas of the rat brain (core, periinfarct and contralateral cortex) after 24h and 3days of permanent ischemia

last: Ramos-Cejudo

first: María

last: Gutiérrez-Fernández

first: Berta

last: Rodríguez-Frutos

first: Mercedes

middle: E

last: Alcaide

first: Fátima

last: Sánchez-Cabo

first: Ana

last: Dopazo

first: Exuperio

last: Díez-Tejedor


title: MGAS5005 vs MGAS5005∆ccpA

status: Public on Jun 04 2008

summary:
The aim of this study was to determine the extent of the CcpA regulon in the M1 serotype MGAS5005.
Kinkel and McIver, 2008 Infection and Immunity
Keywords: group A streptococcus, CcpA

overall_design: 3 biological replicates of MGAS5005 and the isogenic ∆ccpA strain were grown, and RNA was isolated independently 3 times.  The RNA was converted to cDNA and labeled with with either Cy3 or Cy5 using the GE Healthcare CyScribe Post-labelling kit.  The arrays were scanned with GenePix 6.1 and analyzed with Acuity 4.0.

first: Traci

middle: L

last: Kinkel


title: Redirection of metabolism for biological hydrogen production

status: Public on Jun 29 2007

first: Yasuhiro

last: Oda

address: Box 357242, 1705 N.E. Pacific Street, HSB K-354

department: Department of Microbiology

institute: University of Washington

summary:
Photosynthetic microbes can produce the clean-burning fuel hydrogen using one of nature’s most plentiful resources, sunlight 1,2. Anoxygenic photosynthetic bacteria generate hydrogen and ammonia during a process known as biological nitrogen fixation. This reaction is catalyzed by the enzyme nitrogenase and consumes nitrogen gas, ATP and electrons 3. One bacterium, Rhodopseudomonas palustris, has a remarkable ability to obtain electrons from green plant-derived material 4,5 and to efficiently absorb both high and low intensity light energy to form ATP 6. Manipulating R. palustris or a similar organism to produce hydrogen commercially will require us to identify all its genes that contribute to hydrogen production and to understand how this process is regulated in cells. Here we describe mutant strains in which metabolism is redirected such that hydrogen production is uncoupled from nitrogen fixation. Our data indicate that three different single amino acid changes in the transcriptional regulator NifA each yielded strains that produced hydrogen even in the presence of the repressing nitrogen source ammonium and in the absence of specific inducing metabolic signals. We used the mutants to show that, in addition to nitrogenase genes, 18 genes outside of the nitrogenase gene cluster may contribute to hydrogen production. Some of these genes are likely involved in efficient ATP acquisition and in channeling electrons to nitrogenase for reduction of protons to molecular hydrogen. Our results demonstrate that photosynthetic bacteria can be genetically manipulated for sustained production of pure hydrogen in a variety of cultivation conditions in the absence of oxygen, nitrogen or other gases as long as light and an electron donor are supplied.
Keywords: Comparison of transcriptome profiles

overall_design: Transcriptome profile of wild type (CGA009) growing photosynthetically in the presence of amonium an acetate was compare with that of 4 different mutants (CGA570, CGA571, CGA572 and CGA574). We did 2 biological replicates per strain.

first: Federico

last: Rey

first: Erin

middle: K

last: Heiniger

first: Caroline

last: Harwood


title: top1

status: Public on Jan 26 2007

city: Acton

first: Anthony

last: Millgate

address: PO Box 1600

institute: CSIRO

summary:
Thebaine and oripavine accumulating mutant (Norman) verses wildtype.
Keywords = Opium Poppy, Secondary Metabolism
Keywords: other


title: Genomic consequences of background effects on scalloped mutant expressivity in the wing of Drosophila

status: Public on Dec 03 2008

city: East Lansing

first: Ian

last: Dworkin

state: MI

address: 203 Natural Science Bldg. Michigan State University

department: Zoology

institute: Michigan State University

summary:
Genetic background effects contribute to the phenotypic consequences of  mutations, and are pervasive across all domains of life that have been examined, yet little is known about how they modify genetic systems. In part this is due to the lack of tractable model systems that have been explicitly developed to study the genetic and evolutionary consequences of background effects. In this study we demonstrate that phenotypic expressivity of the scalloped[E3]  mutation of Drosophila melanogaster is background dependent, and is the result of at least one major modifier segregating between two standard lab wild-type strains. Microarrays were used to examine the consequences of genetic background effects on the global transcriptome. Expression differences between wild-type strains were found to be as large or larger than the effects of mutations with substantial phenotypic effects, and expression differences between wild-type and mutant varied significantly between genetic backgrounds. Significantly, we demonstrate that the epistatic interaction between sd[E3] and an optomotor blind mutation is background dependent. The results are discussed within the context of developing a complex but more realistic view of the consequences of genetic background effects with respect to mutational analysis, and studies of epistasis and cryptic genetic variation segregating in natural populations

Keywords: Mutant vs wild-type comparison

overall_design: 2 wild-type strains of D. melanogaster (Oregon-R and Samarkand, both marked with white) each with and without the scalloped[E3] mutation. Thus a 2x2 factorial design with a balanced incomplete block (block=slide) design in a full loop configuration with dye swapping.


title: Analysis of gene expression during the onset of muscle hypertrophy in callipyge lambs: time course

status: Public on Sep 19 2006

city: West Lafayette

first: Christopher

middle: A

last: Bidwell

state: IN

address: 125 South Russell Street

department: Animal Sciences

institute: Purdue University

summary:
The callipyge mutation causes postnatal muscle hypertrophy in heterozygous lambs that inherit a paternal callipyge allele (+/CLPG).  Our hypothesis was that the up-regulation of one or both of the affected paternally expressed genes (DLK1 or PEG11) initiates changes in biochemical and physiological pathways in skeletal muscle to induce hypertrophy.
The goal of this study was to identify changes in gene expression during the onset of muscle hypertrophy in order to identify the pathways that are involved in the expression of the callipyge phenotype.  Gene expression was analyzed in longissimus dorsi total RNA from lambs at 10, 20, and 30 days of age using the Affymetrix Bovine Expression Array.
Keywords: time course

overall_design: Longissimus dorsi were collected from 10, 20, and 30 day old callipyge and normal lambs with 2 biological replicates for each group. Total RNA was isolated and hybridized to Affymetrix Bovine Expression arrays. Data were analyzed in SAS and all genotype effects were followed up by qPCR in 42 lambs ranging from 10 to 200 days of age.

first: Jolena

middle: N

last: Fleming-Waddell

first: Lindsay

last: Wilson

first: Gayla

last: Olbricht

first: Tony

last: Vuocolo

first: Keren

last: Byrne

first: Bruce

last: Craig

first: Ross

last: Tellam

first: Noelle

last: Cockett


title: The effects of edema on intestinal smooth muscle

status: Public on Dec 01 2008

city: Houston

first: Karen

last: Uray

state: TX

department: Pediatric Surgery

institute: University of Texas Medical School at Houston

summary:
Intestinal edema induced by a combination of mesenteric venous hypertension and resuscitative fluids (RESUS+VH, E), control was sham operated (CONTROL, C), also included mesenteric venous hypertension only (VH, V) and resuscitative fluid administration only (RESUS, S); samples collected 6 hours after surgery.

Keywords: disease state analysis

overall_design: 4 replicates in each of 4 groups

first: Charles

last: Cox


title: Mga regulon

status: Public on Aug 31 2006

first: Kevin

last: McIver

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: AKT pathway genes define 5 prognostic subgroups in glioblastoma

status: Public on Sep 11 2014

city: San Francisco

first: Joseph

last: Costello

state: CA

department: NeuroSurgery

institute: UCSF

type:
Expression profiling by array
Third-party reanalysis

summary: GBM samples were clusered using gene expression of AKT pathway genes to reveal at least 5 GBM AKT subtypes, having distinct DNA copy number alterations, enrichment in oncogenes and tumor suppressor genes and patterns of expression for PI3K/AKT/mTOR signaling components.

overall_design: Gene expression was profiled on 39 GBM samples plus 6 normal controls from UCSF, as well as 9 GBM samples plus 8 normal controls from MDA. This data was combined with published GBM gene expression data from MDA [GSE4271] and UCLA [GSE4412] obtained on the same platform to reveal GBM subtypes based on AKT pathway genes.

