title: Hematopoietic Fingerprints: an expression database of stem cells and their progeny

status: Public on Nov 21 2007

city: Houston

first: Nathan

last: Boles

state: TX

address: One Baylor Plaza, N1030

department: Pediatrics

institute: Baylor College of Medicine

summary:
Hematopoietic stem cells (HSC) continuously regenerate a complete hematologic and immune system. Very few genes that regulate this process have yet been identified. In order to identify factors governing differentiation, we have compared the transcriptome of highly purified HSC with their differentiated progeny, including erythrocytes, granulocytes, monocytes, NK cells, activated and naïve T-cells, and B-cells. Chromosomal analysis revealed that HSC were more transcriptionally active than other cell types across most chromosomes. Each lineage expressed ~100 to 400 genes uniquely, including many previously uncharacterized genes. Overexpression of two fingerprint genes resulted in a significant bias in differentiation indicating a role in cell fate determination, demonstrating the utility of these data for modulation of specific cell types.
Keywords: Hematopoietic cells, stem cells, wild type cells, Mus musculus

overall_design:
Goal - Expression profiling of hematopoietic cells

Description - Biological replicates of 10 hematopoietic cell types from female C57Bl/6 mice were purified for microarray analysis

Keywords: Hematopoietic cells, stem cells, wild type cells, Mus musculus

Experimental Factors: wild-type female C57Bl/6 CD45.1 Mus musculus

Experimental Design: 25,000- 50,000 cells were FACS sorted, mRNA was purified by RNAqueous (Ambion), DNAse treated with DNAse1, phenol:chloroform:isoamyl alcohol extracted, and amplified through two rounds of in vitro transcription using MessageAmp (Ambion).  Second round was biotinylated with bio-CTP and bio-UTP.

Microarrays: Oligonucleotide, Affymetrix, Moe430 v 2.0

QC:  Biological replicates, correlation coefficient > .95; scale factor <10; 5'/3' ratio < 20


title: IL-6 overexpression-associated gene expression in cholangiocarcinoma cells

status: Public on Jun 26 2008

city: Jacksonville

first: Tushar

last: Patel

state: FL

address: 4500 San Pablo Road

country: USA

institute: Mayo Clinic

summary: The association between chronic inflammation and the development and progression of malignancy is exemplified in the biliary tract where persistent inflammation strongly predisposes to cholangiocarcinoma. The inflammatory cytokine interleukin-6 (IL-6) enhances tumor growth in cholangiocarcinoma by altered gene expression via autocrine mechanisms. We therefore investigated the effect of chronic exposure to IL-6 on gene expression using malignant cholangiocytes stably transfected to overexpress IL-6. Comparison of gene expression identified several genes that were altered by enforced IL-6 expression.

overall_design: Mz-ChA-1 cells were stably transfected with a pTarget vector plasmid containing full length IL-6 under the control of a CMV promoter to generate Mz-IL6. Cells transfected with empty vector were used as control


title: Expression data from T-cell prolymphocytic leukemia (TPLL) and normal T cells

status: Public on Aug 27 2007

city: Essen

first: Ludger

last: Klein-Hitpass

address: Virchowstr. 173

department: Universitaetsklinikum

country: Germany

institute: Institut fuer Zellbiologie

summary:
T-cell prolymphocytic leukemina (T-PLL) is an agressive lymphoma derived from mature T-cells, which is in most cases characterized by the presence of an inv(14)(q11q32) and a characteristic pattern of secondary chromosomal abberations.
We used microarrays to compare the transcriptomes of eight immunomagnetically purified CD3+ normal donor derived peripheral blood cells with five highly purified inv(14)-positive T-PLL blood samples.
Keywords: desease state analysis

overall_design: Purified T-PLL cells and normal T-cells were analyzed on microarrays to identify differentially expressed genes. High-resolution copy number determination using SNP-chip technology and FISH in twelve inv(14)-positive T-PLL showed that differentially expressed genes clustered significantly in regions affectd by recurrent chromosomal imbalances.

