title: Testes gene expression and aging

status: Public on Jan 08 2005

city: Matsumoto

first: Junjie

last: Yao

state: Nagano

address: Asahi 3-1-1

department: Aging and Adaptation

institute: Shinshu university

summary:
14 bp RsaI SAGE analysis of testes from 3 month and 29 month BDF1 mice, and 14 month SAMP1 mice.
Keywords: other

first: J

first: T

last: Chiba

last: Sakai

first: K

last: Hirose

first: M

last: Yamamoto

first: A

last: Hada

last: Kuramoto

last: Higuchi

last: Mori


title: Myelodysplastic Syndromes (MDS) and Acute Myeloid Leukaemia (AML)

status: Public on Jan 10 2005

city: Oxford

first: Andrea

last: Pellagatti

address: John Radcliffe Hospital

department: NDCLS, RDM

country: United Kingdom

institute: University of Oxford

summary:
A 10K cDNA microarray was used to compare neutrophil RNA from 21 MDS patient and 2 AML patients to pooled neutrophil RNA from 7 healthy controls.
Keywords: repeat sample

first: James

middle: S

last: Wainscoat

first: Jacqueline

last: Boultwood


title: Pre–and Post-training arrays/Insulin sensitivity response

status: Public on Feb 14 2005

city: Baton Rouge

first: Margarita

last: Teran-Garcia

state: LA

address: 6400 Perkins Rd

department: Human Genomics

country: USA

institute: Pennington Biomedical Research Center

summary:
Experiment designed to identify differences in gene expression patterns in previously sedentary individuals before an endurance exercise training program. This series compares 2 groups of individuals that display high and low insulin sensitivity (SI) response (HSIR and LSIR) after 20 weeks of exercise (a 4-fold difference in SI response).  There were no differences before training for SI, sex, age, BMI or body fat in the individuals integrating the LSIR and HSIR groups.
Keywords = skeletal muscle
Keywords = exercise-training
Keywords = insulin sensitivity
Keywords: repeat sample


title: Array-based comparative genomic hybridization for distinguishing paraffin-embedded Spitz nevi and melanomas

status: Public on Feb 09 2005

city: Stanford

last: Stanford Microarray Database

state: CA

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

summary:
Distinguishing between Spitz nevus and melanoma presents a challenging task for clinicians and pathologists. Most of these lesions are submitted entirely in formalin for histologic analysis by conventional hematoxylin and eosin-stained sections, and fresh-frozen material for ancillary studies is rarely collected. Molecular techniques, such as comparative genomic hybridization (CGH), can detect chromosomal alterations in tumor DNA that differ between these 2 lesions. This study investigated the ability of high-resolution array-based CGH to serve as a diagnostic test in distinguishing Spitz nevus and melanoma using DNA isolated from formalin-fixed and paraffin-embedded samples. Two of 3 Spitz nevi exhibited no significant chromosomal alterations, while the third showed gain of the short arm of chromosome 11p. The latter finding has previously been described as characteristic of a subset of Spitz nevi. The 2 melanomas showed multiple copy number alterations characteristic of melanoma such as 1q amplification and chromosome 9 deletion. This study has shown the utility of array-based CGH as a potential molecular test in distinguishing Spitz nevus from melanoma. The assay is capable of using archival paraffin-embedded, formalin-fixed material; is technically easier to perform as compared with conventional CGH; is more sensitive than conventional CGH in being able to detect focal alterations; and can detect copy number alterations even with relatively small amounts of lesional tissue as is typical of many skin tumors.
Series_type = clinical_history_design
A clinical history design type is where the organisms clinical history of diagnosis, treatments, e.g. vaccinations, surgery etc.
Keywords: other

middle: D

last: Harvell

first: S

last: Kohler

last: Zhu

last: Hernandez-Boussard

middle: R

last: Pollack

first: Matt

last: Van De Rijn


title: Skeletal muscle of glucocorticoid deprived and treated mice by SAGE

status: Public on Jan 06 2005

city: Quebec City

first: Andre

last: Boivin

state: Quebec

address: 2705 Boul. Laurier

department: SAGE Laboratory

country: Canada

institute: Laval University Hospital Center Research Center

summary:
Forty male C57BL6 mice 12-15 weeks old fed chow ad libitum. 30 mice underwent adrenalectomy (Adx) and 10 others a sham-Adx. Three or 24 h before tissue sampling, groups of 10 mice received an I.P. injection of cortisol (0.1 mg per mice), while the remaining Adx and intact mice received an I.P. injection of the vehicle (ethanol) 24 h prior to the sacrifice. All mice were killed within a period of a few hours. Gastrocnemius muscle were dissected and pooled together for each one of the four groups. Total RNA was isolated by Trizol.
Keywords: other

last: Calvo

first: Mayumi

last: Yoshioka

first: Jonny

last: St-Amand


title: Chlamy genome wide transcription

status: Public on Jan 17 2005

city: Moffett Field

first: Waraporn

last: Tongprasit

institute: NASA Ames Research Center

type: Expression profiling by genome tiling array

summary:
Genome-wide Transcriptional Analysis of Flagellar Regeneration in Chlamydomonas reinhardtii Identifies Orthologs of Ciliary Disease Genes
Keywords: other

first: Viktor

last: Stolc

first: Manoj

middle: P

last: Samanta

first: Wallace

middle: F

last: Marshall


title: toc132_vs_WT

status: Public on Jan 01 2005

city: Chicago

first: christos

last: Noutsos

country: Germany

institute: University of Chicago

summary:
Series of 6 repetitions of hybridization of treatment (toc132) and control (WT) each. Comparison of the Arabidopsis toc132 mutant exhibiting an impaired protein import across the outer chloroplast envelope vs WT. P.Jarvis, unpublished
Keywords: repeat sample

last: Biehl

first: E

last: Richly

first: C

last: Dietzmann

first: J

last: Kurth

first: F

last: Salamini

first: D

last: Leister


title: tic40_vs_WT

summary:
Series of 4 repetitions of hybridization of treatment (tic40) and control (WT) each. Comparison of the Arabidopsis tic40 mutant exhibiting an impaired protein import across the inner chloroplast envelope vs WT. L. Heins et al., EMBO J 21 (2002), pp. 2616-2625
Keywords: repeat sample

first: A


title: toc34_vs_WT

summary: Series of 6 repetitions of hybridization of treatment (toc34) and control (WT) each. Comparison of the Arabidopsis toc34 mutant exhibiting an impaired protein import across the outer chloroplast envelope vs WT.


title: toc120_vs_WT

summary: Series of 6 repetitions of hybridization of treatment (toc120) and control (WT) each. Comparison of the Arabidopsis toc120 mutant exhibiting an impaired protein import across the outer chloroplast envelope vs WT.


title: toc160_vs_WT

summary:
Series of 6 repetitions of hybridization of treatment (toc160) and control (WT) each. Comparison of the Arabidopsis toc160 mutant exhibiting an impaired protein import across the outer chloroplast envelope vs WT. P. Jarvis, unpublished
Keywords: repeat sample


title: L30min_vs_0h

summary:
Series of 6 repetitions of hybridization of treatment (L30min) and control (0h) each. Comparison of plants exposed to light for 30 min after a 12 h dark period versus 12 h dark adapted plants. E. Richly et al., EMBO Rep. 4 (2003), pp. 491–498
Keywords: repeat sample


title: Phytophthora sojae, races 1, 2,5 and 7 on soybean at 48h

city: London

first: Mark

last: Gijzen

state: ON

address: 1391 Sandford St

department: Agriculture & AgriFood Canada

institute: SCPFRC London

summary:
Examination of soybean hypocotyls cv Harosoy (Rps7) 48h after inoculation with P.sojae from race 1, race 2, race 5 and race 7
Keywords: other

sample_organism:
Glycine max
Phytophthora sojae

platform_organism:
Glycine max
Phytophthora sojae

first: Pat

last: Moy

first: Dinah

last: Qutob

first: B

last: Chapman

first: Ian

last: Atkinson


title: stem_vs_leaf

summary:
Series of 6 repetitions of hybridization of treatment (stem) and control (leaf) each. Comparison of stem tissue versus leaf tissue.
Keywords: repeat sample


title: tatA_vs_WT

summary:
Series of 4 repetitions of hybridization of treatment (tatA) and control (WT) each. Comparison of the Arabidopsis tata antisense line that is defective in the ion gradient dependent twin-arginine translocation (TAT) pathway for uptake from the stroma into, or passage through, the thylakoid membrane in the chloroplasts of higher plants versus WT. J. Marques, unpublished
Keywords: repeat sample


title: sut2_vs_WT

summary:
Series of 12 repetitions of hybridization of treatment (sut2) and control (WT) each. Comparison of the Arabidopsis sut2 mutant lacking plasma-membrane sucrose sensor/transporter versus WT. L. Barker et al., Plant Cell 12 (2000), pp. 1153-64
Keywords: repeat sample


title: root_vs_leaf

summary:
Series of 4 repetitions of hybridization of treatment (root) and control (leaf) each. Comparison of root tissue versus leaf tissue.
Keywords: repeat sample


title: HLrec_2h_vs_0h

summary:
Series of 6 repetitions of hybridization of treatment (HLrec_2h) and control (0h) each. Comparison of plants recovered for 2 h in normal light at 80 µE after 1 h of exposure to light stress at 1000 µE versus plants grown under normal light conditions of 80 µE. E. Richly et al., EMBO Rep. 4 (2003), pp. 491–498
Keywords: repeat sample


title: red20micE_vs_white20micE

summary:
Series of 4 repetitions of hybridization of treatment (red20micE) and control (white20micE) each. Comparison of plants grown for 48 hours at 20µE red light versus plants exposed for 48 hours at 20µE to white light. E. Lopez, unpublished
Keywords: repeat sample


title: red200micE_vs_white20micE

summary:
Series of 6 repetitions of hybridization of treatment (red200micE) and control (white20micE) each. Comparison of plants grown for 48 hours at 200µE red light versus plants exposed for 48 hours at 20µE to white light. E. Lopez, unpublished
Keywords: repeat sample


title: red200micE_vs_red20micE

summary:
Series of 4 repetitions of hybridization of treatment (red200micE) and control (red20micE) each. Comparison of plants grown for 48 hours at 200µE red light versus plants exposed for 48 hours at 20µE to red light. E. Lopez, unpublished
Keywords: repeat sample


title: psbs_vs_WT

summary:
Series of 6 repetitions of hybridization of treatment (psbs) and control (WT) each. Comparison of the Arabidopsis psbs mutant lacking Photosystem I protein PSII-S versus WT. X.P. Li et al., Proc Natl Acad Sci U S A 99 (2002), pp. 15222-15227
Keywords: repeat sample


title: psao_vs_WT

summary:
Series of 6 repetitions of hybridization of treatment (psao) and control (WT) each. Comparison of the Arabidopsis psao mutant lacking Photosystem I protein PSI-O versus WT. A. Dietzmann, D. Leister, unpublished
Keywords: repeat sample


title: psan_vs_WT

summary:
Series of 6 repetitions of hybridization of treatment (psan) and control (WT) each. Comparison of the Arabidopsis psan mutant lacking Photosystem I protein PSI-N versus WT. A. Dietzmann, D. Leister, unpublished
Keywords: repeat sample


title: psah2k_vs_WT

summary:
Series of 4 repetitions of hybridization of treatment (psah2k) and control (WT) each. Comparison of the Arabidopsis psah2k doublemutant lacking Photosystem I protein PSI-E1 and PSI-K versus WT. C. Varotto  et al, Plant Physiol. 129 (2002), pp. 616-624
Keywords: repeat sample


title: GAP_Culture_conditions

city: Lynchburg

first: Michael

last: Price

state: VA

address: 1971 University Blvd.