first: A

last: Joy

last: Ramesh

first: I

last: Smirnov

first: M

last: Reiser

last: Misra

first: W

last: Shapiro

first: G

middle: B

last: Mills

first: S

last: Kim

first: B

middle: G

last: Feuerstein


title: Integrative Molecular Concepts Modeling of Prostate Cancer Progression

status: Public on Dec 17 2006

city: Ann Arbor

first: Scott

last: Tomlins

address: 1400 E. Medical Center Dr., 5410 CCGC

institute: University of Michigan

summary:
Using laser capture microdissection to isolate over 100 specific cell populations, we report the profiling of prostate cancer progression from benign epithelium to metastatic disease. By analyzing these expression signatures in the context of over 15,000 “molecular concepts”, or sets of biologically connected genes, we generated an integrative model of prostate cancer progression.
Keywords: disease state analysis

overall_design:
Experiment Design:
• Type of experiment:  This study used microarray experiments to profile prostate cancer progression through the isolation of pure cell populations using laser capture microdissection (LCM) and OmniPlex Whole Transcriptome (WTA) Amplification.
• Experimental factors:  This study profiled various pure cell populations isolated by LCM from prostate tissue.
• The number of hybridizations performed in the experiment:  A total of 104 hybridizations were performed.
• The type of reference used for the hybridizations:  A single commercially available pool of benign prostate tissue (CPP, Clontech) was used as the reference in all hybridizations.  For the reference sample, 10 ng of CPP total RNA was converted into a WTA cDNA library in a volume of 25 µl and five 5 µl aliquots were amplified by WTA PCR and purified. Five ng aliquots of the pooled products were subjected to a second WTA PCR amplification in the presence of amino-allyl dUTP and all products were pooled before labeling to ensure equal representation across all of the hybridizations.
• Hybridization design:   For all hybridizations, the experimental prostate sample isolated by LCM was labeled with Cy5 and the common reference of benign pooled prostate as described above was labeled with Cy3.
• Quality control steps taken:  In order to assess biological and technical reproducibility, we captured identical regions from two specimens (PCA_11 and MET_HR_3) and subjected one sample, PCA_30, to two hybridizations. For PCA_11, adjacent regions of the same section were captured and treated as separate samples. For MET_HR_3, two separate foci of the liver metastasis (from separate frozen blocks) were captured and treated as separate samples. For PCA_30, two aliquots of the primary WTA PCR products were separately subjected to a second round of WTA PCR amplification. Replicates from PCA_30 and MET_HR_3 were also hybridized to arrays from each of the print runs utilized in this study.
Samples used, extract preparation and labeling:
• The origin of the biological sample (for instance, name of the organism, the provider of the sample) and its characteristics:  All samples used were of human origin.  The table in the MIAME Checklist (Supplmentary Methods) summarizes the samples used. Hybridizations are named according to the class of sample profiled and the background color is the same as shown in Figure S3. Two print runs were used during the course of the study and the indicated run for each hybridization is given. For prostate cancer samples, the Gleason patterns present on the sample section used are indicated, as well as the Gleason patterns of the actual cells isolated by LCM.  A unique case number for all profiled samples is given.  Descriptions of samples are given where applicable, including the location of metastatic foci.
• Manipulation of biological samples and protocols used: Laser Capture Microdissection (LCM) was performed from frozen tissue sections with the SL Microtest device using µCUT software (MMI). Approximately 10,000 cells were captured for each sample. Serial sections were used if cells could not be obtained from a single section. Total RNA was isolated from captured cells with the RNAqueous Micro kit (Ambion) and treated with DNAse I according to the manufacturer's instructions. RNA quantification was perfomed using Ribogreen (Molecular Probes).
• Protocol for preparing the hybridization extract: For each sample, total RNA (~10ng) in a volume of 25 µl was converted into an OmniPlex WTA cDNA library and amplified by WTA PCR using reagents and protocols according to the beta-commercial TransPlex WTA kit (Rubicon Genomics, Ann Arbor, MI). For each sample, a single 10 µl aliquot of the WTA cDNA library was amplified by WTA PCR and products were purified. Four or five 5 ng aliquots of product were subjected to a second WTA PCR amplification in the presence of amino-allyl dUTP for post amplification labeling and products were pooled before proceeding with the hybridization. Yields after all WTA PCR amplifications were between 2 to 5 μg per reaction, and reaction progress was monitored in real time using SYBR green I (Molecular Probes) on the iCycler IQ (BioRad) or ABI 7300 Real Time PCR system (Applied Biosystems). Real-time PCR amplifications were terminated at or before plateau phase as measured by fluorescence incorporation to preserve maximum representation.
• Labeling protocol(s):  For all WTA amplified cDNA samples with amino-allyl dUTP incorporated (10-20 ug), nuclease free water was added to 500 ul, the sample was transferred to a Microcon YM-30 filter, and centrifuged at 13,000 rcf at RT for 12 minutes.  The spin column was inverted in a new collection tube and centrifuged at 13,000 rcf for 2 min at RT.  The amount of sample was measured and the volume was adjusted to 5 ul with nuclease free water. For labeling, 5 ul of 1 M sodium bicarbonate (pH 9.0) was added and allowed to incubate at RT for 15 min.  Nine ul of anhydrous DMSO were added to Mono Reactive Cy3 and Cy5 dye packs (Amersham, Buckinghamshire, England), mixed thoroughly, and 1 ul of the proper dye was added to each sample.  The labeling mixture was incubated in the dark at RT for 1 hour.  The reaction was stopped by the addition of 9 ul of 4 M Hydroxylamine for 15 min.   For each labeling mixture, RNase free water was added to 100 ul, 500 ul of PB buffer was added and Cy3 and Cy5 mixtures were added to separate Qiaquick (Qiagen, Valencia, CA) spin columns and centrifuged at 13,000 rcf.  Columns were washed twice with 700 ul of buffer PE, and centrifuged dry at 13,000 rcf for 2 min.  To elute, 60 ul of EB buffer was placed on the column, incubated for 5 min and centrifuged at 13,000 rcf for 1 min.  The Cy3 labeled and Cy5 labeled cDNA for each hybridization were mixed and 1.5 ul were used for analysis on a ND-1000 spectrophotometer.
• External controls (spikes):  Not utilized

Hybridization procedures and parameters:
• The protocol and conditions used during hybridization, blocking and washing: For hybridization, 40 ug of human Cot-1 DNA (Invitrogen, Carlsbad, CA) was added to 120 ul of labeled cDNA, the probe was transferred to a Microcon YM-30 filter and centrifuged at 13,000 rcf for 6 min at RT.  The spin column was inverted in a new collection tube and centrifuged at 13,000 rcf for 2 min at RT.  The eluted probe volume was adjusted to 18.6 ul with nuclease free water and the following were added: 4 ul of yeast tRNA (10 ug/ul, Invitrogen, Carlsbad, CA), 4.9 ul of 20X SSC and 0.84 ul of 10% SDS.  The probe was denatured at 100 Co for 3 min and centrifuged at 13,000 rcf for 45 sec.  The probe was added directly to the microarray and a cover slip was added.  Slides were hybridized overnight in DIE-TECH 1 or 5 slide hybridization chambers in a 65 Co water bath.  After hybridization, cover slips were removed by incubation in 2x SSC / 0.05% SDS.  Slides were then washed in 2x SSC / 0.05% SDS for 5 min and 0.2x SSC / 0.05% SDS for five minutes.  Slides were then washed in 0.2x SSC for 10 sec and centrifuged dry at 500 rpm for 5 min.

Measurement data and specifications:
• Type of scanning hardware and software used:  Microarrays were scanned using a GenePix 4000B scanner (Axon Instruments, Union City, CA).
• Type of image analysis software used:  Images were gridded and spots were quantified using GenePix Pro 4.0 software (Axon Instruments, Union City, CA).
• A description of the measurements produced by the image-analysis software and a description of which measurements were used in the analysis:  The measurements made by GenePix Pro 4.0 are described in the sample files. For all hybridizations, the log2 normalized Median of Ratios (as described below) was used.

