title: Budding yeast Wapl controls sister chromatid cohesion maintenance and the chromosome condensation status [BrdU-ChIP].

city: London

first: Rahul

last: Thadani

address: 44 Lincoln's Inn Fields

institute: Cancer Research UK

summary: Cohesin acetylation by Eco1 during DNA replication establishes sister chromatid cohesion. We show that acetylation makes cohesin resistant to Wapl activity from S-phase until mitosis. Wapl turns out to be a key regulator of cohesin dynamics on chromosomes by controling cohesin maintenance following its establishment in S-phase and its role in chromosome condensation.

overall_design: The Affymetrix Saccharomyces cerevisiae Chip Tiling 1.0F Arrays were used to analyze the incorporation of BrdU in Saccharomyces cerevisiae in S-phase arrested cells.

first: Lidia

last: Lopez-Serra

first: Armelle

last: Lengronne

first: Vanessa

last: Borges

first: Gavin

last: Kelly

first: Frank

last: Uhlmann


title: Copy number analysis in de novo and therapy-related myeloproliferative neoplasms

status: Public on Nov 24 2012

city: Chicago

first: Megan

middle: E.

last: McNerney

state: Illinois

address: 900 East 57th Street, KCBD 5128

department: Pathology

country: USA

institute: The University of Chicago

type:
SNP genotyping by SNP array
Genome variation profiling by SNP array

summary: Loss of chromosome 7 and del(7q) [-7/del(7q)] are recurring cytogenetic abnormalities in hematologic malignancies, including acute myeloid leukemia and therapy-related myeloid neoplasms, and associated with an adverse prognosis.  We performed  SNP array analysis on de novo and therapy-related myeloid neoplasms and identified a 2.17 Mb commonly deleted segment on chromosome band 7q22.1 containing CUX1, a gene encoding a homeodomain-containing transcription factor. Haploinsufficiency of the highly conserved ortholog, cut, led to hemocyte overgrowth and tumor formation in Drosophila melanogaster.  Similarly, haploinsufficiency of CUX1 gave human hematopoietic cells a significant engraftment advantage upon transplantation into immunodeficient mice. These data identify CUX1 as a conserved, haploinsufficient tumor suppressor frequently deleted in myeloid neoplasms.

overall_design: We performed SNP-array analysis of 34 primary patient samples with de novo or therapy-related myeloid leukemia and one acute myeloid leukemia cell line, UoCM1.  For patient samples, DNA was obtained from the white blood cells of bone marrow or peripheral blood leukemia specimens.  Cytogenetic analysis revealed clonal -7/del(7q) in 17 of the cases.

middle: E

first: Christopher

middle: D

last: Brown

first: Xiaoyue

last: Wang

first: Elizabeth

middle: T

last: Bartom

first: Subhradip

last: Karmakar

first: Chaitanya

last: Bandlamudi

first: Shan

last: Yu

first: Jinkyung

last: Ko

first: Barry

middle: P

last: Sandall

first: Thomas

last: Stricker

first: John

last: Anastasi

first: Robert

middle: L

last: Grossman

middle: M

last: Cunningham

first: Michelle

last: LeBeau

first: Kevin

last: White


title: The maternal transcriptome of the crustacean Parhyale hawaiensis is inherited asymmetrically to invariant cell lineages of the ectoderm and mesoderm

status: Public on Nov 19 2012

city: Basel

first: Peter

last: Nestorov

address: Maulbeerstr. 66

country: Switzerland

institute: FMI

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

overall_design: Refer to individual Series


title: The maternal transcriptome of the crustacean Parhyale hawaiensis is inherited asymmetrically to invariant cell lineages of the ectoderm and mesoderm [rest_8cell_embryonic_vs_mesoderm]

summary:
The embryo of the crustacean Parhyale hawaiensis has a total, unequal and invariant early cleavage. It specifies cell fates earlier than other arthropods like Drosophila, as individual blastomeres of the 8-cell stage are allocated to the germ layers and the germline. Furthermore, the 8-cell stage is amenable to embryological manipulations. These unique features make Parhyale a suitable system for elucidating germ layer specification in arthropods. Since asymmetric localization of maternally provided RNA is a widespread mechanism to specify early cell fates, we asked whether this is also true for Parhyale. A candidate gene approach did not find RNAs that are asymmetrically distributed at the 8-cell stage. Therefore, we designed a high-density microarray from 9400 recently sequenced ESTs (1) to identify maternally provided RNAs and (2) to find RNAs that are differentially distributed among cells of the 8-cell stage.
Maternal-zygotic transition takes place around the 32-cell stage, i.e. after the specification of germ layers. By comparing a pool of RNAs from early embryos without zygotic transcription to zygotic RNAs of the germband, we found that more than 15% of the targets on the array were enriched in the maternal transcript pool. A screen for asymmetrically distributed RNAs at the 8-cell stage revealed 129 transcripts, which were associated with germ-layer-specific GO-terms. Cross-correlation analysis of the microarray experiments indicated that half of the asymmetrically distributed RNAs at the 8-cell stage are degraded before the start of zygotic transcription. Finally, we performed knock-down experiments for two of these genes and observed cell-fate-related defects of embryonic development.

overall_design:
microarray analysis of the 8-cell stage embryonic transcriptome - mesoderm progenitors vs. rest
Institution: Max Planck Institute for Developmental Biology, Tuebingen, Germany
Time of experiment: April 2008 to April 2009

first: Florian

last: Battke

first: Mitchell

last: Levesque

first: Matthias

last: Gerberding


title: Aorta profiling HMDP

status: Public on Nov 18 2012

city: Los Angeles

first: Calvin

last: Pan

address: 675 Charles Young Dr South

institute: UCLA

summary: Identify genes in the aorta whose expressions under genetic regulation in the Hybrid Mouse Diversity Panel (HMDP). The HDMP is comprised of classical inbred and recombinant inbred wild-type mice. The RMA values of genes were used for genome-wide association as described in Bennett et al. Genome Research 2010 (PMID 20054062). These data were used to identify candidate genes at loci associated with atherosclerosis.

overall_design: Genome-wide association study (GWAS) for expression in aorta of inbred strains.

first: Aldons

middle: J

last: Lusis

first: Brian

last: Bennett

first: Ayca

last: Erbilgin


title: An eQTL study in the Japanese population [genotype]

status: Public on Nov 27 2012

city: Kodaira

first: Daimei

last: Sasayama

address: 4-1-1 Ogawahigashi-machi

country: Japan

type:
Genome variation profiling by SNP array
SNP genotyping by SNP array

summary: A genome-wide eQTL analysis was performed in whole blood samples collected from 76 Japanese subjects. RNA microarray analysis was performed for 3 independent samples that were genotyped in a genome-wide scan. The correlations between the genotypes of 534,404 autosomal single nucleotide polymorphisms (SNPs) and the expression levels of 30,465 probes were examined for each sample. The SNP-probe pairs with combined correlation coefficients of all 3 samples corresponding to P < 3.10 × 10-12 (i.e., Bonferroni-corrected P < 0.05) were considered significant. SNP-probe pairs with a high likelihood of cross-hybridization and SNP-in-probe effects were excluded to exclude false positive results. We identified 102 cis-acting and 5 trans-acting eQTL regions. The cis-eQTL regions were widely distributed both upstream and downstream of the gene, as well as within the gene.

overall_design: RNA microarray data obtained from 3 independent samples originally recruited for other studies investigating the gene expression levels in psychiatric disorders were used in the present study. For the purpose of the present analyses, genomic DNA was collected from 24 subjects (13 men and 11 women, mean age [SD] = 39.9 [7.6] years) in sample 1, 24 subjects in sample 2 (12 men and 12 women, 34.1 [11.5] years), and 28 subjects (14 men and 14 women, 41.4 [11.8] years) in sample 3. Some of the subjects had depressive symptoms, but all were physically healthy and without clinically significant systemic disease (e.g., malignant disease, diabetes mellitus, hypertension, renal failure, or endocrine disorders). Subjects were recruited from the outpatient clinic of the National Center of Neurology and Psychiatry Hospital, Tokyo, Japan, through advertisements in free local information magazines or through our website announcement. All the subjects were biologically unrelated Japanese individuals who resided in the same geographical area (western Tokyo). The study protocol was approved by the ethics committee at the National Center of Neurology and Psychiatry, Japan. Written informed consent was obtained from every subject after the study was explained to them. Venous blood was collected between 1100 and 1200 h in PAXgene tubes (Qiagen, Valencia) from each subject and was incubated at room temperature for 24 h for RNA stabilization. RNA was extracted from whole blood according to the manufacturer’s guidelines by using the PAXgene Blood RNA System Kit (PreAnalytix GmbH, Hombrechtikon, Switzerland). The RNA was quantified by optical density readings at A260nm by using the NanoDrop ND-1000 (Thermo Scientific, Rockford). Gene expression analysis was performed using Agilent Human Genome 4 × 44 K arrays (Agilent Technologies, Santa Clara). Raw signal data for each of the 3 independent samples were analyzed separately by the GeneSpring GX software (Agilent Technologies). Data were filtered according to the expression level for quality control to eliminate genes that were below the 20th percentile threshold. The expression value of each gene was normalized to the median expression value of all genes in each chip. A total of 30,465 probes were included in the analysis.   Genomic DNA was obtained from venous blood samples. Genotyping was performed by Riken Genesis (Yokohama, Japan) using the Illumina HumanOmni1-Quad BeadChip (Illumina, Inc., San Diego). A total of 713,495 autosomal SNPs were assessed for quality using the PLINK v1.07 software. All SNPs with a call rate below 95%, a deviation from Hardy-Weinberg equilibrium at an error level of P < 0.001, or a minor allele frequency of less than 10% were excluded. The remaining 534,404 SNPs were used for further analysis.

first: Hiroaki

last: Hori

first: Seiji

last: Nakamura

first: Ryo

last: Miyata

first: Toshiya

last: Teraishi

first: Kotaro

last: Hattori

first: Miho

last: Ota

first: Noriko

last: Yamamoto

first: Teruhiko

last: Higuchi

first: Naoji

last: Amano

first: Hiroshi

last: Kunugi


title: Differentially expressed genes during disuse atrophy.

status: Public on Nov 10 2012

city: Boston

first: Susan

last: Kandarian

state: MA

address: 635commonwealth ave, Rm444

department: Health Sciences

institute: Boston University

summary:
To identify atrophy genes directly targeted by Bcl-3 transactivator at a genome wide level, we performed whole transcript expression array and ChIP-seq for muscles from weight bearing or 5-day hind limb unloaded mice.
Genes that showed increased expression with unloading and a Bcl-3 peak in the promoter (from ChIP-seq data) were considered as Bcl-3 direct targets during disuse atrophy. Using ChIP array, we identified 241 direct targets for Bcl-3. Our data describe Bcl-3 as a global regulator both of the proteolysis and the change in energy metabolism that are essential components of muscle atrophy due to disuse.

overall_design: Disuse skeletal muscle atrophy was induced by hind limb unloading. Weight bearing (WB) or 5-day hind limb unloaded (HU) muscles were harvested for total RNA isolation and processed for whole transcript expression profiling. We chose to examine gene expression and Bcl-3 binding from 5-day unloaded muscles because our previous time course study of disuse atrophy suggested that most genes are differentially regulated at this time point, and thus, would best represent the time for Bcl-3 binding to the gene targets of the NF-kB transcriptional network.

