title: Diffuse large B-cell lymphoma

last: Stanford Microarray Database

summary:
Diffuse large B-cell lymphoma (DLBCL), the most common subtype of non-Hodgkin's lymphoma, is clinically heterogeneous: 40% of patients respond well to current therapy and have prolonged survival, whereas the remainder succumb to the disease. We proposed that this variability in natural history reflects unrecognized molecular heterogeneity in the tumors. Using DNA microarrays, we have conducted a systematic characterization of gene expression in B-cell malignancies. Here we show that there is diversity in gene expression among the tumors of DLBCL patients, apparently reflecting the variation in tumor proliferation rate, host response and differentiation state of the tumor. We identified two molecularly distinct forms of DLBCL which had gene expression patterns indicative of different stages of B-cell differentiation. One type expressed genes characteristic of germinal center B cells ('germinal center B-like DLBCL'); the second type expressed genes normally induced during in vitro activation of peripheral blood B cells ('activated B-like DLBCL'). Patients with germinal center B-like DLBCL had a significantly better overall survival than those with activated B-like DLBCL. The molecular classification of tumors on the basis of gene expression can thus identify previously undetected and clinically significant subtypes of cancer.
This study is described more fully in Alizadeh AA et al.(2000) Nature 403:503-11
Keywords: other

first: A

middle: A

last: Alizadeh

first: M

middle: B

last: Eisen

middle: E

last: Ma

first: I

last: Lossos

last: Rosenwald

first: J

last: Boldrick

first: H

last: Sabet

first: T

last: Tran

first: X

last: Yu

middle: I

last: Powell

first: L

last: Yang

first: G

last: Marti

last: Moore

last: Hudson

last: Lu

first: D

last: Lewis

last: Tibshirani

last: Sherlock

first: W

last: Chan

last: Greiner

last: Weisenburger

last: Armitage

last: Warnke

last: Staudt


title: Antibody Arrays Figure 7

status: Public on Jun 27 2002

city: Stanford

last: Stanford Microarray Database

state: CA

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

country: USA

institute: Stanford Microarray Database (SMD)

summary:
Protein microarrays for highly parallel detection and quantitation of specific proteins and antibodies in complex solutions.
This study is described more fully in Haab, Dunham, and Brown, Genome Biology 2001 2(2): research0004.1-0004.13
Keywords: other

first: B

last: Haab

middle: J

last: Dunham

first: P

middle: O

last: Brown


title: Antibody Arrays Figure 1

last: DunhaM


title: Group2

status: Public on Jan 03 2002

city: Cambridge

first: Iain

last: Eaves

address: Hills Road

department: Medical genetics

country: United Kingdom

institute: Cambridge Institute for Medical Research

summary:
Replicate group 2 for GSE11. All samples were processed in parallel to minimize any variation introduced during target preparation.
Keywords: parallel sample

first: Linda

middle: S

last: Wicker

first: Ghassan

last: Ghandour

first: Paul

last: Lyons

first: Laurence

last: Peterson

first: John

last: Todd

first: Richard

last: Glynne


title: Global profile of germline gene expression in C. elegans

status: Public on Jul 24 2001

summary:
We used DNA microarrays to profile gene expression patterns in the C. elegans germline and identified 1416 germline-enriched transcripts that define three groups. The sperm-enriched group contains an unusually large number of protein kinases and phosphatases. The oocyte-enriched group includes potentially new components of embryonic signaling pathways. The germline-intrinsic group, defined as genes expressed similarly in germlines making only sperm or only oocytes, contains a family of piwi-related genes that may be important for stem cell proliferation. Finally, examination of the chromosomal location of germline transcripts revealed that sperm-enriched and germline-intrinsic genes are nearly absent from the X chromosome, but oocyte-enriched genes are not.
This research has been described more fully in Reinke V et al.(2000) Mol Cell 6:605-16
Keywords: other