• Data selection and transformation procedures:  Arrays were auto-gridded by GenePix 4.0.  Features flagged by GenePix as not found during grid

first: Arul

last: Chinnaiyan


title: Himalaya v 292

status: Public on Jul 25 2006

first: Andrew

last: Spriggs

summary:
Himalaya v 292
Keywords: Mutant Analysis

platform_organism:
Hordeum vulgare
Triticum aestivum

overall_design: Four biological replicates were used for the comparison and the dyes were swapped among the test and control samples for labeling two of the replicates. For each replicate, 50 ?g of total RNA was used for both the Cy3 and Cy5 dyes (Amersham Pharmacia, UK), following the two-step labeling method of Schenk et al. (2000). The control plant, 'Himalaya' was labeled with Cy3 in the un-swapped replicates. The dyes were reversed among the replicate experiments to minimize any bias in cDNA incorporation and photo-bleaching of the fluorescent dyes. The pre-hybridization of the microarray slides, hybridization of samples and subsequent washing of the slides to remove unbound target was performed as per the supplied protocol for the CMT-GAPSTM coated microscope slides (Corning USA). The slides were scanned with a GenePix 4000A microarray scanner (Axon Instruments, Union, CA, USA). The features were analyzed using the GenePix Pro 4 software and unsatisfactorily segmented features were either manually adjusted or discarded to ensure the integrity of the data obtained.

first: Bryan

last: Clarke

first: Gavin

last: Kennedy


title: Boxed Experiment of Renal, brain and lung macrophages

status: Public on Feb 16 2008

city: St Lucia

first: Darrin

middle: F

last: Taylor

state: Qld

address: Research Rd

department: Genomics and Bioinformatics

institute: Institute for Molecular Bioscience, Uni of Qld

summary:
Three way boxed experiment comparing EGFP positive renal, lung and brain macrophages.
Keywords: Direct pairwise comparison

overall_design: Each "arm" of the comparison is a pairwise comparison containing a dye swap to eliminate dye bias.

first: Kyra

last: Woods

first: Fiona

last: Rae

first: Tedjo

last: Sasmono

first: Naomi

last: Campanale

first: Dmitry

last: Ovchinnikov

first: Sean

last: Grimmond

first: David

last: Hume

first: Sharon

middle: D

last: Ricardo

first: Melissa

middle: H

last: Little


title: SF370 vs SF370.10R (corR-)

status: Public on Jul 19 2007

first: Kevin

last: McIver

summary:
The aim of this study was to elucidate genes affected by a mutation in the M1 SF370 CovR-repressed TCS corR (Spy1587).  Leday et al 2007
Keywords: wild type vs corR-

overall_design: series contains wild type (SF370) and corR- (SF370.10R) from three independent isolations. cDNA ratios from these isolations as well as their dye swap are included

first: Temekka

last: Leday

first: Deborah

last: Ribardo

first: James

last: Conery


title: Total Lung Control vs Lung Macrophage

status: Public on Jul 04 2007

summary:
Direct comparison of FACS sorted EGFP positive Lung macrophages vs pooled Total Lung extract
Keywords: Direct pairwise comparison

overall_design: Pairwise comparison containing a dye swap to eliminate dye bias.


title: Polyphosphate affects gene expression and viability of Porphyromonas gingivalis W83

status: Public on May 30 2008

city: Seoul

first: Ji-Hoi

last: Moon

address: 1 Hoeki-Dong, Dongdaemoon-Ku

department: Oral Microbiology

country: South Korea

institute: School of Dentistry, Kyung Hee University

summary:
Polyphosphate (polyP) is a ubiquitous and abundant compound found in bacteria, fungi, algae, plant, and animals. Among roles of intracellular polyP in bacteria are resistance and survival in the stationary phase of the growth against stress and stringent condition. Therefore, intracellular polyP is considered as a virulence factor of bacteria. In contrast, exogenous polyP has an antimicrobial activity against a variety of microorganisms. To date, much has been numerous studies of antibacterial effect of polyP against gram positive bacteria and fungi while relatively little reports have been published concerning gram negative bacteria. Here we describe bactericidal effect of polyP against gram negative periodontopathic bacterium, Porphyromonas gingivalis, and the transcriptional change by polyP in this bacterium. The bacterial growth was inhibited by polyP (chain length of P3~P75) at concentration of 0.02~0.03%, but not by Pi and PPi at the concentrations. polyP75 was chosen for further experiments, which suppressed the further growth of P. gingivalis as low as 0.03%. polyP75 completely killed the bacterial cells at the concentration of 0.035%. Microarray analysis was employed to identify genes that showed a greater than 1.5-fold difference in the expression by polyP75 at the concentration of 0.03%. It was found that 155 genes were up-regulated and 173 were down-regulated. Down-regulated genes include groups of energy metabolism-related genes, cell envelope-related genes, and genes in relation to biosynthesis of cofactors, prosthetic groups and carriers. Among the down-regulated genes were several involved in DNA replication, cell division protein, and biosynthesis of purines, pyrimidines, nucleosides and nucleotides. In contrast, a large number of ribosomal proteins, transciptional regulators and transposases were up-regulated. Oxidative stress-related genes and iron storage proteins also appeared to be increased in the expression. Real-time PCR confirmed up- and down-regulation of some selected genes. The overall results suggest that polyP has a bactericidal activity against P. gingivalis, interfering with translation, energy metabolism, DNA replication, cell division, and biosynthesis of purines, pyrimidines, nucleoside and nucleotides. polyP may be used as an agent for prevention and treatment of periodontal infections.
Polyp-treated vs. untreated intensity ratio data linked below as a supplementary file.
Keywords: agent response

overall_design: Twenty μg of each total RNA sample was used in separate hybridization experiments on identical arrays. The whole genome of 1,909 genes of P. gingivalis W83 (GenBank accession no. NC_002950) was submitted to NimbleGen System Inc. (Madison, WI) for microarray design and manufacture using maskless, digital micromirror technology. Five replicates of the genome were included per chip. An average of 19 different 60-base oligonucleotides (60-mer probes) represented each gene in the genome. Sixty-mer probes were selected such that each probe had at least three mismatches compared to all other 60-mers in the target genome. A quality control check (hybridization) was performed for each array, which contained on-chip control oligonucleotides. The arrays were analyzed using an Axon GenePix 4000B microarray scanner with associated software (Molecular Devices Corp., Sunnyvale, CA). Gene expression levels were calculated with NimbleScan Version 2.3 (NimbleGen). Relative signal intensities for each gene were generated using the Robust Multi-Array Average algorithm. The data were processed based on quantile normalization method using the R package. This normalization method aims to make the distribution of intensities for each array in a set of arrays the same. The background-adjusted, normalized, and log transformed intensity values were then analyzed using GeneSpring GX 7.3.1 (Silicon Genetics, Palo Alto, CA).

first: Jin-Yong

last: Lee


title: Nas1 KO mice versus WT mice total kidney comparison

status: Public on Jan 24 2008

summary:
Pairwise comparison of total kidney RNA extracted from Nas1 knockout mice versus total kidney RNA extracted from wildtype mice
Keywords: Direct pairwise comparison

overall_design: Pairwise comparison containing a dye swap to eliminate dye bias

first: Brooke

last: Gardiner

first: Paul

last: Dawson

first: Soohyun

first: Daniel

last: Markovich


title: Cotton ovule development

status: Public on Nov 03 2005

first: Andrew

last: Spriggs

summary:
Cotton ovule development, mutant vs wild type, Comparisons of DP16 0 dpa ovule
Keywords: WildType vs Mutant

overall_design: 7 comparisons and one 0 dpa control. The 1A/DP16 & 4A/DP16 comparisons have 8 slides each, 4 Biological replicates, each biological replicate having 2 technical replicates. Dyes were swapped between technical replicates. The SL1-7-1/DP16 comparison has 6 slides, 3 Biological replicates, each biological replicate having 2 technical replicates. Dyes were swapped between technical replicates. The 5B/DP16, fl/Xu-142, OI/II+N & 53/DP16 comparisons have 4 slides each, 2 Biological replicates, each biological replicate having 2 technical replicates. Dyes were swapped between technical replicates. The 0 dpa control experiment has 3 slides , 3 Biological replicates, no technical replicates and no dye swapping.