first: Robert

middle: W

last: Jackman

first: Chia-Ling

last: Wu

middle: C


title: Cyto2.7M copy number analysis of eight diffuse large B-cell samples and one matched blood sample

status: Public on Nov 26 2012

city: Aalborg

first: Julie

middle: Støve

last: Bødker

address: Sdr. Skovvej 15

department: Department of Heamatology

country: Denmark

institute: Aalborg University Hospital

summary: We performed a comparison analysis of the Affymetrix arrays SNP6.0 genome wide array (SNP6.0) and cytogenetic 2.7M whole-genome array (Cyto2.7M) using nine human samples. We compared the two array types with respect to four parameters including the size and breakpoints of the alterations detected, the actual CN assigned to the CNVs as well as long stretches of loss of heterozygosity. Overall, we found very good consistency between the two types of array on all parameters compared, even in regions with very complex changes. This GEO submission contains the Cyto2.7M data. GEO submission, GSE37977 contains the SNP6.0 data.

overall_design:
DNA was extracted from eight samples of diffuse-large B-cell lymphoma with complex genomic rearrangements using the DNeasy Blood & Tissue kit (Qiagen) following manufactures instructions. DNA was also included from one matched blood sample where mononuclear cells were isolated from the blood sample by Ficoll-Paque Plus (GE Health Care, Uppsala, Sweden) and stored in 10 % DMSO and 20 % serum at – 80 oC. For DNA extraction, the cells were thawed, washed twice in PBS and genomic DNA extracted using the DNeasy Blood & Tissue kit (Qiagen). The DNA was eluted in water and the concentration measured using a Nanodrop (Thermo Scientific).
Copy number analysis of Affymetrix cytogenetic 2.7M whole-genome arrays was performed on eight diffuse large B-cell samples and one matched blood sample.

middle: S

first: Claus

last: Gyrup

first: Preben

last: Johansen

first: Alexander

last: Schmitz

first: Jakob

last: Madsen

first: Hans

last: Johnsen

first: Martin

last: Boegsted

first: Karen

last: Dybkær

first: Mette

last: Nyegaard


title: Transcriptome comparison of S. pyogenes strains MGAS2221 and 2221ΔrivRX

status: Public on Dec 01 2012

city: Reno

first: Paul

last: Sumby

state: NV

address: 1554 N. Virginia St.

department: Microbiology & Immunology

institute: University of Nevada

summary: The rivR gene encodes a putative transcriptional regulator, while the rivX gene encodes a putative small regulatory RNA.  To determine the RivRX regulon during exponential phase growth in THY broth we compared parental strain MGAS2221 with isogenic rivRX mutant strain 2221ΔrivRX.

overall_design: GAS strains were grown in THY broth to mid-exponential phase, corresponding to an O.D.600 of 0.5.  A 4.5ml aliquot of each GAS culture was added to 9ml of RNAprotect (Qiagen Inc.).  Following addition of RNAprotect, samples were incubated at room temperature for 5 mins before centrifuging.  Supernatant was removed and the pellets quick frozen in liquid nitrogen and stored at -80 °C until ready to use.  RNA isolation, cDNA synthesis, and use of our custom Affymetrix microarray was as previously described (Perez et al., 2009)


title: The maternal transcriptome of the crustacean Parhyale hawaiensis is inherited asymmetrically to invariant cell lineages of the ectoderm and mesoderm [late_vs_early_embryonic]

first: Peter

last: Nestorov

overall_design:
microarray analysis of early vs late embryonic transcriptomes
Institution: Max Planck Institute for Developmental Biology, Tuebingen, Germany
Time of experiment: April 2008 to April 2009

first: Florian

last: Battke

first: Mitchell

last: Levesque

first: Matthias

last: Gerberding


title: Comparison of the oxacillin stress response in vraS and vraT mutants

status: Public on Nov 30 2012

city: CHICAGO

first: Susan

last: Boyle-Vavra

state: IL

address: 900 E 57th Street

institute: University of Chicago

summary: To determine the role of the second gene in the vra operon (vraT) in the stress response to oxacillin, we compared the oxacillin induction profiles in a vraT deletion strain to that of a vraSR mutant in a USA300 MRSA strain background.

sample_organism: Staphylococcus aureus subsp. aureus USA300

overall_design: Nonpolar deletion of vraT and insertional inactivation of vraS was constructed in MRSA strain USA300.

first: Shouhui

last: Yin

last: Daum


title: The maternal transcriptome of the crustacean Parhyale hawaiensis is inherited asymmetrically to invariant cell lineages of the ectoderm and mesoderm [rest_8cell_embryonic_vs_ectoderm]

overall_design:
microarray analysis of the 8-cell stage embryonic transcriptome - ectodermal progenitors vs. rest
Institution: Max Planck Institute for Developmental Biology, Tuebingen, Germany
Time of experiment: April 2008 to April 2009


title: Microarray Analysis of microRNA Expression during Axolotl Limb Regeneration

status: Public on Nov 06 2012

city: New Haven

first: Edna

last: Holman

state: CT

address: 266 Whitney Ave. KBT-442

department: Molecular, Cellular and Developmental Biology

institute: Yale University

summary: The salamander microRNA expression between mid-bud limb regenerating blastemas (17 days post amputation) and non-regenerating stump tissues was compared by microarray analysis.

platform_organism:
Danio rerio
Gallus gallus
Lemur catta
Ateles sp.
Gorilla gorilla
Pan troglodytes
Homo sapiens
Bos taurus
Mus musculus
Rattus norvegicus
Human alphaherpesvirus 1
Human betaherpesvirus 5
human gammaherpesvirus 4
JC polyomavirus
Human immunodeficiency virus 1
Monodelphis domestica
Human gammaherpesvirus 8
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design:
LC Sciences arrays: Six paired samples were analyzed: three mid-bud 17dpa blastemas (bl), and three non-regenerating stumps (st). Three arrays were hybridized comparing two paired samples each time. Biological dye-swaps were made by labeling bl samples once with Cy3 and twice with Cy5; st samples were labeled accordingly twice with Cy5 and once with Cy3.  Multiple arrays averaged into a single Sample record.
Supplementary files:
GSE29727_LC_MultiArray_SimpleNormalizedData.txt.gz
GSE29727_LC_signal_ratio_mean_SD.txt.gz
GSE29727_LC_t-Test_st-vs-bl.txt.gz

Exiqon arrays: Six paired samples were analyzed: three mid-bud 17dpa blastemas (bl), and three non-regenerating stumps (st). Six arrays were hybridized comparing each sample labeled with Hy3 against a common reference sample made by pooling all the samples and labeling it with Hy5. Multiple arrays not averaged, represented as multiple Sample records.
Supplementary file: GSE29727_Exiqon_matrix_complete.txt

first: Craig

last: Crews


title: miRNA expression profile from ANGPTL1 overexpression lung cancer cell

city: Taipei

first: Tsang-Chih

last: Kuo

address: No. 1, Section 1, Jen-Ai Road

country: Taiwan

institute: National Taiwan University

summary:
ANGPTL1-overexpressed CL1-5 cells were used to identify miRNAs which regulate EMT, cancer invasion and metastasis.
We used microRNA Taqman Low Density Array to identify candidate miRNAs

overall_design: ANGPTL1-overexpressed CL1-5 cells were analyzed compare to vector control (pcDNA3.1) CL1-5 cells

first: Jen-Liang

last: Su

first: Min-Liang


title: Distribution of EBP50 binding motifs.

status: Public on Nov 16 2012

first: Yih-Jyh

last: Shann

address: No.155, Sec.2, Linong Street

institute: Nation Yang-Ming University

type: Genome binding/occupancy profiling by genome tiling array

summary: The aim of this study is to identify EBP50 binding sequence.

overall_design: Chip-on-chip experiment with chromatin immunoprecipated with anti-EBP50 antibody is labeled with Cy5 and mock IP (Input DNA) is labeled with Cy3.

first: Yu-Yu

last: Lin

first: Yung-Ho

last: Hsu

first: Hsin-Yi

last: Huang

first: Chi-Ying

middle: F

first: Shu-Cheng

last: Wei

first: Chi-Ling

last: Chen

first: Tzuu-Shuh

last: Jou.


title: Gastric cancer tumor tissue samples and cell lines vs normal sample

status: Public on Nov 05 2012

city: San Francisco

first: Xin

state: CA

institute: UCSF

type: Genome variation profiling by genome tiling array

summary: We analyzed DNA copy number alterations in 64 human gastric cancer samples and 8 gastric cancer cell lines using bacterial artificial chromosome (BAC) arrays based comparative genomic hybridisation (aCGH).

overall_design: Gastric cancer tumor tissue samples and cell lines vs normal blood samples

first: Biao

last: Fan


title: Transcriptome response to genistein in zebrafish embryos

status: Public on Nov 01 2012

city: Aachen

first: Viktoria

last: Schiller

state: NRW

address: Forckenbeckstrasse 6

department: UNIFISH

country: Germany

institute: Fraunhofer IME

summary: To test wether endocrine disruption is detectable in zebrafish at the transcriptome level, we exposed newly fertilized zebrafish embryos to low doses of genistein (EC10 and EC20) for 48 hours.

overall_design: Newly fertilized embryos (<2hpf) were exposed to 2.2 mg/l (EC10) and 2.4 mg/l (EC20) genistein for 48 hours. Since aceton was used as a solvent for genistein, an acetone solvent control in addition to the water (ISO) control was included in the study. Overall, four replicates were performed per condition, each consisting of 24 pooled embryos.

first: Arne

last: Wichmann

first: Ralf

last: Kriehuber

first: Markus

last: Hecker

first: Martina

last: Fenske


title: microRNA expression in young and elder mouse tissues

first: Hirohiko

last: Hohjoh

state: Tokyo

address: 4-1-1 Ogawahigashi

institute: National Institute of Neuroscience, NCNP

summary: We investigated expression profiles of miRNAs in various tissues of young and elder mice by means of DNA microarray. The results suggested that there was a difference in the expression of miRNAs between young and elder mice.

overall_design: Small RNA samples prepareed from various tissues of young and elder mice were examined by means of Genopal®-MICM DNA chips.

first: Akiko

last: Eda

first: Tatsunobu

last: Fukushima


title: microRNA expression in various tissues of klotho-deficient and wild-type mice

summary: The expression profiles of miRNAs in klotho-deficient and wild-type mice were examined by means of Genopal®-MICM DNA chips. The data suggested that there was a difference in the expression of miRNAs between klotho-deficient and wild-type mice.

overall_design: Small RNA samples prevared from 5-week-old klotho-deficient and wild-type mice were examined.


title: Analyses of senescence-associated miRNAs in various mouse tissues

overall_design: Refer to individual Series


title: Transcriptomic study of Sphingomonas sp. LH128 inoculated into phenanthrene-contaminated soil

status: Public on Oct 20 2012

city: Heverle

first: Tekle Tafese

last: Fida

address: Kastelpark Arenberg 220

department: Earth and environmental Science

country: Belgium

institute: KU Leuven

summary: The survival, pollutant degradation activity and transcriptome response was monitored in Sphingomonas sp. LH128 inoculated into soil. Cultivable cell numbers were determined by plating, while phenanthrene degradation was monitored by HPLC. The genetic base for the adaptive strategy of LH128 in soil was investigated by using microarray consisting 7,200 gene-coding ORFs. During 4 hours of incubation, 510 genes were differentially expressed (317 increased and 193 reduced expression) while 610 genes were differentially expressed (318 increased and 292 reduced) after 10 days of incubation. Genes with increased expression comprised of gene encoding PAH catabolic enzymes, stress resistance, oxidative stress tolerance, outer membrane proteins/porins and efflux pump proteins while the downregulated genes comprised of genes encoding flagellar biosynthesis, ribosomal proteins and ATPase.