first: V

last: Reinke

last: Smith

first: J

last: Nance

last: Wang

first: C

last: Van Doren

first: R

last: Begley

first: S

last: Jones

first: E

last: Davis

last: Scherer

last: Ward

middle: K

last: Kim


title: Diurnal and Circadian-Regulated Genes in Arabidopsis

status: Public on Jul 20 2001

last: Stanford Microarray Database

summary:
Plants respond to day/night cycling in a number of physiological ways. At the mRNA level, the expression of some genes changes during the 24-hr period. To identify novel genes regulated in this way, we used microarrays containing 11,521 Arabidopsis expressed sequence tags, representing an estimated 7800 unique genes, to determine gene expression levels at 6-hr intervals throughout the day. Eleven percent of the genes, encompassing genes expressed at both high and low levels, showed a diurnal expression pattern. Approximately 2% cycled with a circadian rhythm. By clustering microarray data from 47 additional, unrelated experiments, we identified groups of genes regulated only by the circadian clock. These groups contained the already characterized clock-associated genes LHY, CCA1, and GI, suggesting that other key circadian clock genes might be found within these clusters.
This research has been described more fully in Schaffer R et al.(2001) Plant Cell 13:113-123
Keywords = circadian rhythm
Keywords: other

last: Schaffer

last: Landgraf

first: M

last: Accerbi

last: Simon

last: Larson

last: Wisman


title: Genetic diversity among Helicobacter pylori strains

status: Public on Jul 25 2001

summary:
Helicobacter pylori colonizes the stomach of half of the world's population, causing a wide spectrum of disease ranging from asymptomatic gastritis to ulcers to gastric cancer. Although the basis for these diverse clinical outcomes is not understood, more severe disease is associated with strains harboring a pathogenicity island. To characterize the genetic diversity of more and less virulent strains, we examined the genomic content of 15 H. pylori clinical isolates by using a whole genome H. pylori DNA microarray. We found that a full 22% of H. pylori genes are dispensable in one or more strains, thus defining a minimal functional core of 1281 H. pylori genes. While the core genes encode most metabolic and cellular processes, the strain-specific genes include genes unique to H. pylori, restriction modification genes, transposases, and genes encoding cell surface proteins, which may aid the bacteria under specific circumstances during their long-term infection of genetically diverse hosts. We observed distinct patterns of the strain-specific gene distribution along the chromosome, which may result from different mechanisms of gene acquisition and loss. Among the strain-specific genes, we have found a class of candidate virulence genes identified by their coinheritance with the pathogenicity island.
Keywords: other

first: N

last: Salama

first: K

last: Guillemin

first: T

last: McDaniel

first: G

last: Sherlock

first: L

last: Tompkins

last: Falkow


title: NOD model of  type 1 diabetes

status: Public on Nov 21 2001

first: Iain

last: Eaves

summary:
We used high density oligonucleotide arrays to measure the relative expression levels of >39,000 genes and ESTs in the NOD mouse (a murine model of T1D and other autoimmune conditions), four NOD-derived diabetes resistant congenic strains and two nondiabetic control strains. Owing to the importance of T cells in the development of T1D we decided to target two organs, the spleen and thymus.  We profiled gene expression in thymi from four week old female mice and spleens from three month old female mice.  For each of the 14 strain-tissue combinations (7 strains x 2 tissues) we performed two independent replicate experiments, making the total number of hybridizations performed 28.  In each case, an RNA population from a pool of two or three organs was generated to minimize the chances of within strain variation masking genuine variation between the strains.  To minimize any variation introduced during target preparation, all samples within a given replicate group were processed in parallel.  Three samples from group two (spleen: B10.H2g7_S2 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gsm594 (GSM594); thymus: B10.H2g7_T2 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gsm608 (GSM608), B10.H2g7 Idd3_T2 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gsm609 (GSM609)) and one from group one (spleen B10.H2g7_S1 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gsm587 (GSM587) failed a preliminary quality control check.  Consequently, the steps involved in preparing labelled cRNA from the initial starting material had to be repeated for these four samples at a later date.  A subsequent comparison of the variation seen between samples within the same replicate group (samples processed in parallel) versus samples in distinct replicate groups (samples processed at different times) revealed that the variation between the two groups (i.e. owing to independent sample preparation) was higher than the small amount of variation between the closely matched strains.  Ignoring the variability introduced during sample preparation was therefore likely to result in spurious changes being detected and genuine strain-specific differences in gene expression being masked.  Consequently, we decided to exclude the four samples that had had to be prepared independently owing to failing initial quality control.
Keywords = NOD, diabetes, congenic
Keywords: other

first: Linda

last: Wicker

first: Ghassan

last: Ghandour

last: Lyons

last: Peterson

last: Todd

last: Glynne


title: Group1

summary:
Replicate group 1 for GSE11.  All samples were processed in parallel to minimize any variation introduced during target preparation.
Keywords: parallel sample