department: Biology & Chemistry

institute: Liberty University

summary:
Gene expression analysis of A. parasiticus grown under conditions conducive and nonconductive for aflatoxin production was evaluated using glass slide microarrays containing 765 ESTs.
Aflatoxins (AF) produced by Aspergillus flavus and A. parasiticus are responsible for approximately $270M in losses annually in the corn, peanut, cotton, and tree nut industries of the United States.  In an attempt to develop effective control procedures, research has focused on elucidating  the pathway of aflatoxin biosynthesis with the goal of identifying potential targets for intervention.  Research to date points to the involvement of complex and likely overlapping regulatory circuits.  To better understand the regulation by nutritional and environmental factors, a targeted cDNA microarray consisting of genes associated with AF production was employed to investigate the influence of nitrogen source, carbon source, temperature, and pH on AF production.  For each nutritional or environmental parameter examined, a condition conducive for aflatoxin production was compared with a condition that was non-conducive.  Three replicate cultures for each condition were grown.  Cultures were grown for 24 hours and harvested.  AF production for each culture was quantified and tissues were stored separately at -80C. For array hybridization, tissue samples for each condition were pooled and RNA extracted using Trizol reagent.
Keywords = aspergillus
Keywords = aflatoxin
Keywords = regulation
Keywords = secondary metabolism
Keywords: other

sample_organism:
Aspergillus flavus
Aspergillus parasiticus

first: Shannon

middle: B

last: Conners

first: Sabrina

last: Tachdjian

first: Robert

middle: M

last: Kelly

first: Gary

middle: A

last: Payne


title: toc75_vs_WT

first: christos

last: Noutsos

summary:
Series of 6 repetitions of hybridization of treatment (toc75) and control (WT) each. Comparison of the Arabidopsis toc75 mutant exhibiting an impaired protein import across the outer chloroplast envelope vs WT. P. Jarvis, unpublished
Keywords: repeat sample


title: psak_vs_WT

summary:
Series of 6 repetitions of hybridization of treatment (psak) and control (WT) each. Comparison of the Arabidopsis psak mutant lacking Photosystem I protein PSI-K versus WT. C. Varotto  et al, Plant Physiol. 129 (2002), pp. 616-624
Keywords: repeat sample

last: Biehl

first: E


title: psah2_vs_WT

summary:
Series of 6 repetitions of hybridization of treatment (psah2) and control (WT) each. Comparison of the Arabidopsis psah2 mutant lacking Photosystem I protein PSI-H2 versus WT. C. Varotto  et al, Plant Physiol. 129 (2002), pp. 616-624
Keywords: repeat sample

last: Richly

first: C


title: psag_vs_WT

summary:
Series of 8 repetitions of hybridization of treatment (psag) and control (WT) each. Comparison of the Arabidopsis psag mutant lacking Photosystem I protein PSI-G versus WT. C. Varotto  et al, Plant Physiol 129 (2002), pp. 616-624
Keywords: repeat sample

last: Dietzmann

first: J


title: HLrec_2d_vs_0h

summary:
Series of 6 repetitions of hybridization of treatment (HLrec_2d) and control (0h) each. Comparison of plants recovered for 48 h in normal light at 80 µE after 1 h of exposure to light stress at 1000 µE versus plants grown under normal light conditions of 80 µE. E. Richly et al., EMBO Rep. 4 (2003), pp. 491–498
Keywords: repeat sample

last: Kurth

first: F


title: psae2_vs_WT

summary:
Series of 6 repetitions of hybridization of treatment (psae2) and control (WT) each. Comparison of the Arabidopsis psae2 mutant lacking Photosystem I protein PSI-E2 versus WT. A. Ihnatowicz, D. Leister, unpublished
Keywords: repeat sample

last: Salamini

first: D


title: psae1_vs_WT

summary:
Series of 6 repetitions of hybridization of treatment (psae1) and control (WT) each. Comparison of the Arabidopsis psae1 mutant lacking Photosystem I protein PSI-E1 versus WT. C. Varotto et al., Plant J 22 (2000), pp. 115-124
Keywords: repeat sample

first: A

last: Leister


title: prors1_vs_WT

summary:
Series of 6 repetitions of hybridization of treatment (prors1) and control (WT) each. Comparison of the Arabidopsis prors1 mutant lacking prolyl tRNA synthetase versus WT. P. Pesaresi, D. Leister, unpublished
Keywords: repeat sample


title: prpl11_vs_WT

summary:
Series of 6 repetitions of hybridization of treatment (prpl11) and control (WT) each. Comparison of the Arabidopsis prpl11 mutant lacking the plastid ribosomal protein PRPL11 versus WT. P. Pesaresi et al., Plant J 27 (2001), pp. 179-189
Keywords: repeat sample


title: ppi1_vs_WT

summary:
Series of 6 repetitions of hybridization of treatment (ppi1) and control (WT) each. Comparison of the Arabidopsis ppi1 mutant defective in import of chloroplast precursor proteins versus WT. S. Kubis et al., Plant Cell 15 (2003), pp. 1859-1871
Keywords: repeat sample


title: psaf_vs_WT

summary:
Series of 6 repetitions of hybridization of treatment (psaf) and control (WT) each. Comparison of the Arabidopsis psaf antisense line lacking Photosystem I protein PSI-F versus WT. A. Haldrup et al., J Biol Chem 275 (2000), pp. 31211-31218
Keywords: repeat sample


title: pete2_vs_WT

summary:
Series of 6 repetitions of hybridization of treatment (pete2) and control (WT) each. Comparison of the Arabidopsis pete2 mutant lacking one of the two isoforms of plastocyanin versus WT. Both grown on MS media. M. Weigel et al., J. Biol. Chem. 278 (2003), pp. 31286–31289.
Keywords: repeat sample


title: HL_1h_vs_0h

summary:
Series of 6 repetitions of hybridization of treatment (HL_1h) and control (0h) each. Comparison of plants exposed to light stress at 1000 µE for 1 h versus plants grown under normal light conditions of 80 µE. E. Richly et al., EMBO Rep. 4 (2003), pp. 491–498
Keywords: repeat sample


title: pete1_vs_WT

summary:
Series of 6 repetitions of hybridization of treatment (pete1) and control (WT) each. Comparison of the Arabidopsis pete1 mutant lacking one of the two isoforms of plastocyanin versus WT. Both grown on MS media. M. Weigel et al., J. Biol. Chem. 278 (2003), pp. 31286–31289.
Keywords: repeat sample


title: ppi2_vs_WT

summary:
Series of 8 repetitions of hybridization of treatment (ppi2) and control (WT) each. Comparison of the Arabidopsis ppi2 mutant defective in import of chloroplast precursor proteins versus WT. J. Bauer et al., Nature 203 (2000), pp. 203-207
Keywords: repeat sample


title: pete1_pete2_vs_WT

summary:
Series of 6 repetitions of hybridization of treatment (pete1_pete2) and control (WT) each. Comparison of the Arabidopsis pete1 pete2 doublemutant lacking both isoforms of plastocyanin versus WT. Both grown on MS media. M. Weigel et al., J. Biol. Chem. 278 (2003), pp. 31286–31289.
Keywords: repeat sample


title: petc_vs_WT

summary:
Series of 4 repetitions of hybridization of treatment (petc) and control (WT) each. Comparison of the Arabidopsis petc mutant lacking the Rieske protein of cyt b6f complex versus WT. D. Maiwald et al., Plant Physiol 133 (2003), pp. 191-202
Keywords: repeat sample


title: pam48_vs_WT

summary:
Series of 6 repetitions of hybridization of treatment (pam48) and control (WT) each. Comparison of the Arabidopsis pam48 mutant with altered photosynthesis and defective in an unknown protein versus WT. E. Richly et al., EMBO Rep. 4 (2003), pp. 491–498
Keywords: repeat sample


title: pam46_vs_WT

summary:
Series of 6 repetitions of hybridization of treatment (pam46) and control (WT) each. Comparison of the Arabidopsis pam46 mutant with altered photosynthesis and defective in an unknown protein versus WT. E. Richly et al., EMBO Rep. 4 (2003), pp. 491–498
Keywords: repeat sample


title: pSuc_6h_vs_H2O

summary:
Series of 6 repetitions of hybridization of treatment (pSuc_6h) and control (H2O) each. Comparison of plants treated for 6 h in MS+60mMSuc versus H2O treatment. K. Deuschle, W. Frommer, unpublished
Keywords: repeat sample


title: pSuc_3h_vs_H2O

summary:
Series of 6 repetitions of hybridization of treatment (pSuc_3h) and control (H2O) each. Comparison of plants treated for 3 h in MS+60mMSuc versus H2O treatment. K. Deuschle, W. Frommer, unpublished
Keywords: repeat sample


title: pSuc_vs_H2O

summary:
Series of 14 repetitions of hybridization of treatment (pSuc) and control (H2O) each. Comparison of plants grown on MS media containing 2% Sucrose versus plants grown on untreated MS media.
Keywords: repeat sample


title: pSuc_30min_vs_H2O

summary:
Series of 6 repetitions of hybridization of treatment (pSuc_30min) and control (H2O) each. Comparison of plants treated for 30 min in MS+60mMSuc versus H2O treatment. K. Deuschle, W. Frommer, unpublished
Keywords: repeat sample


title: pStaupAsc_vs_pAsc

summary:
Series of 6 repetitions of hybridization of treatment (pStaupAsc) and control (pAsc) each. Comparison of plants treated for 4 h with 2µM Staurosporin followed by 4 h treatment with 4 h 25 mM Ascorbat (pH 5,5) versus treatment for 4 h with H2O followed by treatment of 4 h with 25 mM Ascorbat (pH 5,5). A. Kandlbinder, K.J. Dietz, unpublished
Keywords: repeat sample


title: pStaupAsc_vs_H2O

summary:
Series of 6 repetitions of hybridization of treatment (pStaupAsc) and control (H2O) each. Comparison of plants treated for 4 h with 2µM Staurosporin followed by 4 h treatment with 4 h 25 mM Ascorbat (pH 5,5) versus 8 h treatment with H20. A. Kandlbinder, K.J. Dietz, unpublished
Keywords: repeat sample


title: pPro_6h_vs_H2O

summary:
Series of 6 repetitions of hybridization of treatment (pPro_6h) and control (H2O) each. Comparison of plants treated for 6 h with 100 mM proline to toxic levels of cellular proline versus H2O treatment.
Keywords: repeat sample


title: 3weeks_vs_4weeks

summary:
Series of 4 repetitions of hybridization of treatment (3weeks) and control (4weeks) each. Comparison of 3 weeks old plants versus 4 weeks old plants.
Keywords: repeat sample


title: prors2_vs_WT

summary:
Series of 6 repetitions of hybridization of treatment (prors2) and control (WT) each. Comparison of the Arabidopsis prors2 mutant lacking prolyl tRNA synthetase versus WT.  P. Pesaresi, D. Leister, unpublished
Keywords: repeat sample


title: pStau_vs_H2O

summary:
Series of 6 repetitions of hybridization of treatment (pStau) and control (H2O) each. Comparison of plants treated for 4 h with H2O followed by 4 h treatment with 25 mM Staurosporin (pH 5,5) versus 8 h treatment with H20. A. Kandlbinder, K.J. Dietz, unpublished
Keywords: repeat sample


title: pPro_3h_vs_H2O

summary:
Series of 6 repetitions of hybridization of treatment (pPro_3h) and control (H2O) each. Comparison of plants treated for 3 h with 100 mM proline to toxic levels of cellular proline versus H2O treatment.
Keywords: repeat sample


title: pPro_30min_vs_H2O

summary:
Series of 6 repetitions of hybridization of treatment (pPro_30min) and control (H2O) each. Comparison of plants treated for 30 min with 100 mM proline to toxic levels of cellular proline versus H2O treatment.
Keywords: repeat sample


title: pPro_2d_vs_H2O

summary:
Series of 6 repetitions of hybridization of treatment (pPro_2d) and control (H2O) each. Comparison of plants treated for 48 h with 100mM proline to toxic levels of cellular proline versus no treatment. K. Deuschle, W. Frommer, unpublished
Keywords: repeat sample


title: pPar_vs_H2O

summary:
Series of 6 repetitions of hybridization of treatment (pPar) and control (H2O) each. Comparison of plants treated with benzoquinone herbicide paraquat 30' after reexposure to light (after one 12h dark period) versus 30' after reexposure to light and treatment with H20 as control. E. Richly et al., EMBO Rep. 4 (2003), pp. 491–498
Keywords: repeat sample


title: pmildew_vs_no_mildew

summary:
Series of 6 repetitions of hybridization of treatment (pmildew) and control (no_mildew) each. Comparison of plants 2 days after mildew infection versus no infection.
Keywords: repeat sample


title: pParL_vs_pParD

summary:
Series of 6 repetitions of hybridization of treatment (pParL) and control (pParD) each. Comparison of plants treated with benzoquinone herbicide paraquat 30' after reexposure to light (after one 12h dark period) versus treatment with paraquat and incubation for 12h in darkness. E. Richly et al., EMBO Rep. 4 (2003), pp. 491–498
Keywords: repeat sample