first: Jan

last: Dürig

first: Stefanie

last: Bug

first: Tanja

last: Boes

first: Thomas

last: Jöns

first: Jose

middle: I

last: Martin-Dubero

first: Lana

last: Harder

first: Michael

last: Baudis

first: Ulrich

last: Dührsen

first: Reiner

last: Siebert


title: Tumor and stroma from breast by LCM

status: Public on Sep 30 2007

city: Bethesda

first: Stefan

last: Ambs

state: MD

address: 37 Convent Dr Bldg 37 Room 3050

institute: NCI

summary:
Tumor epithelium and surrounding stromal cells were isolated using laser capture microdissection of human breast cancer to examine differences in gene expression based on tissue types from inflammatory and non-inflammatory breast cancer
Keywords: LCM

overall_design: We applied LCM to obtain samples enriched in tumor epithelium and stroma from 15 IBC and 35 non-IBC cases to study the relative contribution of each component to the IBC phenotype and to patient survival.

first: Brenda

last: Boersma

first: Mark

last: Reimers


title: Response of potato and tobacco plants to photoperiod changes

status: Public on Sep 01 2007

city: Rockville

first: Jia

last: Liu

address: 9712 Medical Center Drive

institute: Plant Genomics

summary:
Plants of Solanum tuberosum ssp andigena, which tuberize only under SD conditions, were grown in growth chambers under non-inductive LD conditions and half of the plants were transferred to inductive SD conditions for 1 or 15 days, whilst the rest of the plants were kept as controls in LD. Transgenic potato plants with reduced phyB levels, which tuberize irrespective of photoperiod, were also grown in LD conditions. All the plants, irrespective of treatment, were harvested 14 hours after the beggining of the photoperiod (i.e. immediately before dusk for plants on LD, and 8 hours after dusk for the plants on SD). A similar experimental protocol was used with plants of N. tabacum cv Hicks that flower at the same time irrespective of photoperiod and the isogenic line N. tabacum cv Hicks carrying the Maryland Mammoth mutant allele, which flower only on SD (i.e. the plants were grown under LD for 55 or 41 days in LD and then transferred for 1 or 15 days to SD conditions, respectively, whilst control plants were grown 56 days in LD). Finally, Nicotiana silvestris plants that flower only on LD were grown in non-inductive SD and then half of the plants were transferred to inductive LD conditions for 1 or 15 days. In all cases we harvested only the leaves, the organ in which daylength perception takes place and photoperiodic responses are initiated. SD conditions in this experiments were 8 hours of light/ 16 hours of darkness, 160 uEinstein, 22 °C. LD conditions were 16 hours of light/ 8 hours of darkness, 80 uEinstein, 22 °C. RNA was extracted with TRIZOL.
Keywords: Direct comparison / Balanced Block Design

sample_organism:
Nicotiana sylvestris
Nicotiana tabacum
Solanum tuberosum subsp. andigenum

overall_design: 28 hybs total

first: Marcelo

last: Yanovsky


title: LSAGE Library Human Renal Glomeruli

status: Public on Jun 13 2007

city: Edmonton

first: Barbara

middle: Jutta

last: Ballermann

state: Alberta

address: HMRC 261

department: Medicine

country: Canada

institute: University of Alberta

summary:
Glomeruli were isolated from the kidney of a 72 yo male patient.  The kidney was surgically removed due to renal cell carcinoma.  The glomeruli were isolated from uninvolved renal parenchyma.  Histology (H&E) of glomeruli and interstitium was normal.
Keywords: Kidney Subcompartment

overall_design: Glomeruli were isolated using the sieving technique in ice-cold PBS, followed by isolation of total RNA with RNeasy kit.  RNA was judged intact by agarose gel electrophoresis.  SAGE library was custom-synthesized by Genzyme Corportation.