overall_design: Transcriptomic response of phenanthrene degrading Sphingomonas sp. LH128 inoculated into phenanthrene contaminated soil after 4h and after 10 days of incubation was studied using genome-wide gene expression analysis. For this purpose, the strain was pregrown in minimal medium and inoculated at appropriated celld densitites. RNA was extracted both from soil and and from initial inoculum and cDNA was synthesized and labeled with Cy3. Transcriptomic response in soil of three replicates per conditions after both incubation duration were analyzed and compared with the initial inoculum

first: T

last: Tekle

first: S

last: Moreno

first: H

last: Heipeier

first: P

last: Breugelmans

first: W

last: Roling

first: J

middle: R

last: Van Der Meer

first: D

last: Springael


title: Transcriptome analysis of annotated coding genes and sORF in 16 organs and 17 environmental conditions at A. thaliana

status: Public on Sep 30 2012

city: Iizuka

first: Kousuke

last: Hanada

state: Fukuoka

address: 680-4 Kawazu

department: Department of Bioscience and Bioinformatics

institute: Kyushu Institute Technology

summary: There are 16 organ samples (dry seeds, 24H imbibed seeds, 48H imbibed seeds, juvenile rosette, adult rosette, senescence leaves, cauline leaves, stems, young buds, mature flower buds, flowers, young siliques, mature siliques and old siliques) with triplicates. There are 17 samples of different environmental samples (0 h white, 1 h white, 6 h white, 24 h white, dark, blue, far-red and red lights, control, cold 2h, cold 6h, hot 2h, hot 6h, NaCl 2h, NaCl 6h, dry 2h and dry 6h) with triplicates.

overall_design: For 12 organs, three lines of plants were grown in soil under the long-day conditions of 16 hours light at 22℃. Samples were collected from each of juvenile rosette leaves, adult rosette leaves, cauline leaves, stems, young flower buds (sepals were closed and petals are not visible), mature flower buds (petals are visible), flowers, young siliques filled with white seeds, mature siliques filled with green seeds, old yellowing siliques (2-month-old) and senescence rosettes. Root tissues were collected from 2-week-old plants growing on 1% agar plates containing Murashige and Skoog (MS). Callus were collected from cultured CIM (callus induction medium) containing B5 medium supplemented with 20 g liter–1 glucose, 0.5 mg liter–1 2,4-D, and 0.1 mg liter–1 kinetin. Dry seed was defined to be after-ripened seeds for 4 weeks. Imbibed seeds are collected from seeds imbibed on the moistened paper for 24 and 48 hours under the continuous light at 22℃. In light irradiations, wild type (WT) seeds were plated on MS plates. For the time course experiment of white light, the plates were placed at 4°C in darkness for at least 2 days prior to receiving 6 h red light irradiation to synchronize germination. Then, plates were placed in the dark for 3 days and then exposed to white fluorescent light (100 μmol m–2 s–1) for 1, 6 and 24 h. For monochromatic light experiment, WT seedlings were grown in continuous red light, blue light, far-red light, or darkness for 6 days after red light irradiation. The light intensity used was 0.17 μmol m–2 s–1 for red light, 1.16 μmol m–2 s–1 for blue light and 0.53 μmol m–2 s–1 for far-red light. All abiotic stress samplings were collected from plants grown for 2 weeks on MS plates under 2 and 6 hours of abiotic stress conditions at the continuous light at 22℃. For drought stress treatment, plants were transferred and dehydrated onto the dried filter paper in the covered plastic dishes. For heat and cold stress treatments, the covered plastic dishes with plants were transferred directly from 22 to 37 and 2℃ respectively. For salinity stress treatment, plants were transferred onto the filter paper moistened with MS plates including 200mM NaCl.

first: Mieko

last: Higuchi

first: Masanori

last: Okamoto

first: Takeshi

last: Yoshizumi

first: Minami

last: Shimizu

first: Maho

last: Tanaka

first: Yoko

last: Horii

first: Mika

last: Kawashima

first: Keiko

last: Matsui

first: Tetsuro

last: Toyoda

first: Kazuo

last: Shinozaki

first: Motoaki

last: Seki


title: Whole blood response of Pigs to infection with Porcine Reproductive and Respiratory Syndrome Virus (PRRSV)

status: Public on Sep 26 2012

city: East Lansing

first: juan

middle: p

last: steibel

state: MI

address: 1205 I Anthony Hall

institute: Michigan State University

summary:
Porcine reproductive and respiratory disease (PRRS) is the most important disease in swine industry worldwide. However, strategies such as vaccination and good biosecurity are not consistently successful to eliminate PRRSV. Although some gene expression pathways have been explored recently, host molecular pathways blocked by PRRSV and the protective immune response expressed in pigs resistant to PRRSV are largely unknown. In order to answer these questions, we herein characterize changes in blood gene expression in pigs responding differentially to infection  with a well characterized type 2 (North American) PRRSV isolate. Samples are those collected through the PRRS Host Genetics Consortium (PHGC).
Samples were those from Tempus tube collected blood of PHGC pigs selected from four response groups according to their serum viral load (0-21 days post infection) and weight gain (0-42 dpi) and characterized as low vs. high viral load and low vs high weight gain .

overall_design: block reference design was used to accommodate samples from 4 treatment groups.

first: Maria

last: Arceo

first: Catherine

last: Ernst

first: Joan

middle: K

last: Lunney

first: Nancy

last: Raney

first: Raymond

last: Rowland

first: Juan

last: Steibel


title: Expression analysis of tomato plants TYLCV resistant, susceptible and resistant line silenced in the hexose transporter (LeHT1) gene before and 7 days after inoculation of tomato with Tomato yellow leaf curl virus  (TYLCV).

city: Rehovot

first: Dagan

last: Sade

address: Hertzel

country: Israel

institute: Hebrew University of Jerusalem

summary:
Investigation of whole genome gene expression level changes in a resistance  susceptible  and  LeHT1-silenced resistance tomato plants, infected with TYLCV and compared to the non infected control.
Two inbred tomato lines (named R and S) were used issued  from a breeding program  describe by Vidavsky and Czosnek, 1998, and Silencing of the hexose transporter gene LeHT1 and the properties of these plants have been described  by Eybishtz et al., 2010.

overall_design:
The array was designed to include all the known tomato genes retrieved from TIGR and Sol Genomics public databases. Following filtration for redundancies, 25,591 known genes and 7,335 uncertain or unknown genes were retrieved The data were transferred to Roche NimblGen company (http://www.nimblegen.com/) who has generated a 60-mer oligonucleotide array where each of the ~30,000 tomato genes is represented by at least two specific probes, and unrelated controls. Each slide contains four arrays of ~70,000 oligos.
TYLCV resistant and susceptible lines infection with TYLCV and LeHT1  silenced TYLCV resistant line infected with TYLCV

first: Henry

last: Czosnek

first: Inber

last: Plaschke


title: Bilberries reduce low-grade inflammation and subacute endotoxemia in individuals with features of metabolic syndrome - microarray/QPCR profiling of dietary effects of bilberries in PBMCs

status: Public on Sep 15 2012

city: Kuopio

first: Otto

middle: Taavetti

last: Mykkänen

address: Yliopistonranta 1

department: Public Health and Clinical Nutrition

country: Finland

institute: University of Eastern Finland

type:
Expression profiling by array
Expression profiling by RT-PCR

summary:
Obesity and its consequences on cardiometabolic health have been associated to low-grade inflammation. The most diverse source of dietary anti-inflammatory compounds is polyphenols and especially anthocyanins, which are major polyphenols in bilberries (Vaccinium myrtillus).
We investigated the effects of a bilberry-rich diet on glucose and lipid metabolism, inflammation and gene expression profile in peripheral blood mononuclear cells (PBMCs) in subjects with overweight and other features of the metabolic syndrome.  The study was a randomized, controlled clinical intervention using 2-arm parallel group design. The participants in the bilberry group (BB, n = 15) consumed bilberries or berry products equivalent of 400 g fresh bilberries daily for 8 weeks, while the participants in the control group (C, n = 12) were asked to maintain their habitual diet.
The microarray profiling was done from 3 subjects in the BB group and further QPCR expression analyses from all subjects in both groups at the start and end of the intervention (weeks 0 and 8). From 50 differentially expressed transcripts (P<0.005), five candidate genes; WDSUB1, COX7B, RGS18, DAPP1 and TICAM1, were randomly selected for QPCR analyses from PBMCs in both groups.  To further explore the interplay of dietary change and activated pathways in PBMCs, 11 additional genes were selected for QPCR. The selected transcripts were from the LPB, RIPK-1, Ly96 (MD2), CD19, MMD, TNFRSF12A, CD72, CCR2, IL17RC, IL17R and MAP3K7IP2 genes.  Our results indicate that regular bilberry intake may reduce endotoxemia and chronic inflammation, the latter especially by directing the immunity away from overactive innate cell mediated responsiveness. Bilberry consumption may decrease cardiovascular and metabolic risk in the long term.

overall_design:
The microarray profiling was done in PBMCs from 3 subjects in BB group and further QPCR expression analyses in PBMCs from 15 subjects in the BB group and 12 subjects in the C group.

For QPCR expression analyses;
Time point (biological replicate):
0 wk: baseline PBMCs1 - 15, baseline PBMCc1- 12
Time point (biological replicate):
8 wk: bilberry PBMCs1 - 15, bilberry PBMCc1 - 12
Non-normalized data with triplicate samples (technical replicate) of each bilogical replicates (replicate1-3)

first: Michiel

last: Adriaens

first: Pirkka

middle: V

last: Kirjavainen

first: Leena

last: Pulkkinen

first: Hannu

first: Riitta

last: Törrönen

first: Majukka

last: Kolehmainen


title: Expression Analysis of WR99210-treated Mycobacterium tuberculosis H37Rv

status: Public on Sep 18 2012

city: Seattle

first: Molly

last: Nixon

state: WA

address: 307 Westlake Ave N Ste 500

institute: Seattle Biomedical Research Institute

summary:
Investigation of whole genome gene expression level changes in Mycobacterium tuberculosis treated with the DHFR inhibitor WR99210, compared to untreated cells.
The antimycobacterial properties of WR99210 are further described in Gerum, A., Ulmer, J., Jacobus, D., Jensen, N., Sherman, D., and C. Sibley. 2002. Novel Saccharomyces cerevisiae screen identifies WR99210 analogues that inhibit Mycobacterium tuberculosis dihydrofolate reductase. Antimicrob Agents Chemother 46(11):3362-3369 [PMID:12384337]

overall_design: A nine chip experiment in which total RNA was collected from H37Rv after treatment with 100 uM WR99210 for 0, 4, and 24 hours.  Three separate cultures/biological replicates were interrogated for both treated and untreated cultures.  Labeled cDNA was hybridized to NimbleGen spotted oligo tiling arrays covering both strands of the M. tuberculosis genome at ~200 bp intervals between 60-mer probes.

first: David

last: Sherman


title: The Transcriptional and Gene Regulatory Network of Lactococcus lactis MG1363 during Growth in Milk

status: Public on Sep 12 2012

city: Groningen

first: Anne

middle: de

last: Jong

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: university of Groningen

summary: In the present study we examine the changes in the expression of genes of Lactococcus lactis subspecies cremoris MG1363 during growth in milk. To reveal which specific classes of genes (pathways, operons, regulons, COGs) are important, we performed a transcriptome time series experiment. Global analysis of gene expression over time showed that L. lactis adapted quickly to the environmental changes. Using upstream sequences of genes with correlated gene expression profiles, we uncovered a substantial number of putative DNA binding motifs that may be relevant for L. lactis fermentative growth in milk. All available novel and literature-derived data were integrated into network reconstruction building blocks, which were used to reconstruct and visualize the L. lactis gene regulatory network. This network enables easy mining in the chrono-transcriptomics data. A freely available website at http://milkts.molgenrug.nl gives full access to all transcriptome data, to the reconstructed network and to the individual network building blocks.