title: pCO2_6d_vs_0d

summary:
Series of 6 repetitions of hybridization of treatment (pCO2_6d) and control (0d) each. Comparison of plants  grown for 6 d at high-CO2 levels of (1 % (v/v) CO2) versus normal CO2 levels. E. Richly et al., EMBO Rep. 4 (2003), pp. 491–498
Keywords: repeat sample


title: pFe_vs_H2O

summary:
Series of 6 repetitions of hybridization of treatment (pFe) and control (H2O) each. Comparison of plants grown under oxidative stress due to high-iron concentrations versus no treatment. C. Varotto, unpublished
Keywords: repeat sample


title: pCO2_1d_vs_0d

summary:
Series of 4 repetitions of hybridization of treatment (pCO2_1d) and control (0d) each. Comparison of plants  grown for 1 d at high-CO2 levels of (1 % (v/v) CO2) versus normal CO2 levels. E. Richly et al., EMBO Rep. 4 (2003), pp. 491–498
Keywords: repeat sample


title: pBro_vs_H2O

summary:
Series of 6 repetitions of hybridization of treatment (pBro) and control (H2O) each. Comparison of plants treated with nitrile herbicide bromoxynil 30' after reexposure to light (after one 12h dark period) versus 30' after reexposure to light and treatment with H20 as control. E. Richly et al., EMBO Rep. 4 (2003), pp. 491–498
Keywords: repeat sample


title: pCO2_10d_vs_0d

summary:
Series of 4 repetitions of hybridization of treatment (pCO2_10d) and control (0d) each. Comparison of plants  grown for 10 d at high-CO2 (1 % (v/v) CO2) versus normal CO2 levels.  E. Richly et al., EMBO Rep. 4 (2003), pp. 491–498
Keywords: repeat sample


title: 2weeks_vs_4weeks

summary:
Series of 6 repetitions of hybridization of treatment (2weeks) and control (4weeks) each. Comparison of 2 weeks old plants versus 4 weeks old plants.
Keywords: repeat sample


title: pAsc_vs_H2O

summary:
Series of 6 repetitions of hybridization of treatment (pAsc) and control (H2O) each. Comparison of plants treated with 4 h with H2O followed by treatment of 4 h with 25 mM Ascorbat (pH 5,5) versus 8 h treatment with H20. A. Kandlbinder, K.J. Dietz, unpublished
Keywords: repeat sample


title: pBroL_vs_pBroD

summary:
Series of 6 repetitions of hybridization of treatment (pBroL) and control (pBroD) each. Comparison of plants treated with nitrile herbicide bromoxynil 30' after reexposure to light (after one 12h dark period) versus treatment with bromoxynil and incubation for 12h in darkness. E. Richly et al., EMBO Rep. 4 (2003), pp. 491–498
Keywords: repeat sample


title: mak3_vs_WT

summary:
Series of 6 repetitions of hybridization of treatment (mak3) and control (WT) each. Comparison of Arabidopsis mak3 mutant defective in cytoplasmic N-acetyltransferase versus WT. P. Pesaresi et al., Plant Cell 15 (2003), pp. 1817-1832
Keywords: repeat sample


title: pStaupAsc_vs_pStau

summary:
Series of 6 repetitions of hybridization of treatment (pStaupAsc) and control (pStau) each. Comparison of plants treated for 4 h with 2µM Staurosporin followed by 4 h treatment with 4 h 25 mM Ascorbat (pH 5,5) versus treatment for 4 h with H2O followed by 4 h treatment with 25 mM Staurosporin (pH 5,5). A. Kandlbinder, K.J. Dietz, unpublished
Keywords: repeat sample


title: laf6_D_vs_WT_D

summary:
Series of 6 repetitions of hybridization of treatment (laf6_D) and control (WT_D) each. Comparison of Arabidopsis laf6 mutant lacking the atABC1-transporter versus WT, both dark adapted. S.G. Moeller et al., Genes Dev 15 (2001), pp. 90-103
Keywords: repeat sample


title: kn09pPro_2d_vs_WT

summary:
Series of 6 repetitions of hybridization of treatment (kn09pPro_2d) and control (WT) each. Comparison of the proline-hypersensitive Arabidopsis kn09 mutant blocked in mitochondrial proline catabolism and treated with proline (roots treated with MS+100mM proline for 48 h) versus WT (roots treated with MS+100mM Glc for 48 h). K. Deuschle et al., Plant J 27 (2001), pp. 345-356
Keywords: repeat sample


title: kn09_vs_WT

summary:
Series of 6 repetitions of hybridization of treatment (kn09) and control (WT) each. Comparison of the proline-hypersensitive Arabidopsis kn09 mutant blocked in mitochondrial proline catabolism (roots treated with MS+100mM Glc for 48 h) versus WT (roots treated with MS+100mM Glc for 48 h). K. Deuschle et al., Plant J 27 (2001), pp. 345-356
Keywords: repeat sample


title: hcf145_vs_WT

summary:
Series of 10 repetitions of hybridization of treatment (hcf145) and control (WT) each. Comparison of Arabidopsis hcf145 mutant defective in the assembly of photosystem I versus WT. L. Lezhneva et al., Plant J 37 (2004), pp. 174-185
Keywords: repeat sample


title: 2h_rec_vs_LA

summary:
Series of 6 repetitions of hybridization of treatment (2h_rec) and control (LA) each. Comparison of plants recovered for 2 h in light after 1 h of darkness versus light adapted plants.
Keywords: repeat sample


title: gun5_vs_WT

summary:
Series of 8 repetitions of hybridization of treatment (gun5) and control (WT) each. Comparison of Arabidopsis gun5 mutant lacking a ChlH subunit of Mg-chelatase versus WT. R.E. Susek et al., Cell 74 (1993), pp. 787-799; N. Mochizuki et al., Proc Natl Acad Sci U S A 98 (2001), pp. 2053-2058
Keywords: repeat sample


title: gun1_vs_WT

summary:
Series of 8 repetitions of hybridization of treatment (gun1) and control (WT) each. Comparison of Arabidopsis gun1-1 mutant defective in plastid signaling (protein unknown) versus WT. R.E. Susek et al., Cell 74 (1993), pp. 787-799
Keywords: repeat sample


title: fluL_vs_WT

summary:
Series of 6 repetitions of hybridization of treatment (fluL) and control (WT) each. Comparison of Arabidopsis flu mutant lacking FLU, a regulator of chlorophyll biosynthesis versus WT. Both harvested 30' after reexposure to light after 12h dark period. R. Meskauskiene et al., Proc Natl Acad Sci U S A 98 (2001), pp. 12826-12831
Keywords: repeat sample


title: cue1_vs_WT

summary:
Series of 6 repetitions of hybridization of treatment (cue1) and control (WT) each. Comparison of Arabidopsis cue1-1 mutant lacking phosphoenol pyruvate translocator versus WT. S.J. Streatfield et al., Plant Cell 11 (1999), pp.1609-1622
Keywords: repeat sample


title: blue20micE_vs_white20micE

summary:
Series of 8 repetitions of hybridization of treatment (blue20micE) and control (white20micE) each. Comparison of plants  grown for 48 hours at 20µE blue light versus plants exposed for 48 hours at 20µE to white light. E. Lopez, unpublished
Keywords: repeat sample


title: blue200micE_vs_white20micE

summary:
Series of 6 repetitions of hybridization of treatment (blue200micE) and control (white20micE) each. Comparison of plants  grown for 48 hours at 200µE blue light versus plants exposed for 48 hours at 20µE to white light. E. Lopez, unpublished
Keywords: repeat sample


title: mCO2_4d_vs_0d

summary:
Series of 10 repetitions of hybridization of treatment (mCO2_4d) and control (0d) each. Comparison of plants grown for 96 h at low-CO2 (0.003 % (v/v) CO2) versus plants grown at normal CO2 level. E. Richly et al., EMBO Rep. 4 (2003), pp. 491–498
Keywords: repeat sample


title: atpd_vs_WT

summary:
Series of 4 repetitions of hybridization of treatment (atpd) and control (WT) each. Comparison of Arabidopsis atpd mutant lacking ATP synthase delta subunit versus WT. D. Maiwald et al., Plant Physiol 133 (2003), pp. 191-202
Keywords: repeat sample


title: pCK_vs_H2O

summary:
Series of 6 repetitions of hybridization of treatment (pCK) and control (H2O) each. Comparison of cytokinin-treated (2 h) cell culture versus untreated cell culture. T. Schmüllig, unpublished
Keywords: repeat sample


title: blue200micE_vs_blue20micE

summary:
Series of 6 repetitions of hybridization of treatment (blue200micE) and control (blue20micE) each. Comparison of plants  grown for 48 hours at 200µE blue light versus plants exposed for 48 hours at 20µE to blue light. E. Lopez, unpublished
Keywords: repeat sample


title: mCO2_2d_vs_0d

summary:
Series of 6 repetitions of hybridization of treatment (mCO2_2d) and control (0d) each. Comparison of plants grown for 48 h at low-CO2 (0.003 % (v/v) CO2) versus plants grown at normal CO2 level. E. Richly et al., EMBO Rep. 4 (2003), pp. 491–498
Keywords: repeat sample


title: atc6_vs_WT

summary:
Series of 6 repetitions of hybridization of treatment (atc6) and control (WT) each. Comparison of the Arabidopsis atc6 mutant lacking cytochrom c6 protein versus WT. M. Weigel et al., Trends Plant Sci 8 (2003), pp. 513-517
Keywords: repeat sample


title: aap6_vs_WT

summary:
Series of 6 repetitions of hybridization of treatment (aap6) and control (WT) each. Comparison of the Arabidopsis aap6 mutant lacking the amino acid transporter protein AAP6 of xylem parenchyma versus WT. W.N. Fischer et al., Plant J. 29 (2002), pp. 717-731
Keywords: repeat sample


title: laf6_L_1h_vs_WT_D

summary:
Series of 6 repetitions of hybridization of treatment (laf6_L_1h) and control (WT_D) each. Comparison of Arabidopsis laf6 mutant lacking the atABC1-transporter versus WT. laf6 exposed to normal light for 1 h after dark adaptation, WT dark adapted. S.G. Moeller et al., Genes Dev 15 (2001), pp. 90-103
Keywords: repeat sample


title: mec_wou_vs_no_wou

summary:
Series of 6 repetitions of hybridization of treatment (mec_wou) and control (no_wou) each. Comparison of plants 2 days after mechanical wounding versus untreated plants.
Keywords: repeat sample


title: aap3_vs_WT

summary:
Series of 6 repetitions of hybridization of treatment (aap3) and control (WT) each. Comparison of the Arabidopsis aap3 mutant lacking the amino acid transporter protein AAP3 of roots versus WT. W.N. Fischer et al., Plant J. 29 (2002), pp. 717-731
Keywords: repeat sample


title: 1week_vs_4weeks

summary:
Series of 4 repetitions of hybridization of treatment (1week) and control (4weeks) each. Comparison of 1 week old plants versus 4 weeks old plants.
Keywords: repeat sample


title: pete2_soil_vs_WT

summary:
Series of 6 repetitions of hybridization of treatment (pete2_soil) and control (WT) each. Comparison of the Arabidopsis pete2 mutant grown on soil and lacking one of the two plastocyanin protein isoforms versus WT. M. Weigel et al., J. Biol. Chem. 278 (2003), pp. 31286–31289.
Keywords: repeat sample


title: atpc_vs_WT

summary:
Series of 10 repetitions of hybridization of treatment (atpc) and control (WT) each. Comparison of Arabidopsis atpc1-1 mutant lacking ATP synthase gamma subunit versus WT. C.D. Bosco et al., J Biol Chem 279 (2004), pp. 1060-1069
Keywords: repeat sample


title: pete1_soil_vs_WT

summary:
Series of 8 repetitions of hybridization of treatment (pete1_soil) and control (WT) each. Comparison of the Arabidopsis pete1 mutant grown on soil and lacking one of the two plastocyanin protein isoforms versus WT. M. Weigel et al., J. Biol. Chem. 278 (2003), pp. 31286–31289.
Keywords: repeat sample


title: PSII_vs_PSI

summary:
Series of 6 repetitions of hybridization of treatment (PSII) and control (PSI) each. Comparison of plants grown under PSII-specific light versus plants grown under PSI-specific light. E. Richly et al., EMBO Rep. 4 (2003), pp. 491–498
Keywords: repeat sample