first: Paul

first: Laurence

first: John


title: UV Exposure in Wild-Type and SOS-Deficient E. coli

status: Public on Jul 30 2001

last: Stanford Microarray Database

summary:
UV Irradiation of the wild-type and lexA MG1655 Escherichia coli. Cells were irradiated at ~2x10^8 cells/ml in the Davis medium by 15-W germicidal lamp (254 nm, 0.66J/m^2/sec). Set also includes respective controls for unirradiated cells collected at 20 and 60 min time points. Comparison between lexA mutant and the isogenic wild-type prior the UV treatment is also included as part of the set.
The SOS response in UV-irradiated Escherichia coli includes the upregulation of several dozen genes that are negatively regulated by the LexA repressor. Using DNA microarrays containing amplified DNA fragments from 95.5% of all open reading frames identified on the E. coli chromosome, we have examined the changes in gene expression following UV exposure in both wild-type cells and lexA1 mutants, which are unable to induce genes under LexA control. We report here the time courses of expression of the genes surrounding the 26 documented lexA-regulated regions on the E. coli chromosome. We observed 17 additional sites that responded in a lexA-dependent manner and a large number of genes that were upregulated in a lexA-independent manner although upregulation in this manner was generally not more than twofold. In addition, several transcripts were either downregulated or degraded following UV irradiation. These newly identified UV-responsive genes are discussed with respect to their possible roles in cellular recovery following exposure to UV irradiation.
Data from the set are presented and analysed in the manuscript "Comparative gene expression profiles following UV exposure in wild type and SOS deficient Escherichia coli." Courcelle J; Khodursky A; Peter B; Brown PO; Hanawalt PC, Genetics 158: 41-64 May 2001
Keywords: other

first: J

last: Courcelle

first: A

last: Khodursky

first: B

last: Peter

first: P

last: Brown

middle: C

last: Hanawalt


title: Topoisomerase function in E. coli replication fork movement

summary:
Analysis of topoisomerase function in bacterial replication fork movement: use of DNA microarrays.
We used DNA microarrays of the Escherichia coli genome to trace the progression of chromosomal replication forks in synchronized cells. We found that both DNA gyrase and topoisomerase IV (topo IV) promote replication fork progression. When both enzymes were inhibited, the replication fork stopped rapidly. The elongation rate with topo IV alone was 1/3 of normal. Genetic data confirmed and extended these results. Inactivation of gyrase alone caused a slow stop of replication. Topo IV activity was sufficient to prevent accumulation of (+) supercoils in plasmid DNA in vivo, suggesting that topo IV can promote replication by removing (+) supercoils in front of the chromosomal fork.
This study is detailed in Khodursky AB et al.(2000) Proc Natl Acad Sci U S A 97:9419-24
Keywords: other

last: Schmid

last: DeRisi

first: D

last: Botstein

middle: R

last: Cozzarelli


title: Prp4-1 temperature shift

status: Public on Apr 16 2002

city: Santa Cruz

first: Manuel

last: Ares

institute: UC Santa Cruz

summary:
Prp4-1 and wt strains were grown at 26°C to A600 of 1.0, then an equal volume of 48°C media was added to bring the temperature to 37°C.  Both strains were allowed to grow at 37°C and samples were taken at 0 (before shift), 5, 15, 30, 60, and 120 mins after shift to restrictive temperature.
Keywords = splicing
Keywords: time-course

first: Tyson

last: Clark


title: Non-essential mRNA processing factors

summary:
Set of experiments done on yeast deletion strains of various non-essential mRNA processing factors.