first: Yingru

last: Wu


title: Total Brain Control vs Brain Macrophage

first: Darrin

last: Taylor

summary:
Direct comparison of FACS sorted EGFP positive brain macrophages vs pooled Total Brain extract
Keywords: Direct pairwise comparison

first: Kyra

last: Woods

first: Fiona

last: Rae

first: Tedjo

last: Sasmono

first: Naomi

last: Campanale

first: Dmitry


title: Expression data from Callipyge muscle types (ST, LD, SS, SM) at birth (T=0) and 12 weeks (T=12)

status: Public on Oct 04 2006

city: Brisbane

first: Ross

last: Tellam

state: QLD

address: 306 Carmody Road St.Lucia

department: Level 6 Queensland Biosciences Precinct

institute: CSIRO Animal, Food and Health Sciences

summary:
Microarrays were used for transcription profiling of skeletal muscle samples taken at birth, when the phenotype was not expressed, and 12 weeks of age from Callipyge and wild type sheep. The genes that underlie the expression of the phenotype rather than result from the fibre type change in the affected muscle have been identified.
We used microarrays to detail the global programme of gene expression underlying the hypertrophy phenotype and identified distinct classes of regulated genes during this process. A working model that links the muscle hypertrophy phenotype with a core group of transcriptional coregulators is proposed.
Keywords: Genotype X muscle X  time course study

overall_design: Gene expression analyses were performed primarily on longissimus dorsi skeletal muscle (LD) from Wild type (NN) and Callipyge (NCpat) sheep using Bovine Affymetrix GeneChip microarrays. Two developmental time-points were investigated in this study: newborn (within 5 days of birth; T0) and 11-12 weeks post-birth (T12). The muscle hypertrophy phenotype developed over the first 2-3 months and was associated with a significant change in muscle fibre type (Carpenter et al., 1996; Cockett et al., 1994; 1996; Kerth et al., 2003). One of the objectives of the gene expression analysis was to delineate between those genes that underlie the muscle hypertrophy in Callipyge sheep and those that result from the fibre type change in the affected muscle. To address this issue a comparison was undertaken of gene expression in wild type skeletal muscles with differing fibre type compositions to identify fibre type specific genes. These samples were taken from NN animals at T12. The three skeletal muscles used in this analysis were semimembranosis (SM), semitendinosis (ST) and longissimus dorsi (LD).

first: Tony

last: Vuocolo

first: Keren

last: Byrne

first: Jason

last: White

first: Sean

last: McWilliam

first: Toni

last: Reverter

first: Noelle

last: Cockett


title: Gene expression profiling of patients with severe acute respiratory syndrome (SARS)

status: Public on Jul 31 2007

city: Toronto

first: Mark

middle: J

last: Cameron

state: Ontario

address: 3-913 TMDT, MaRS Centre, 101 College St.

country: Canada

institute: UHN

summary:
We used cDNA microarrays to systematically analyze host responses in SARS-infected individuals from onset of symptoms to discharge from hospital or death.  We modeled gene expression in 60 datasets from 40 unique patients of varied clinical evolution with emphasis on correlating innate and adaptive immune responses with discrete clinical phases of the disease.
Keywords: Comparative patient class comparision, SARS patients relative to healthy controls

overall_design: Peripheral blood was collected in 5 ml heparinized blood collection tubes from study participants upon presentation to the hospital.  The median length between onset of symptoms consistent with SARS and presentation to the hospital was 2 days (range 0-7 days).  Peripheral blood specimens were then collected longitudinally every five days during hospitalization and at discharge from the hospital.  Whole blood RNA was stabilized and purified using Paxgene Blood Collection Tubes and Paxgene RNA kits (Qiagen, Mississauga, ON, Canada).  Sufficient RNA yields were obtained after Paxgene Whole Blood RNA isolation for 70 samples from 40 unique SARS patients and 10 healthy controls (HC1-10) and amplified using MessageAmp kits (Ambion).  Replicate measurements or dye swaps were not possible due to severe limitations in RNA quantity.  All samples (Cy5) were hybridized against amplified reference RNA (Cy3) (Stratagene, La Jolla, CA).  Longitudinal ANOVA were performed to select significantly altered genes in the pre-crisis (acute) phase of SARS (0-8 days since onset, n=22), crisis phase for non-severe SARS patients (8+ days since onset, n=15) and crisis phase for severe SARS patients (8+ days since onset, n=23).

first: David

last: Kelvin

first: Peter

last: Wilkinson


title: M6 Mga+ vs Mga-

first: Kevin

last: McIver

summary:
The transcriptional regulator Mga of Streptococcus pyogenes (the group A streptococcus, GAS) is known to directly activate several virulence genes important for colonization and immune evasion during exponential growth.  Transcriptome analysis comparing two mga-1 serotypes (M1 SF370, M6 JRS4) and one mga-2 serotype (M4 GA40634) against their isogenic mga-inactivated strains uncovered a broader Mga regulon profile containing both activated and repressed genes with predicted functions primarily related to the uptake and metabolism of sugars.  Although the divergent M1 and M4 Mga profiles were similar in size and content, the M6 JRS4 strain was clearly distinct, even from other M6 strains.  Real-time RT-PCR and northern blot analysis validated our microarray results and confirmed that established core Mga regulon genes directly activated by Mga (emm, scpA, sof, fba) exhibited the highest activation levels across all strains tested.  A novel ORF (Spy2036) encoding a cytosolic hypothetical protein was highly activated in all three serotypes and was called gene regulated by Mga or grm.  Mga was shown to bind directly to Pgrm, which overlaps the Mga-regulated Psof in OF+ strains, suggesting that grm is part of the core Mga regulon and is able to activate two divergently transcribed genes from a single site in a class II background.  Both class and serotype specific Mga-regulated genes, such as speB, were apparent.  In fact, Mga activated speB as long as it was expressed in the wild type strain, although direct binding of Mga to the PspeB promoter could not be demonstrated.  Thus, Mga is able to both directly and indirectly regulate genes shown to be important for virulence and the metabolic homeostasis of GAS.
Keywords: Wild-type vs Mga-

overall_design: series contains Mga+ (JRS4) and Mga- (JRS519) from three independent isolations.  cDNA ratios from these isolations as well as their dye swaps are included.

first: Deborah

last: Ribardo


title: M1 Mga+ vs Mga-

overall_design: series contains Mga+ (SF370) and Mga- (KSM165L) from three independent isolations.  cDNA ratios from these isolations as well as their dye swap are included


title: GAS M3 serotype, exponential versus stationary phase

status: Public on Jun 28 2007

city: Atlanta

first: June

last: Scott

state: GA

address: 1510 Clifton Road

department: Microbiology and Immunology

institute: Emory University

summary:
MGAS315 is a wild type strain. RNA isolated in exponential phase and stationary phase were compared
Keywords: Growth phase comparison

overall_design: Paired RNA samples were prepared (Ex and St) from nine independent cultures of MGAS315. Reference RNA consisted of pooled RNA from each preparation, labelled with Cy5

first: Timothy

last: Barnett


title: Grain Hardness

first: Andrew

last: Spriggs

summary:
A microarray analysis of wheat grain hardness
Keywords: Cultivar Comparison

overall_design: For both the Heron and Falcon NIL, whole wheat heads were harvested at 6, 15 and 25 days post anthesis (DPA) from glass house grown material and stored at -80 OC. For the other wheat cultivars analysed, heads at approximately 9-10 DPA were used. Eight to ten developing caryopses at the same age and morphological stage of development were selected from a head to represent a sample. Seed collected from a different head represented a replicate sample. Total RNA was isolated from the whole seed following the method of Higgins et al. (1976) with the following modification to remove starch. After the lithium chloride precipitation, the RNA pellet was resuspended in 250 ?l water. Then 3.5 ?l of 3 M sodium acetate (pH 5.3) and 125 ?l ethanol were added and the sample was centrifuged for 10 minutes at 4 OC. The supernatant was transferred to a fresh tube and the RNA was ethanol-precipitated by the addition of 21.5 ?l of 3 M sodium acetate (pH 5.3) and 375 ?l ethanol. The recovery of RNA varied from 0.06-0.5 ?g RNA per mg of tissue and this was dependent on the developmental stage of the seeds used for extraction of the RNA. For the labelling procedure, 50 ?g of total RNA was used for both the Cy3 and Cy5 dyes (Amersham Pharmacia, UK), following the two-step labelling method of Schenk et al. (2000). The Cy3 control (hard wheat) and Cy5 sample (soft wheat) were swapped among the replicate experiments to minimise any bias in cDNA incorporation and photo-bleaching of the fluorescent dyes. The pre-hybridisation of the microarray slides, hybridisation of the target cDNA and subsequent washing of the slides to remove unbound target was performed as per the supplied protocol for the CMT-GAPSTM coated microscope slides (Corning USA). The slides were scanned with a GenePix 4000A microarray scanner (Axon Instruments, Union, CA, USA). The features were analysed using the GenePix Pro 4 software and unsatisfactorily segmented features were either manually adjusted or discarded to ensure the integrity of the data obtained.

first: Bryan

last: Clarke

first: Sadequr

last: Rahman


title: Transcriptome analysis of Paracoccidioides brasiliensis cells undergoing the Mycelium-to-Yeast transition

status: Public on Oct 18 2005

city: Santo André

first: Luiz

middle: R.

last: Nunes

state: SP

address: Rua Santa Adélia 166

department: Centro de Ciências Naturais e Humanas

country: Brazil

institute: UFABC - Universidade Federal do ABC

summary:
Paracoccidioides brasiliensis is a thermodimorphic fungus associated with paracoccidioidomycosis (PCM), a prevalent systemic mycosis in South America. In humans, infection starts by inhalation of fungal propagules, which reach the pulmonary epithelium and transform into the yeast parasitic form. Thus, the mycelium-to-yeast transition is of particular interest because conversion to yeast is essential for infection. We have used a P. brasiliensis biochip, carrying sequences of 4,692 genes from this fungus to monitor gene expression at several time points of the mycelium-to-yeast morphological shift (from 5 to 120 h).
Keywords: Time Course

overall_design:
Microarray hybridizations were carried out with RNA obtained from cells harvested at 5, 10, 24, 48, 72 and 120 h after setting the temperature shift from 26 to 37oC. The RNA obtained from the original mycelial culture was taken as reference (t = 0 h).