middle: J

first: Wolfgang

last: Fierlbeck

first: Jenny

last: Sorensson-Nystrom


title: Gene Expression Profiling of Hepatocellular Carcinoma

status: Public on Oct 25 2007

first: Xin

middle: Wei

last: Wang

address: 37 Convent Drive

department: Laboratory of Human Carcinogenesis

institute: National Cancer Institute

summary:
To identify the prognostic subtypes of hepatocellular carcinoma with potential progenitor cell origin.
Keywords: disease state design

overall_design: We used our in-house oligonucleotide microarray data of 238 HBV-positive HCC cases.


title: Differential expression analysis of genes relevant to the moult cycle of Portunus pelagicus

status: Public on Jan 03 2008

city: Maroochydore DC

first: Anna

middle: Viktoria

last: Kuballa

state: Queensland

address: University of the Sunshine Coast

department: Faculty of Science, Health and Education

country: Australia

institute: University of the Sunshine Coast

summary:
A holistic approach to examine differential gene expression profiles of transcripts relevant to the moulting process, across all moult cycle stages, was used in this study.  Custom cDNA microarrays were constructed for P. pelagicus.  The printed arrays contained 5000 transcripts derived from both the whole organism, and from individual organs such as the brain, eyestalk, mandibular organ and Y-organ from all moult cycle stages.  A total of 556 clones were sequenced from the cDNA libraries used to construct the arrays.  These cDNAs represented 217 singlets and 62 contigs, resulting in 279 unique putative genes. Moult cycle-related differential expression patterns were observed for many transcripts.
Keywords: cyclic moult stage comparison of the crab Portunus pelagicus

overall_design: In order to identify differential gene expression across moult stages, two consecutive moult stages were compared on each array in a dual colour (Cy3 and Cy5) experiment.  RNA samples were pooled across subjects in order to reduce the effect of biological variation (nine subjects were pooled across a total of three arrays) for each moult stage comparison.  Equal amounts of total RNA from three crabs in one moult stage, were pooled, and compared against equal amounts of total RNA pooled from three crabs in another moult stage, on one array.  This was repeated three times in total, the different moult stages were labelled with Cy3 or Cy5 respectively.  Consecutive moult stages were compared in the following format; postmoult (Cy3) with intermoult (Cy5), intermoult (Cy3) with early premoult (Cy5), early premoult (Cy3) with late premoult (Cy5), late premoult (Cy3) with ecdysis (Cy5), and ecdysis (Cy3) with postmoult (Cy5).

middle: V

first: Abigail

last: Elizur


title: Transcriptome of irradiated keratinocyte stem cells

status: Public on May 05 2007

city: Evry

first: Walid

last: Rachidi

address: 2 rue Gaston Crémieux

country: France

institute: CEA

summary:
To characterise the response of keratinocyte stem cells to ionizing radiation, gene profiling was performed using oligonucleotide microarrays (26068 probes). Cells were seeded in culture plates after cell sorting, irradiated the next day (2 Gy at 15 hours in culture), and RNA was prepared 3 hours after exposure. LOWESS normalisation was applied.
Keywords: keratinocyte stem cells, irradiation, transcriptome

overall_design: dye-swap hybridization were performed. Slides were scanned with a Genepix 4000 microarray scanner (Axon Instruments, Molecular devices, Sunnyvale, CA). For each hybridized spot, the Cy3 and Cy5 fluorescence values were obtained by using Genepix Pro 4.0 software (Axon Instruments) and were saved as a result file

first: Ghida

last: Harfouche

first: Gilles

last: Lemaitre

first: Pierre

last: Vaigot

first: Franc

last: Amiot

first: Michele

last: Martin


title: Identification of rust-induced genes in poplar using Populus PICME 28K cDNA microarrays