title: fluD_vs_WT

summary:
Series of 6 repetitions of hybridization of treatment (fluD) and control (WT) each. Comparison of Arabidopsis flu mutant lacking FLU, a regulator of chlorophyll biosynthesis, versus WT. Both harvested after a period of 12 h darkness. R. Meskauskiene et al., Proc Natl Acad Sci U S A 98 (2001), pp. 12826-12831
Keywords: repeat sample


title: PSII_DCMU_vs_PSI

summary:
Series of 6 repetitions of hybridization of treatment (PSII_DCMU) and control (PSI) each. Comparison of plants grown under PSII-specific light and treated with the electron transport inhibitor DCMU versus plants grown under PSI-specific light without DCMU treatment. T. Pfannschmidt, unpublished
Keywords: repeat sample


title: PSII_DCMU_vs_PSII

summary:
Series of 6 repetitions of hybridization of treatment (PSII_DCMU) and control (PSII) each. Comparison of plants grown under PSII-specific light and treated with the electron transport inhibitor DCMU versus plants grown under PSII-specific light without DCMU treatment. T. Pfannschmidt, unpublished
Keywords: repeat sample


title: ML4c_rec_24h_vs_ML_4C

summary:
Series of 6 repetitions of hybridization of treatment (ML4c_rec_24h) and control (ML_4C) each. Comparison of plants recovered for 24 h in medium light at 20 °C after a period of 24 h of exposure to photoinhibitory conditions in medium light at 4 °C  versus plants exposed to photoinhibitory conditions of medium light at 4 °C for 24 h. A. Haldrup, unpublished
Keywords: repeat sample


title: ML4c_rec_24h_vs_ML_20C

summary:
Series of 6 repetitions of hybridization of treatment (ML4c_rec_24h) and control (ML_20C) each. Comparison of plants recovered for 24 h in medium light at 20 °C after a period of 24 h of exposure to photoinhibitory conditions in medium light at 4 °C  versus plants grown under medium light at 20 °C. A. Haldrup, unpublished
Keywords: repeat sample


title: ML_4C_vs_ML_20C

summary:
Series of 6 repetitions of hybridization of treatment (ML_4C) and control (ML_20C) each. Comparison of plants exposed to photoinhibitory conditions of medium light at 4 °C for 24 h versus plants grown under medium light at 20 °C. A. Haldrup, unpublished
Keywords: repeat sample


title: L_1h_vs_D

summary:
Series of 6 repetitions of hybridization of treatment (L_1h) and control (D) each. Comparison of plants exposed to light for 1 h after a over night dark period versus over night dark adapted plants.
Keywords: repeat sample


title: Chlamydomonas nonphotosynthetic mutants

status: Public on Dec 31 2004

city: Kenosha

first: David

middle: C

last: Higgs

state: WI

address: 900 Wood Rd.

department: Biological Sciences

institute: University of Wisconsin-Parkside

summary:
Microarray analysis of two nonphotosynthetic nuclear mutants (mcd1-1, mcd1-2) that affect chloroplast RNA stability to identify affected organellar genes (chloroplast and mitochondrial). Further, the photosynthetic suppressor (mcd2-1) that suppresses mcd1-2 was included to determine which genes respond directly to the RNA stabilty phenotype and which respond to the nonphotosynthetic phenotype.
Keywords: repeat sample

first: Brian

last: Erickson

last: Stern


title: Screening for candidate clock-controlled genes

status: Public on Dec 29 2004

city: Nagoya

first: Masahiro

last: Ishiura

state: Aichi

address: Furo-cho, Chikusa-ku

department: Gene Center

country: Japan

institute: Nagoya University

summary:
Microarrays were hybridized with a mixture of solutions containing LL2 cDNA labeled with Cy3 or Cy5 (dye-swap) and LL14 cDNA labeled with Cy5 or Cy3 (dye-swap).
Keywords: repeat sample

first: Ken-ichi

last: Kucho

first: Yuka

last: Tsuchiya

first: Yasuhide

last: Okumoto

first: Manabu

last: Harada

first: Masao

last: Yamada


title: effect of neuregulin on cardiocytes

city: Berne 9

first: Martin

last: Flück

state: Bern

address: Bühlstrase 26

department: Department of Anatomy

country: Switzerland

institute: University of Berne

summary:
Parallel treatment of adult rat primary cultured cardiocytes with neuregulin 1 beta or media only for 24 hours
Keywords: parallel sample

first: Marie-Noëlle

last: Giraud

first: Christian

last: Zuppinger

first: Thomas

last: Suter


title: toc90_vs_WT

first: christos

last: Noutsos

summary: Series of 6 repetitions of hybridization of treatment (toc90) and control (WT) each. Comparison of the Arabidopsis toc90 mutant exhibiting an impaired protein import across the outer chloroplast envelope vs WT.

last: Biehl

first: E

last: Richly

first: C

last: Dietzmann


title: Electrical pacing of mouse muscle

status: Public on Dec 24 2004

city: Copenhagen

first: Peter

last: Schjerling

address: Bispebjerg Bakke 23, M81

department: Institute of Sports Medicine Copenhagen, ISMC

country: Denmark

institute: Bispebjerg Hospital

summary:
Mice were electrically stimulated by implanting a pacer. The hindlimb muscles received low frequency stimulation for three hours and the tibialis anterior muscle was harvested at different time points after the stimulation. Sham operated control mice were included in the experiment.
mRNA was pooled from 6 mice at each time point and hybridized to the arrays together with mRNA from untreated mice (reference).
Keywords: time-course

first: Kristian

last: Vissing

first: Paul

last: Rosenberg

first: Kelly

last: Hutcheson


status: Public on Dec 22 2004

city: Bunkyo-ku

first: Katsuhiko

last: Shirahige

state: Tokyo

address: 1-1-1 Yayoi

department: Research Center for Epigenetic Disease

institute: The University of Tokyo

summary:
This series is a supplementary data set for the manuscript titled "Postreplicative recruitment of Cohesin to double-strand breaks is required for DNA repair"
All data shown in the paper plus duplicate experiments were registered (15 ChIP-chip data).

Experimental design:

1. Type of experiment:
ChIP (Chromatin immunoprecipitation) analysis hybridized to high density oligonucleotide arrays. The S. cerevisiae chromosome VI array described by Katou et al. (2003) Nature 424, 1078-83 and the newly developed S. cerevisiae chromosomes III-VIa have been used.

2. Experimental factors:
Distribution of the sister chromatid cohesion protein Scc1, before and after induction of a DNA double strand break (dsb) on chromosome III, V and VI in G2/metaphase cells were analysed (Benomyl arrested cells).

3. Number of hybridizations performed:
ChIP analysis: 15

4. Hybridisation design:
ChIP analysis: comparison of ChIP fraction with SUP (supernatant) fraction

5. Quality control:
Duplication of experiments, confirmation of recruitment of  the analysed protein to a dsb by induction of breaks at three different positions in the genome. Mock hybridisation of samples immunoprecipitated from cells containing no tag recognized by antibody used. Checking of the ChIP fraction by Western blotting.

6. URL of supplemental website:
GEO Accession number: GSE1905
Web site: http://chromosomedynamics.bio.titech.ac.jp

Samples used, extract preparation and labeling:

1. Origin of the biological sample
Budding yeast (Saccharomyces cerevisiae).

2. Manipulation of the samples and the protocols used:
Mitotic budding yeast cells were synchronised in G2/M with Benomyl (80 ug/ml) Cells were fixed 30 minutes at room temperature plus over night in 1% formaldehyde at 4C.

3. Protocols for preparing extracts:
ChIP analysis: Extract preparation was processed following the Shirahige lab protocol (http://chromosomedynamics.bio.titech.ac.jp ). 5x10^8 cells were disrupted using Multi-Beads Shocker (MB400U, YASUI KIKAI, Osaka).
Whole cell extract was sonicated to obtain 400-600 bp genomic DNA fragments. Anti-Flag monoclonal antibody M2 (Sigma-Aldrich Co., St Louis, MO) coupled to Dynabeads (Dynal, protein A Dynabeads) were used for chromatin immunoprecipitation. The immunprecipates were eluted and incubated over night at 65¨¬C to reverse the cross-link. Immunoprecipitated genomic DNA was incubated with proteinase K, extracted 2 times with phenol/chloroform/isoamylalcohol, precipitated, resuspended in TE and incubated with RnaseA. The DNA was then purified using the Qiagen PCR purification kit, and concentrated by ethanol precipitation. The DNA was amplified by PCR after random priming. 10 ug of amplified DNA was digested with Dnase I to a mean size of 100 bp. After Dnase I inactivation at 95¨¬C, fragments were labelled as detailed below.

4. Labeling protocol
DNA fragments were end-labeled by addition of 25 U of Terminal Transferase and 1 nmol Biotin-N6ddATP (NEN) for 1 hour at 37C as previously described by Winzeler et al. (Science. 281, 1194-1197, 1998). The entire sample was used for hybridization.

5. Hybridization procedures and parameters:
Hybridization, blocking and washing were carried out as previously described (http://chromosomedynamics.bio.titech.ac.jp). Each sample was hybridized to the array in 150 ul containing 6xSSPE; 0.005% TritonX-100; 15 ug fragmented denatured salmon sperm DNA (Gibco-BRL); 1 nmole 3’biotin labelled control oligonucleotide (oligo B2, Affymetrix). Samples were denatured at 100C for 10 minutes, and then put on ice before being hybridized for 16 hours at 42C in an hybridization oven (GeneChip Hybri.
Oven 320, Affymetrix). Washing and scanning protocol (FlexMidi-euk2v3-450) provided by Affymetrix was performed automatically on a fluidics station (GeneChip fluidics station 400, Affymetrix).

6. Measurement data and specifications:
S. cerevisiae arrays were scanned using the HP GeneArray Scanner
(Affymetrix) at an emission wavelength of 560 nm, resolution 7.5 uM. Grids were aligned to scans following the library array description. Primary data analyses were carried out using Affymetrix Microarray Suite Ver.5.0 software to obtain signal intensity, fold change value, change p-value and detection p-value.
The detailed information of this analysis is available at http://www.affymetrix.com/support/technical/whitepapers/sadd_whitepaper.pdf
and
http://www.affymetrix.com/support/technical/technotes/statistical_reference_
guide.pdf
To discriminate significant signals for binding to DNA (dark grey signals), signals from the ChIP fraction scan were compared to the SUP (supernatant) fraction scan using the 3 following criteria: first, the signal reliability was judged by the detection p-value of each locus (p-value <=0.025); secondly, reliability of binding ratio was judged by change p-value (p- value <=0.025); thirdly, only clusters of at least 3 contiguous loci responding to the 2 previous criteria were selected as significantly enriched locus. The light grey signals represent the statistically not significantly enriched signals. The software to present the result
(chr6viewer) is available at http://everythingchromovi.gsc.riken.go.jp. The raw and transformed data files are available at GEO database website and at our web site http://chromosomedynamics.bio.titech.ac.jp.