Each time point was analyzed with four independent hybridizations (two pairs of dye-swap hybridizations). The hybridizations labeled as "Exp1" and "Exp2" have been performed with independent RNA preparations. Since each biochip carried two replicas of the arrayed genes, a total of eight samples were generated for each timepoint.

The data has been filtered, normalized and adjusted as described in the "data processing" box for each individual sample. Dye swap consistency checking has been performed between equivalent experimental pairs with the aid of the software TIGR MIDAS v2.19 and inconsistent spots have been flagged and excluded from further analyses.

The values obtained from each dye swap pair have been averaged and consolidated into a single data file, generating a total of 24 hybridization files (four from each timepoint). These files have been loaded into the software TIGR MIDAS v. 3.03. Experiments were then normalized and genes that displayed statistically significant modulation were identified by one-way ANOVA, considering p < 0.01 as a cutoff value.

A list of statisticaly significant, modulated genes was created, showing the average log ratio for each one of these genes, within each time point

first: Regina

last: Oliveira

first: Daniela

last: Leite

first: Vivian

last: da Silva

first: Maria

last: Goldman

first: Rosana

last: Puccia

last: Travassos

first: Francisco

last: Nobrega

first: Marina

middle: P

first: Gustavo


title: M4 Mga+ vs Mga-

middle: S

overall_design: series contains Mga+ (M4) and Mga- (M4.586) from three independent isolations.  cDNA ratios from these isolations as well as their dye swaps are included


title: Cotton Fibre/Non Fibre

status: Public on Jun 27 2006

summary:
0dpa Fibre vs epidermal laser capture microdisection comparison
Keywords: Development

overall_design: Total RNA was isolated from each cell type (fibre initial or non-fibre epidermal pavement cell) from both Plant 1 and Plant 2.  Hence, there were two biological replicates of each cell-type.  Sub-samples of each cell type, designated here as technical replicates, were taken as separate batches of cells from different groups of ovules, but each from the same pair of plants.  In particular, there were four sub-samples of fibre initial cells from plant 1 and two from plant 2 and two sub-samples of non-fibre epidermal from plant 1 and four from plant 2. The complete experiment involved three dye-swap pairs using a total of 6 arrays.

first: Yingru

last: Wu

first: Danny

last: Llewellyn


title: Hypoxic Stress

status: Public on May 18 2005

summary:
GLB1, a class 1 haemoglobin gene from Arabidopsis thaliana (GLB1) is essential for plant survival following hypoxic stress.
Keywords = haemoglobin, hypoxic stress, stress
Keywords: other

first: Peter

middle: W

last: Hunt


title: Human Melanoma vs Normal Human DNA

status: Public on Jun 05 2007

city: boston

first: bin

last: feng

state: MA

address: 44 binney street

institute: dfci

summary:
Highly rearranged and mutated cancer genomes present major challenges in the identification of pathogenetic events driving the cancer process.  Here, we engineered lymphoma-prone mice with chromosomal instability to assess the utility of mouse models in cancer gene discovery and the extent of cross-species overlap in cancer-associated copy number aberrations.  Integrating with targeted re-sequencing, our comparative oncogenomic studies efficiently identified FBXW7 and PTEN as commonly deleted or mutated tumor suppressors in human T-cell acute lymphoblastic leukemia/lymphoma (T-ALL).  More generally, the murine cancers acquire widespread recurrent clonal amplifications and deletions targeting loci syntenic to alterations present in not only human T-ALL but also diverse tumors of hematopoietic, mesenchymal and epithelial types. These results thus support the view that murine and human tumors experience common biological processes driven by orthologous genetic events as they evolve towards a malignant phenotype.  The highly concordant nature of genomic events encourages the use of genome unstable murine cancer models in the discovery of biologically relevant driver events in human cancer.
Keywords: comparative genomic hybridization

overall_design: 123 Melanoma samples  were analyzed. Normal Human DNA was used as reference. Most samples were hybridized with dye-swap replica.

first: B

last: Feng

first: R

last: Maser

first: A

last: Protopopov

first: O

last: Kabbarah

first: C

last: Nogueira

last: Brennan

first: L

last: Chin

last: Depinho


title: GAS M6 serotype, wild-type vs covR mutant

status: Public on Dec 19 2005

first: June

last: Scott

summary:
JRS4 is our wild-type M6 serotype strain and JRS948 is the isogenic covR strain.
Keywords: 2-channel

overall_design: Four separate RNA preparations from each strain (RNA #A-D) were hybridized to duplicate arrays. Reference RNA consisted of pooled RNA from each preparation, labelled with Cy5.

first: Tracy

last: Dalton

first: Timothy

middle: C

last: Barnett

middle: R


title: Cotton promoter discovery

status: Public on Jun 01 2006

first: Andrew

last: Spriggs

summary:
Genomic approaches to the discovery of promoters for sustained expression in cotton (Gossypium hirsutum L.) under field conditions: expression analysis in transgenic cotton and Arabidopsis of a Rubisco small subunit promoter identified using EST sequence analysis and cDNA microarrays.
Keywords: Promoter Discovery

overall_design: RNAs from 8-week old plants were compared to RNAs from 10-, 14-, 20- and 22-week old plants on separate arrays each with a dye swap. The 20 and 22 weeks hybridisations each had a biological replicate (each with a dye swap) as well as a second independent hybridisation (with dye swap) with one of the 22 week RNAs. One of the 22-week slides was of low quality and had to be discarded.

first: Ranamalie

last: Amarasinghe


title: Udt1-1 anther and Wild type_anther

status: Public on Oct 01 2005

city: Yongin

first: Yeon-Ki

last: Kim

state: Kyonggido

address: 38-2 Nam-dong

institute: Genomics and Genetics Institute, GreenGene Biotech

summary:
A series of microarray experiments by using RNA sources from UDT1-1 mutant type- and wild type-anthers at stages from meiosis to young microspore.
In conjuction, microarray experiments by using RNA sources from wild type_Palea/lemmas in the flowering stage and wild type anther at pollen mitosis were performed in a time course design and compared to the microarrays of UDT1-1 mutant type- and wild type-anthers.
Keywords: time-course

first: K-H

last: Jung

first: M-J

last: Han

first: Y

first: I

last: Hwang

first: Y-K

first: BH

last: Nahm

first: G

last: An


title: Infected hypocotyl time course

status: Public on Apr 21 2005

institute: CSIRO Plant Industry

summary:
Time course of Fusarium wilt infection of cotton hypocotyl tissues
Keywords = cotton, Fusarium wilt, AtsC, virulence, in planta expressed genes
Keywords: other

first: Helen

last: McFadden


title: ATAF2 repression

status: Public on Apr 20 2005

summary:
The transcription factor ATAF2 represses the expression of pathogenesis-related genes in Arabidopsis
Keywords = ATAF2, NAC-Domain, PR, gene expression regulation, wounding, transcription factor
Keywords: other

first: Christian

last: Delessert


title: RNA co-immunoprecipitations with yeast She proteins

status: Public on Dec 21 2005

city: Stanford

last: Stanford Microarray Database

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

summary:
RNA co-immunoprecipitations with C-terminal protein A-tagged She proteins. One liter of cells were cultured at 30 degrees in YPAD medium and collected during exponential growth by centrifugation.  Cells were washed twice and broken mechanically with glass beads. Extracts were incubated with IgG-agarose beads (Sigma).  The beads were washed four times, and She proteins were released from the beads by cleavage with TEV-protease (Invitrogen).  RNA was isolated by phenol/chloroform extraction and isopropanol precipitation from TEV eluates, which corresponds to the purified fraction, and from extracts (input).  Both RNA samples, input and purified, were reverse transcribed and labeled with the fluorescent dyes Cy3 and Cy5 (Amersham), respectively.  The samples were mixed and competitively hybridized to yeast DNA microarrays containing all yeast genes
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

overall_design: Computed

first: Andre

last: Gerber


title: Flowering Mutant Experiment

status: Public on Apr 09 2005

city: Canberra

summary:
Collection of Flowering mutants
Keywords = flowering, growth and development, gene structure and expression
Keywords: other

first: Iain

last: Wilson


title: DP16 Time Course

summary:
DP16 ovules of -4, -2, 2  dpa compared to 0 dpa
Keywords: Time Course

overall_design: 4 timepoints at -4 dpa, -2 dpa, 0 dpa and +2 dpa. -4, -2 and +2 dpa have 4 slides each, 2 Biological replicates, each biological replicate having 2 technical replicates. Dyes were swapped between technical replicates. 0 dpa has 3 slides , 3 Biological replicates,no technical replicates and no dye swapping.