status: Public on Mar 15 2007

city: Champenoux

first: Sebastien

last: Duplessis

address: INRA Centre Grand Est - Nancy

department: UMR 1136 IAM

institute: INRA

summary:
Microarray expression profiling was carried out in poplar leaves upon infection with rust in order to identify genes expressed during tree defense response. For this purpose, we inoculated detached leaves of the interamerican hybrid poplar Populus trichocarpa x Populus deltoides 'Beaupré' grown in greenhouse with spores of avirulent strain 93ID6 of the pathogenic rust fungus Melampsora larici-populina (incompatible interaction, I48). Besides, we mock-inoculated 'Beaupré' leaves with water (control condition, T48). Detached leaves were maintained in vitro in controled conditions to allow fungal infection and colonization of plant tissue. Leaves were sampled 48 hours post-inoculation after that the fungus attempt to penetrate plant cells in mesophyll. Competitive hybridization between transcripts of incompatible interaction (I48) and control condition (T48) was done on Populus PICME 28K cDNA microarray.
Keywords: Time-course infection of plant tissue, defense response, cDNA microarray

platform_organism:
Populus trichocarpa x Populus deltoides
Populus euphratica
Populus tremula x Populus alba

overall_design: Three biological replicates of comparison between I48 and T48 treatments were tested, and one was discarded because of post-processing hybridization problems. Comparison between the two biological replicates served to identify consistent expression data in this experiment.

first: Sébastien

first: Cécile

last: Rinaldi

first: Annegret

last: Kohler

first: Francis

first: Pascal

last: Frey


title: Identification and characterization of the changed and stable transcripts during mouse oocyte maturation

status: Public on Sep 05 2006

city: Bar Harbor

first: You-Qiang

last: Su

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

summary:
There is massive destruction of transcripts during maturation of mouse oocytes.  The objective of this project was to identify and characterize the transcripts that are degraded versus those that are stable during the transcriptionally silent germinal vesicle (GV)-stage to metaphase II (MII)-stage transition using the microarray approach.  A system for oocyte transcript amplification using both internal and 3’-poly(A) priming was utilized to minimize the impact of complex variations in transcript polyadenylation prevalent during this transition.  Transcripts were identified and quantified using Affymetrix Mouse Genome 430 v2.0 GeneChip.  The significantly changed and stable transcripts were analyzed using Ingenuity Pathways Analysis and GenMAPP/MAPPFinder to characterize the biological themes underlying global changes in oocyte transcripts during maturation.  It was concluded that the destruction of transcripts during the GV to MII transition is a selective rather than promiscuous process in mouse oocytes.  In general, transcripts involved in processes that are associated with meiotic arrest at the GV-stage and the progression of oocyte maturation, such as oxidative phosphorylation, energy production, and protein synthesis and metabolism, were dramatically degraded.  In contrast, transcripts encoding participants in signaling pathways essential for maintaining the unique characteristics of the MII-arrested oocyte, such as those involved in protein kinase pathways, were the most prominent among those stables.
Keywords: Developmental stage (mature vs. immature) comparison

overall_design: Comparison immature GV-stage oocyte (3 biological replicates) with mature MII-stage oocytes (3 biological replicates)

first: Koji

last: Sugiura

first: Yong

last: Woo

first: Karen

last: Wigglesworth

first: Sonya

last: Kamadar

first: Jason

last: Affourtit

first: John

last: Eppig


title: MMP101

status: Public on Sep 20 2005

city: Seattle

last: Leigh

state: WA

department: Microbiology

institute: University of Washington

summary:
Methanococcus maripaludis is a methanogenic archaeon. Within its genome, there are two operons for membrane associated hydrogenases, eha and ehb. To investigate the regulation of ehb on the cell, an S40 mutant was constructed in such a way that a portion of the ehb operon was replaced by pac cassette in the wild type parental strain S2 (done by Whitman's group at the University of Georgia). Four samples of each strain were grown in batch culture. Differences in transcriptional expression between S40 and S2 were measured using cDNA arrays, with flip dye experiments for each biological replicate.
Keywords: mutant, archaea, carbon, hydrogenase, methanogen

overall_design: 16 replicates were used for the experiment. Four biological replicates of the wild type (S2) and mutant (S40) strains where compared using dye flips. Each slide contained two copies of the array yielding four technical replicates for each biological replicate.