Keywords = splicing
Keywords: repeat sample

first: Charles

middle: W

last: Sugnet


title: Microarray-based CGH in human cancer cell lines

status: Public on Feb 12 2002

city: San Francisco

first: Donna

middle: G

last: Albertson

department: Comprehensive Cancer Center

institute: University of California San Francisco

type: Genome variation profiling by genome tiling array

summary:
This series represents the data set from the paper Assembly of microarrays for genome-wide measurement of DNA copy number appearing in Nat Genet 2001 Nov;29(3):263-4 and it's web supplement.
Specimen procurement, labeling, hybridization and imaging protocols from Nat Genet 2001 Nov;29(3):263-4 web supplement:
Specimens.  We obtained GM03563, GM00143, GM05296, GM07408, GM01750, GM03134, GM13330, GM03576, GM01535, GM07081, GM02948, GM04435, GM10315, GM13031 and GM01524 cell strains from the NIGMS Human Genetics Cell Repository (Coriell Institute for Medical Research), and cultured them under the recommended conditions.  We cultured cell lines BT474, HCT116, T47D, MPE600, COLO320, SW837, MDA-MB-231, MDA-MB-453 and HT29 under the recommended conditions.  To isolate DNA from confluent cell cultures, we collected cells from T75 flasks and then incubated them overnight at 55 C in a 3 ml solution containing 0.01 M Tris, pH 7.5, 0.001 M EDTA, pH 8, 0.5% SDS and 0.1 g/l proteinase K.  We added 1 ml of saturated NaCl solution and 10 ml of ethanol to the cell lysate and collected the DNA by spooling.  We removed excess liquid and then dissolved the DNA in 1 ml of H2O.  We isolated DNA from breast tumor specimens as described previously.
DNA labeling.  We labeled DNA by nick translation or random priming.  For nick translation, we used a 400 l reaction containing 10 g DNA, 50 mM Tris, pH 7.6, 5 mM MgCl2, 0.02 mM each dATP, dTTP and dGTP, 0.2 mM Cy3- or Cy5-dCTP (Amersham), 0.2 U DNA Polymerase I (Gibco BRL), and 30 l DNAseI/PolI enzyme mix (Gibco BRL).  We incubated the reaction at 15 C for 60 min after which we stopped the reaction by incubation at 70 C for 10 min.  We removed unincorporated nucleotides using a Sephadex G-50 spin column.  We labeled genomic DNA by random priming in a 100 l reaction containing 0.003 - 0.6 g DNA, 1x random primers solution (BioPrime DNA Labeling System, Gibco BRL), 1 mM Tris, pH 7.6, 0.1 mM EDTA, 0.2 mM each of dATP, dTTP and dGTP, 0.1 mM dCTP, 0.4 mM Cy3 or Cy5-dCTP (Amersham) and 160 U Klenow fragment (BioPrime DNA Labeling System, Gibco BRL). We incubated the DNA with the random primers solution at 100 C for 10 min in a total volume of 84 l, prior to adding the other reagents and then incubated the 100 l reaction overnight at 37 C.  We removed unincorporated nucleotides using a Sephadex G-50 column.
Hybridization.  We combined test and reference DNAs (~2 g of input genomic DNA for nick translation or ~0.6 g of input genomic DNA for random prime labeling) with Cot-1 DNA (80-100 g; Gibco BRL) and precipitated them with ethanol.  We collected the precipitate by centrifugation and allowed the precipitate to dry in air for 10 min before re-dissolving it in a 50 l hybridization mixture containing 50% formamide, 2 x SSC, 10% dextran sulfate, 4% SDS and 500 g yeast tRNA, pH 7.  We incubated the hybridization mixture at 70 C for 10-15 min to denature the DNA and subsequently continued incubation at 37 C for 60 min to allow blocking of repetitive sequences.  We applied a ring of rubber cement closely around the array to form a well, into which we added 50 l of slide blocking solution containing 500 g salmon sperm DNA in 50% formamide, 2 x SSC, 10% dextran sulfate and 4% SDS, pH 7.   We created an airtight hybridization chamber by placing a silicone gasket (PGC Scientific) around the array and rubber cement ring, placing a slide on top of it and clamping with binder clips.  After a 30 min incubation at room temperature, we opened the chamber, removed approximately three-quarters of the blocking solution, added the denatured and re-annealed hybridization mixture and then re-sealed the chamber.  We placed the arrays on a slowly rocking table (~1 rpm) at 37 C to allow hybridization to occur over 16-72 h.  After hybridization, we rinsed off the excess hybridization fluid with PN buffer (PN: 0.1 M sodium phosphate, 0.1% nonidet P40, pH 8), then washed once in 50% formamide, 2 x SSC, pH 7 at 45 C for 15 min, and finally in PN buffer at room temperature for 15 min.  After draining excess liquid from the arrays, we mounted them in a solution containing 90% glycerol, 10% PBS and 1 M DAPI, and then sealed them with a cover slip.  We drained excess glycerol-DAPI solution onto a paper tissue.
Imaging and analysis.  We acquired 16 bit 1024x1024 pixel DAPI, Cy3 and Cy5 images using a custom built CCD camera system, although we have also used commercial laser scanners for this purpose.  We used ?UCSF SPOT? software (A.N.J. manuscript submitted) to automatically segment the spots based on the DAPI images, perform local background correction and to calculate various measurement parameters, including log2ratios of the total integrated Cy3 and Cy5 intensities for each spot.  We used a second custom program SPROC to associate clone identities and a mapping information file with each spot so that the data could be plotted relative to the position of the BACs on the September, 2000 freeze of the draft human genome sequence (http://genome.ucsc.edu).  SPROC also implements a filtering procedure to reject data based on a number of criteria, including low reference/DAPI signal intensity and low correlation of the Cy3 and Cy5 intensities with a spot.  The SPROC output consists of averaged ratios of the triplicate spots for each clone, standard deviations of the triplicates and plotting position for each clone on the array, as well as other clone information stored in the database, such as STS content (Tables A and B).  We edited the data files to remove ratios on clones for which only one of the triplicates remained after SPROC analysis and/or the standard deviation of the log2ratios of the triplicates was > 0.2.
Keywords: other