first: Yingru

last: Wu


title: 1h_D_vs_LA

status: Public on Jan 01 2005

city: Chicago

first: christos

last: Noutsos

institute: University of Chicago

summary:
Series of 6 repetitions of hybridization of treatment (1h_D) and control (LA) each. Comparison of light adapted plants exposed to darkness for 1h versus light adapted plants.
Keywords: repeat sample

first: A

last: Biehl

first: E

last: Richly

first: C

last: Dietzmann

first: J

last: Kurth

first: F

last: Salamini

first: D

last: Leister


title: Age-associated alteration of gene expression patterns in mouse oocytes

status: Public on Aug 20 2004

city: Baltimore

first: Minoru

last: Ko

address: 251 Bayview Blvd, Suite 100, 10C

department: National Institute on Aging

institute: NIH

summary:
Decreasing oocyte competence with maternal aging is a major factor in human infertility. To investigate the age-dependent molecular changes in a mouse model, we compared the expression  profiles of metaphase II oocytes collected from 5-6 week old mice with those collected from 40-42 week old mice using the  NIA 22K 60-mer oligo microarray.
Keywords: other

first: Toshio

last: Hamatani

first: Geppino

last: Falco

first: Mark

last: Carter

first: Hidenori

last: Akutsu

first: Carole

last: Stagg

first: Alexei

last: Sharov

first: Dawood

last: Dudekula

first: Vincent

last: VanBuren


title: SL2_vs_Kc167_Dif_Expr

status: Public on May 27 2003

city: Mississauga

first: Zak

last: Razak

state: ON

address: 3359 Mississauga Road

department: Zoology Department

institute: University of Toronto

summary:
The expression profiles of Drosophila Kc167 and SL2 cells were compared on the CDMC_Drosophila_7k2 array platform.  Three independent RNA samples from each cell line were isolated and compared in a pairwise fashion.  Dye-flip experiments were also performed.  See Neal et al. 2003 for results and discussion.
Keywords = Kc167
Keywords = SL2
Keywords = Drosophila
Keywords: other

first: Scott

last: Neal

first: Meredith

last: Gibson

first: Anthony

last: So

first: Jon

middle: T

last: Westwood


title: 10s oxidative stress

status: Public on Feb 19 2005

city: Albuquerque

first: Sushmita

last: Roy

state: NM

institute: Biology, University of New Mexico

summary:
This series represents the rapid response to oxidative stress
Keywords: time-course

last: Aragon

first: Margaret

last: Werner-Washburne


title: M1 and M6 serotypes, Wild-type vs. Mga- GAS

status: Public on Apr 06 2005

city: College Park

first: Kevin

last: McIver

address: 3124 Biociences Research Bldg. (413)

institute: University of Maryland, College Park

summary:
JRS4 is our wild-type M6 serotype GAS and JRS519 is our Mga- M6 serotype GAS.  SF370 is our wild-type M1 serotype GAS and KSM165L is our Mga- M1 serotype GAS.

Table 1:  Genomic Normalization
Description:  Step by Step instructions for the removal of outlier
background data and any ORF data that did not meet threshold of 2SD
above background average, using original data from gpr file provided in
each of the sample files.

Table 2:  M1 Mga+ vs Mga-
Description:  Step by Step instructions for the removal of outlier data
as compared across all possible data points for each ORF.  Data points
after genomic normalization are used with resultant averages and
standard deviations for each ORF computed.

Table 3: M6 Mga+ vs Mga-
Description:  Step by Step instructions for the removal of outlier data
as compared across all possible data points for each ORF.  Data points
after genomic normalization are used with resultant averages and
standard deviations for each ORF computed.
Keywords: repeat sample

first: Deborah

last: Ribardo


title: CHX Treatment

status: Public on Nov 03 2005

first: Andrew

last: Spriggs

address: GPO Box 1600

summary:
Cycloheximide treatment of cotton ovules
Keywords: Antibiotic Treatment

overall_design: Single timepoint, 6 slides, 3 Biological replicates, each biological replicate having 2 technical replicates. Dyes were swapped between technical replicates.

first: Yingru

last: Wu


title: Kc167_Inter-slide_Variability_Test

summary:
A large batch of Drosophila Kc167 total RNA was prepared and was used for 3 homotypic hybridizations in order to evaluate the inter-slide variability using the CDMC_Drosophila_7k2 platform.  See Neal et al. 2003 for results and discussion.
Keywords = Kc167
Keywords = Drosophila
Keywords = Platform Variability
Keywords: other

middle: L


title: Arabidopsis Transcriptome

status: Public on Oct 24 2004

city: NEW HAVEN

first: Ligeng

last: Ma

state: CT

address: 165 Prospect

department: Molecular, Cellular & Developmental Biology

institute: Yale University

summary:
Sample groupings for this project are as follows:

Cauline leaf vs Cultured Cell :
- Cauline leaf, p1; Exp:Red; Ref: Green (Cy5:Cy3)
- Cauline leaf, p2; Exp:Red; Ref: Green (Cy5:Cy3)
- Cauline leaf, p3; Exp:Red; Ref: Green (Cy5:Cy3)

Cotyledon light vs Cotyledon dark :
- Cotyledon, CP1; Exp:Red; Ref: Green (Cy5:Cy3)
- Cotyledon, CP2; Exp:Red; Ref: Green (Cy5:Cy3)

Cotyledon light vs Cultured cell :
- Cotyledon, cn1; Exp:Green; Ref: Red (Cy3:Cy5)
- Cotyledon, cn2; Exp:Green; Ref: Red (Cy3:Cy5)

Cotyledon dark vs Cultured cell :
- Cotyledon dark, n1; Exp:Green; Ref: Red (Cy3:Cy5)
- Cotyledon dark, n2; Exp:Green; Ref: Red (Cy3:Cy5)
- Cotyledon dark, n3; Exp:Green; Ref: Red (Cy3:Cy5)

Germinating seed vs Cultured cell :
- Germinating seed, gn1; Exp:Green; Ref: Red (Cy3:Cy5)
- Germinating seed, gn2; Exp:Green; Ref: Red (Cy3:Cy5)
- Germinating seed, gn3; Exp:Green; Ref: Red (Cy3:Cy5)

Hypocotyl light vs Hypocotyl dark :
- Hypocotyl, hldn1; Exp:Red; Ref: Green (Cy5:Cy3)
- Hypocotyl, hldn2; Exp:Red; Ref: Green (Cy5:Cy3)

Hypocotyl light vs Cultured cell :
- Hypocotyl light, hln1; Exp:Green; Ref: Red (Cy3:Cy5)
- Hypocotyl light, hln2; Exp:Green; Ref: Red (Cy3:Cy5)

Petal vs Cultured cell :
- Petal, pn1; Exp:Green; Ref: Red (Cy3:Cy5)
- Petal, pn2; Exp:Green; Ref: Red (Cy3:Cy5)
- Petal, pn3; Exp:Green; Ref: Red (Cy3:Cy5)

1DBP vs Cultured cell :
- Pistil 1DBP, pin1; Exp:Green; Ref: Red (Cy3:Cy5)
- Pistil 1DBP, pin2; Exp:Green; Ref: Red (Cy3:Cy5)
- Pistil 1DBP, pin3; Exp:Green; Ref: Red (Cy3:Cy5)

Pistil 1DPP vs Cultured cell :
- Pistil 1DPP, psn1; Exp:Green; Ref: Red (Cy3:Cy5)
- Pistil 1DPP, psn2; Exp:Green; Ref: Red (Cy3:Cy5)
- Pistil 1DPP, psn3; Exp:Green; Ref: Red (Cy3:Cy5)
- Pistil 1DPP, psn4; Exp:Green; Ref: Red (Cy3:Cy5)