title: MMP qualitative and quantitative mass spectrometry

first: Murray

last: Hackett

address: HSB H330 1959 NE Pacific Street

department: Chemical Engineering

summary:
Methanococcus maripaludis is a methanogenic archaeon. Within its genome, there are two operons for membrane associated hydrogenases, eha and ehb. To investigate the regulation of ehb on the cell, an S40 mutant was constructed in such a way that a portion of the ehb operon was replaced by pac cassette in the wild type parental strain S2 (done by Whitman's group at the University of Georgia). The S40 and S2 strains were grown in 14N and 15N media with acetate separately. A biological replicate was made by switching the media. Mass spectrometry based quantitative proteomics were done on the mixtures to investigate the differences in expression patterns between S40 and S2.
Keywords: isotope labeling mass spectrometry, quantitative proteomics

platform_organism:
Methanococcus maripaludis
Methanococcus maripaludis S2

overall_design:
Methanococcus maripaludis is a methanogenic archaeon.  Within its genome, there are two operons for membrane associated hydrogenases, eha and ehb. To investigate the regulation of ehb on the cell, an S40 mutant was constructed in such a way that a portion of the ehb operon was replaced by pac cassette in the wild type parental strain S2 (done by Whitman's group at the University of Georgia). Thus the S40 mutant can be selected from the S2 background by puromycin screening. The S40 and S2 strains were grown in 14N and 15N media with acetate separately. A biological replicate was made by switching the media, i.e. "flipping" the isotopes. Samples were mixed together then, after that, the mixed sample was separated to soluble part (CE part) and particulate part (PT part).
Trypsin digestion was done after treating the sample with RapiGest, DTT and iodoacetamide. Then, an YMC C18 column was used to make fractions from F1 to F5. A two dimensional capillary HPLC column was used to load the sample. The capillary column contains two parts, a strong cation exchange column (SCX) and a reverse phase part (RP), which is an Aqua C18 column. Seven different salt concentrations of ammonium acetate were used to elute the sample from SCX to the C18. Then, a gradient of acetonitrile was performed to elute the peptides from the C18 part. Electrospray ionization was done at 2.4 kv. MS1 and MS2 spectra were collected on a ThermoFinnigan LCQ. Raw files were processed by SEQUEST software and DTASelect v1.9. The Xcorr criteria used in DTASelect were 1.9 for singly charged, 2.0 for doubly charged, 3.3 for triply charged. The data were processed by SEQUEST separately using 14N and 15N amino acid modification parameters. So after DTASelect, two sets of protein identification tables were created from each dataset.
A program calculating the protein expression ratios in S40 and S2 was written by Fred Taub in the FileMaker 6.0 environment. The scheme of the program is shown in Fig.2.  First, from the DTASelect-filter.txt file, for each CID scan file, calculate the corresponding isotope ion's m/z. Then, go back to the raw file data, finding the full scan from which the CID scan came. Compare the intensity of the full scans right before and behind this full scan in the reconstructed ion current chromatogram (RIC chromatogram). Use the most intense one among the three for the calculation of protein's ratio. Then, for each peptide from the same or very close full scan, compare the calculated ratio both from 14N DTASelect-filter.txt and 15N DTASelect-filter.txt files. Assign confidence values A, B, or C to each ratio pair by the following rules: if the ratios from both DTASelect-filter.txt files are the same, assign them to confidence A level; if they are different, assign B; if one side is missing, then assign C value. Then, each protein's 14N/15N ratio was calculated as the mean value of all unique peptides identified for the protein that have the highest confidence value.
After the protein ratios were produced for each sample, CE1, CE2, PT1 and PT2, all the data were normalized and combined to make a final report of the expression pattern of S40/S2. All the ratios before assigning confidence values were used in this calculation. The detection of outliers was done in two steps. For the first stage, Dixon's Q-test was used; then, at the second stage, a MAD modified z-score test (18) with >3.5 cutoff was used. By Dixon's Q-test, 300 records were detected as outliers from 21524 records, which is 0.72%. Then, by MAD modified z-score test, 1520 records were detected as outliers from the remaining 21224 records, which is 7.2%.