first: Antoine

middle: M

last: Snijders

first: Norma

last: Nowak

first: Richard

last: Segraves

first: Stephanie

last: Blackwood

first: Nils

first: Jeffery

last: Conroy

first: Greg

last: Hamilton

first: Anna

last: Hindle

first: Bing

last: Huey

first: Karen

last: Kimura

first: Sindy

last: Law

first: Ken

last: Myambo

first: Joel

last: Palmer

first: Bauke

last: Ylstra

first: Jingzhu

middle: P

last: Yue

first: Joe

last: Gray

first: Ajay

middle: N

last: Jain

first: Daniel

last: Pinkel


title: E. coli response to MMC

status: Public on Feb 26 2002

city: Bethesda

first: Pavel

last: Khil

state: MD

address: 5 Memorial Dr.

institute: NIDDK

summary:
Changes in gene expression after treatment of E. coli cultures with mitomycin C were assessed using gene array technology. Unexpectedly, a large number of genes (nearly 30% of all genes) displayed significant changes in their expression level.  Analysis and classification of expression profiles of the corresponding genes allowed us to assign this large number of genes into a dozen to two dozen small clusters of genes with similar expression profiles.  This assignment allowed us to describe systematically the changes in the level of gene expression in response to DNA damage.  Among the damage-induced genes more than a hundred are novel.  From those genes involved in DNA metabolism that have not been previously shown to be induced by DNA damage, for example, the mutS gene involved in mismatch repair is especially noteworthy.  In addition to the SOS response, we observed the induction of other stress response pathways such as those of oxidative stress and osmotic protection.  Among the genes that are down-regulated in response to DNA damage are numerous protein biosynthesis genes. Analysis of the gene expression data highlighted the essential involvement of sigmaS regulated genes and the general stress response network in the response to DNA damage.
Keywords = DNA damage, recA, SOS
Keywords: other

first: R. Daniel

last: Camerini-Otero


title: Tryptophan metabolism response in E. coli

last: Stanford Microarray Database

summary:
DNA microarray analysis of gene expression in response to physiological and genetic changes that affect tryptophan metabolism in Escherichia coli.
We investigated the global changes in mRNA abundance in Escherichia coli elicited by various perturbations of tryptophan metabolism. To do so we printed DNA microarrays containing 95% of all annotated E. coli ORFs. We determined the expression profile that is predominantly dictated by the activity of the tryptophan repressor. Only three operons, trp, mtr, and aroH, exhibited appreciable expression changes consistent with this profile. The quantitative changes we observed in mRNA levels for the five genes of the trp operon were consistent within a factor of 2, with expectations based on established Trp protein levels. Several operons known to be regulated by the TyrR protein, aroF-tyrA, aroL, aroP, and aroG, were down-regulated on addition of tryptophan. TyrR can be activated by any one of the three aromatic amino acids. Only one operon, tnaAB, was significantly activated by the presence of tryptophan in the medium. We uncovered a plethora of likely indirect effects of changes in tryptophan metabolism on intracellular mRNA pools, most prominent of which was the sensitivity of arginine biosynthetic operons to tryptophan starvation.
This study is detailed in Khodursky AB et al.(2000) Proc Natl Acad Sci U S A 97:12170-5
Keywords: other

first: A

last: Khodursky

first: B

last: Peter

first: N

last: Cozzarelli

first: D

last: Botstein

first: P

last: Brown

first: C

last: Yanofsky


title: Adaptive evolution in yeast

summary:
A Saccharomyces cerevisiae population was cultured for many generations under conditions to which it is not optimally adapted. These experiments were designed to investigate adaptive evolution under natural selection.
This study is described in more detail in Ferea TL, et al. 1999. Proc Natl Acad Sci USA 96:9721-6
Keywords: other

first: T

middle: L

last: Ferea

first: R

middle: F

last: Rosenzweig