title: Diagnostic miniarray of childhood acute lymphoblastic leukemia (ALL)

status: Public on Jul 04 2005

first: Gerolamo

last: Lanfranchi

summary:
We developed and validated a diagnostic miniarray to recognize different subtypes of ALL. We analyzed blindly the gene expression profiling of 17 patients: 10 ALL-B, 5 ALL-T and 2 MLL/AF4. This miniarray was able to assign all samples to the correct class. We compared the transcription profiles of the leukemic samples by miniarray competitive hybridisation against an arbitrary total RNA reference prepared from normal human bone marrow.

ALL-B patients:	GSM50368, GSM50369, GSM50370, GSM50371, GSM50372, GSM50373, GSM50374, GSM50375, GSM50376, GSM50377

ALL-T patients:	GSM50379, GSM50380, GSM50381, GSM50382, GSM50383

ALL-B patients with the specific chromosomal aberration MLL/AF4:	GSM50384, GSM50385
Keywords = Acute lymphoblastic leukemia
Keywords = human bone marrow
Keywords = transcriptional profiling
Keywords = miniarray

Reference: Haematologica 2005;90:890-898
Keywords: ordered

first: Lucia

last: Tombolan

first: Marta

last: Campo Dell'Orto

first: Benedetta

last: Accordi

first: Geertruy

last: te Kronnie

first: Chiara

last: Romualdi

first: Nicola

last: Vitulo

first: Giuseppe

last: Basso


title: Gene expression profiling of children affected by acute lymphoblastic leukemia

city: Padova

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

country: Italy

institute: University of Padova

summary:
We have examined gene expression profiling of 18 children with acute lymphoblastic leukemia (ALL). In particular, the ALL patients are subdivided in three different subtypes by morphological, immunophenotypic and cytogenetical parameters: 10 ALL-B, 5 ALL-T and 3 ALL-B with the specific chromosomal aberration MLL/AF4. We compared the transcription profiles of the leukemic samples by microarray competitive hybridization against an arbitrary total RNA reference prepared from normal human bone marrow. Two replicates of each experiment were done using different microarray slides, in which the sample and reference RNAs labeled either with Cy3 or Cy5 fluorochromes were crossed in both combinations.

ALL-B patients:	GSM49966, GSM49967, GSM49969, GSM49970, GSM49971, GSM49972, GSM49973, GSM49974, GSM49976, GSM49977, GSM49978, GSM49979, GSM49980, GSM49981, GSM49982, GSM49983, GSM49984, GSM49985, GSM49986, GSM49987

ALL-T patients:	GSM49988, GSM49989, GSM49990, GSM49991, GSM49992, GSM49993, GSM49994, GSM49995, GSM49996, GSM49997

ALL-B patients with the specific chromosomal aberration MLL/AF4:	GSM49999, GSM50001, GSM50004, GSM50005, GSM50006, GSM50007
Keywords = Acute lymphoblastic leukemia (ALL)
Keywords = human bone marrow
Keywords = gene expression profiling

Reference: Haematologica 2005;90:890-898
Keywords: ordered

first: Cristiano

last: De Pittà


title: Ips pini JHIII male & female timecourse

status: Public on Jun 16 2005

city: Reno

first: Christopher

middle: Ian

last: Keeling

state: NV

address: 1664 North Virginia Street

department: Department of Biochemistry/Mail Stop 330

country: USA

institute: University of Nevada, Reno

summary:
This series examines gene expression in the anterior midgut at several time points (2, 4, 8, & 16 h) after topical application of juvenile hormone III (JHIII) or acetone (control) to adult beetles of both sexes.
Keywords = North American pine engraver beetle
Keywords = anterior midgut
Keywords = juvenile hormone
Keywords = pheromone biosynthesis
Keywords = Coleoptera
Keywords = Scolytidae
Keywords: other

middle: I

first: Sharon

last: Young

first: Claus

last: Tittiger


title: ENCODE transcript mapping for human placental poly(A)+ RNA and human NB4 cell line total RNA

status: Public on Jun 04 2005

city: New Haven

first: Olof

last: Emanuelsson

state: CT

address: 260 Whitney Avenue

institute: Yale University

type: Expression profiling by genome tiling array

summary:
not available
Keywords: other

overall_design:
Transcript mapping on maskless array synthesizer (MAS) ENCODE arrays for 3 different biological replicates of placental poly(A)+ RNA (each with either 2 or 3 technical replicates): GSM52610, GSM52611, GSM52612, GSM52613, GSM52614, GSM52615, and GSM52616.

Keywords = placenta poly(A)+ RNA, ENCODE, tiling array, maskless photolithography, transcription mapping

Transcript mapping on maskless array synthesizer (MAS) ENCODE arrays for 3 different biological replicates of NB4 total RNA (each with 2 technical replicates): GSM52617, GSM52618, GSM52619, GSM52620, GSM52621, and GSM52622.

Keywords = NB4 cell line total RNA, ENCODE, tiling array, maskless photolithography, transcription mapping

Transcript mapping on maskless array synthesizer (MAS) ENCODE arrays for 3 different biological replicates of placental poly(A)+ RNA (each with either 2 or 4 technical replicates) using the protocol described in Bertone et al, Science 306 (2004): GSM52649, GSM52650, GSM52651, GSM52652, GSM52653, GSM52654, GSM52655, and GSM60239.