6. Array Design
1. General array design: in situ synthesized arrays by Affymetrix
2. Availability of arrays: commercially available from Affymetrix
3. Location and ID of each spot on arrays: available at our web site
(http://chromosomedynamics.bio.titech.ac.jp) and from Affymetrix on request
4. Probe type: oligonucleotide
5. The arrays used in this study can be purchased from Affymetrix:
Chromosome VI S.cerevisiae: rikDACF, P/N# 510636
Chromosome III,IV,V,VIa S.cerevisiae: SC3456a520015F, P/N# 520015
Keywords: other

first: Lena

last: Strom

first: Camilla

last: Sjogren


title: tpt1_vs_WT

summary:
Series of 6 repetitions of hybridization of treatment (tpt1) and control (WT) each. Comparison of the Arabidopsis tpt1 mutant exhibiting a reduction of triose phosphate (TP)-specific transport activities in chloroplasts to below 5%. A. Schneider et al., Plant J 32 (2002), pp. 685-699
Keywords: repeat sample

first: A

first: J

last: Kurth

first: F

last: Salamini

first: D

last: Leister


title: Conditioned Taste Aversion experiment

city: San Juan

first: Humberto

last: Ortiz-Zuazaga

state: PR

address: PO BOX 23334

department: High Performance Computing facility

institute: University of Puerto Rico

summary:
Conditioned Taste Aversion experiment
Keywords: other

first: Ricardo

last: Chiesa

middle: G

first: Sohaira

last: Morales

first: Javier

last: Pérez

first: Julio

last: García

first: Sandra

last: Peña de Ortiz


title: PSI_DCMU_vs_PSI

first: christos

last: Noutsos

summary:
Series of 6 repetitions of hybridization of treatment (PSI_DCMU) and control (PSI) each. Comparison of plants grown under PSI-specific light and treated with the electron transport inhibitor DCMU versus plants grown under PSI-specific light without DCMU treatment. T. Pfannschmidt, unpublished
Keywords: repeat sample

last: Biehl

first: E

last: Richly

first: C

last: Dietzmann


title: Time-course of mdx and wild type mice

status: Public on Dec 20 2004

city: Leiden

first: Rolf

last: Turk

address: Wassenaarseweg 72

department: Center for Human and Clinical Genetics

country: Netherlands

institute: Leiden University Medical Center

summary:
Time-course microarray data set of mdx and wild type mice ranging from 1-20 weeks of age
Keywords: time-course


title: Comparative transcriptome analysis of early interaction events in Scots pine root tissues following challenge (1dpi)

status: Public on Dec 21 2004

city: Raleigh

first: Debbie

middle: Ross

last: Craig

state: NC

address: 840 Main Campus Drive

department: Forestry

institute: North Carolina State University

summary:
Comparative transcriptome analysis of early interaction events in Scots pine root tissues following challenge with a pathogenic, saprophytic or symbiotic fungus. Seedlings of P. sylvestris (19 days post germination) were transferred to wet, sterile filter paper on Petri-plates. Thereafter, the roots of the seedlings were inoculated with the mycelial homogenate of either Heterobasidion annosum (FP5, P-type) a pathogenic root rot fungus which attacks Norway spruce, Scots pine and broad leaf trees or Laccaria bicolor, an obligate ectomycorrhizal symbiont or  Trichoderma aureoviride- an obligate saprotroph. Thereafter, incubated for 30 minutes, during which time some hyphae adhered to the roots. The inoculated seedlings (ten) were then transferred to another wet sterile filter paper placed on 1% water agar in Petri dishes. A second set of moist sterile filter paper was laid over the roots. The region of the Petri-dish containing the roots was covered with aluminium foil and the edges of the plate sealed with parafilm. The seedlings were then incubated for 24 hr  under a photoperiod of 16h light at 20 ºC. Control seedlings were ‘inoculated’ with sterile distilled water.
Keywords: other

last: Asiegbu

last: Olson

first: G

last: Li

last: Adomas

first: T

last: Chu

last: Heller

first: M

last: Karlsson

last: Nahalkova

first: L

last: van Zyl

first: R

last: Wolfinger

last: Sederoff

last: Dean

last: Finlay

last: Stenlid


title: Quantitative microarray profiling of alternative splicing in mouse tissues

city: Toronto

first: Qun

last: Pan

address: 160 College St.

institute: University of Toronto

summary:
We describe the application of a new microarray platform, which combines information from exon body and splice-junction probes, to analyze the regulation of 3126 alternative splicing events in ten mouse tissues. The details of the methods and algorithms are described in this paper: Revealing global regulatory features of mammalian alternative splicing using a quantitative microarray platform (Molecular Cell, Dec., 2004)
Keywords = A new quantitative alternative splicing microarray platform
Keywords: other

first: Ofer

last: Shai

first: Christine

last: Misquitta

first: Wen

last: Zhang

first: Arneet

middle: L

last: Saltzman

first: Naveed

last: Mohammad

first: Tomas

last: Babak

first: Henry

last: Siu

first: Timothy

last: Hughes

first: Quaid

last: Morris

first: Brendan

middle: J

last: Frey

first: Benjamin

last: Blencowe


title: Genes regulated by FGF2 in mouse cortical neuron culture

status: Public on Dec 15 2004

city: Glasgow

first: Tomoko

last: Iwata

address: Beatson Laboratories, Garscube Estate, Switchback Road, Bearsden

department: Division of Cancer Sciences & Molecular Pathology

institute: Faculty of Medicine, University of Glasgow

summary:
We have performed the hybridisation in triplicate using total RNA samples pooled from three independent batches of primary cortical neuron culture derived from E14.5 CD1 mouse brains on one day in vitro (1DIV). We stimulated the cells with 50 ng/ml FGF2 in the presence of 10 μg/ml heparin for 4 hours, and the expression of genes were compared to those in the absence of FGF2. The data were obtained from the three experiments with the best possible conditions and strict measures were applied for the purpose of quality control. Seventeen features representing housekeeping genes in the array (GAPDH, HPRT and S16, S9, and S8 ribosomal proteins) gave average value of Ratio of Medians (ROM), 1.20 ± 0.28, which was confirmed to be acceptable. Total RNA was extracted from cells in the growing phase by using RNA Clean (Hybaid) according to the manufacturer’s instruction and further purified with RNeasy mini kit (Qiagen). Direct labelling of 20 µg of total RNA primed with Oligo(dT) was performed in the presence of Cy-5 and Cy-3-dUTP (Amersham Pharmacia Biotech) using SuperScript II (Invitrogen). The Cy5- and Cy3-labelled cDNA samples were then mixed and purified with GFX DNA purification kit (Amersham Pharmacia Biotech). The samples were added with 1.2 µg of salmon sperm DNA and 5 µg of Poly(dA) and dried in SpeedVac at 60°C. The high-density glass microarray chips were prepared at the EMBL core facility by spotting the PCR products prepared from the NIA 15k cDNA mouse clone set. Array slides were pre-hybridized in 6x SSC, 0.5% SDS, 1% BSA at 42°C for 1 hour and incubated in a boiled water for 2 min shortly prior to hybridisation. The cDNA samples were resuspended in 15 µl of hybridisation buffer (50% formamide, 6x SSC, 0.5% SDS and 5% Denhardt’s) and denatured by incubating at 95°C for 2 min. Hybridisation was at 42oC for 16 hours. The slides were washed for 10 min each with 2 x SSC, then with 0.5 x SSC, 0.1%SDS, followed by 0.1 x SSC, 0.1%SDS, at room temperature. Scanning was performed with GenePix 4000B (Axon). Quality control was performed, firstly by eye, to confirm scanner alignment and absence of significant bubbles and scratches. Scatter plots were further used to eliminate the unacceptable hybridisation data. The multiple spike-in controls RNA template were added to the sample upon direct labelling, and the successful labelling and hybridisation was confirmed in each hybridisations. GenePix Pro grogram calculates the Normalisation Factor of each hybridisation, based on the premise that the arithmetic mean of the ratios from every feature on the given array should be equal to 1. Normalisation was therefore performed by multiplying the Factor to Ratio of Medians (ROM) in each gene. The program also identifies features that did not give good alignment to the expected spotted area as “flagged” spots, indicative of the impaired-quality hybridisation of the specific genes.
Keywords = NIA mouse 15k
Keywords = cortical neuron
Keywords = FGF
Keywords: other

first: Ruediger

last: Klein

first: Wilhelm

last: Ansorge


title: Hearts_tissue_expression_profile_2

status: Public on Dec 14 2004

city: Palo Alto

first: Svetlana

last: Shchegrova

institute: Agilent Technologies, Inc

summary:
Expression profiles in Adult Heart and Fetal Heart normal tissues.
Keywords: other


title: Gene expression profiling of the superior olivary complex using serial analysis of gene expression

status: Public on Dec 13 2004

city: Kaiserslautern

first: Hans Gerd

last: Nothwang

institute: University of Kaiserslautern

summary:
SAGE profile of the rat superior olivary complex (SOC). Rats were 60 days old (P60).
Keywords: other

first: H

first: Alexander

last: Koehl

first: Nicole

last: Schmidt

first: Anne

last: Rieger

first: Sara

last: Pilgram

first: Ivica

last: Letunic

first: Peer

last: Bork

first: Florentina

last: Soto

first: Eckhard

last: Friauf


title: Hep3B time-course

status: Public on Dec 10 2004

city: ROUEN

first: Jean

middle: Philippe

last: SALIER

address: Bvd Gambetta

department: Inserm Unit 519

country: France

institute: Faculty of Medicine and Pharmacy

summary:
A time-course (T0, 15, 30 min, 1, 3, 6 or 16 hours) of mRNA abundance changes was studied in the human Hep3B hepatoma cell line challenged with a pro-inflammatory cytokine-enriched medium (CM,conditionned medium) vs control medium (NCM,non conditionned medium). Paired cultures prepared from a same batch of trypsinized cells were challenged with CM vs NCM for a given length of time and this was repeated in three independent experiments (S1,S2,S3).
Keywords: time-course

first: Cedric

last: Coulouarn

first: Gregory

last: Lefebvre

first: Maryvonne

last: Daveau

first: Jean-Philippe

last: Salier


title: Vitamin E plus and minus

city: Aberdeen

first: Janice

middle: E

last: Drew

state: Scotland

address: Greenburn Road

institute: Rowett Research Institute

summary:
Clontech Atlas Stress array of rat distal colon of rats fed on vitamin E sufficient or deficient diets.
Keywords: ordered

first: Claus

last: Mayer


title: Differential expression under hypoxia in zebrafish

first: Christoph

middle: Peter

last: Bagowski

institute: Leiden University

summary:
The local background was subtracted from the fluorescent value of each spot. Feature intensities were extracted from scanned microarray images using GenePix Pro 5.1. (Axon Instruments). The images were visually inspected, and spots from low-quality areas of the array were flagged and excluded from further analysis. Spots were also excluded from analysis if both the combined fluorescent intensity for both channels was less than 1.4 times that of the local background and the pixel-by-pixel correlation coefficient of the spot was less than 0.4. The fluorescence ratios were normalized as previously described (Turton and Gant oncogene 2001website). A hierarchical clustering algorithm (M. Eisen Brown and Botstein PNAS 98 website) was applied to those genes that fulfilled all of the following conditions: they were not flagged; they were differentially expressed (equal or higher than 1.5 fold upregulated or equal or lower than 2 fold downregulated); they had p-values equal or less than 0.02;  and they were consistent on at least 4 out of the 5 arrays.
Keywords: repeat sample

first: David

last: van der Meer

first: Jelani

middle: T

last: Leito


title: Major Patterns of B Cell Gene Expression Changes in Response to Short-Term Stimulation with 33 Single Ligands

status: Public on Dec 09 2004

city: Pasadena

first: Sangdun

last: Choi

address: 1200 E. California Blvd

department: Biology

institute: California Institute of Technology

summary:
We examined the major patterns of changes in gene expression in mouse splenic B cells in response to stimulation with 33 single ligands for 0.5, 1, 2, and 4 h. We found that ligands known to directly induce or costimulate proliferation, namely, anti-IgM (anti-Ig), anti-CD40 (CD40L), LPS, and, to a lesser extent, IL-4 and CpG-oligodeoxynucleotide (CpG), induced significant expression changes in a large number of genes. The remaining 28 single ligands produced changes in relatively few genes, even though they elicited measurable elevations in intracellular Ca2+ and cAMP concentration and/or protein phosphorylation, including cytokines, chemokines, and other ligands that interact with G protein-coupled receptors. A detailed comparison of gene expression responses to anti-Ig, CD40L, LPS, IL-4, and CpG indicates that while many genes had similar temporal patterns of change in expression in response to these ligands, subsets of genes showed unique expression patterns in response to IL-4, anti-Ig, and CD40L.
Keywords: other

first: Rebecca

last: Hart

first: Mi Sook

last: Chang

first: Jong-Woo

last: Kim

first: Yun Anna

last: Cao

first: Sun Young

last: Lee

first: Angela

last: Alexander

first: Joella

last: Grossoehme

first: Zhen

last: Yan

first: Robert

last: Hsueh


title: RAvs.ND

city: Berlin

first: Ute

last: Ungethuem

department: Core Center for Functional Genome Research

institute: Charité University Hospital

summary:
Rheumatoid arthritis (RA) is a chronic, inflammatory joint disease of unknown etiology and pronounced inter-patient heterogeneity. To characterize RA at the molecular level and to uncover key pathomechanisms, we performed whole-genome gene expression analyses. Synovial tissues from rheumatoid arthritis patients were compared to those from to normal donors.
Keywords: repeat sample

overall_design: Rheumatoid in comparison to normal donors were investigated. For both groups samples derived from individual patients and or pools of patients were hybridised.