Root dark vs Cultured cell :
- Root dark, rdn1; Exp:Green; Ref: Red (Cy3:Cy5)
- Root dark, rdn2; Exp:Green; Ref: Red (Cy3:Cy5)

Root light vs Cultured cell :
- Root light, rln1; Exp:Green; Ref: Red (Cy3:Cy5)
- Root light, rlp1; Exp:Red; Ref: Green (Cy5:Cy3)

Root light vs Root dark :
- Root light vs dark, rldp1; Exp:Red; Ref: Green (Cy5:Cy3)
- Root light vs dark, rldp2; Exp:Red; Ref: Green (Cy5:Cy3)

Rosette leaf vs Cultured cell :
- Rosette leaf, rfp1; Exp:Red; Ref: Green (Cy5:Cy3)
- Rosette leaf, rfp2; Exp:Red; Ref: Green (Cy5:Cy3)
- Rosette leaf, rfp3; Exp:Red; Ref: Green (Cy5:Cy3)

Sepal vs Cultured cell :
- Sepal, sn1; Exp:Green; Ref: Red (Cy3:Cy5)
- Sepal, sn2; Exp:Green; Ref: Red (Cy3:Cy5)

Silique 3DPP vs Cultured cell :
- Silique 3DPP, s3n1; Exp:Green; Ref: Red (Cy3:Cy5)
- Silique 3DPP, s3n2; Exp:Green; Ref: Red (Cy3:Cy5)
- Silique 3DPP, s3n3; Exp:Green; Ref: Red (Cy3:Cy5)

Silique 8DPP vs Cultured cell :
- Silique 8DPP, s8n1; Exp:Green; Ref: Red (Cy3:Cy5)
- Silique 8DPP, s8n2; Exp:Green; Ref: Red (Cy3:Cy5)
- Silique 8DPP, s8n3; Exp:Green; Ref: Red (Cy3:Cy5)

Stamen vs Cultured cell :
- Stamen, smn1; Exp:Green; Ref: Red (Cy3:Cy5)
- Stamen, smn2; Exp:Green; Ref: Red (Cy3:Cy5)
- Stamen, smn3; Exp:Green; Ref: Red (Cy3:Cy5)

Hypocotyl dark vs Cultured cell :
- Hypocotyl dark, hn1; Exp:Green; Ref: Red (Cy3:Cy5)
- Hypocotyl dark, hn2; Exp:Green; Ref: Red (Cy3:Cy5)

Stem vs Cultured cell :
- Stem, stp1; Exp:Red; Ref: Green (Cy5:Cy3)
- Stem, stp2; Exp:Red; Ref: Green (Cy5:Cy3)
- Stem, stp3; Exp:Red; Ref: Green (Cy5:Cy3)

Keywords: other


title: Global gene expression profiling during pituitary thyrotroph, somatotroph, and lactotroph differentiation.

status: Public on Sep 02 2005

first: Tom

middle: Eric

last: Porter

address: Building #142

department: Animal and Avian Sciences

institute: University of Maryland

summary:
The anterior pituitary is comprised of five major hormone-secreting cell types which differentiate during embryonic development in a  temporally distinct manner.  Microarrays containing 5,128 unique cDNAs expressed in the neuroendocrine system were produced and used to identify genes with  potential involvement in onset of thyroid-stimulating hormone beta-subunit, growth hormone, and prolactin gene transcription during chick embryonic  development.  We identified 352 cDNAs that were differentially expressed (P < 0.05 and the highest mean at least 1.6-fold greater than the lowest mean) on  embryonic day 10, 12, 14, or 17, the period of thyrotroph, somatotroph, and lactotroph differentiation in the chicken.  Consistent with cellular ontogeny in  the chick anterior pituitary gland, thyroid-stimulating hormone beta-subunit mRNA increased steadily between embryonic day 10 and embryonic day 17, growth  hormone mRNA increased between embryonic day 12 and embryonic day 17, and PRL mRNA did not increase until embryonic day 17.  Expression of 149 cDNAs  increased in a manner similar to thyroid-stimulating hormone beta-subunit mRNA and 67 decreased between embryonic day 10 and embryonic day 17, and some of  these are likely associated with thyrotroph differentiation.  Similarly, expression of 74 and 66 genes changed in a manner over the 4 ages that is consistent  with them having a potential role in induction of growth hormone and prolactin mRNA, respectively.  Among these candidate genes are numerous transcription  factors and signaling molecules that have not previously been implicated in pituitary development.
Keywords: time course during development (4 ages)

overall_design: Four biological replicates each of chicken pituitary embryonic day 10, embryonic day 12, embryonic day 14, and embryonic day 17  amplified antisense RNA were analyzed using neuroendocrine cDNA microarrays in a reference design.  Each experimental sample (embryonic day 10, 12, 14, or  17) was labeled with Cy3 and hybridized with an aliquot of the Cy5 reference pool, which was generated from all sixteen RNA samples.

first: Laura

middle: E

last: Ellestad

first: Wilfrid

last: Carre

first: Michael

last: Muchow

first: Sultan

last: Jenkins

first: Xiaofei

last: Wang

first: Larry

last: Cogburn


title: Changes in pituitary gene expression between embryonic day 17 and post-hatch day 3.

summary:
A major research focus in our laboratory is the development of the chicken pituitary gland.  As this tissue does not yield sufficient RNA  to analyze using cDNA microarrays, mRNA must be amplified by reverse transcription with an oligo-dT primer containing the T7 RNA polymerase promoter site  followed by in vitro transcription using T7 RNA polymerase.  Therefore, this preliminary study investigating differential gene expression between embryonic  day 17, when all the major cell types in the chick anterior pituitary gland have differentiated, and post-hatch day 3 was conducted to verify that amplified  antisense RNA could be used in conjunction with our neuroendocrine microarrays containing 5,128 unique cDNAs to detect changes in gene expression.  Of the  662 cDNAs that were expressed at significantly different levels between the two ages (P < 0.05, n=3 samples/age), 159 exhibited substantial differences where  the higher mean was at least 1.6-fold greater than the lower mean.  The majority of the genes (117) increased between e17 and d3.  Several genes which may  play a role in neuroendocrine development were identified, including many transcription factors, signaling molecules, and morphogeneic factors.
Keywords: time course during development (2 ages)

overall_design: Three biological replicates each of chicken pituitary embryonic day 17 and post-hatch day 3 amplified antisense RNA were analyzed  using neuroendocrine cDNA microarrays in a reference design.  Each experimental sample (embryonic day 17 or post-hatch day 3) was labeled with Cy3 and  hybridized with an aliquot of the Cy5 reference pool, which was generated from all six RNA samples.

middle: A


title: Characterization of Glucocorticoid-Induced Changes in Gene Expression in the Embryonic Pituitary Gland.

status: Public on Jun 14 2006

summary:
We have previously shown that corticosterone (CORT) can induce premature differentiation of somatotrophs in the chicken embryo.  CORT induction of GH mRNA is indirect, in that protein synthesis inhibition blocks its inducing effect.  In this study, we used a custom chicken microarray to analyze global gene expression in the embryonic pituitary gland and to identify potential direct targets of CORT that may regulate its induction of somatotroph differentiation.  Our microarray analysis revealed 25 direct early targets of CORT.
Keywords: Duration of corticosterone treatment on gene expression levels

overall_design: Four biological replicates each of the twelve treatment groups from cultured chicken embryonic day 11 pituitary cells amplified antisense RNA were analyzed using DEL-MAR 14K Integrated Systems Microarray in a reference design.  Each experimental sample was labeled with Cy3 and hybridized with an aliquot of the Cy5 reference pool, which was generated from all forty-eight RNA samples.


title: Chitin elicitation timecourse

status: Public on Sep 09 2005

last: Stanford Microarray Database

summary:
Chitin oligomers, released from fungal cell walls by endochitinase, induce defense and related cellular responses in many plants. However, little is known about chitin responses in the model plant Arabidopsis. We describe here a large scale characterization of gene expression patterns in Arabidopsis in response to chitin treatment using an Arabidopsis microarray consisting of 2,375 EST clones representing putative defense-related and regulatory genes. Transcript levels for 71 ESTs, representing 61 genes, were altered >3-fold in chitin-treated seedlings relative to control seedlings. A number of transcripts exhibited altered accumulation as early as 10 min after exposure to chitin, representing some of the earliest changes in gene expression observed in chitin-treated plants. Included among the 61 genes are those that have been reported to be elicited by various pathogen-related stimuli in other plants. Additional genes, including genes of unknown function, were also identified broadening our understanding of chitin-elicited responses. Among transcripts with enhanced accumulation, one cluster was enriched in genes with both the W-box promoter element and a novel regulatory element. In addition, a number of transcripts had decreased abundance, encoding several proteins involved in cell wall strengthening and wall deposition. The chalcone synthase promoter element was identified in the upstream regions of these genes, suggesting that pathogen signals may suppress expression of some genes. These data indicate that Arabidopsis will be an excellent model to elucidate mechanisms of chitin elicitation in plant defense.
Groups of assays that are related as part of a time series.
Keywords: time_series_design

first: Katrina

last: Ramonell


title: Liver gene transcription during energy balance perturbations in C57/BL/J6 mice.