Keywords = placenta poly(A)+ RNA, ENCODE, tiling array, maskless photolithography, transcription mapping

first: Ugrappa

last: Nagalakshmi

first: Zheng

last: Lian

first: Joel

middle: S

last: Rozowsky

first: Alexander

middle: E

last: Urban

first: Sherman

last: Weissman

first: Mike

middle: P

last: Snyder

first: Mark

last: Gerstein


title: Rice Transcriptome - Slide A; Slide B

status: Public on May 24 2005

city: NEW HAVEN

first: Ligeng

last: Ma

address: 165 Prospect

department: Molecular, Cellular & Developmental Biology

summary:
[Oryza sativa Genome Oligo Set Version 1.0 was designed by Beijing Genomics Institute (BGI) and contain 60,727 70mer oligos representing both indica and japonica genomes. All oligos were designed from cDNAs, expreseed sequence tag (EST) sequences, predicted genes of BGI rice genome build and other public resources. Mapping to TIGR rice genome pseudommolecues release 2 is based on the BLAST results, if a oligo has greater than 97% identity to a gene sequence from TIGR pseudomolecules, the oligo represents that gene. Rice 30K Operon Version 1.0 -70 mer oligos. The array is in 48 pin conformation. It has 25 columns and 25 rows in each of 4 x 12 subarrays. This is the slideA of the two slide sets.
Platform_catalog_number: XDEN-A
Platform_coating: poly L lysine
Platform_manufacture_protocol: Omnigrid 100 contact printer; TeleChem Stealth SMP3 split pins; See http://keck.med.yale.edu/dnaarrays/printing
Platform_manufacturer: Keck Biotechnology Resource Lab at Yale
Platform_support: glass slide
Platform_technology: spotted oligonucleotide
]
Series_sample_order: Sample 1-15 Slide A; Sample 16-30 Slide B
Keywords: other


title: JHIII-MF & feeding-M

status: Public on Dec 31 2004

summary:
This series examines gene expression in the anterior midgut at several time points (2, 4, 8, & 16 h for males, 8 h for females) after topical application of juvenile hormone III (JHIII) or acetone (control) to adult beetles.  In addition, gene expression in male anterior midguts were examined 24 h after phloem feeding or in unfed beetles.
Keywords: North American pine engraver beetle; anterior midgut; juvenile hormone; pheromone biosynthesis; Coleoptera; Scolytidae

Publication reference:

Reference Type: Book Section
Authors: Tittiger, Claus; Keeling, Christopher I.; Blomquist, Gary J.
Year: 2005
Title: Some insights into the remarkable metabolism of the bark beetle midgut.
Editor: Romeo, J.T.
Book Title: Chemical ecology and phytochemistry of forest ecosystems
City: Toronto
Publisher: Elsevier
Volume: 39
Pages: 57-78
Series Title: Recent Advances in Phytochemistry

Keywords: other

first: Gary

middle: J

last: Blomquist


title: Comparison of Dll1tm1Gos and wt embryos at E10.5

status: Public on Mar 01 2005

city: Munich - Neuherberg

first: Johannes

last: Beckers

state: Bavaria

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

country: Germany

institute: GSF - National Research Center

summary:
Comparison of pooled Dll1tm1Gos and wildtype E10.5 embryo samples.
4 dual-color DNA-chip hybridizations on a non-commercial cDNA chip and 9 dual-color hybridisations on a commercial chip (Atlas Glass Mouse 1) of cDNAs from a pool of embryos were made.
Keywords: other

first: Christine

last: Machka


title: Global transcription analysis of immature avian erythrocytic progenitors

status: Public on Nov 30 2004

city: Villeurbanne Cedex

first: Olivier

last: Gandrillon

address: 16 rue Raphael Dubois

country: France

institute: Universite' Claude Bernard Lyon I

summary:
The molecular mechanisms regulating the cell fate decision between self-renewal and differentiation/apoptosis in stem and progenitor cells are poorly understood. Here, we report the first comprehensive identification of genes potentially involved in the switch from self-renewal toward differentiation of primary, non-immortalized erythroid avian progenitor cells (T2EC cells). We used the Serial Analysis of Gene Expression (SAGE) technique in order to identify and quantify the genome fraction functionally active in a self-renewing versus a differentiating cell population. We generated two SAGE libraries and sequenced a total of 37,589 tags, thereby obtaining the first transcriptional profile characterization of a chicken cell. Tag identification was performed using a new relational database (Identitag) developed in the laboratory, which allowed a highly satisfactory level of identification. Among 123 differentially expressed genes, 11 were investigated further and for nine of them the differential expression was subsequently confirmed by real-time PCR. The comparison of tag abundance between the two libraries revealed that only a small fraction of transcripts was differentially expressed. The analysis of their functions argue against a prominent role for a master switch in T2EC cells decision-making, but are in favor of a critical role for coordinated small variations in a relatively small number of genes that can lead to essential cellular identity changes.
Keywords: other

first: Francesca

last: Damiola

first: Celine

last: Keime

first: Sandrine

last: Gonin-Giraud

first: Sebastien

last: Dazy


title: Evolution of gene expression in the Drosophila melanogaster subgroup update and extension

status: Public on May 12 2005

city: Cambridge

first: Scott

middle: A

last: Rifkin

state: MA

address: 16 Divinity Ave

department: OEB

institute: Harvard University

summary:
http://www.nature.com/ng/journal/v33/n2/abs/ng1086.html.
Little is known about broad patterns of variation and evolution of gene expression during any developmental process. Here we investigate variation in genome-wide gene expression among Drosophila simulans, Drosophila yakuba and four strains of Drosophila melanogaster during a major developmental transition?the start of metamorphosis. Differences in gene activity between these lineages follow a phylogenetic pattern, and 27% of all of the genes in these genomes differ in their developmental gene expression between at least two strains or species. We identify, on a gene-by-gene basis, the evolutionary forces that shape this variation and show that, both within the transcriptional network that controls metamorphosis and across the whole genome, the expression changes of transcription factor genes are relatively stable, whereas those of their downstream targets are more likely to have evolved. Our results demonstrate extensive evolution of developmental gene expression among closely related species.