sample_organism: Lactococcus cremoris subsp. cremoris MG1363

overall_design: 12 time points

last: de Jong

first: Morten

middle: E

last: Hansen

first: Oscar

last: Kuipers

first: Mogens

last: Kilstrup

first: Jan

last: Kok


title: Gene expression profiling in murine mesenchymal stem cells treated with local anesthetics (ropivacaine)

status: Public on Aug 31 2012

city: Edmonton

first: Eliana

last: Lucchinetti

address: HMRC 408

country: Canada

institute: University of Alberta

summary: Mesenchymal stem cells (MSCs) are recruited from the blood stream to tumors, healing wounds or sites of tissue injury by multiple growth factors and chemokines where they differentiate into e.g. fibroblasts or endothelial cells. Engrafted at the sites of tissue damage, they secrete growth factors and cytokines that facilitate healing. Inhibition of MSC proliferation by prolonged application of local anesthetics (commonly used after surgery) could delay wound closure and promote wound dehiscence.

overall_design: Culture-expanded bone-marrow-derived murine MSCs wewre treated in vitro with 100 uM ropivacaine for 24 hours (4 samples). Untreated MSCs served as controls.The collected cells were immediately frozen in liquid nitrogen and later used for RNA isolation and subsequent microarray hybridization. Gene-level analysis was performed. Exon-level analysis will be also performed.

first: Michael

last: Zaugg


title: Gene expression analysis of wild type Pectobacterium wasabie SCC3193 compared to a SCC3193 inactivation mutant of rsmA

status: Public on Aug 24 2012

city: Helsinki

first: Martin

last: Broberg

address: Viikinkaari 5D

department: Biosciences

institute: University of Helsinki

summary: Posttranscriptional regulator RsmA is part of a regulatory system that controls production of plant cell wall degrading enzymes (PCWDEs), motility and other virulence factors among the Pectobacterium spp of plant pathogens. We constructed the knockout mutation of rsmA gene in Pectobacterium wasabiae strain SCC3193. The rsmA- strain has three times lower growth rate but increased virulence when compared to wild type. To explain this phenotype we compared wild type and rsmA- mRNA levels using genome wide microarray. We found that the synthesis of all known virulence factors and flagella is upregulated, while cell division and peptidoglycan synthesis is down regulated in rsmA- strain. The TCA cycle is directed fully to energy production, indicating low energetic status of the cell that is a probable reason for the low growth rate of the mutant. Growth experiments showed that the enzymatic activities of extracellular virulence factors polygalacturonase and pectate lyase are very high throughout the growth curve even without induction by plant component. Wild type cells are rod shaped in liquid media, but elongated and hyperflagellated in swarm plate containing potato tuber extract and in potato tuber. The rsmA- strain exhibits the same conditional phenotype, but differentiation into swarmer cells is faster and cell elongation more pronounced. Virulence experiments in potato tuber showed that although rsmA- strain causes bigger tissue maceration, its ability to compete with the natural bacterial community in the host is decreased. We conclude that the lack of RsmA switches the cells to infective phenotype characterized by expression of virulence factors and swarming. The lack of control over these energy costly processes is probably the reason for decreased growth rate and fitness.

overall_design: Gene expression analysis from P. wasabie SCC3193 wildtype and SCC3193 rsmA mutant was performed on RNA samples extraxcted from the rsmA mutant (at 40 and 48 hours) and wildtype (at 24 hours). The strain were grown on 1.5% agar M9 minimal media plates supplemented with 10% potato extract. Three biological replicates were used from each strain at each time point.

first: Viia

last: Kõiv

first: Liis

last: Andresen

first: Jekaterina

last: Frolova

first: Panu

last: Somervuo

first: Petri

last: Auvinen

first: Tapio

last: Palva

first: Minna

last: Pirhonen

first: Andres

last: Mäe


title: α-catulin play a role in lung cancer metastasis

status: Public on Aug 16 2012

first: Tse-Ming

last: Hong

address: 128 Academia Road, Section 2, Nankang

institute: Academia Sinica

summary: Background: α-catulin may functions as an oncoprotein, sustaining proliferation by preventing cellular senescence and promoting cancer cell migration. In this study, we investigated the mechanism of α-catulin in cancer cell migration and metastasis in lung cancer. Method: α-catulin mRNA expression was isolated from A549/AS2neo (control) and A549/AS2neo-α-catulin stable cells. The Phalanx Human OneArray microarray analysis was performed to identify α-catulin downstream genes. Results: Overexpression of α-catulin increased cancer cell migration and metastasis. By using Phalanx Human OneArray microarray we have identified panel of genes altered by α-catulin overexpression, consisting of CDC42, intergrins and genes related to cytoskeleton remodeling. Conclusion: α-catulin is an oncoprotein and promotes lung cancer cell migration and metastasis.

overall_design: Two-condition experiment, Vector vs. alpha-catulin overexpression cells.The cDNAs encoding full-length human alpha-catulin were amplified and subcloned into lentiviral pLKO_AS2.neo which generated full-length alpha-catulin. Vector control or alpha-catulin lentivirus were transduced into A549 cells and G418 was used to select stable cells.

first: C

middle: H

last: Liang

first: T

first: Y

last: Chen


title: Comparative transcriptomic analysis of acute host responses during 2009 pandemic H1N1 influenza infection in mouse, macaque, and swine (swine dataset)

last: Katze

address: Rosen Building 960 Republican St.

department: Microbiology

institute: University of Washington

summary:
Background: The 2009 pandemic H1N1 influenza virus emerged in swine and quickly became a major global health threat. In mouse, non-human primate, and swine infection models, the pH1N1 virus efficiently replicates in the lung and induces pro-inflammatory host responses; however, whether similar or different cellular pathways were impacted by pH1N1 virus across independent infection models remains to be further defined. To address this, we have performed a comparative transcriptomic analysis of acute host responses to a single pH1N1 influenza virus, A/California/04/2009 (CA04), in the lung of mice, macaques and swine.

Results: Despite similarities in the clinical course, we observed differences in inflammatory molecules elicited, and the kinetics of their gene expression changes across all three species. The retinoid X receptor (RXR) signaling pathway controlling pro-inflammatory and metabolic processes was differentially regulated during infection in each species, though the heterodimeric RXR partner, pathway associated signaling molecules, and gene expression patterns differed in each species.

Conclusions: By comparing transcriptional changes in the context of clinical and virological measures, we identified differences in the host transcriptional response to pH1N1 virus across independent models of acute infection. Antiviral resistance and the emergence of new influenza viruses have placed more focus on developing drugs that target the immune system. Underlying overt clinical disease are molecular events that suggest therapeutic targets identified in one host may not be appropriate in another.

overall_design: The goal of this experiment was to use global gene expression profiling to understand swine lung host responses to pandemic H1N1 influenza A/Californica/04/2009 (CA04) virus infection and compare acute host responses across independent species. Four-week-old crossbred pigs (Sus Scrofa) were inoculated intratracheally with either 10^6 TCID50/pig egg-derived 2009 pandemic influenza A/California/04/2009 virus (n = 5) or mock inoculated with non-infectious cell culture supernatant (control; n = 4). Animals were euthanized on day 7 post-infection and lung samples were used for microarray.

first: Jennifer

last: Tisoncik Go

first: Sarah

last: Belisle

first: Nicolas

last: Tchitchek

first: Terrence

last: Tumpey

first: Wenjun

last: Ma

first: Juergen

middle: A

last: Richt

first: Heinz

last: Feldmann

middle: G


title: Francisella tularensis Schu4 gene expression during infection of mouse spleen

status: Public on Aug 04 2012

city: Fort Collins

first: Luke

last: Kingry

state: CO

address: 2025 IDRC at Foothills Campus Delivery

institute: Colorado State University

summary: Francisella tularensis is classified as a Category A priority pathogen and causes fatal disseminated disease in humans upon inhalation of less than 50 bacteria. Although drugs are available for treatment, they are not ideal because of toxicity and delivery, and in some cases relapse upon withdrawal. We have an ongoing program in the development of novel FabI enoyl-ACP-reductase enzyme inhibitors for Francisella and other select agents. To establish ftFabI in F. tularensis as a clinically relevant drug target, we demonstrated that the enzyme is essential for growth in vitro and that ftfabI is not transcriptionally altered in the presence of exogenous fatty acids. Inhibition of ftFabI results in loss of viability that is not rescued by exogenous fatty acids supplementation. Importantly, whole-genome transcriptional profiling of F. tularensis with DNA microarrays from infected tissues revealed that ftfabI and de novo fatty acid biosynthetic genes are transcriptionally active during infection. This is the first demonstration that the FabI enoyl-ACP-reductase enzyme encoded by F. tularensis is essential and that de novo fatty acid biosynthetic components are transcriptionally active during infection in the mouse model tularemia.

sample_organism: Francisella tularensis subsp. tularensis SCHU S4

overall_design: 2 C57BL/6 mice were infected with Francisella tularensis strain Schu4 via the intranasal route. Spleen tissue was harvested at 120 hours post-infection and total RNA was isolated immediately after harvest. RNA was pooled and host polyA-tailed RNA and ribosomal RNA were depleted using hybridization probes coupled to magnetic beads. The resulting sample was enriched for bacterial mRNA, and dye labeled using random hexamer primed RT and Cy3-labeled dUTPs. Labeled cDNA was hybridized in triplicate to custom whole genome cDNA microarrays and scanned using a GenePix 4000B.

first: Richard

last: Slayden


title: Identification of Ligands for the human gamma-delta TCR

status: Public on Jul 28 2012

city: London

first: Adrian

last: Hayday

address: St Thomas' Street

department: Immunobiology

country: United Kingdom

institute: King's College London, Guy's Campus

summary:
 T cells bearing gamma delta T cell antigen receptors (TCRs) function in lymphoid stress surveillance. However, the contribution of gamma delta TCRs to such responses is unclear. Here we found that the TCR of a human V gamma4Vdelta5 clone directly bound endothelial protein C receptor (EPCR), which allowed gamma delta T cells to recognize both endothelial cells targeted by cytomegalovirus and epithelial tumors. EPCR is a major histocompatibility complex–like molecule that binds lipids analogously to the antigen-presenting molecule CD1d. However, the V gamma4Vdelta5 TCR bound EPCR independently of lipids, in an antibody-like way. Moreover, the recognition of target cells by gamma delta
T cells required a multimolecular stress signature composed of EPCR and costimulatory ligand(s). Our results demonstrate how a gamma delta TCR mediates recognition of broadly stressed human cells by engaging a stress-regulated self antigen.

overall_design: 2E9 is an antibody that blocks gd-TCR recognition of human cells that are the targets of the clone LES. 2E9 also stains cells that are targeted by LES. Therefore, to identify the TCR ligand expressed by 2E9-positive cells, Gene Expression was compared in two cell lines that stain with 2E9 (K562 and U937) versus two cell lines that do not (Hutu80 and Huh7).

first: Tobias

last: Silberzahn

first: Julie

last: Deschanet


title: Molecular Signatures of cardiac defects in Down syndrome lymphoblastoid cell lines (congenital heart disease)

status: Public on Aug 15 2012

city: Paris

first: Luce

last: Dauphinot

address: 47 boulevard de l'hôpital

department: ICM

country: France

institute: INSERM U1127-CNRS UMR7225-UPMC

summary: Molecular Signatures of cardiac defects in Down syndrome lymphoblastoid cell lines. In this study, we want to identify genes and pathways specifically dysregulated in atrioventricular septal defect and /or atrial septal defect + ventricular septal defect in case of trisomy 21.

overall_design: Total RNA obtained from DS lymphoblastoid cell lines without congenital heart disease compared to cell lines from DS with congenital heart disease.