first: Henning

last: Witt


title: Fob3b vs F-line

status: Public on Dec 16 2004

city: Bar Harbor

first: Ioannis

last: Stylianou

state: ME

address: 600 Maine Street

institute: The Jackson Laboratory

summary:
Liver and BAT expression differences between the fat F-line, and congenic Fob3b-line. Normalised data appended as follows:

TABLE 1: LIVER - 1st set (7.5K) of the 2 slide NIA NIH 15K set
-source1 = F-line liver male - 2 pools each made from 5 different individuals
-source2 = Fob3b-line (aka Fchr15D-line) liver male - 2 pools each made from 5 different individuals
-values are normalised using mixed model across 6 slides:
1 F-line vs Fline
2 Fob3b-line vs Fob3b-line
3 F-line pool1 vs Fob3b-line pool1
4 F-line pool1 vs Fob3b-line pool1 -dye swap
5 F-line pool2 vs Fob3b-line pool2
6 F-line pool2 vs Fob3b-line pool2 -dye swap

TABLE 2: LIVER - 2nd set (7.5K) of the 2 slide NIA NIH 15K set
-source1 = F-line liver male - 2 pools each made from 5 differnt individuals
-source2 = Fob3b-line (aka Fchr15D-line) liver male - 2 pools each made from 5 differnt individuals
-values are normalised using mixed model across 6 slides:
1 F-line Vs F-line
2 Fob3b-line vs Fob3b-line
3 F-line pool1 vs Fob3b-line pool2
4 F-line pool1 vs Fob3b-line pool2 dye swap
5 F-line pool2 vs Fob3b-line pool1
6 F-line pool2 vs Fob3b-line pool1 dye swap

TABLE 3: Brown Adipose Tissue (BAT) 1st (7.5K) array set of 15K NIA NIH set
-source1 = F-line male BAT from 2 pools each made from 5 different individuals
-source2 = Fob3b-line (aka Fchr15D-line) male BAT from 2 pools each made from 5 different individuals
-values are normalised using mixed model across 4 slides:
1 F-line pool1 vs Fob3b-line pool1
2 F-line pool1 vs Fob3b-line pool1 dye swap
3 F-line pool2 vs Fob3b-line pool2
4 F-line pool2 vs Fob3b-line pool2 dye swap

TABLE 4: Brown Adipose Tissue (BAT) 2nd (7.5K) array of the 15K NIA NIH set
-source1 = F-line male BAT (2 pools each from 5 individual mice)
-source2 = Fob3b-line (aka Fchr15D-line) male BAT (2 pools each from 5 individual mice)
-values are normalised using mixed model across 4 slides:
1 F-line pool1 vs Fob3b-line pool1
2 F-line pool1 vs Fob3b-line pool1 dye swap
3 F-line pool2 vs Fob3b-line pool2
4 F-line pool2 vs Fob3b-line pool2 dye swap
Keywords = Obesity
Keywords = Fob3b
Keywords = QTL
Keywords = congenic
Keywords: other

first: Michael

last: Clinton

first: Clare

last: Pritchard

first: Zuzzana

last: Lallane

first: Lutz

last: Bünger

first: Grahame

last: Bulfield

first: Simon

last: Horvat


title: Golden-mantled ground squirrel (Spermophilus lateralis) hibernating heart transcriptome

status: Public on Dec 03 2004

city: Pacific Grove

first: Andrew

last: Gracey

institute: Stanford University

summary:
This series represents the heart transcriptome for animals sampled during summer, interbout arousal, and late torpor
Keywords = squirrel, heart, hibernation
Keywords: other

middle: Y


title: 13-lined ground squirrel (Spermophilus tridecemlineatus) hibernating liver transcriptome

summary:
This series represents the liver transcriptome for animals sampled during summer, interbout arousal, and late torpor
Keywords = squirrel, liver, hibernation
Keywords: other


title: Golden-mantled ground squirrel (Spermophilus lateralis) hibernating brain transcriptome

summary:
This series represents the brain transcriptome for animals sampled during summer, interbout arousal, and late torpor.
Note that the brain expression data for interbout aroused animals was not analyzed in our publication because the group consisted of just 2 animals.
Keywords = squirrel, brain, hibernation
Keywords: other


title: yeast hsf1-R206S/F256S mutant

city: Kanazawa

first: Hiroshi

last: Sakurai

state: Ishikawa

address: 5-11-80 Kodatsuno

department: School of Health Sciences

institute: Kanazawa University

summary:
Effect of hsf1-R206S/F256S mutation on heat-induced transcription of genes is analyzed. Total RNA was isolated from HSF1 wild type and hsf1-R206S/F256S cells grown at 39oC for 15 min. Probe cDNA was primed by oligo(dT) and was synthesized in the presence of 33P-dCTP. Hybridization was carried out using the same GF100 GeneFilter. Value higher than 30 in HSF1 wild type cells is confident. Values from duplicate experiments were averaged, and the average fold changes were calculated.
Keywords = yeast
Keywords = HSF1
Keywords: other


title: The Role of Stationary Phase in Gene Regulation and Mating Competence in Candida albicans

status: Public on Dec 01 2004

city: Iowa City

first: Rui

last: Zhao

state: IA

institute: The University of Iowa

summary:
This set of microarray experiments examines differential gene expression in Candida albicans mating mixtures of opaque a/a and alpha/alpha cells during schmooing and fusion.
Keywords = gene regulation
Keywords = Candida albicans
Keywords = mating
Keywords = microarray
Keywords: other

first: Shawn

last: Lockhart

first: Kathleen

last: Yeater

first: Lois

last: Hoyer

first: Karla

last: Daniels

first: David

last: Soll


title: Differential expression of Aspergillus genes as a result of disrupting maf1

first: Ahmad

last: Fakhoury

department: Plant Pathology

summary:
We identified a 14-3-3 homolog (maf1) in an EST library made under conditions conducive to aflatoxin biosynthesis. Disruption of this gene in A. flavus by site directed mutagenesis abolished aflatoxin production. The maf1 mutant was morphologically similar to wild type but had reduced conidiation and growth on some media. DNA expression analysis of the wild type and maf1 mutant revealed that the mutation affected the expression profile of a set of genes associated with aflatoxin production.
Keywords = Aspergillus
Keywords = aflatoxin
Keywords = 14-3-3
Keywords: repeat sample

first: Gary

last: Payne


title: Golden-mantled ground squirrel (Spermophilus lateralis) hibernating liver transcriptome

summary:
This series represents the liver transcriptome for animals sampled during summer, interbout arousal, and late torpor
Keywords = squirrel
Keywords = liver
Keywords = hibernation
Keywords: other


title: Differential Renal Gene Expression in Pre-hypertensive and Hypertensive SHR

city: RTP

first: NIEHS

last: Microarray Core

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary:
This study examined the renal gene expression profiles between spontaneously-hypertensive rats (SHR) and Wistar-Kyoto (WKY) rats at a pre-hypertensive stage (3 weeks of age) and hypertensive stage (9 weeks of age).  In addition, age-related changes in gene expression patterns were examined from 3 to 9 weeks in both WKY and SHR.  Five to six individual kidney samples of the same experimental group were pooled together and quadruplicate hybridizations were performed on the NIEHS Rat v2.1, 2.2 and 3.0 arrays.
Keywords: other

first: J

last: Seubert

first: F

last: Xu

last: Graves

last: Collins

first: S

middle: O

last: Sieber

first: R

middle: S

last: Paules

first: D

last: Kroetz

last: Zeldin


title: Proteomic analysis of Rasagiline

city: Haifa

first: Yotam

last: Sagi

address: 2 Efron st.

department: Department of Pharmacology , Faculty of Medicine

country: Israel

institute: Technion - Israel institute of Technology

summary:
The effect of rasagiline or MPTP on midbrain protein expression profile
Keywords: repeat sample

first: Silvia

last: Mandel

first: Moussa

last: Youdim


title: Gene Analysis of Rasagiline

summary:
Gene expression profile of Rasagiline  vs. water oral treatment
Keywords = Rasagiline
Keywords = gene
Keywords: repeat sample


title: DNase II-deficient fetal liver

city: Kyoto

first: Shigekazu

last: Nagata

address: Yoshida. Sakyo-ku

department: Department of Medical Chemistry

institute: Graduate School of Medicine, Kyoto University

summary:
The liver of DNase II-deficient embryos contains numerous macrophages carrying undigested DNA, and the embryos die in feto. Here, we examined the gene expression in the wild-type (GSM32833) and DNase II-/- (GSM32834) fetal liver, and found that a set of interferon (IFN)-inducible genes is strongly activated in the DNase II-/- fetal liver. When the DNase II-/- mice were crossed to IFN type I receptor (IFN-IR)-null mice, the mice deficient in both DNase II and IFN-IR genes were born apparently normally, indicating that the type I IFN and its inducible genes had the lethal effect on the mouse development. To examine which genes induced by IFN is responsible to kill the embryos, the gene expression of the fetal liver of DNase II-/- IRF-IR-/- embryos (GSM32835) was also examined.
Keywords: other

first: Hideyuki

last: Yoshida

first: Yasutaka

last: Okabe

first: Hidehiro

last: Fukuyama

first: Kohki

last: Kawane


title: Serial time induction by TPA on BCBL-1 cells in the absence or presence of viral replication inhibitor cidofovir

city: Bethesda

first: Michael

last: Lu

state: MD

address: 10 Center Drive, Blg. 10, Rm 10S255

department: HIV and AIDS Malignancy Branch

institute: National Cancer Institute

summary:
BCBL-1 cells were induced with 20 ng/ml TPA either in the absence (U) or presence (+) of 100 µM cidofovir (CDV) treatment and collected at 0, 6, 8, 10, 12, 24, 36, 48, 72, 96 hours (h) post-TPA addition, and compared against untreated (U), uninduced latent BCBL-1 reference cells. Three biological repeats were performed.
Keywords = Kaposi's sarcoma-associated herpesvirus
Keywords = KSHV
Keywords = human herpesvirus type 8
Keywords = HHV-8
Keywords = primary effusion lymphoma (PEL) cells
Keywords = body-cavity based lymphoma-1 (BCBL-1) cells
Keywords = lytic induction
Keywords = 12-O-tetradecanoylphorbol-13-acetate (TPA)
Keywords = viral replication inhibition
Keywords = cidofovir (CDV)
Keywords: time-course

platform_organism:
Homo sapiens
Human gammaherpesvirus 8

first: Jacqueline

last: Suen

first: Carolina

last: Frias

first: Ruth

last: Pfeiffer

first: Mong-hsun

last: Tsai

first: Eric

last: Chuang

first: Steven

last: Zeichner


title: Ambrosino series 1

first: Tomoko

last: Iwata

summary:
Hybridizations were performed in triplicate, using total of 7 RNA samples extracted from 3 independent batches of proliferating cardiomyocyte cell line derived from p38alpha knockout mouse. In two hybridizations (Ambrosino 1, Ambrosino 2), the RNAs from p38alpha-/- and wt cells were labeled with Cy-5 and Cy-3-dUTP, respectively, whereas in the third hybridization (Ambrosino 3), the dyes were swapped. The multiple spike-in control RNA templates were added to the sample upon direct labeling, and the successful labeling and hybridization was confirmed in each hybridizations. Twelve housekeeping genes in the array (GAPDH, HPRT and S16, S9, and S8 ribosomal proteins) gave average value of Ratio of Medians (ROM), 1.30 ± 0.26, which was confirmed to be acceptable. GenePix Pro program calculates the Normalization Factor, based on the premise that the arithmetic mean of the ratios from every feature on the given array should be equal to 1. Normalization was therefore performed by multiplying the Factor to ROM in each gene. The program also identifies features that did not give good alignment to the expected spotted area as “flagged” spots, indicative of the impaired-quality hybridization of the specific genes. All flagged genes were removed from the list before further analysis. The genes that passed all these criteria were sorted by ROM and those that showed more than ±1.5 fold changes were selected in the data table from each hybridization. Finally, the data tables from the 3 independent hybridizations were compared and only those genes that appeared in all 3 experiments were selected in the final list (manuscript submitted).
Keywords = NIA mouse 15K
Keywords = cardiomyocytes
Keywords = p38alpha MAPK
Keywords: repeat sample

first: Concetta

last: Ambrosino

first: Ruediger

last: Klein

first: Angel

middle: R

last: Nebreda


title: CEA_SGF:E00009#switch_lympho_mega

city: Evry

first: Thierry

last: Kortulewski

address: 2 rue Gaston Cremieux

institute: CEA/DRR/SGF/LGRH

summary:
we analyzed the gene expression profile of newly produced transgenic bone marrow subpopulations and compared it to the expression patterns obtained from cells isolated from wild type mice at different stages of the hematopoietic differentiation process. These populations were enriched in HSC, CMP, CD41+ c-kit+ and CD41+ c-kit- populations for the myelo-megakaryocytic lineage; and for the B lymphoid lineage, the populations were enriched in CLP, Pro-B and mature B lymphocytes. To produce comparable profiles total bone marrow RNA was used as a common reference.
Keywords: repeat sample


title: Leucine starvation series

city: Chicago

first: Kimberly

last: Dittmar

state: IL

department: Biochemistry and Molecular Biology

institute: University of Chicago

summary:
These data represent the ratios of charged to total tRNA for E. coli auxotrophic strain CP78 during starvation for leucine over a time course of 32 minutes.
Keywords: time-course

platform_organism:
Escherichia coli
Bacillus subtilis
Saccharomyces cerevisiae


title: Skeletal Muscle Response

status: Public on Nov 24 2004

first: Sangdun

last: Choi

summary:
To improve our understanding of the genetic reprogramming during the early phase of skeletal adaptation in response to endurance training, we employed cDNA microarray analysis to examine changes in mRNA expression in mouse plantaris muscle after a single bout voluntary running. Control untrained mice were compared with with R3h, R12h, P3h, P6h, P12h, P24h and R4w mice.  We conclude that a single bout of voluntary running is sufficient to induce active remodeling processes, including cell proliferation, by a coordinated regulation of the genome in response to signals elicited from increased neuromuscular activity.