Extended from the original publication by updating annotation to release 4.0 and using 8 arrays for each strain/species.  All Drosophila yakuba arrays are new.

see also:  PMID: 15122255.  http://www.nature.com/ng/journal/v36/n6/abs/ng1355.html  Gu Z, Rifkin SA, White KP, Li WH Duplicate genes increase gene expression diversity within and between species.
Keywords: repeat sample

sample_organism:
Drosophila melanogaster
Drosophila simulans
Drosophila yakuba

first: Junhyong

last: Kim

first: Kevin

last: White


title: Evaluation of Microarray Gene Identification Methods Using Spike-In Experiments

status: Public on May 03 2005

city: Singappore

first: Althea

last: Chua

country: Singapore

institute: Bioinformatics Institute

summary:
Due to the lack of controlled microarray experimental data, evaluation of gene identification methods has been performed using simulated data.  As the ability of these approaches to mimic actual experimental data is questionable, conclusions drawn can be misleading. We applied spike-in approaches to develop experimental benchmark data and used it to evaluate various gene identification methods.
mRNA that correspond to specific spots on a microarray were obtained by in-vitro transcription of selected clones. They were then spiked in at 11 varying concentrations to a common pool of mRNA, creating a set of known differentially expressed genes.
mRNA was obtained from mouse ATCC CRL1606 hybridoma cells. From self hybridization results 200 genes that consistently exhibited a log ratio value close to 0 were randomly selected across a range of intensity.  In-vitro transcripts of these 200 genes were obtained from their respective clones. From RNA gel electrophoresis and test array results, 169 of the 200 transcripts were deemed successful. Experiments were then conducted by spiking these 169 transcripts to the common pool of mRNA extracted from the hybridoma cells. With exception of the spiked in genes, the experimental set-up is identical to a self hybridization. This experiment is thus different from other microarray experiments as the set of differentially expressed genes is known as they have been artificially created.
Spiked in genes were introduced at 11 concentrations: 0pmol (self hybridization), 0.025pmol, 0.05pmol, 0.10pmol, 0.15pmol, 0.20pmol, 0.25pmol, 0.5pmol, 0.75pmol 1pmol and 2pmol.   For concentrations 0pmol, 0.05pmol, 0.10pmol, 0.25pmol, 0.50pmol and 0.75pmol, 6 replicates were obtained.  For concentrations 0.025pmol, 0.15pmol, 0.20pmol, 1pmol and 2pmol, 3 replicates were obtained. Dye swaps were not performed for these experiments.
Keywords: other


title: Probing miRNAs with microarrays:  tissue specificity and functional inference

status: Public on Oct 09 2004

city: Toronto

first: Tomas

last: Babak

state: ON

address: 112 College St

department: Banting and Best Department of Medical Research

country: Canada

institute: Best Institute

summary:
We describe a method to detect miRNAs using microarrays, in which the miRNAs are directly hybridized to the array. We used this method to analyze miRNA expression across 16 mouse organs and tissues. More than half of the 78 miRNAs detected were expressed in specific adult tissues. By comparing miRNA levels to mRNA levels determined in a parallel microarray analysis of the same tissues, we found that the expression of target mRNAs predicted on the basis of sequence similarity is biased towards the tissues in which the corresponding miRNA is expressed.  The remainder of the data comprises of absolute expression levels of a comprehensive survey of other mouse noncoding RNA.  The expression levels were measured using multiple independent probes that were tiled across each transcript.
Keywords: other

first: Wen

last: Zhang

first: Quaid

last: Morris

first: Benjamin

last: Blencowe

first: Timothy

middle: R

last: Hughes


title: Embryonic E14.5 telencephalon vs adult forebrain

status: Public on Jul 31 2004

city: Naples

first: Massimo

last: Zollo

state: Naples

address: Via Pietro Castellino,111

department: TIGEM/ZOLLO

institute: TIGEM (Telethon Institute of genetics and Medicine)

summary:
TESS_E14.5_Adult series:
Set of microarray expreriments used to identify genes of TESS library preferentially expressed in Embryonic E14.5 mouse telencephalon
Keywords: other


title: TAcKLE - Transcriptome Amplification and cDNA Labeling for Expression analysis

status: Public on Aug 13 2004

city: Heidelberg

first: Joerg

last: Schlingemann

address: Technologiepark III, Im Neuenheimer Feld 280

department: Molecular Biology (B060)

institute: German Cancer Research Center (DKFZ)