first: M

first: Yi

last: Zhang

first: Tiansong

last: Wang

first: Qiangwei

last: Xia


title: Analysis of transcription in the Drosophila melanogaster testis

status: Public on Jul 16 2003

first: Brian

last: Oliver

address: 50 South Drive

department: LBG

institute: NIDDK, NIH

summary:
Identification and annotation of all the genes in the sequenced Drosophila genome is a work in progress. Wild-type testis function requires many genes and is thus of potentially high value for the identification of transcription units. We therefore undertook a survey of the repertoire of genes expressed in the Drosophila testis by computational and microarray analysis. We generated 3141 high-quality testis expressed sequence tags (ESTs). Testis ESTs computationally collapsed into 1560 cDNA set used for further analysis. Of those, 11% correspond to named genes, and 33% provide biological evidence for a predicted gene. A surprising 47% fail to align with existing ESTs and 16% with predicted genes in the current genome release. EST frequency and microarray expression profiles indicate that the testis mRNA population is highly complex and shows an extended range of transcript abundance. Furthermore, >80% of the genes expressed in the testis showed onefold overexpression relative to ovaries, or gonadectomized flies. Additionally, >3% showed more than threefold overexpression at p <0.05. Surprisingly, 22% of the genes most highly overexpressed in testis match Drosophila genomic sequence, but not predicted genes. These data strongly support the idea that sequencing additional cDNA libraries from defined tissues, such as testis, will be important tools for refined annotation of the Drosophila genome. Additionally, these data suggest that the number of genes in Drosophila will significantly exceed the conservative estimate of 13,601.
Keywords: other

first: Justen

last: Andrews

first: Gerard

middle: G

last: Bouffard

first: Chris

last: Cheadle

first: Jining

last: Lü

first: Kevin

last: Becker


title: Discovery and validation of expression data for the Genomics of Acute Myeloid Leukemia Program at Washington University

status: Public on Feb 12 2008

city: St Louis

first: Jacqueline

last: Payton

state: MO

address: 4320 Forest Park Avenue, Suite 211

institute: Washington University School of Medicine

summary:
Activating mutations in tyrosine kinase (TK) genes (e.g. FLT3 and KIT) are found in more than 30% of patients with de novo acute myeloid leukemia (AML); many groups have speculated that mutations in other TK genes may be present in the remaining 70%. We performed high-throughput re-sequencing of the kinase domains of 26 TK genes (11 receptor TK and 15 cytoplasmic TK) that are expressed in most AML patients, using genomic DNA from the bone marrow (tumor) and matched skin biopsy samples (germline) from 94 patients with de novo AML; sequence variants were validated in an additional 94 AML tumor samples (14.3 million base pairs of sequence were obtained and analyzed). We identified known somatic mutations in FLT3, KIT, and JAK2 TK genes at the expected frequencies, and found four novel somatic mutations, JAK1V623A, JAK1T478S, DDR1A803V and NTRK1S677N, once each in four respective patients out of 188 tested. We also identified novel germline sequence changes encoding amino acid substitutions (i.e. non-synonymous changes) in 14 TK genes, including TYK2, which had the largest number of non-synonymous sequence variants (11 total detected). Additional studies will be required to define the roles that these somatic and germline TK gene variants play in AML pathogenesis.