Keywords = Mouse skeletal muscle
Keywords = plantaris
Keywords = voluntary running
Keywords: time-course

first: Xuebin

last: Liu

first: Ping

last: Li

first: Takayuki

last: Akimoto

first: Sun Young

last: Lee

first: Curtis

last: Gumbs

first: Mei

last: Zhang

first: Zhen

last: Yan


title: Male BALB/c Mouse Testosterone-Treated Submandibular/Lacrimal/Meibomian Glands

city: Boston

first: Nathaniel

last: Treister

state: MA

address: 20 Staniford Street

institute: Schepens Eye Research Institute

summary:
Series includes pooled (n = 5 mice per biological replicate) samples from lacrimal, meibomian, and submandibular glands of male palcebo- and testosterone-treated BALB/c mice. All experiments were run in triplicate (pooled biological replicates) on CodeLink Mouse Uniset I Microarrays.

Keywords: repeat sample

first: David

last: Sullivan

first: Stephen

last: Richards

first: Tomo

last: Suzuki


title: Male/Female BALB/c Mouse Submandibular/Sublingual/Parotid/Lacrimal/Meibomian  Glands

summary:
Series includes pooled (n = 5 mice per biological replicate) samples from submandibular, sublingual, parotid, lacrimal, and meibomian glands of BALB/c mice. Both male and female samples were analyzed on CodeLink Mouse Uniset I Microarrays.
Keywords: repeat sample


status: Public on Nov 19 2004

city: Vancouver

first: Josh

middle: D

last: Neufeld

state: BC

address: #300-6174 University Blvd.

department: Department of Microbiology & Immunology

institute: University of British Columbia

summary:
Comparison of hexachlorocyclohexane (HCH) contaminated soils from Spain with a community-specific microarray.

These results are being submitted for publication and represent the first use of microarrays for analysis of soil DNA and the first community-specific microarray design.
Keywords: other

first: William

middle: W

last: Mohn

first: Victor

last: de Lorenzo


title: The hibernating phenotype assessed through transcript screening

first: Andrew

last: Gracey

state: CA

summary:
Mammalian hibernation is a dramatic physiological transition that involves the controlled reduction of regulated body temperature and the consequent depression of all physiological processes.  The resulting reduction of metabolism and associated energy expenditure permits survival during extended periods of poor food availability in winter. To date our understanding of the molecular events that give rise to the hibernating phenotype is fragmentary and incomplete. Here, we present a large-scale gene expression screen to explore the transcriptional changes that are associated with the torpid phenotype of the hibernating golden-mantled ground squirrel, Spermophilus lateralis.  Expression profiles for liver, cardiac tissue, and brain isolated from summer active, torpid, and interbout aroused animals were generated by hybridization to a squirrel microarray composed of >12,000 cDNA probes.  We reveal that the transcriptional changes associated with torpor are modest and generally involve less than 2-fold changes in mRNA level.  By profiling the distribution of gene ontological terms in the lists of differentially expressed genes we were able to identify the functional themes that distinguish the summer awake and hibernating phenotypes.  In all tissues, the pattern of differential gene expression is consistent with a switch to lipid metabolism during hibernation.  In liver, we detected an expression signature suggestive of a profound depression in urea metabolism and detoxification pathways.  This expression signature was reproduced in transcript data collected from liver of the13-lined ground squirrel, S. tridecemlineatus, suggesting that this phenotype is conserved between closely related species.  The transcriptional changes in cardiac tissue were interpreted as a component of the bradycardia associated with torpor.  The function of the differentially expressed transcripts in brain is less transparent, likely due to heterogeneity among the responses of different cell populations in this complex organ.
Keywords: other

sample_organism:
Ictidomys tridecemlineatus
Callospermophilus lateralis

first: Daryl

last: Williams

first: Elaine

last: Epperson

first: Weizhong

first: Margaret

last: Hughes

first: Ruth

last: Taylor

first: Jane

last: Rogers

first: Sandra

last: Martin

last: Cossins


title: mouse sciatic nerve profile of CMT1A peripheral neuropathy model, caused by PMP22 overexpression

status: Public on Nov 13 2004

city: Amsterdam

first: Anneloor

last: ten Asbroek

address: Meibergdreef 9

institute: Academic Medical Center

summary:
profiles of normal and diseased sciatic nerve of young adult mice
Keywords: other

first: Camiel

last: Verhamme

first: Marjon

last: van Groenigen

first: Ruud

last: Wolterman

first: Maryla

middle: M

last: de Kok-Nazaruk

first: Frank

last: Baas


title: Glycoconjugate expression profiling in mouse postnatal cerebellar development

status: Public on Nov 15 2004

city: La Jolla

first: Steven

last: Head

address: 10550 N Torrey Pines Rd

institute: The Scripps Research Institute

summary:
We used a custom Affymetrix GeneChip, the "GLYCOv2" array, to measure differences in gene expression patterns from adult and postnatal day 7 (P7) mouse cerebellum RNA.
Keywords = Cerebellum, microarray, development, glycoconjugates, glycosyltransferases, proteoglycans, gene expression
Keywords: other

platform_organism:
Homo sapiens
Mus musculus

first: Frances

middle: I

last: Smith

first: Qiang

last: Qu

first: Timothy

last: Gilmartin


title: Alternative Splicing in 5 Tissues

status: Public on Nov 22 2004

city: Los Angeles

first: Christopher

last: Lee

department: Dept. of Chemistry & Biochemistry

institute: University of California, Los Angeles

summary:
Alternative splicing microarray data in five normal tissues (brain, muscle, liver, bone marrow, testes) for 316 human genes.
Keywords: other

first: Keith

last: Le

first: Katherine

last: Mitsouras

first: Meenakshi

last: Roy

first: Qi

last: Wang

last: Xu

first: Stanley

middle: F

last: Nelson


title: Immune-stimulated Peyer's patch

status: Public on Nov 16 2004

city: St. Paul

first: Cheryl

last: Dvorak

state: MN

address: 1971 Commonwealth Avenue

department: Veterinary and Biomedical Sciences

institute: University of Minnesota

summary:
RNA from all normal tissues were pooled in equal amounts and used to create the normal tissue library. RNA from all immune stimulated tissues (Salmonella infection, CT+LPS, and PBC, with and without cycloheximide) were pooled in equal amounts and used to create the immune stimulated tissue library. The subtracted library was created by combining the normal and immune stimulated libraries and by subtracting porcine fibroblast RNA.
Keywords: other


title: SML1 synthetic lethality

status: Public on Nov 05 2004

city: Baltimore

first: Xuewen

last: Pan

address: 733 N. Broadway, Room 331

department: Department of Molecular Biology and Genetics

institute: Johns Hopkins University School of Medicine

summary:
Assessment of synthetic lethality between an sml1 null mutation and Yeast Deletion mutations
Keywords = SML1
Keywords = yeast
Keywords = deletion
Keywords = synthetic lethality
Keywords = tag
Keywords = barcode
Keywords: repeat sample

first: Daniel

last: Yuan

first: Dong

last: Xiang

first: Xiaoling

first: Sharon

last: Sookhai-Mahadeo

first: Joel

last: Bader

first: Philip

last: Hieter

first: Forrest

last: Spencer

first: Jef

last: Boeke


title: TUB1 synthetic haploinsufficiency

summary:
Assessment of growth impairment resulting from a heterozygous tub1 null mutation as compared to that from a heterozygous ura3 null mutation
Keywords = TUB1
Keywords = URA3
Keywords = yeast
Keywords = deletion
Keywords = synthetic haploinsufficiency
Keywords = tag
Keywords = barcode
Keywords: repeat sample


title: Pool controls

summary:
Determination of how two critical procedural steps in the dSLAM protocol ('diploid synthetic lethality assessed by microarray') affect results
Keywords = yeast
Keywords = deletion
Keywords = synthetic lethality
Keywords = tag
Keywords = barcode
Keywords: ordered


title: CDC102 synthetic lethality

summary:
Assessment of synthetic lethality between a temperature-sensitive allele of CDC102 and Yeast Deletion mutations
Keywords: repeat sample


title: CIN8 Synthetic Lethality

summary:
Assessment of synthetic lethality between a cin8 deletion mutation and Yeast Deletion mutations.
Keywords = CIN8
Keywords = yeast
Keywords = deletion
Keywords = synthetic lethality
Keywords = tag
Keywords = barcode
Keywords: repeat sample


title: Fhl1 and lfh1 ChIP-chip

status: Public on Nov 09 2004

first: Joseph

last: Wade

address: 240 Longwood Ave

department: BCMP

institute: Harvard Medical School

type: Genome binding/occupancy profiling by array

summary:
Fhl1-9myc ChIP-chip, YPD, OD600=0.8, 2 arrays with duplicate spotting of yeast intergenic regions.