first: Clementine

last: Ripoll

first: Isabelle

last: Rivals

first: Emilie

last: Ait Yahya-Graison

first: Evelyne

last: Paly

first: Clothilde

last: Mircher

first: Andre

last: Ravel

first: Yann

last: Grattau

first: Henry

last: Blehaut

last: Megarbane

first: Guy

last: Dembour

first: Benedicte

last: de Freminville

first: Renaud

last: Touraine

first: Nicole

last: Creau

first: Marie-Claude

last: Potier

first: Jean-Maurice

last: Delabar


title: ChIP-chip analysis to determine GLI2 binding sites

status: Public on Jul 11 2012

city: Houston

first: Pawel

last: Stankiewicz

state: TX

address: One Baylor Plaza

department: Molecular Human Genetics

institute: Baylor College of Medicine

summary: Chromatin immunoprecipitation with anti-GLI2 antibody was conducted in human pulomonary microvascular endothelial cells (HPMECs) to determine GLI2 binding sites upstream of FOXF1. An unanticipated and tremendous amount of the non-coding sequences of the human genome are transcribed. Long non-coding RNAs (lncRNAs) are non-protein coding transcripts longer than 200 nucleotides and their functions remain enigmatic. We demonstrate that deletions of lncRNA genes cause a lethal lung developmental disorder, Alveolar Capillary Dysplasia with Misalignment of Pulmonary Veins (ACD/MPV), with parent of origin effects. We identify non-coding overlapping deletions 250 kb upstream to FOXF1 in nine patients with ACD/MPV that arose de novo specifically on the maternally inherited chromosome and delete a fetal lung-specific EST, part of an lncRNA. These deletions define distant cis-regulatory region that harbors a differentially methylated CpG island, binds GLI2 depending on the methylation status of this CpG island, and physically interacts with and up-regulates the FOXF1 promoter, consistent with the absence of the fetal lung-transcribed lncRNA perturbing FOXF1 regulation. LncRNA-mediated chromatin interactions may be responsible for position effect phenomenon and potentially cause many disorders of human development.

overall_design: ChIP-chip HPMECs transfected to overxpress GLI2; 2 biological replicates

first: Katarzyna

last: Kolodziejska

first: Zhishuo

last: Ou

first: Richard

last: Person


title: Detection of non-coding deletion CNVs upstream to FOXF1 [Agilent-030795]

summary: Genomic copy number analysis in patients with ACD/MPV. An unanticipated and tremendous amount of the non-coding sequences of the human genome are transcribed. Long non-coding RNAs (lncRNAs) are non-protein coding transcripts longer than 200 nucleotides and their functions remain enigmatic. We demonstrate that deletions of lncRNA genes cause a lethal lung developmental disorder, Alveolar Capillary Dysplasia with Misalignment of Pulmonary Veins (ACD/MPV), with parent of origin effects. We identify non-coding overlapping deletions 250 kb upstream to FOXF1 in nine patients with ACD/MPV that arose de novo specifically on the maternally inherited chromosome and delete a fetal lung-specific EST, part of an lncRNA. These deletions define distant cis-regulatory region that harbors a differentially methylated CpG island, binds GLI2 depending on the methylation status of this CpG island, and physically interacts with and up-regulates the FOXF1 promoter, consistent with the absence of the fetal lung-transcribed lncRNA perturbing FOXF1 regulation. LncRNA-mediated chromatin interactions may be responsible for position effect phenomenon and potentially cause many disorders of human development.potentially cause many disorders of human development.

overall_design: CNVs were identified by array CGH with custom-designed 16q24.1 region specific (1Mb flanking FOXF1) 44K oligonucleotide microarrays (Agilent technologies) in 3 patients with ACD.

first: Przemyslaw

last: Szafranski


title: Biofilms of the PAH-degrading Sphingomonas sp. LH128 on solute stress when actively degrading and growing on phenanthrene

status: Public on Jun 18 2012

first: Tekle Tafese

last: Fida

summary: This study examines the transcriptomic response of biofilms of the PAH-degrading Sphingomonas sp. LH128 on solute stress when actively degrading and growing on the PAH compound. To address the effect of solute stress on bacterial physiology and transcriptomic response, NaCl was used as osmolyte. Both acute and chronic solute stress was invoked to assess differences in short-term and long-term responses.

overall_design: Transcriptomic response of phenanthrene degrading Sphingomonas sp. LH128 biofilms as a response to short-term and long-term solute (NaCl) stress was studied using genome-wide gene expression analysis. For this purpose, the strain was grown in customized continuous glass flow chambers that contain solid phenanthrene as a sole carbon source and that allow easy recovery of biofilm cells for transcriptomic and physiological analysis. A NaCl stress of 450 mM was imposed on LH128 biofilms growing on phenanthrene crystals coated on glass slides either for 4 hours (acute stress) or for 3 days (chronic stress). RNA was extracted from the biofilm and cDNA was synthesized and labeled with Cy3. Transcriptomic response in the stressed biofilms of three replicates per conditions were analyzed and compared with non-stressed

first: TEKLE

middle: T

first: PHILIP

last: Breugelmans

first: ROB

last: Lavigne

first: EDITH

last: Coronado

first: DAVID

last: Johnson

first: JAN

last: van der Meer

first: ANTONIA

middle: P

last: Mayer

first: HERMANN

last: Heipieper

first: JOHAN

last: Hofkens

first: DIRK

last: Springael


title: Detection of non-coding deletion CNVs upstream to FOXF1 [Agilent-022084]

status: Public on Jul 06 2012

city: Rotterdam

first: Erwin

last: Brosens

state: - If in U.S, Select a State -

address: Dr molewaterplein 50

department: Clinical genetics

institute: ErasmusMC

summary:
Genomic copy number analysis in patients with ACD/MPV. An unanticipated and tremendous amount of the non-coding sequences of the human  genome are transcribed. Long non-coding RNAs (lncRNAs) are non-protein coding  transcripts longer than 200 nucleotides and their functions remain enigmatic. We  demonstrate that deletions of lncRNA genes cause a lethal lung developmental disorder,  Alveolar Capillary Dysplasia with Misalignment of Pulmonary Veins (ACD/MPV), with  parent of origin effects. We identify non-coding overlapping deletions 250 kb upstream  to FOXF1 in nine patients with ACD/MPV that arose de novo specifically on the  maternally inherited chromosome and delete a fetal lung-specific EST, part of an  lncRNA. These deletions define distant cis-regulatory region that harbors a differentially  methylated CpG island, binds GLI2 depending on the methylation status of this CpG  island, and physically interacts with and up-regulates the FOXF1 promoter, consistent  with the absence of the fetal lung-transcribed lncRNA perturbing FOXF1 regulation.  LncRNA-mediated chromatin interactions may be responsible for position effect  phenomenon and potentially cause many disorders of human development.potentially cause many disorders of human development.
CNVs were identified by array CGH with custom-designed 16q24.1 region specific (1Mb flanking FOXF1) 44K oligonucleotide microarrays (Agilent technologies) in 3 patients with ACD.  This Series contains data for only two patients

overall_design: custom targeted oligoarray, normal reference vs patient sample

first: E

first: A

last: de Klein

first: D

last: Tibboel


title: Placental gene expression in pregnancies established after the transfer of day 7 blastocysts derived from in vitro (IVP), somatic cell nuclear transfer (SCNT) and in vivo (AI) embryos

status: Public on Jun 06 2012

city: Bonn

first: Dessie

last: Salilew-Wondim

address: Endenicher Allee 15

department: Animal breeding and husbandry group

institute: University of Bonn

summary: Aberrant placental gene expression associated with culture condition and/or deficiencies in transcriptome reprogramming are hypothesized to be the major cause of SCNT and IVP inefficiencies. Therefore, the main objective of this study was to invesitgate the dysregulated genes, molecular pathways and functional alteration in bovine placentas derived from SCNT and IVP pregnancies compared to their AI counterparts

overall_design: Day 7 blastocysts derived from AI, IVP or SCNT were transferred to synchronized cows. The pregnant animals were slaughtered at day 50 of the gestation period and the placentas were then recovered and used for transcriptome analysis using GeneChip bovine genome array

first: Dawit

last: Tesfaye

first: M

middle: M

last: Hossain

first: Eva

last: Held

first: Franca

last: Rings

first: Ernst

last: Tholen

first: Christian

last: Looft

first: Karl

last: Schellander

first: Michael

last: Hoelker


title: Expression profiling by array of Salmonella enterica serovar Typhimurium (SL1344) qseC mutant x wild type

status: Public on Jun 01 2012

city: Dallas

first: Cristiano

middle: Gallina

last: Moreira

address: 6000 Harry Hines Blvd.

institute: UT Southwestern Medical Center

summary:
“Stress, survival and virulence: the multi-faceted host/microbial interactions.”
Bacteria employ epinephrine and norepinephrine, which converge to distinct bacterial crucial processes, like survival and pathogenicity.  A novel stress periplasmic membrane protein belonging to previously described BOF family, protein renamed here SrpP, and together with membrane sensor kinase QseC has an essential role in stress response and virulence of S. Typhimurium.  SrpP employs its predicted binding pocket, specifically the SrpPE110 residue, and interacts with lipid A modification enzyme, LpxO dioxygenase.  Upon this interaction SrpP in S. Typhimurium finely manages multiple membrane functions to culminate in survival upon stress and pathogenesis in vivo, connecting host-stress chemical signaling to cell stress in bacteria.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

overall_design: Comparison of sensor histidine kinase qseC mutant expression levels versus wild type strain.

first: Stephen

last: Libby

first: Ferric

last: Fang

first: Vanessa

last: Sperandio


title: Microarray analysis of gene expression profiles in human neuroblastoma cells exposed to Amyloid beta-Zn and Amyloid beta-Cu complexes

status: Public on May 01 2012

city: Padua

first: Karina

last: Fincati

address: V.le G. Colombo, 3

department: Department of Biology, University of Padua

country: Italy

institute: CNR-Institute for Biomedical Technologies

summary:
Abnormal metal accumulation is associated with Alzheimer’s disease (AD) and has a relevant role in affecting amyloid beta-peptide (Abeta) aggregation and neurotoxicity.In the present study, employing a microarray analysis of 35,129 genes, we analyzed gene expression profile changes due to exposure to Abeta-Zn or Abeta-Cu complexes in neuronal-like cells (SH-SY5Y).
Microarray data indicated that Abeta-Zn or Abeta-Cu complexes selectively alter expression of genes mainly related to cell death, inflammatory responses, and apoptosis.Taken together these findings indicate that Abeta-Zn or Abeta-Cu show some commonalities in affecting AD-related target functions. The overall modulatory activity on these genes supports the idea of a possible net result leading to mechanisms that counteract toxic effects of Abeta-Zn or Abeta-Cu.

overall_design: Analysis used a neuronal cell lines, the SH-SY5Y, exposed to either AB,  the AB-Cu or AB-Zn complex or Cu or Zn alone. The SH-SY5Y without treatment were used that a control. For the exposure to AB, six replicates were performed (three dye swap and three non-dye swap), while for exposure to AB-Cu, AB-Zn, Zn and Cu two replicates each were made (one dye swap and one non-dye swap).