summary:
To characterize the properties and evaluate the performance of the TAcKLE procedure, a novel method providing effective transcriptome amplification for expression analyses on oligonucleotide microarrays, we performed 20 two-color hybridizations using self-spotted Operon 27k arrays. A single source of universal human reference RNA (pooled from 10 cell lines) and RNA extracted from healthy breast tissue was used for all experiments to avoid differences in transcript abundance imposed by the RNA preparation. RNA was either amplified by one or two rounds of linear isothermal RNA amplification (starting from 2000 ng, 200 ng, 20 ng or 2 ng), followed by Cy-dUTP incorporation using Klenow fragment, or labeled directly by reverse transcription of 40 µg RNA with Cy-dUTP. For all quantities of starting material, one co-hybridization of reference RNA, two hybridizations of breast versus reference RNA as well as one hybridization of reference versus breast RNA were performed. In case of amplified RNA, all dye labeling reactions were made from distinct target preparations. Hybridizations were performed for 16 h at 42 °C in a GeneTAC Hybridization Station (Genomic Solutions) using UltraHyb hybridization buffer (Ambion). Hybridized microarrays were scanned at 5 µm resolution on a GenePix 4000B microarray scanner (Axon Instruments). For all hybridizations, raw signal intensities were normalized applying variance stabilization (W. Huber et al., Bioinformatics 18 Suppl 1, 2002).
Keywords = amplification
Keywords = labeling
Keywords = protocol
Keywords = spotted
Keywords = human
Keywords = long oligonucleotide
Keywords = oligo
Keywords = 70mer
Keywords = Operon
Keywords: other

first: Olaf

last: Thuerigen

first: Grischa

last: Toedt

first: Heidi

last: Kramer

first: Peter

last: Lichter

first: Meinhard

last: Hahn


title: Mouse QRNA novel ncRNA prediction array

status: Public on Mar 08 2005

summary:
We used this array as described in Babak, Blencowe, anf Hughes (2005), to screen novel ncRNA predictions.  See author supplementary data for more detailed probe information.
Keywords: parallel sample


title: Intestinal cells infected with Vibrio cholerae

status: Public on Oct 14 2004

city: Baltimore

first: James

last: Kaper

state: MD

department: Center for Vaccine Development

institute: University of Maryland School of Medicine

summary:
Each sample was infected with a different strain of V. Cholerae
Keywords = Cholerae
Keywords: parallel sample

first: Neil

last: Stokes

first: Xin

last: Zhou

first: Stephen

last: Meltzer

middle: B


title: Retinoic acid-induced neuroblastoma cells

summary:
TESS_Neuro2A series

Set of microarray expreriments used to identify genes of TESS library differentially expressed in Murine Neuroblastomas cells Neuro2A induced with Retinoic Acid treatment for 24 h, 48 h, 72 h, 96 h and 7 days
Keywords: time-course


title: Maskless photolithography genome tiling experiment

status: Public on Oct 29 2004

first: Paul

last: Bertone

summary:
This experiment was designed to identify transcribed sequences across the human genome, particularly those distinct from previously annotated genes. To measure global transcriptional activity a series of high-density oligonucleotide tiling arrays was constructed to represent sense and antisense strands of the entire nonrepetitive sequence of the genome (1.5 Gb). A total of 51,874,388 36mer oligonucleotide probes, positioned every 46 nt on average, were synthesized via maskless photolithography at a feature density of approximately 390,000 probes per slide. The arrays were hybridized to fluorescence-labeled cDNA reverse-transcribed from triple-selected poly (A)+ liver tissue RNA.
Keywords = transcription
Keywords = gene expression
Keywords = human
Keywords: other


title: mouse RPE/choroid age comparison - ATLAS arrays

status: Public on Sep 30 2003

city: Davis

first: Sharon

middle: A.

last: Boylan

state: CA

address: 2403 Tupper Hall

department: Biological Chemistry

institute: University of California, Davis

summary:
Young mice were compared to old mice (2 month vs 24 month) to determine gene changes that occur with aging in the mouse retinal pigmented epithelium/choroid of the eye.
Keywords = retinal pigmented epithelium
Keywords = aging
Keywords = choroid
Keywords: other

first: Hisashi

last: Ida

first: Andrea

middle: L

last: Weigel

first: Leonard

middle: M

last: Hjelmeland


title: Time course of oxidative stress responses in yeast, caused by Menadione or hydrogen peroxide

status: Public on Feb 04 2005

city: Palo Alto

first: Michael

last: Shapira

address: 300 Pasteur Dr. Lane Bldg. room L309

department: Genetics

institute: Stanford University

summary:
Oxidative stress caused by Menadione or Hydrogen peroxide in synchronized Saccharomyces cerevisiae cultures. Alpha factor synchronized cultures (0.2-0.4 OD), treated at the beginning of S phase (25 min after release from G1 arrest) with either 2 mM Menadione (MD) or 0.24 mM Hydrogen peroxide (HP), show cell cycle effects. Cells treated with MD arrested at G1. Cells treated with HP delayed at S and then, after removal of HP at 135 minutes , continued the cell cycle, only to arrest at G2/M. Growth was carried out in 30C with shaking (295 rpm).
Two time course experiments were performed with each oxidative stress agent, designated as H2O2 and H2O2_II,  MD and MD_II.
Keywords = oxidative stress
Keywords = menadione
Keywords = hydrogen peroxide
Keywords = time course
Keywords = cell cycle
Keywords = yeast
Keywords: other

first: Eran

last: Segal

first: David

last: Botstein


title: A genomic view of estrogen actions in human breast cancer cells

status: Public on Oct 27 2004

city: Avellino

first: Angelo

last: Facchiano

address: via Roma 52A/C

institute: Institute of Food Science

summary:
Changes in the expression of 8400 genes were monitored by cDNA microarray analysis during the first 32 h of human breast cancer (BC) ZR-75.1 cell stimulation with a mitogenic dose of 17beta-estradiol, a timing which corresponds to completion of a full mitotic cycle in hormone-stimulated cells. Hierarchical clustering of 344 genes whose expression either increases or decreases significantly in response to estrogen reveals that the gene expression program activated by the hormone in these cells shows 8 main patterns of gene activation/inhibition. This newly identified estrogen-responsive transcriptome represents more than a simple cell cycle response, as only a few affected genes belong to the transcriptional program of the cell division cycle of eukaryotes, or showed a similar expression profile in other mitogen-stimulated human cells. Indeed, based on the functions assigned to the products of the genes they control, estrogen appears to affect several key features of BC cells, including their metabolic status, proliferation, survival, differentiation and resistance to stress and chemotherapy, as well as RNA and protein synthesis, maturation and turn-over rates.
Keywords: time-course