In this ongoing study, we have performed high-throughput sequencing of whole genomes, exomes, and transcriptomes, as well as SNP and expression microarrays, and methylation microarrays, using genomic DNA or RNA from the bone marrow (tumor) and matched skin biopsy samples (germline) from over 300 patients with de novo AML. These samples are also part of the Cancer Genome Atlas (TCGA) study of AML.

overall_design: 304 patient samples analysed.

first: Tim

last: Ley

first: Michael

middle: H

last: Tomasson

first: Jackie

middle: E


title: Metastatic potential of melanomas defined by specific gene expression profiles with no BRAF signature (Mannheim).

status: Public on Jun 27 2006

city: Zürich

first: Keith

middle: S

last: Hoek

address: private

country: Switzerland

institute: Currently unaffilliated

summary:
The molecular biology of metastatic potential in melanoma has been studied many times previously and changes in the expression of many genes have been linked to metastatic behaviour. What is lacking is a systematic characterization of the regulatory relationships between genes whose expression is related to metastatic potential.  Such a characterization would produce a molecular taxonomy for melanoma which could feasibly be used to identify epigenetic mechanisms behind changes in metastatic behaviour. To achieve this we carried out three separate DNA microarray analyses on a total of 86 cultures of melanoma.  Significantly, multiple testing correlation revealed that previous reports describing correlations of gene expression with activating mutations in BRAF or NRAS were incorrect and that no gene expression patterns correlate with the mutation status of these MAPK pathway components. Instead, we identified three different sample cohorts (A, B and C) and found that these cohorts represent melanoma groups of differing metastatic potential. Cohorts A and B were susceptible to TGFbeta-mediated inhibition of proliferation and had low motility.  Cohort C was resistant to TGFb and demonstrated high motility. Meta-analysis of the data against previous studies linking gene expression and phenotype confirmed that cohorts A and C represent transcription signatures of weakly and strongly metastatic melanomas, respectively. Gene expression co-regulation suggested that signalling via TGFbeta-type and Wnt pathways underwent considerable change between cohorts. These results suggest a model for the transition from weakly to strongly metastatic melanomas in which TGFbeta-type signalling upregulates genes expressing vasculogenic/extracellular matrix remodeling factors and Wnt signal inhibitors, coinciding with a downregulation of genes downstream of Wnt signalling.
Keywords: class discovery study (differential metastatic potential)

overall_design: In this data set 45 melanoma cultures were analyzed.

first: Natalie

middle: C

last: Schlegel

first: Patricia

last: Brafford

first: Antje

last: Sucker

first: Selma

last: Ugurel

first: Rajiv

last: Kumar

first: Barbara

middle: L

last: Weber

first: Katherine

last: Nathanson

first: David

last: Phillips

first: Meenhard

last: Herlyn

first: Dirk

last: Schadendorf

first: Reinhard

last: Dummer


title: UB/OC-1 differentiation

status: Public on Jul 08 2002

city: Sheffield

first: Marcelo

middle: Nicolas

last: Rivolta

state: Yorkshire

address: Western Bank

department: Biomedical Science

country: United Kingdom

institute: University of Sheffield

summary:
This study explores the profiles of genes expressed during conditional differentiation of inner ear hair cell precursors in vitro. The cell line UB/OC-1 was derived from mouse embryonic organs of Corti (Rivolta et al, Proc. R. Soc. Lond. B 265: 1595-1603, 1998) and it can be induced to differentiate upon a temperature shift. The study has been replicated in two separate populations of cells, named Exp A and Exp B. Exp A includes daily time points from 0 to 9 days, then 11 and 14 days. Exp B includes days 0, 2, 4, and 9. The manuscript associated to this work is Rivolta et al., Genome Research 12(7):1091-1099, 2002.
Keywords: time-course

middle: N

first: Antony

last: Halsall

first: Claire

middle: M

last: Johnson

middle: A

last: Tones

first: Matthew

last: Holley