first: Denise

last: Drago

first: Valentina

last: Gatta

first: Stefano

last: Sensi

first: Paolo

last: Zatta


title: Small non-coding differentially-methylated copy-number variants, involving lncRNAs, cause a lethal lung developmental disorder

first: Pawel

last: Stankiewicz

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

overall_design: Refer to individual Series


title: Regulation of synovial DKK1 expression by local glucocorticoid metabolism in inflammatory arthritis

status: Public on Apr 24 2012

city: University of Birmingham

first: Rowan

middle: Samuel

last: Hardy

state: West Midlands

address: 2nd floor IBR

department: Clinical and Experimental Medicine

institute: University oif Birmingham

summary: Inflammatory arthritis is associated with bone loss and fractures due to abnormal bone remodelling. Bone remodelling is 'uncoupled' with bone resorption increased and bone formation suppressed. These changes resemble those seen in patients treated with therapeutic glucocorticoids, and in both of these situations, altered wnt signalling is implicated. Recent studies have highlighted the importance of the synovial fibroblast in mediating abnormal bone remodelling during inflammation. The wnt antagonist dickkopf-1 (DKK1) is secreted by synovial fibroblasts in response to inflammation, and this protein has been proposed to be a master regulator of bone remodelling in inflammatory arthritis. Here we show that DKK1 expression by primary human synovial fibroblasts is more potently regulated by glucocorticoids than pro-inflammatory cytokines. Glucocorticoids, but not TNF-alpha, regulated expression of multiple wnt agonists and antagonists in favour of inhibition of wnt signalling. In vitro TNF-alpha and IL1-beta indirectly regulate DKK1 production through increased expression of the glucocorticoid activating enzyme 11beta-hydroxysteroid dehydrogenase type 1 (11beta-HSD1). These results demonstrate that the links between synovial inflammation, altered wnt signalling and bone remodelling may not be direct but are dependent on local activation of endogenous glucocorticoids.

overall_design:
Human fibroblast-like synoviocytes isolated from patients with rheumatoid arthritis treated with either vehicle, TNF or dexamethasone (dex).
Gene arrays for control, TNF and dexamethasone treatments were performed on three separate synovial fibroblast cell lines isolated from three rheumatoid arthritis patients. All fold changes displayed are the combined results of the three separate fibroblast lines.

first: Mark

last: Cooper


title: Gene expression analysis in MZ twins discordant for IAR [in vitro]

status: Public on Apr 15 2012

city: Linköping

first: Fredrik

last: Barrenas

address: Sandbäcksgatan 7, level 2

department: Dept of Clinical and Experimental Medicine

country: Sweden

institute: Linköping University Hospital

summary: Gene expression analysis in CD4+ T cells extracted from allergen-challenged PBMCs, isolated from discordant MZ twins with IAR

overall_design: MZ twins discordant for intermittent allergic rhinitis (IAR)

first: Mikael

last: Benson


title: Characterization of whole blood gene and while blood cell expression profiles of dietary-induced hyperlipidemia in miniature pigs

status: Public on Apr 25 2012

city: Tsukuba

first: Junko

last: Takahashi

state: Ibaraki

address: 1-1-1 Umezono

institute: National Institute of Advanced Industrial Science and Technology　(AIST)

summary: Miniature pigs are useful model animal for gene expression studies on dietary-induced hyperlipidemia, because they have similar digestive physiology to human. Two typical dietary components were used for dietary-induced hyperlipidemia miniature pig models. One is a high-fat and high-cholesterol diet (HFCD) containing 15% lard and 2% cholesterol, the other is a high-fat, high-cholesterol and high-sucrose diet (HFCSD) containing 15% lard, 2% cholesterol and 37% sucrose.

overall_design: Whole blood gene expression in HFCD, HFCSD and control male miniature pigs was measured at 10, 19 and 27 weeks of feeding periods.　White blood cell gene expression in HFCD, HFCSD and control male miniature pigs was measured at 27 weeks of feeding period.

first: Hitoshi

last: Iwahashi


title: Refinement and discovery of new hotspots of copy number variation associated with autism spectrum disorder

status: Public on Sep 30 2012

first: Megan

middle: Y

last: Dennis

address: 3720 15th Ave NE

department: Department of Genome Sciences

summary: Rare DNA copy-number variation (CNV) plays an important role in the underlying genetic etiology of autism and intellectual disability.  Although large numbers of copy-number variants (CNVs) have been recently implicated in autism, most are large affecting many genes and specificity of these lesions with respect to classically defined autism as opposed to more broadly defined developmental delay is unclear.  We exploited the repeat architecture of the genome to target smaller regions (n=1340 hotspots, median size 15 kbp) flanked by repetitive sequence among 2,240 autism simplex patients and a subset of unaffected parents.

overall_design: 3,088 test samples and 2 references (NA12878 and NA18507) and an additional 1,214 test samples and 2 references (NA12878 and NA18507)

first: Santhosh

last: Girirajan

first: Carl

last: Baker

first: Maika

last: Malig

first: Bradley

last: Coe

first: Catarina

middle: D

last: Campbell

first: Kenneth

last: Mark

first: Tiffany

last: Vu

first: Can

last: Alkan

first: Ze

last: Cheng

first: Raphael

last: Bernier

first: Evan

last: Eichler


title: Gene expression profiling of endothelial cell apoptosis induced by serum withdrawal

status: Public on Jul 20 2012

city: Cambridge

first: Muna

last: Affara

address: Tennis Court Road

department: Pathology

institute: University of Cambridge

summary: To understand the regulatory relationships among EC transcripts during apoptosis using serum withdrawal time series microarray data and use this to identify master regulators of endothelial cell apoptosis.

overall_design: In the study presenty here, HUVEC isolates from 10 different individuals were pooled. The extracted RNA was hybridised onto the microarray at different timepoints following treatment with serum withdrawal. The time course was replicated 3 times using three different pools of 10 HUVEC isolates.

first: D

middle: S

last: Charnock-Jones

first: Cristin

last: Print


title: Transcriptional responses of human monocyte-derived macrophages (HMDM) to lipopolysaccharide (LPS) - Illumina arrays

status: Public on Mar 29 2012

city: Brisbane

first: Kate

last: Schroder

state: QLD

address: University of Queensland, St Lucia

country: Australia

institute: Institute for Molecular Bioscience

summary: These microarrays were performed for use in a genome-wide scan for LPS-regulated genes in human monocyte-derived macrophages, in order to construct a list of LPS-regulated genes for detailed interrogation on custom microarrays (see GSE19482 for custom array analysis).

overall_design: Human monocyte-derived macrophages (HMDM) were stimulated with the TLR4 agonist, lipopolysaccharide, over a time course (0, 0.5, 2, 6, 24h) and analysed in biological duplicate (each of which represents a pool of two independent blood donors), in total representing 4 macrophage preparations from independent blood donors, by commercial Illumina microarray.

first: Katharine

last: Irvine

first: Matthew

middle: J

last: Sweet


title: Nordihydroguaiaretic Acid Improves Metabolic Dysregulation and Aberrant Hepatic Lipid Metabolism in Mice by Both PPAR-alpha-Dependent and -Independent Pathways

status: Public on Mar 30 2012

city: Palo Alto

first: Haiyan

last: Zhang

address: 3801 Miranda Ave

department: Geriatric Research, Education and Clinical Center

institute: VA Palo Alto Health Care System

summary: To test whether NDGA attenuate dyslipidemia and hepatic steatosis by enhancing fatty acid oxidation through activation of PPAR-α. Using wild type (WT, C57BL/6) fed with chow diet as control, WT mice were either fed with high-fat diet or high-fat diet with NDGA (2.5g/kg food); ob/ob mice were fed with either chow or chow with NDGA (2.5 g/kg food), and maintained on the respective diets for 16 weeks. The expression of lipid metabolism related genes in the liver of these mice were analyzed using Phalanx GPL6845 platform (Mouse OneArray V1). Together with other biochemical/physiological data, our results suggest that the beneficial actions of NDGA on dyslipidemia and hepatic steatosis in ob/ob mice are exerted primarily through enhanced fatty acid oxidation and energy utilization via the activation of PPAR- α receptor activity.

overall_design: To examine the changes in gene expression in liver of WT and ob/ob mice with different NDGA diet treatment, RNA isolated from 3 animals of each group were used for studies of gene expression profiles. Phalanx GPL6845 platform (Mouse OneArray V1) was used for the microarrays analysis.

first: H

first: W

last: Shen

first: F

middle: B

last: Kraemer

first: Y

last: Cortez

first: S

last: Azhar


title: Conservation and divergence in Toll-like receptor 4-regulated gene expression in primary human versus mouse macrophages

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Transcriptome analysis of circulating monocytes in obese patients before and three months after bariatric surgery

status: Public on May 24 2012

city: Leuven

first: Paul

last: Holvoet

address: Herestraat 49, PB 705

department: Department of Cardiovascular Diseases

summary: Low-grade chronic inflammation plays an important role in the development of obesity and obesity-associated disorders such as insulin resistance, type 2 diabetes, the metabolic syndrome and atherosclerosis. One possible link between obesity and inflammation is the enhanced activation of circulating monocytes making them more prone to infiltration into the adipose and vascular tissues of obese persons. Furthermore, weight loss after bariatric surgery is associated with less inflammation. Transcriptome analysis of circulating monocytes from control and obese patients before and after bariatric surgery will potentially provide insights into the pathophysiology of obesity and associated disorders and supply biomarkers for diagnostic purpose. The cohort comprised 6 lean age-matched controls (BMI: 20.3±0.5 kg/m2, mean±SEM) and 18 obese individuals without clinical symptoms of cardiovascular disease (BMI: 45.1±1.4 kg/m2, P<0.001 compared with lean controls). These 18 morbidly obese subjects were referred to our hospital for bariatric surgery. Before they were included, individuals were evaluated by an endocrinologist, an abdominal surgeon, a psychologist and a dietician. Only after multidisciplinary deliberation, the selected patients received a laparoscopic Roux-en-Y gastric bypass. CD14+ monocytes were collected before and three months after bariatric surgery (BMI: 37.5±1.3 kg/m2, P<0.001 compared with before weight loss), total RNA was extracted and subjected to genome-wide expression analysis.

overall_design: Samples consisted of CD14+ monocytes from 6 lean controls and 18 morbidly obese patients before and three months after bariatric surgery. The 6 lean controls were also used to make 6 control pools.

first: B

last: Geeraert

first: N

last: Benhabilès

first: P


title: Characterization of the transcriptome profiles related to globin gene switching during in vitro erythroid maturation

status: Public on Jan 14 2012

city: Augusta

first: Biaoru

last: Li

state: GA

department: Pediatrics

institute: MCG

summary: The fetal and adult globin genes in the human b-globin cluster on chromosome 11 are sequentially expressed to achieve normal hemoglobin switching during human development. The pharmacological induction of fetal g-globin (HBG) to replace abnormal adult sickle bS-globin is a successful strategy to treat sickle cell disease; however the molecular mechanism of g-gene silencing after birth is not fully understood. Therefore, we performed global gene expression profiling using primary erythroid progenitors grown from human peripheral blood mononuclear cells to characterize protein expression patterns during the g-globin to b-globin (g/b) switch observed throughout in vitro erythroid differentiation. We confirmed erythroid maturation in our culture system using cell morphologic features defined by Giemsa staining and the g/b-globin switch by reverse transcription-quantitative PCR (RT-qPCR) analysis. We observed maximal g-globin expression at day 7 with a switch to a predominance of b-globin expression by day 28 and the g/b-globin switch occurred around day 21. Expression patterns for transcription factors including GATA1, GATA2, KLF1 and NFE2 confirmed our system produced the expected pattern of expression based on the known function of these factors in globin gene regulation. Subsequent gene expression profiling was performed with RNA isolated from progenitors harvested at day 7, 14, 21, and 28 in culture. Three major gene profiles were generated by Principal Component Analysis (PCA). For profile-1 genes, where expression decreased from day 7 to day 28, we identified 2,102 genes down-regulated >1.5-fold. Ingenuity pathway analysis (IPA) for profile-1 genes demonstrated involvement of the Cdc42, phospholipase C, NF-Kb, Interleukin-4, and p38 mitogen activated protein kinase (MAPK) signaling pathways. Transcription factors known to be involved in g-and b-globin regulation were identified. The transcriptome analysis completed with erythroid progenitors grown in vitro identified groups of genes with distinct expression profiles, which function in metabolic pathways associated with cell survival, hematopoiesis, blood cells activation, and inflammatory responses. This study represents the first report of a transcriptome analysis in human primary erythroid progenitors to identify transcription factors involved in hemoglobin switching.  Our results also demonstrate that the in vitro liquid culture system is a good model to define mechanisms of global gene expression and the DNA-binding protein and signaling pathways involved in globin gene regulation.