first: Luigi

last: Cicatiello

first: Claudio

last: Scafoglio

first: Lucia

last: Altucci

first: Massimo

last: Cancemi

first: Guido

last: Natoli

first: Giovanni

last: Iazzetti

first: Raffaele

last: Calogero

first: Nicoletta

last: Biglia

first: Michele

last: De Bortoli

first: Christian

last: Sfiligoi

first: Piero

last: Sismondi

first: Francesco

last: Bresciani

first: Alessandro

last: Weisz


title: Differentiated vs undifferentiated neural stem cells

last: Zollo

summary:
TESS_NSC series:
Set of microarray expreriments used to identify genes of TESS library differentially expressed in Neural stem cells induced or not to differentiation
Keywords: other


title: Evaluation of the chicken transcriptome by SAGE of B cell and the DT40 cell line

status: Public on Oct 06 2004

city: Neuherberg

first: Randolph

last: Caldwell

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute for Molecular Radiobiology

institute: GSF-National Reseearch Center

summary:
These libraries represent total RNA from bursal tissue of 20 day old CB-inbred chicks and the ALV induced bursal cell line DT40 Cre1 cells.
Keywords = chicken transcriptome SAGE Bursal cell DT40
Keywords: other

first: Matthias

last: Wahl

first: Andrjez

last: Kierzek

first: Hiroshi

last: Arakawa

first: Eduardo

last: Eyras

first: Nina

last: Hubner

last: Jung

first: Manuel

last: Soeldenwagner

first: Manuella

last: Cervelli

first: Yan-Dong

last: Wang

first: Volkmar

last: Liebscher

first: Jean-Marie

last: Buerstedde


title: Transcriptome analysis of monocytic leukemia cell differentiation

status: Public on Oct 23 2004

city: Montpellier

first: David

last: Piquemal

address: 1682, rue de la Valsière

institute: ACOBIOM

summary:
The human leukemia cell line U937 is a well-established model for studying monocytic cell differentiation. We used a modified protocol (SADE) of serial analysis of gene expression (SAGE) and developed a SADE linker-anchored PCR assay to investigate the pattern of expression of known genes and to identify new transcripts in proliferating cells and during cell growth arrest and differentiation. We implemented new informatic tools to compare expression profiles before and after exposure of cells to differentiation inducers. From the analysis of 47,388 tags, we identified 13,806 distinct transcripts, 265 of which showed significant variations (P<0.01). Among 1219 well-identified genes, major changes concerned transcription and translation components, cytoskeleton, and macrophage-specific genes. Nearly half of the tags, some of them expressed at high levels, matched partially characterized genes or ESTs, or revealed yet-unknown transcripts, providing a wealth of new candidate genes that may reveal novel aspects of terminal monocytic differentiation.
Keywords = 12213207
Keywords: other

first: Therese

last: Commes

first: Laurent

last: Manchon

first: Mireille

last: Lejeune

first: Conchita

last: Ferraz

first: Denis

last: Pugnere

first: Jacques

last: Demaille

first: Jean-Marc

last: Elalouf

last: Marti


title: Mouse Expression Database

status: Public on Sep 01 2004

city: Cincinnati

first: Bruce

last: Aronow

state: OH

institute: Cincinnati Children's Hospital Medical Center

summary:
This series of mouse expression database represents samples contributed by researchers at University of Cincinnati and Cincinnati Children's Hospital
profiles
Keywords: other

first: Joanna

last: Groden

first: Mitchell

last: Cohen

first: Michael

middle: D

last: Bates

first: Dan

last: Wiginton

first: Chris

last: Erwin

first: Kathleen

last: Anderson

first: Sandra

last: Degen

first: Susan

last: Waltz

first: Belinda

last: Peach

first: Thomas

last: Doetschman

first: Jeff

last: Molkentin

first: Jonathan

last: Katz

first: Steve

last: Potter

first: Jorge

last: Bezerra

last: Mucenski

first: James

last: Lessard

first: MaryBeth

last: Genter

first: Amy

last: Moseley

first: Jianhua

last: Zhang

last: Lehman

first: Ming

last: Xu

first: John

last: Maggio

first: Linda

last: Parysek

first: R

last: Hirsch

last: Dedman


title: Sex-dependent and growth hormone (GH)-dependent gene expression

status: Public on Mar 27 2004

city: Boston

first: David

middle: J.

last: Waxman

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

institute: Boston University

summary:
A series of dual-channel gene expression profiles obtained using MWG Rat 5K microarrays (~5535 unique rat genes) and MWG Rat Liver microarrays (~1353 unique rat genes with 999 of these genes also represented on the Rat 5K microarray)  was used to examine the sex-dependent and GH-dependent differences in gene expression in adult rat liver.  This series is comprised of 8 randomly chosen pairings of independent male and female rat liver cDNA samples and 8 randomly chosen pairings of independent male and continuous GH-treated male rat liver cDNA samples, totaling 16 samples.  Half of the samples were hybridized to the MWG Rat 5K microarrays and the other half were hybridized to the MWG Rat Liver microarrays.  Comparison of the set of sex-dependent genes with the set of GH-responsive genes shows that 90% of male-dominant genes are suppressed in male rats treated with a female pattern of GH.  Approximately 73% of female-dominant genes were up-regulated in the continuous GH-treated male rats.
Keywords = Growth hormone
Keywords = liver sexual dimorphism
Keywords = cytochrome P450
Keywords = liver gene expression
Keywords = dual channel cDNA microarray
Keywords: repeat sample