status: Public on May 16 2003

city: Cambridge

first: R.

middle: Michael

last: Raab

address: 77 Massachusetts Avenue

department: Chemical Engineering

institute: Massachusetts Institute of Technology

summary:
A control group consisting of nine C57/BL/6J mice was maintained on a normal diet consisting of Purina Rodent Chow (Harlan Teklad, catalog #5008, 6.5% fat, 49% carbohydrate, 23% protein, 3.5 kcal/ g). The experimental group consisted of nine mice grown on a specialty high-fat diet (Harlan Teklad, catalog #TD88137, 42.16% fat, 42.81% carbohydrate, 15.02% protein, 4.53 kcal/ g). Mice were maintained for ten weeks on their respective diets in a controlled environment with standard light and feeding schedule.  Two days before tissue harvest, the experimental group on the high-fat diet was divided into one group of five and one group of four mice. The first group continued on the high-fat diet for the final two days, while the second group fasted. Mouse weights were recorded two days prior, and the day of tissue harvest. At the end of the fasting period liver tissue samples were harvested from each mouse.

RNA was purified from the liver tissue samples. Each tissue was homogenized in 1 mL of STAT-60 (Tel-Test, Inc., Friendswood, TX) and the homogenate was mixed with 200 uL of chloroform. The aqueous phase was removed, and mixed with 500 uL of isopropanol to precipitate the RNA. The resulting RNA pellet was washed with 500 uL of 70% ethanol and allowed to air dry. The pellet was dissolved in RNase free water (Ambion, TX), quantified by UV spectroscopy, and stored at -80C.

Total RNA control samples (Universal Mouse Reference RNA, catalog # 740100, Stratagene) were labeled using Cy3 dCTP (Perkin-Elmer), and liver total RNA experimental samples were labeled using Cy5 dCTP (Perkin-Elmer) during reverse transcription. For reverse transcription 10 ug of total RNA was mixed with 2 uL of 10X Cy-labeled dCTP, 2 uL of 100 mM DTT (Invitrogen), 4 uL of 5X First Strand Buffer (Invitrogen), 2 uL of a dNTP mixture containing 5 mM dGTP, dATP, dTTP and 2 mM dCTP (Invitrogen), 2 uL of 0.5 mg/ mL oligo-dT18-20 (Invitrogen), and 2 uL of Superscript II reverse transcriptase (Invitrogen). The control RNA samples were additionally mixed with 2 uL of random hexamers. The reaction mixtures were incubated at 42 C for two hours. After the reverse transcription reactions, the RNA templates were degraded by addition of 2 uL of 1 N NaOH and incubation at 65 C for 10 minutes. The alkaline conditions were neutralized by addition of 2 uL of 1 N HCl. Liver cDNA samples were then mixed with a control cDNA sample, and the mixtures were cleaned using a QIAquick Nucleotide Removal kit (Qiagen) as described by the manufacturer's instructions. The cleaned samples were concentrated in a speed vacufuge (Eppendorf) for 20 minutes at 65 C, and were dissolved in 32 uL of prewarmed hybridization buffer (Clontech Laboratories), quantified, and hybridized to prepared oligonucleotide microarrays. Hybridization occurred overnight at 55 C using Corning hybridization chambers. The following day the arrays were washed in Glass Hybridization Wash Solution (Clontech Laboratories), then in 1X SSC, and finally in 0.1X SSC. The arrays were dried by centrifugation and scanned using a GenePix 4000B scanner (Axon Instruments). The resulting data was downloaded and formatted in Excel (Microsoft), and analyzed using Matlab (The MathWorks, Inc.).

Microarrays were prepared using GAPS glass slides (Corning), and a Virtek arrayer (Bio-Rad). Arrays contained 16,847 features, printed from a synthesized oligonucleotide mouse library (Operon). The library was suspended in 3X SSC, centrifuged, and loaded into the arrayer. Arrays were printed at approximately 50% humidity. Once printed, the probes were crosslinked using a UV Stratalinker (Stratagene). The slides were then
blocked for 15 minutes in a 250 mL mixture containing 15.7 g/ L succinic anhydride (Fluka AG), 239 mL 1-methyl-2-pyrrolidinone (EM Science), and 10.7 mL of 1 M boric acid (Fisher), pH 8.0. They were cleaned by rinsing twice in 250 mL of milli-Q water, followed by 250 mL of 95% ethanol (Pharmco Products). After blocking, they were dried using filtered air and stored in the dark at room temperature.

In this experiment the gene expression data of the control mice is given by samples GSM6592, GSM6593, GSM6594, and GSM6595.  The gene expression data of the high-fat mice is given by samples GSM6599, GSM6600, GSM6601, and GSM6602.  The gene expression data of the fasted mice is given by samples GSM6596, GSM6597, and GSM6598.
Keywords = mouse, liver, energy homeostasis, gene expression, microarrays
Keywords: repeat sample

first: R. Michael

first: John

last: Bullen

first: Joanne

last: Kelleher

first: Christos

last: Mantzoros

first: Gregory

last: Stephanopoulos


title: Kc167_RNA_Quant_Eval

first: Zak

last: Razak

summary:
Three different amounts, 20 ug (GSM6155), 40 ug (GSM6157) and 80ug (GSM6158), of total Kc167 RNA were used in homotypic labelings to determine the optimal amount of RNA necesary to produce the most useable data using the CDMC_Drosophila_7k2 array.  See Neal et al. 2003 for results and discussion.
Keywords = Kc167
Keywords = Drosophila
Keywords = RNA amount
Keywords: other

first: Scott

last: Neal

first: Meredith

last: Gibson

first: Anthony

middle: K

last: So

first: Jon

last: Westwood


title: Saprophytically grown Fov

first: Andrew

last: Spriggs

department: Bioinformatics Group

summary:
Fov Infected cotton root tissue
Keywords = cotton, Fusarium wilt, AtsC, virulence, in planta expressed genes
Keywords: other

first: Helen

last: McFadden


title: Effect of varying illumination

status: Public on Apr 21 2003

city: Houston

first: Samuel

last: Kaplan

department: Microbiology and Molecular Genetics

institute: University of Texas Health Science Center at Houston

summary:
Rhodobacter sphaeroides 2.4.1 illuminated with either lumiline bulbs at 10W/m2 or tungsten bulbs at 100W/m2.
Sparged with 95%N/5%CO2.
Keywords: other

first: Jung

last: Roh

first: William

last: Smith


title: infected root time course

summary:
Time course of fusarium wilt infection of cotton root tissues
Keywords = cotton, Fusarium wilt, AtsC, virulence, in planta expressed genes
Keywords: other


title: zzMex67 co-IPed RNA vs. Total RNA  (zzMex67IP_v_TotalRNA)

status: Public on Nov 25 2002

city: Boston

first: Haley

last: Hieronymus

address: 1 Jimmy Fund Way SM922

institute: Harvard Medical School and Dana-Farber Cancer Institute

summary:
Comparison of cDNA from RNA IPed with zzMex67 to that from total RNA; resulting analysis gives Mex67 binding level relative to total abundance for each mRNA
Keywords: repeat sample

first: Pamela

last: Silver


title: zzYra1 co-IPed RNA vs. Total RNA  (zzYra1IP_v_TotalRNA)

summary:
Comparison of cDNA from RNA IPed with zzYra1 to that from total RNA; resulting analysis gives Yra1 binding level relative to total abundance for each mRNA
Keywords: repeat sample


title: zzYra1 co-IPed RNA vs. zzMex67 co-IPed RNA  (zzYra1IP_v_zzMex67IP)

summary:
Comparison of cDNA from RNA co-IPed with zzYra1
to cDNA from RNA co-IPed with zzMex67
Keywords: repeat sample


title: total RNA from mex67-6 at 37C vs. Mex67 WT at 37C (mex67-5TS_v_Mex67WT)

summary:
Comparison of cDNA from RNA of mex67-5 temperature-sensitive mutant to RNA from Mex67 wildtype strain both at the non-permissive temperature of 37C
Keywords: repeat sample