overall_design: Peripheral blood mononuclear cells were isolated from three normal donors using Histapaque-1.077. The mononuclear cells were grown in three independent cultures using the one-phase protocol as previously published. Cells were cultured in alphaMEM containing 30% fetal bovine serum, 1% deionized BSA with penicillin (100 U/mL) and streptomycin (0.1 mg/mL) at 37°C and 5% CO2. The following growth factors were added on day 0: stem cell factor (50 ng/mL), interleukin-3 (10 ng/mL) and erythropoietin (4 U/mL).  Approximately 1.5 million cells were harvested from each culture (triplicate samples) on day 7, 14, 21 and 28 for microarray analysis on the whole-genome Illumina HumanWG-6 V2 Expression BeadChip.

first: Betty

last: Pace

first: Wei

first: Michael

last: Strory

first: Lianghao

last: Ding


title: MB_xenograft_models

status: Public on Apr 05 2012

first: Hon-chiu

middle: Eastwood

last: Leung

address: 1102 Bates Street  Room C1030.09

summary: Classification of medulloblastoma xengrafts models

overall_design: primary human patient medulloblastoma samples were implanted into the corresponding position in SCID mice, the subsequent tumors gene expression profiles were compared with those of primary tumor samples to see if the overall transcriptomes were preserved. Repeat of each sample was the same labeled aRNA loaded onto another chip. Control samples include normal fetal brain, and normal adult cerebellum.


title: mRNA degradation in Mycobacterium tuberculosis under aerobic conditions

status: Public on Mar 08 2012

city: Seattle

first: Tige

last: Rustad

address: 307 Westlake Avenue N, Suite 500

department: Pathobiology

institute: Seattle Biomedical Research Institute

summary:
Transcription was arrested using 50 ug/ul of rifampin leaving RNA degradation as the sole vector responsible for mRNA abundance.
mRNA half-lives were calculated from the decay of signal intensity from T0.

overall_design: Four replicates were sampled after 0, 5 10, 15, 20, and 30 minutes of mRNA decay for a total of 24 arrays.

first: William

last: Brabant


title: 2009 pandemic H1N1 virus causes disease and upregulation of genes related to inflammatory and immune response, cell death, and lipid metabolism in pigs

status: Public on Feb 13 2012

last: Katze

address: Rosen Building 960 Republican St.

institute: University of Washington

summary:
This study used virological, histological, and global gene expression data to compare the virulence of two 2009 pH1N1 isolates from human (A/California/04/2009) and swine (A/swine/Alberta/25/2009) to that of a 1918-like classical swine influenza virus (A/swine/Iowa/1930) in a pig model of infection.
The overall goal of this study was to characterize the clinical, histological, virological and global gene expression responses to three distinct influenza A isolates in an experimental pig model of influenza infection. We compared the pathogenesis of two pH1N1 viruses, one derived from a human patient (A/CA/04/09 [CA09]) and the other from swine (A/swine/Alberta/25/2009 [Alb09]), with that of the 1918-like classical swine influenza virus (A/swine/Iowa/1930 [IA30]) in the pig model. Both pH1N1 isolates induced clinical symptoms such as coughing, sneezing, decreased activity, fever, and labored breathing in challenged pigs, but IA30 virus did not cause any clinical symptoms except fever. Although both the pH1N1 viruses and the IA30 virus caused lung lesions, the pH1N1 viruses were shed from the nasal cavities of challenged pigs whereas the IA30 virus was not. Microarray was used to assess global gene expression in the lungs at 3 and 5 days post-infection.

overall_design: Crossbred pigs fwere obtained from a healthy herd free of SIV and porcine reproductive and respiratory syndrome virus. These studies included two experiments: the classical H1N1 SIV (IA30) study was completed at Kansas State University's biosafety level 2 (BSL-2) facility in compliance with the Institutional Animal Care and Use Committee at Kansas State University, and the pH1N1 virus study was completed at the Central States Research Center (CSRC), Inc., BSL-3 facility (Oakland, NE), in compliance with the Institutional Animal Care and Use Committee at CSRC. In each experiment, 10 pigs were inoculated with noninfectious cell culture supernatant as controls. For the classical H1N1 SIV experiment, 10 4-week-old crossbred pigs were inoculated intratracheally with 10^6 50% tissue culture infective doses (TCID50)/pig of egg-derived IA30 virus. For the pH1N1 virus experiment, 10 4-week-old crossbred pigs were inoculated intratracheally with 10^6 TCID50/pig of either egg-derived CA/09 or Alb/09 virus. Five animals per group were euthanized at 3 and 5 days postinfection (dpi), respectively.

first: Wenjun

last: Ma

first: Sarah

last: Belisle

first: Derek

last: Mosier

first: Xi

first: Evelyn

last: Stigger-Rosser

first: Qinfang

last: Liu

first: Chuanling

last: Qiao

first: Jake

last: Elder

first: Richard

last: Webby

first: Juergen

last: Richt


title: mRNA degradation in Mycobacterium tuberculosis with DosR ectopically induced

summary:
After induction of DosR from a tet regulated promoter (uninduced controls were treated with an equivalent ammount of the solvent, DMSO), transcription was arrested using 50 ug/ul of rifampin leaving RNA degradation as the sole vector responsible for mRNA abundance.
mRNA half-lives were calculated from the decay of signal intensity from T0.

overall_design: Three replicates for each condition (DosR induced and uninduced) were sampled after 0, 10, 20, 30, and 60 minutes of mRNA decay for a total of 30 arrays.


title: Patterns of histone H3 Lysine 27 monomethylation and erythroid cell-type specific gene expression [expression]

status: Public on Dec 06 2011

city: New Haven

first: Vince

last: Schulz

address: 333 Cedar St. LMP 4085

department: Department of Pediatrics

institute: Yale University

summary:
ERYTHROID CELL-TYPE SPECIFIC GENE EXPRESSION
Post-translational histone modifications, acting alone or in a context-dependent manner, influence numerous cellular processes via their regulation of gene expression. Monomethylation of histone H3 lysine 27 (K27me1) is a poorly understood histone modification. Some reports describe depletion of K27Me1 at promoters and transcription start sites (TSS), implying its depletion at TSS is necessary for active transcription, while others have associated enrichment of H3K27me1 at TSS with increased levels of mRNA expression. Tissue- and gene-specific patterns of H3K27me1 enrichment and their correlation with gene expression were determined via chromatin immunoprecipitation on chip microarray (ChIP-chip) and human mRNA expression array analyses. Results from erythroid cells were compared to those in neural and muscle cells. H3K27me1 enrichment varied depending on levels of cell-type specific gene expression, with highest enrichment over transcriptionally active genes. Over individual genes, the highest levels of H3K27me1 enrichment were found over the gene bodies of highly expressed genes. In contrast to H3K4me3, which was highly enriched at the TSS of actively transcribing genes, H3K27me1 was selectively depleted at the TSS of actively transcribed genes. There was markedly decreased to no H3K27me1 enrichment in genes with low expression. At some locations, H3K27 monomethylation was also found to be associated with chromatin signatures of gene enhancers.

overall_design: The gene expression profiles of three replicates of 4 human cell lines were obtained using Illumina microarrays.

first: Laurie

last: Steiner

first: Vincent

first: Yelena

last: Maksimova

first: Clara

last: Wong

first: Patrick

last: Gallagher


title: Macaca Fascicularis Differential Gene Expression Following Stroke: Control versus Tat-NR2B9c Treated Cortex at 1 hour and 6 hours following middle cerebral aretry occlusion (MCAO)

status: Public on Feb 08 2012

city: Toronto

first: DJ

last: Cook

state: ON

address: 11-414MCl, 399 Bathurst St

institute: University of Toronto

summary: Differential gene expression comparison between cortex of placebo and PSD-95 inhibitor (Tat-NR2B9c), treated cynomolgus macaques at 1 and 6 hours after middle cerebral artery occlusion.  The purpose of this study was to identify changes in differential gene expression in the cortex of animals receiving strokes across the two time points and bewtwee the two treatment groups.  Differential gene expression was defined as the ratio of fluroescene detected for expressed sequence tags in the left, unoperated cortex versus the contralateral, right, ischemic cortex at each time point.  Two colour, Agilent, 4x44k whole genome macaca mulata microarrays with sample rna hybridized to Cy5 channel and universal macaca mulatta rna control on the Cy3 channel were obtained for each hemisphere.  Comparisons between treatment groups at each time point and within in each treatment group across each time point were made to detect differential gene expression.  Significant differential gene expression was defined as greater than 2-fold change and p<0.05 by T-test.

sample_organism:
Macaca fascicularis
Macaca mulatta

overall_design: Three condition experiment comparing the effect of treatment with placebo versus Tat-NR2B9c administered 5 min after MCAO with tissue samples collected 1h and 6h after MCAO and a second comparison of gene expression within each treatment group between 1h and 6h: 3 biological replicates in each group

first: Michael

last: Tymianski

first: D


title: Gene expression in HEK293 cells with hSNRK-GFP or GFP

status: Public on Oct 31 2011

city: Chicago

first: Amy

last: Rines

address: 303 E. Chicago Ave.  Tarry 14-735

institute: Northwestern University

summary: Analysis of gene expression changes with human SNRK-GFP overexpression.  The purpose of the study was to determine the expression of the genes that are altered by SNRK in order to obtain evidence about what cellular functions SNRK regulates.

overall_design: Total RNA obtained from HEK293 cells 48 hours after transfection with human SNRK-pEGFPN3 or pEGFPN3

middle: K

first: Hossein

last: Ardehali


title: Change in expression of genes after retinoic acid treatment of stellate cells: dose response

status: Public on Dec 30 2011

city: London

first: Hemant

last: Kocher

address: Charterhouse Square

institute: Barts and the London

summary:
We evaluated the change in expression of genes after treatment of stellate cells with retinoic acid to understand how the stellate cells can de-differentiate and effect their physiological behaviour in pathological conditions. We then tested the changes in the gene expression in 2D and 3D culture conditions for pancreatic stellate cells and in a pancreatic cancer model.

Keywords: gene expression change, dose response, matrix conditions

overall_design: We treated a pancreatic stellate cell line on plastic or Matrigel with 1 or 10 micromolar dose of all-trans retinoic acid (ATRA). RNA was extracted and hybridized on Illumina Human microarrays. We looked for target genes regulated by ATRA and evaluated for dose repsonse and change due to background culture conditions.

first: Claude

last: Chelala

first: Fieke

last: Froeling

last: Dobson

first: Charles

last: Mein

first: Ian

middle: R

last: Hart


title: mRNA degradation in Mycobacterium tuberculosis

first: Tige

last: Rustad

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

sample_organism:
Mycobacterium tuberculosis H37Rv
Mycolicibacterium smegmatis MC2 155

overall_design: Refer to individual Series

first: William

last: Brabant


title: Change in expression of genes after retinoic acid treatment of stellate cells: time course

summary:
We evaluated the change in expression of genes after treatment of stellate cells with retinoic acid to understand how the stellate cells can de-differentiate and effect their physiological behaviour in pathological conditions. We then tested the changes in the gene expression in 2D and 3D culture conditions for pancreatic stellate cells and in a pancreatic cancer model.