first: Amrita

last: Ahluwalia

first: Karl

middle: H

last: Clodfelter


title: S. cerevisiae mutant with a constitutively activated Ras/cAMP pathway

status: Public on Aug 19 2003

city: Manchester

first: Dawn

last: Jones

country: United Kingdom

institute: UMIST

summary:
Comparison of the transcriptomes of Saccharomyces cerevisiae wild type FY23 and a PDE2 deletion mutant DJ28.
Keywords = PDE2
Keywords = Ras/cAMP pathway
Keywords: other


title: Gene expression analysis reveals chemical-specific profiles

status: Public on Nov 20 2002

city: Thousand Oaks

first: Hisham

middle: K

last: Hamadeh

address: One Amgen Center Drive, Mailstop 5-1-A

department: Toxicology

institute: Currently at: Amgen Inc.

summary:
The application of gene expression profiling technology to examine multiple genes and signaling pathways simultaneously promises a significant advance in understanding toxic mechanisms to ultimately aid in protection of public health. Public and private efforts in the new field of toxicogenomics are focused on populating databases with gene expression profiles of compounds where toxicological and pathological endpoints are well characterized. The validity and utility of a toxicogenomics is dependent on whether gene expression profiles that correspond to different chemicals can be distinguished. The principal hypothesis underlying a toxicogenomic or pharmacogenomic strategy is that chemical-specific patterns of altered gene expression will be revealed using high-density microarray analysis of tissues from exposed organisms. Analyses of these patterns should allow classification of toxicants and provide important mechanistic insights. This report provides a verification of this hypothesis. Patterns of gene expression corresponding to liver tissue derived from chemically exposed rats revealed similarity in gene expression profiles between animals treated with different agents from a common class of compounds, peroxisome proliferators [clofibrate (ethyl-p-chlorophenoxyisobutyrate), Wyeth 14,643 ([4-chloro-6(2,3-xylidino)-2-pyrimidinylthio]acetic acid), and gemfibrozil (5-2[2,5-dimethylphenoxy]2-2-dimethylpentanoic acid)], but a very distinct gene expression profile was produced using a compound from another class, enzyme inducers (phenobarbital).
Keywords: other


title: TGF-b signaling and response

status: Public on Jan 02 2004

city: Bronx

first: Weijia

state: NY

address: 1300 Morris Park Ave

department: Medicine

institute: Albert Einstein College of Medicine

summary:
This work evaluates new and specific therapeutic targets and molecular diagnostic markers connected to the TGF-b response system in chronic fibrotic diseases.
Keywords: other


title: Gene expression profiling of Arabidopsis floral homeotic mutants

status: Public on May 02 2004

city: Pasadena

first: Frank

last: Wellmer

address: 1200 E. California Blvd.

department: Biology 156-29

institute: California Institute of Technology

summary:
The gene expression profiles of inflorescences of the floral homeotic mutants apetala1, apetala2, apetala3, pistillata, and agamous were compared to  wild-type inflorescences using a flower-specific  cDNA array (GSM21001-21015) and a "whole-genome" oligonucleotide array (Operon) (GSM21016-21035). All experiments were performed at least in triplicate.

This SuperSeries is composed of the SubSeries listed below.

first: Jose

last: Riechmann

first: Marcio

last: Alves-Ferreira

first: Elliot

last: Meyerowitz


title: Replication and Protein binding profile of chromosome VI of S.cerevisiae

status: Public on Aug 27 2003

city: Bunkyo-ku

first: Katsuhiko

last: Shirahige

state: Tokyo

address: 1-1-1 Yayoi

department: Research Center for Epigenetic Disease

country: Japan

institute: The University of Tokyo

type: Genome binding/occupancy profiling by genome tiling array

summary:
Type of experiment: ChIP-chip (Chromatin immunoprecipitation on DNA chip) analyses of replication related, checkpoint related proteins and BrdU incorporated regions at 300bp resolution. Newly developed S.cerevisiae chromosome VI tiling array produced by affymetrix was used.

Experimental factors:Distribution of various replication and checkpoint related proteins on chromosome VI during S-phase (with or w/o hydroxy urea). Distribution of BrdU incorporated regions on chromosome VI during S-phase with hydroxy urea. Wild type, tof1 deletion mutant, mrc1 deletion mutant, rad9 deletion mutant, sml1 deletion mutant, and sml1 mec1 tel1 triple deletion mutant were also investigated. The results of 74 hybridization files presented in the paper are shown.

The type of reference used for the hybridizations, if any: For the analysis of FLAG tagged protein, we usually used Cdc45-3XHA as an internal reference. For the analysis of HA tagged protein, POL1-3XFLAG was usually analyzed simultaneously as a reference.

Hybridization design: Comparison of ChIP fraction with SUP fraction for protein binding profile. For the analyses of BrdU incorporated regions, anti BrdU antibody bound fraction was compared with SUP (Sup of purified DNA from cells at G1 phase) fraction. During a course of these experiments, we found that S-phase Sup fractions were essentially the same among different genetic backgrounds and did not affect the binding profiles. Based on this observation we use standardized Sups for all experiments. No locus was scored as significantly enriched in the control ChIP experiment using HU treated untagged cells.