AND

Ifh1-9myc ChIP-chip, cells grown in YPD, OD600=0.8, 2 arrays with duplicate spotting of yeast intergenic regions.
Keywords = Fhl1
Keywords: other

middle: B

last: Hall

first: Kevin

last: Struhl


title: LCD1-overexpression synthetic lethality

summary:
Assessment of synthetic lethality between an overexpressed LCD1 gene and Yeast Deletion mutations
Keywords = LCD1
Keywords = overexpression
Keywords = yeast
Keywords = deletion
Keywords = synthetic lethality
Keywords = tag
Keywords = barcode
Keywords: repeat sample


title: Benomyl dose-response

summary:
Synthetic lethality of Yeast Deletion strain mutations in haploid cells with various concentrations of Benomyl
Keywords = Benomyl
Keywords = yeast
Keywords = deletion
Keywords = tag
Keywords = barcode
Keywords: dose response


title: Oryza Sativa and Magnaporthe Grisea LongSAGE

status: Public on Nov 08 2004

city: Tucson

first: Carol

last: Soderlund

state: AZ

address: 303, Forbes Building

department: BIO5 Institute

institute: University of Arizona

summary:
LongSAGE library in this series are from 'Whole Genome Analysis of Pathogen-Host Recognition and Subsequent Responses in the Rice Blast Patho-System' project. This work is supported by NSF-PGRP #0115642.
Keywords: other

sample_organism:
Oryza sativa Japonica Group
Pyricularia oryzae 70-15

first: Malali

last: Gowda

first: Eric

last: Stahlberg

first: Venu

last: Reddyvari Channarayappa

first: Shankaraganesh

last: Manikantan

first: Vishal

last: Pampanwar

first: Jamie

last: Hatfield

first: Brandon

last: Childers

first: Chatchawan

last: Jantasuriyarat

first: Yeisoo

last: Yu

first: HyeRan

last: Kim

first: Rod

last: Wing

first: Ralph

last: Dean

first: Cari

first: Guo-Liang


title: Changes in genome-wide occupancy of core transcriptional regulators during stress

status: Public on Nov 03 2004

city: University Park

first: Frank

last: Pugh

state: PA

address: 452 North Frear Laboratory

institute: The Pennsylvania State University

summary:
Organisms respond to heat stress by reprogramming gene expression.  Here we show that genome-wide reprogramming involves enhanced assembly of the TFIID and SAGA regulatory pathways at heat induced genes, and disassembly of the TFIID pathway at heat-repressed genes.  While TFIID and SAGA are recruited to heat-induced genes, only SAGA appears to be associated with achieving maximal induction.  Mot1, an ATP-dependent inhibitor of the TATA binding protein TBP, assembles at heat-induced SAGA-regulated genes, but functions to attenuate rather than promote activation.  Changes in promoter occupancy of bromodomain factor Bdf1 are tightly linked to changes in TFIID occupancy, which further supports the notion that the two work together.  Bdf1 is inhibitory to a number of SAGA-regulated genes and dissociates when these genes are activated, suggesting that Bdf1 normally blocks transcription complex assembly at these genes.  These linkages in reprogramming of factor occupancy at promoters provide direct evidence for two functionally distinct transcription assembly pathways, and reveal unexpected cross-talk between the pathways.
Keywords = Chromatin Immunoprecipitation
Keywords = Microarray
Keywords = TBP
Keywords: other

first: Sara

last: Zanton

first: B


title: RAKE microRNA

status: Public on Nov 01 2004

city: Philadelphia

first: Don

last: Baldwin

address: 277 John Morgan, 3620 Hamilton Walk

department: Pathology and Lab Medicine

institute: University of Pennsylvania

summary:
MicroRNAs (miRNAs) are small regulatory RNAs, which serve fundamental biological roles across eukaryotic species. We describe a novel method for high throughput miRNA detection. The technique is termed RNA-primed, Array-based, Klenow Enzyme (RAKE) assay, because it involves on-slide application of the Klenow fragment of DNA polymerase to extend unmodified miRNAs hybridized to immobilized DNA probes. We used RAKE to study human cell lines and brain tumors. We show that the RAKE assay is sensitive and specific for miRNAs and is ideally suited for rapid expression profiling of all known miRNAs. RAKE offers unique advantages for specificity over Northern blots or other microarray-based expression profiling platforms.  Furthermore, we demonstrate that miRNAs can be isolated and profiled from formalinfixed paraffin-embedded tissue, which opens up new opportunities for analyses of small RNAs from archival human tissue. The RAKE assay is theoretically versatile and may be used for other applications, such as viral gene profiling.
Keywords = microRNA
Keywords: ordered

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Arabidopsis thaliana
Homo sapiens
Mus musculus
Rattus norvegicus

first: Peter

last: Nelson

middle: A

first: Marie

last: Scearce

first: Carl

last: Oberholtzer

first: John

last: Tobias

first: Zissimos

last: Mourelatos


title: jejunal Peyer’s patch (JPP) gene expression relative to jejunal mesenteric lymph node (j-MLN) gene expression.

first: Kendra

middle: A.

last: Hyland

address: 1971 Commonwealth Ave.

institute: University of Minneosta

summary:
Although immune mechanisms have been described for Peyer’s patch function, in discriminating food nutrients and commensal microflora from pathogenic challenge, an understanding of gene expression patterns associated with normal intestinal homeostasis is lacking. The effects of commensal bacterial colonization on global gene expression in the small intestine of germ-free mice have been described (1, 2). However, no studies have compared expression patterns of various healthy lymphoid tissues in conventionally-raised pigs or other species. The objective of this study was to investigate the pattern of normal gene expression in jejunal Peyer’s patches (JPP) of healthy pigs. We hypothesized that gene expression of intact jejunal Peyer's patch is characterized by genes associated with absorption and secretory functions as well as genes associated with GALT-specific immune functions.
Eight hybridizations were performed, with dye swaps of JPP mRNA from four juvenile pigs.  Each hybridization compared JPP from an individual pig to the jejunal mesenteric lymph node reference sample, which was pooled from all juvenile pigs in the study. However, two of the hybridizations resulted in poor quality data, and were excluded from further analysis.
Normalization, hierarchical clustering, data visualization, and statistical analysis were performed by GeneSpring version 6.2 (Silicon Genetics, Redwood, CA). GeneSpring standardized the intensities for each spot by subtracting the local background, and then normalized globally by locally weighted linear regression (Lowess). A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead.  Spots with a flag value of “0” were excluded. The intensity of negative control DNA-containing spots was used to additionally exclude low intensity data.  Negative controls include the gene for Arabidopsis thaliana homeodomain-like protein (AY054571); 200 ng/microl Poly(dA) (Amersham, Piscataway, NJ); a 461 bp fragment of the kanamycin-resistant gene, amplified from the pET24b+ plasmid (Novagen, Madison, WI); PRRS virus strain VR-2332 (PRU87392) ORFs 2, 3, 4, 5, 6 and 7; pCMVSport 6 plasmid (Invitrogen, Carlsbad, CA); and pGEM-T plasmid (Promega, Madison WI).  The mean intensity of the negative controls for both Cy3 and Cy5 was calculated for each slide, and spots with a mean intensity less than the mean intensity + 2SD were excluded from further analysis.
After normalization, GeneSpring averaged replicate spots for each clone across hybridizations.  GeneSpring used the Cross Gene Error Model, which was based on replicate values.  A Student’s t-test with the Benjamini and Hochberg false discovery rate multiple testing correction (MTC) verified the difference between the natural log of the normalized gene expression ratio (JPP:j-MLN) and a ratio of 1.0. p-values less than 0.05 were considered significant.
Series_references: 1.Fukushima K, Ogawa H, Takahashi K, Naito H, Funayama Y, Kitayama T, Yonezawa H, and Sasaki I. Non-pathogenic bacteria modulate colonic epithelial gene expression in germ-free mice. Scand J Gastroenterol 38: 626-634, 2003.  2. Hooper LV, Wong MH, Thelin A, Hansson L, Falk PG, and Gordon JI. Molecular analysis of commensal host-microbial relationships in the intestine. Science 291: 881-884, 2001.
Keywords: other

first: Juliana

middle: G

last: Machado

first: Hyland

last: Kendra


title: Mouse tissue comparison

status: Public on Oct 29 2004

city: Toronto

first: Mark

last: Robinson

institute: University of Toronto

summary:
An oligonucleotide microarray study of 42,000 new and predicted mouse genes across a comprehensive set of 55 tissues
Keywords: other


title: MPSS analysis of mouse BLK CL.4 and liver cells

status: Public on Oct 26 2004

city: Hayward

first: Daixing

last: Zhou

address: 25861 Industrial Blvd

department: Bioinformatics

institute: Solexa

summary:
MPSS analysis of mouse BLK CL.4 cells and liver cells.  Total RNA, nuclear RNA and post-nuclear RNA examined.
Keywords: other

first: Tom

last: Vasicek

first: Chris

last: Austin

first: Irina

last: Khrebtukova


summary:
MPSS mouse transcriptome analysis project.

See http://www.ncbi.nlm.nih.gov/geo/info/mouse-trans.html for more details.
Keywords: other


title: Human Reticulocyte

status: Public on Oct 23 2004

city: Montpellier

first: David

last: Piquemal

address: 1682, rue de la Valsière

institute: ACOBIOM

summary:
Reticulocytes were purified from fresh blood samples obtained from 10 healthy adult volunteers (5 women and 5 men) after informed consent. The donors had normal blood cell counts, blood smears, hemoglobin electrophoresis, red cells membrane resistance tests and no biological evidence of hemolysis.
Whole blood samples were centrifuged, the supernatant and the buffy coat containing white blood cells (WBC) and platelets were removed. The red cells pellet was then purified using the method described by Brun et al.
Purity, assessed by Hematology Flow Cytometer was 1 leukocyte per 15 millions RBC and efficiency of purification process was 99.8% and 1 platelet per 10 000 RBC.
Keywords: other

first: Beatrice

last: Bonafoux

first: Mireille

last: Lejeune

first: Ronan

last: Quere

first: Aurelie

last: Baudet

first: Lea

last: Assaf

first: Jacques

last: Marti

first: Patricia

last: Aguilar-Martinez

first: Therese

last: Commes


title: Genome-wide binding of Fhl1 and Ifh1 +/- Rapamycin

status: Public on Nov 10 2004

city: Geneva

first: Stephan

middle: B.

last: Schawalder

address: Quai Ansermet 30

department: Departement of Molecular biology

institute: University of Geneva

summary:
Array design

-Platform: amino-silane coated glass slides (GAPS II, Corning)
-S. cerevisiae intergenic regions amplified from S288C genomic DNA (ResGen) using the intergenic region primer oligonucleotides (ResGen) (Harismendy et al. EMBO J. 22(18): 4738-4747, 2003). The primers allow the amplification of the sequence located on either side of elements such as open reading frames, tRNAs, small nuclear RNAs, Ty elements, solo δ, etc. A complete description of the primers can be obtained on the web site (ftp://ftp.resgen.com/pub/genepairs/yeast_intergenic).
-The PCR products were purified and spotted using an automated arrayer (MicroGrid II, BioRobotics)

Experiment design
-Type of experiment: genome wide binding analysis
-Experimental factor: genotype (Wild-Type, Fhl1-myc, Ifh1-myc); drug (rapamycin)
-Number of hybridization performed in the experiment: 15 (four conditions with three to five biological replicates each)
-Reference used for each condition: ChIP from the wild-type strain
-Quality control: one dye-swap per condition

Samples used, extract preparation and labeling
-The origin of the biological sample:
o	Species: S. cerevisiae
o	Cell type: (1) W303; (2) W303+IFH1-13myc-TRP1MX6;(3) W303+FHL1-13myc-HIS3MX6.
-Growth conditions: log phase (2x107/mL) at 30ºC in YPD medium; when indicated rapamycin was added at the final concentration of 200 ng/mL for 90 min.
-Cross-linking for 30 min at 30ºC
-Chromatin immunoprecipitation: Dynabeads M280 coupled to sheep anti-mouse IgG or sheep anti-rabbit IgG and mouse monoclonal antibodies against the myc epitope (culture supernatant of 9E10) were used for immunoprecipitation according to standard techniques.
-Labeling protocol(s): each IP was blunt-ended, ligated to linker DNA, then subjected to Ligation Mediated (LM)-PCR in the presence of amino-allyl dUTP. Labeling was performed for 1 hour at room temperature in the presence of NHS-ester Cy3 or Cy5 in 0.1 M Sodium Carbonate. The labeling reaction was stopped with 2 M Hydroxylamine and the labeled DNA purified.

Hybridization procedures and parameters
-Standard protocols were used

Measurement data and specifications
-Software for scanning: GenePix Pro 4.0 (Axon Instruments, Inc.)
-Scanner: GenePix 4000A (Axon Instruments, Inc.)
Keywords: dose response

first: Mehdi

last: Kabani

first: Urmilla

last: Choudhurry

first: Isabelle

last: Howald

first: Michel

last: Werner

last: Shore


title: interaction with bacteria or bacterial supernatant

city: Sophia Antipolis

first: Chimene

last: Moreilhon

institute: CNRS

summary:
Epithelial cells were in contact either with live bacteria  (S. aureus) or with bacterial supernatant during 3 hours. Three dependant experiment for each condition were performed. RNA from epithelial cells were extracted. Each condition was hybridized on 6 slides (3 slides with their corresponding swap)
Keywords: parallel sample


title: BAC CGH array profiling using Phi29-amplified microdissected samples

city: Lisbon

first: Joana

last: Cardoso

address: Av. Prof Egaz Moniz

country: Portugal

institute: Faculty of Medicine

type: Genome variation profiling by genome tiling array

summary:
Details of the experiment are available within the Nucleic Acid Research, 2004 manuscript "Genomic profiling by DNA amplification of
laser capture microdissected tissues and array CGH", by Cardoso J. et al.
Keywords: other

first: Lia

last: Molenaar

first: Renee

middle: X

last: Menezes

first: Carla

last: Rosenberg

first: Hans

last: Morreau

first: Gabriela

last: Moslein

first: Riccardo

last: Fodde

first: Judith

last: Boer