Keywords: gene expression change, time course

overall_design: We treated a pancreatic stellate cell line on plastic with 1 micromolar all-trans retinoic acid (ATRA) for timepoints of 30 mins, 4 hours, 12 hours, 24 hours and 168 hours. RNA was extracted and hybridized on Illumina Human microarrays. We looked for target genes regulated by ATRA and evaluated for time course change.

middle: E

first: Richard


title: Transcriptome-wide changes in HeLa cell line investigated in response to Heat-shock stress

status: Public on Nov 09 2011

city: New Delhi

first: Mitali

last: Mukerji

state: New Delhi

address: Sukhdev Vihar, Mathura Road

department: Functional Genomics and Molecular Medicine

country: India

institute: CSIR-Institute Of Genomics and Integrative Biology

summary: The repertoire of transcripts that are differentially regulated in response to Heat-shock were studied using Illumina WG-6 v2.0 BeadChip.

overall_design: Study was undertaken with 3 biological replicates for each condition of Heat-Shock Treated and Untreated condition.

first: Rajesh

last: Pandey


title: Early and sustained innate immune response defines pathology and death in nonhuman primates infected by highly pathogenic influenza virus.

status: Public on Nov 01 2011

last: Katze

department: Microbiology

country: USA

summary: This study revealed important similarities but also critical differences between the H5N1 and 1918-reassortant viruses, highlighting aspects of the host–pathogen interface caused by highly virulent influenza viruses.

overall_design: Animals assigned to 4 experimental groups (n = 8) matched for age, weight, and sex, were inoculated by intratracheal, intranasal, tonsillar, and conjunctival routes with a total of 107 pfu of A/Vietnam/1203/2004 (H5N1) virus, A/Texas/36/91 (H1N1) virus or reassortants of this virus containing either 2 (HA, NA) or 3 (HA, NA, NS) genes from the 1918 virus. Two animals per group were scheduled for sacrifice on days 1, 2, 4, and 7. Two additional animals were used as uninfected control animals and killed on day 7. Oligoarray analyses consisted of comparing array profiles of individual lung samples (with representative pathology and degree of infection) from infected animals to pooled equal masses of mRNA from all lung lobes of 7 reference cynomolgus macaques obtained through the tissue program of the University of Washington National Primate Research Center. There are 2 technical array replicates fro each sample.

first: Carole

last: Baskin

first: Helle

last: Bielefeldt-Ohman

first: Terrence

last: Tumpey

last: Sabourin

first: James

last: Long

first: Adolfo

last: García-Sastre

first: Airn-E

last: Tolnay

first: Randy

last: Albrecht

first: ohn

last: Pyles

first: Pam

middle: H

last: Olson

first: Lauri

last: Aicher

first: Elizabeth

last: Rosenzweig

first: Kaja

last: Murali-Krishna

first: Edward

last: Clark

first: Mark

last: Kotur

first: Jamie

middle: L

last: Fornek

first: Sean

last: Proll

first: Robert

last: Palermo

first: Carol


title: Change in expression of genes after retinoic acid treatment of stellate cells

first: Hemant

last: Kocher


title: Identification of Candidate Tumor Suppressor Genes Inactivated by Promoter Methylation in Melanoma

status: Public on Oct 03 2011

city: Herston

first: Derek

middle: John

last: Nancarrow

state: Queensland

address: 300 Herston Road

department: Genetics & Population Health

institute: Queensland Institute of Medical Research

summary: Tumor suppressor genes (TSGs) are sometimes inactivated by transcriptional silencing through promoter hypermethylation. To identify novel methylated TSGs in melanoma, we carried out global mRNA expression proﬁling on a panel of 12 melanoma cell lines treated with a combination of 5-Aza-2-deoxycytidine (5AzadC) and an inhibitor of histone deacetylase, Trichostatin A. Reactivation of gene expression after drug treatment was assessed using Illumina whole-genome microarrays. After qRT-PCR conﬁrmation, we followed up 8 genes (AKAP12, ARHGEF16, ARHGAP27, ENC1, PPP1R3C, PPP1R14C, RARRES1, and TP53INP1) by quantitative DNA methylation analysis using mass spectrometry of base-speciﬁc cleaved ampliﬁcation products in panels of melanoma cell lines and fresh tumors. PPP1R3C, ENC1, RARRES1, and TP53INP1, showed reduced mRNA expression in 35–59% of the melanoma cell lines compared to melanocytes and which was correlated with a high proportion of promoter methylation (>40–60%). The same genes also showed extensive promoter methylation in 6–25% of the tumor samples, thus conﬁrming them as novel candidate TSGs in melanoma.

overall_design: We sought to identify melanoma TSGs silenced by promoter methylation by carrying out an array-based analysis in a well-annotated panel of 12 cell lines after combined treatment with 5AzadC and an inhibitor of histone deacetylase, Trichostatin A (TSA). Expression profiles were generated for each cell line before and after drug treatment using Illumina Sentrix Human-6 Expression version 2 BeadChips. Genes   reactivated   in   all   12   cell   lines   were removed  from  further  analysis  since  they  are likely responding to drug treatment as part of the ‘‘cellular  stress  response,’’  or  due  to  promoter demethylation of genes normally silenced in the melanocytic lineage. Genes were further ﬁltered to  identify  those  with  an  average  of  >4-fold increased  expression  in  at  least  four  samples  in the panel of 12 lines and >10-fold increase in at least one of the cell lines.

first: Vanessa

middle: F

last: Bonazzi

first: Darryl

last: Irwin

first: Nicholas

last: Hayward


title: mRNA degradation in Mycobacterium tuberculosis during cold and hypoxic stress

first: Tige

last: Rustad

summary:
Transcription was arrested using 50 ug/ul of rifampin leaving RNA degradation as the sole vector responsible for mRNA abundance at 20C (cold) or in 0.2%O2 (hypoxia).
mRNA half-lives were calculated from the decay of signal intensity from T0.

overall_design: Three replicates were sampled after 0, 1, 2, and 5 hours of mRNA decay in both cold and hypoxia for a total of 24 arrays.

first: William

last: Brabant


title: Patterns of histone H3 Lysine 27 monomethylation and erythroid cell-type specific gene expression

first: Vince

last: Schulz

state: CT


title: Gene-expression analysis of Oncostatin-M (OSM) signalling in cervical squamous cell carcinomas over-expressing the Oncostatin-M receptor (OSMR)

status: Public on Sep 30 2011

first: Julien

last: Bauer

state: Cambridgeshire

address: Tennis court road

institute: Cambridge University

summary: The type II Oncostatin M receptor (OSMR) serves as the main binding site for the pleiotropic cytokine OSM. We have previously demonstrated a positive correlation between copy number driven OSMR over-expression and adverse clinical outcome in cervical tumours and have also established enhanced angiogenic, migratory and invasive potential as major consequences of OSMR over-expression using cell-line models of cervical cancer. By analysis of gene expression patterns in cell lines and tumours, this study now systematically defines cohorts of genes that are implicated for the phenotypes observed. Importantly, we have identified 15 OSM induced genes that are involved in at least one of these key functions and are up-regulated in both OSMR over-expressing cell-lines and tumours. These genes can serve as markers of OSM signalling in OSMR over-expressing SCCs and represent suitable targets for functional characterisation.

overall_design: Gene expression of 4 cervical SCC cell lines analysed (2 with and 2 without OSMR overexpression) at 6 different time-points,  with 3 replicates at each time-point.

first: Anasuya

last: Chattopadhyay

first: Ian

last: Roberts

first: Xiao

last: Zhang

first: Konstantina

last: Karagavriilidou

first: David

last: Winder

last: Coleman


title: Pandemic Swine-Origin H1N1 Influenza A Virus Isolates Show Heterogeneous Virulence in Macaques

status: Public on Aug 30 2011

first: Michael

last: Katze

summary:
This study used virological, histological, immunological and global gene expression to compare the virlence of two newly emerged 2009 H1N1 isolates (A/Mexico/InDRE4487/2009 and A/Mexico/4108/2009) and current seasonal H1N1 influenza strain (A/Kawasaki/UTK-4/2009) in experimentally infected cynomolgus macaques.
We showed that infection of macaques with two genetically similar but clinically distinct SOIV isolates from the early stage of the pandemic (A/Mexico/4108/2009 and A/Mexico/InDRE4487/2009) resulted in upper and lower respiratory tract infections and clinical disease ranging from mild to severe pneumonia. Disease associated with these SOIV isolates was clearly advanced over the mild infection caused by A/Kawasaki/UTK-4/2009, a current seasonal strain.

overall_design: Total dose of 7 x 10^6 pfu of influenza virus by a combination of different routes: intratracheal (4 ml), intranasal (0.5 ml each nostril), intraocular (0.5 ml each eye), and oral (1 ml).

last: Safronetz

first: Barry

last: Rock

first: Friederike

last: Feldmann

first: Sarah

last: Belisle

first: Douglas

last: Brining

first: Don

last: Gardner

first: Sean

middle: C

last: Proll

first: Andrea

last: Marzi

first: Yoshimi

last: Tsuda

first: Rachel

middle: A

last: LaCasse

first: Lisa

last: Kercher

first: Anthony

last: York

first: Marcus

last: Korth

first: Dan

last: Long

first: Rebecca

last: Rosenke

first: W

last: Shupert

first: Celia

last: Aranda

first: John

last: Mattoon

first: Darwyn

last: Kobasa

first: Gary

last: Kobinger

first: Yan

last: Li

first: Jeffery

last: Taubenberger

first: Jürgen

last: Richt

last: Parnell

first: Hideki

first: Yoshihiro

last: Kawaoka

middle: G

first: Heinz


title: Gene expression profile of Serially Mixed samples of MDA-MB231 and Mouse Astrocytes

status: Public on Sep 24 2011

city: Houston

first: Sangbae

last: Kim

address: 1 Baylor plaza

department: HGSC

institute: Baylor Colleage of Medicine

summary: To test specificity of human microarray probes against mouse mRNA serially mixed human MDA-MB231 cancer cells' mRNAs with mouse Astrocytes were hybridized against human microarray and vice versa by changing the ratios of human and mouse samples from 100% to 0%.

overall_design:
Mixed human: 1 MDA-MB231, 1 MDA231_Astro(91), 2 MDA231_Astro(73), 2 MDA231_Astro(55),2 MDA231_Astro(37),1 MDA231_Astro(19), 1 Astrocytes
Mixed mouse: 1 MDA-MB231, 1 MDA231_Astro(91), 2 MDA231_Astro(73), 2 MDA231_Astro(55),2 MDA231_Astro(37),1 MDA231_Astro(19), 1 Astrocytes

first: Eun-Sung

last: Park

first: Ju-seog

last: Lee

first: Isaiah

last: Fidler


title: Plasma miRNA profile as a predictor for early virological response of  interferon treatment in chronic hepatitis B patients

status: Public on Sep 20 2011

city: shanghai

first: xiaonan

last: zhang

address: caolang road 2901, Jinshan district

department: research unit

country: China

institute: Shanghai public health clinical center

summary: To find novel circulating markers associated with prognosis of interferon therapy,We performed microarray analysis of plasma samples in 94 chronic hepatitis B patients

overall_design: Ninety four HBV patients, who underwent PEG-IFN or conventional interferon treatment were enrolled. Their plasma samples before treatment were collected and subject to miRNA  array analysis. miRNA profiles from 13 formalin fixed formaldehyde embedded liver biopsy samples were also analyzed to evaluate the correlation between liver and plasma.

first: Xiaonan

last: Zhang

first: Zhenghong

last: Yuan