Quality control steps taken: Confirmation of ChIP fraction by Western blotting. Confirmation by conventional ChIP PCR methods for selected locus. Or Duplication.

The origin of the biological sample:
Budding Yeast (Saccharomyces cerevisiae)

Manipulation of biological samples and protocols used:For the preparation of HU-arrested cells, we synchronized yeast cells with alpha-factor (2mM) and then released cells into 200mM HU for 60 min. at 23°C. For the preparation of S-phase cells, cells were released into S-phase without HU and at 16°C collected at the time indicated. These cells were fixed by 1% Formaldehyde and then used for ChIP of protein of interest. For the analyses of BrdU incorporation, the same fraction of cells used for ChIP were fixed by ice cold buffer containing 0.1% Azide, and then used for detection of BrdU incorporated regions.

Protocol for preparing the hybridization extract:We disrupted 1.5X10^8 cells by MULTI-BEADS SHOCKER (MB400U, YASUI KIKAI, Osaka), which was able to keep cells precisely at lower than 6°C during disruption by glass beads. This enabled us to retrieve more than 60% of tagged proteins to soluble fraction routinely. Chromosomal DNA was shared into the average size of 400-600bp by sonication. Anti-HA monoclonal antibody HA.11 (16B12) (CRP Inc., Denver, PA) and anti-FLAG monoclonal antibody M2 (Sigma-Aldrich Co., St Louis, MO) were used for chromatin immuno-precipitation. Immunoprecipitated chromosomal DNA was subsequently purified following the protocol of Young’s lab (http://inside.wi.mit.edu/young/pub/locationanalysis.html). Purified DNA was random primed and amplified by the protocol of Brown’s lab (http://www.microarrays.org). 2ug of amplified DNA was digested with DNaseI to a mean size of 100bp and used for labeling as previously described by Winzeler et al. (Science. 281, 1194-1197, 1998).
For the analysis of BrdU incorporated regions, total DNA from 3X10^8 cells was purified by Qiagen Genomic-tip system (P/N10223, QIAGEN, Germany). DNA was sheared to 300bp by sonication, denatured, and mixed with 2ug of anti-mouse IgG1 dynabeads (P/N110.12, Dynal AS, Norway) bound anti-BrdU monoclonal antibody (2B1D5F5H4E2, MBL, Japan). Immunoprecipitation and purification of antibody bound DNA fraction was carried out following the protocol of Cimbora et al. (Mol. Cel. Biol. 20, 5581-5591, 2000). Purified DNA was random primed and amplified by the Brown’s lab protocol. 2ug of amplified DNA was digested with DNaseI to a mean size of 100bp and used for labeling.

Labeling protocol:DNA was end-labelled with Biotin-N6ddATP by Terminal Transferase as previously described by Winzeler et al. (Science. 281, 1194-1197, 1998)

The protocol and conditions used during hybridization, blocking and washing: Hybridization, blocking and washing steps were carried out as previously described by Winzeler et al. (Science. 281, 1194-1197, 1998). Each sample was hybridized to the array in 150ul containing 6XSSPE, 0.005% TritonX-100, 15ug fragmented denatured salmon sperm DNA (Gibco-BRL), and 1nmole of a 3’-biotin control oligonucleotide (oligo B2 probes) that hybridized to the border features on the array. Samples were heated to 100°C for 10 min., and then cooled on ice. Samples were hybridized for 16h at 42°C in a hybridization oven (GeneChip hybri oven 320, Affymetrix, CA). Washing and staining protocol (Mini_euk1 ver2) provided by Affymetrix was performed automatically on a fluidics station (GeneChip fluidics station 400, Affymetrix, CA).

Measurement data and specifications:Each array was scanned by HP GeneArray Scanner (Affymetrix, CA) at an emission wavelength of 560nm at 7.5uM resolution. Grids were aligned to the scanned images using the know feature of the array. Primary data analyses were carried out using the Affymetrix Microarray Suite Ver.5.0 software to obtain hybridization intensity, fold change value, change p-value, and detection p-value for each locus. For the discrimination of positive and negative signals for the binding, we compared ChIP fraction with Sup (supernatant) fraction by using three criteria as follows. First, the reliability of strength of signal was judged by detection p-value of each locus (p-value lower than 0.025 was considered as significant). Secondly, reliability of binding ratio was judged by change p-value (p-value lower than 0.025 was considered as significant). Thirdly, clusters consisted of at least three contiguous loci which filled above two criteria were selected as significantly enriched locus, because it is apparent that a single site of protein-DNA interaction will result in immuno-precipitation of DNA fragments that hybridized not only to the locus of the actual binding site but also to its neighbors. This third criterion is very unique, make the data highly reliable and can be only applicable to the chip data obtained by our high-resolution tiling array. In the case of BrdU experiment, loci c6-462 to c6-479 (Ty element) and c6-591 to c6-601 (YFR016c) were excluded from calculation, because those loci gave high background in IP fraction even without BrdU treatment. The software to present the result of discriminant analyses (makeps) is available at our web site.

Keywords = DNA replication checkpoint binding profile
Keywords: other

first: Yuki

last: Katou

first: Yutaka

last: Kanoh

first: Masashige

last: Bando

first: Hideki

last: Noguchi

first: Hirokazu

last: Tanaka

first: Toshihiko

last: Ashikari

first: Katsunori

last: Sugimoto


title: Life cycle of Drosophila melanogaster

status: Public on Jan 06 2003

city: New Haven

first: Kevin

last: White

address: 333 Cedar Street

department: Department of Genetics

institute: Yale University School of Medicine

summary:
Molecular genetic studies of Drosophila melanogaster have led to profound advances in understanding the regulation of development. Here we report gene expression patterns for nearly one-third of all Drosophila genes during a complete time course of development. Mutations that eliminate eye or germline tissue were used to further analyze tissue-specific gene expression programs. These studies define major characteristics of the transcriptional programs that underlie the life cycle, compare development in males and females, and show that large-scale gene expression data collected from whole animals can be used to identify genes expressed in particular tissues and organs or genes involved in specific biological and biochemical processes.
Keywords: other

first: M

middle: N

last: Arbeitman

first: E

last: Furlong

first: F

last: Imam

last: Johnson

first: B

last: Baker

last: Krasnow

last: Scott

first: R

middle: W

last: Davis

first: K


title: Serial analysis of gene expression in the corneal endothelium of Fuchs' dystrophy

status: Public on Jul 16 2003

city: Bethesda

first: Elliott

last: Margulies

department: Genome Technology Branch

institute: National Human Genome Research Institute

summary:
PURPOSE: To compare the gene expression profiles of normal human corneal endothelium with Fuchs' corneal endothelium, by using serial analysis of gene expression (SAGE). METHODS: Three pairs of normal human corneas were obtained from eye banks. Thirteen bisected Fuchs' corneal buttons were processed at the time of corneal transplantation. The endothelia of normal and Fuchs'-affected corneas were stripped, and total RNA was isolated. Serial analysis of gene expression (SAGE) was performed to identify and quantify gene transcripts. Genes over- and underexpressed by Fuchs' endothelium were limited to P < 0.01 by the method of Audic and Claverie. RESULTS: A total of 19,136 tags were identified with 9,530 from normal and 9,606 from Fuchs' endothelium. The expression of 18 transcripts was upregulated, and 36 transcripts were downregulated in Fuchs' endothelium compared with normal tissue. Upregulated transcripts included serum amyloid A1 and A2, metallothionein, and apolipoprotein D. Of the downregulated transcripts, 26 matched known genes, 3 matched expressed sequence tags (ESTs), and 7 were unknown to current databases. One downregulated transcript involved a newly reported bicarbonate transporter. Decreased transcripts related to antioxidants and proteins conferring protection against toxic stress were noted in Fuchs' versus normal endothelium including nuclear ferritin, glutathione S-transferase-pi, and heat shock 70-kDa protein. Nine different SAGE tags matching mitochondrial sequences accounted for 25% of the ESTs that were decreased in Fuchs' endothelium. CONCLUSIONS: SAGE analysis comparing normal to Fuchs' endothelium demonstrates diminished expression of mitochondrial, pump function, and antiapoptotic cell defense genes. A complete report of gene expression profiles of normal human corneal endothelium can be found in PMID 12583793.
Keywords: other

first: John

last: Gottsch

first: Gerami

last: Seitzman

first: Amanda

last: Bowers

first: Sean

last: Kim

first: Saurabh

last: Saha

first: Albert

last: Jun

first: Walter

last: Stark

first: Sammy

last: Liu


title: NBFGC cDNA microarray initial test

status: Public on May 21 2003

city: East Lansing

first: Steven

middle: Paul

last: Suchyta

state: MI

address: B215 Anthony Hall

department: Animal Science

institute: Michigan State University

summary:
Initial test of the NBFGC cDNA microarray.
Keywords = bovine, cDNA, microarray, false positive
Keywords: repeat sample

first: Robert

last: Tempelman

first: Paul

last: Coussens


title: total RNA from yra1-1 at 37C vs. Yra1 WT at 37C (yra1-1TS_v_Yra1WT)

status: Public on Nov 25 2002

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 of yra1-1 temperature-sensitive mutant to RNA from Yra1 wildtype strain both at the non-permissive temperature of 37C
Keywords: repeat sample

first: Pamela

last: Silver


title: zzMex67 co-IPed RNA vs. zz co-IPed RNA (zzMex67IP_v_zzIP)

summary:
Comparison of cDNA from RNA IPed with zzMex67 to that from RNA co-IPed with zz tag alone (control IP)
Keywords: repeat sample


title: zzYra1 co-IPed RNA vs. zz co-IPed RNA  (zzYra1IP_v_zzIP)

summary:
Comparison of cDNA from RNA IPed with zzYra1 to that from RNA co-IPed with zz tag alone (control IP)
Keywords: equivalent probe


title: Gene expression in germ line

status: Public on Dec 24 2003

first: Valerie

last: Reinke

address: 333 Cedar St

summary:
Identification of genes expressed in the germ line of C. elegans.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Cerebellar development

status: Public on Apr 26 2001

city: Wako-shi

first: Yoshihiro

last: Kagami

state: Saitama

address: 2-1 Hirosawa

institute: RIKEN Brain Science Institute

summary:
The Affymetrix GeneChip Mu11K was used to analyze the gene expression profile in developing mouse cerebellum (two GeneChips per E18, P7, P14, P21, and P56) to assist in the understanding of the genetic basis of cerebellar development in mice.
The analysis showed 81.6% (10,321/12,654) of the genes represented on the GeneChip were expressed in the postnatal cerebellum, and among those, 8.7% (897/10,321) were differentially expressed with more than a two-fold change in their maximum and minimum expression levels during the developmental time course.
The expression data (mean signal in relative unit) of all of these 897 differentially expressed genes were listed in GSM50(for E18), GSM51(for P7), GSM52(for P14), GSM53(for P21), and GSM54(for P56)  as well as our homepage at http://www.brain.riken.go.jp/labs/lm
Keywords = mouse cerebellum development
Keywords: time-course