title: Rescue of KRAS suppression in HCT116 colon cancer cell line

status: Public on Jul 22 2014

city: Cambridge

first: Diane

last: Shao

address: 7 Cambridge Center

institute: Broad

summary:
Cancer cells that express oncogenic alleles of RAS typically require sustained expression of the mutant allele for survival, but the molecular basis of this oncogene dependency remains incompletely understood. To identify genes that can functionally substitute for oncogenic RAS, we systematically expressed 15,294 open reading frames in a human KRAS-dependent colon cancer cell line engineered to express an inducible KRAS-specific shRNA. We found 147 genes that promoted survival in the setting of KRAS suppression. In this model, the transcriptional co-activator YAP1 rescued cell viability in KRAS-dependent cells upon suppression of KRAS and was required for KRAS-induced cell transformation. Acquired resistance to Kras suppression in a Kras-driven murine lung cancer model also involved increased YAP1 signaling. KRAS and YAP1 converge on the transcription factor FOS and activate a transcriptional program involved in regulating the epithelial-mesenchymal transition (EMT). Together, these findings implicate transcriptional regulation of EMT by YAP1 as a significant component of oncogenic RAS signaling.
We used microarrays to compare gene expression in HCT116 cells in which we suppressed KRAS expression doxycycline-inducible shRNA targeting KRAS compared to cells treated with media alone (no shKRAS induced). We express KRAS, LacZ, and YAP1 in each condition to identify genes transcriptionally involved in the rescue of KRAS suppression.

overall_design: HCT116 cells harboring doxycycline-inducible shKRAS (HCTtetK) expressing either LacZ, KRAS, or YAP1, were treated with doxycycline for 30 hours to suppress KRAS. Untreated (no doxycycline) cells expressing each ORF were used as control. Total RNA was collected using PerfectPure RNA Cultured Cell Kit (5Prime) and expression profiling was performed on Human Genome U133A 2.0 Array (Affymetrix) using the Dana Farber Cancer Institute Microarray Core.

first: Wen

last: Xue

first: Elsa

middle: B

last: Krall

first: Arjun

last: Bhutkar

first: Federica

last: Piccioni

first: Xiaoxing

last: Wang

first: Anna

last: Schinzel

first: Sabina

last: Sood

last: Rosenbluh

first: Jong

middle: W

last: Kim

first: Yaara

last: Zwang

first: Thomas

last: Roberts

first: David

last: Root

first: Tyler

last: Jacks

first: William

last: Hahn


title: PARK2 knockdown in 2 glioma cell lines

status: Public on Apr 11 2014

city: New York

first: Yongxing

last: Gong

state: NY

address: 1275 York Avenue

country: USA

institute: Momerial Sloan-Kettering Cancer Center

summary:
The PARK2 gene was knocked down using 2 independent siRNAs in SNB19 and SF539 cell lines
A non-targeted scramble siRNA was used as the control.

overall_design: Scramble, PARK2 siRNA#1 or PARK2 siRNA#2 was transfected into each cell line, in duplicate, and RNA analyzed using the Affymetrix U133A 2.0 platform.

first: Luc

middle: G

last: Morris

first: Timothy

middle: A

last: Chan


title: Gene Expression Data in Human Monocyte-derived Dendritic Cell (MoDC)  from Young and Aged Donors

status: Public on May 28 2014

city: Irvine

first: Sudhir

last: Gupta

state: CA

address: Med Sci Buld I, C240

department: Medicine

institute: University of California, Irvine

summary:
Dendritic cells (DCs) are major antigen-presenting cells that play a key role in initiating and regulating innate and adaptive immune responses. DCs are critical mediators of tolerance and immunity. The functional properties of DCs changes with age.
The purpose of this study was to define the age-associated molecular changes in DCs by gene array analysis using Affymatrix GeneChips. We identified up and down-regulated gene expression changes in DC from aged donors compared to young donors.

overall_design: Total 9 MoDC RNA samples from four young donors (20-27 years) and five aged donors (77-84 years) were analyzed using Affymetrix HG-U133A_2 Gene Arrays to compare differential gene expression changes in MoDC between aged and young groups

first: Jia-ning

last: Cao


title: Functional analysis of ABCB5 in melanoma cells

status: Public on Jun 17 2014

city: Boston

first: Markus

middle: Hermann

last: Frank

state: Massachusetts

address: 300 Longwood Avenue

institute: Boston Children's Hospital

summary: Functional analysis of ABCB5 in A375 and G3361 melanoma cells, by comparing stably-transfected controls to ABCB5-shRNA-targeted cells.

overall_design: 12 samples total. Replicates n=3 for the following 4 groups: A375 pSUPER-retro-puro-Vector vs. A375 pSUPER-retro-puro-ABCB5-KD; G3361 pSUPER-retro-puro-shCNTRL vs. G3361 pSUPER-retro-puro-ABCB5-KD.

first: Brian

middle: J

last: Wilson

middle: H


title: Human blood monocyte response to IL-17A in culture

status: Public on Apr 30 2014

first: Mayte

last: Suarez-Farinas

address: 1425 Madison Ave, L2-70C, Box 1077,

institute: Mount SinaiSchool of Medicine

summary: The levels of IL-17 are elevated in the serum of psoriasis patients. However, the effects of IL-17 on circulating leukocytes bearing the IL-17 receptors are not fully understood. Of particular interest are monocytes, as the activation and recruitment of effector monocytes underlies the pathobiology of a number systemic inflammatory diseases, including psoriasis co-morbidities, such as atherosclerosis, metabolic regulation in adipose tissue and psoriatic arthritis.  Human monocytes highly express both IL-17RA and IL-17RC and chemotraffick in response to IL-17. We explored the impact of IL-17 on blood monocytes. Using cDNA microarray, , we molecularly characterized how human blood monocytes respond to IL-17A in vitro.

overall_design: total RNA was extratced from CD14+ monocytes (isolated from human blood) after 24hr culture with or without IL-17A (200ng/mL)

last: Suárez-Fariñas

first: Claire

middle: Q

last: Wang

first: Kristine

middle: E

last: Nograles

first: James

last: Krueger


title: Whole genome expression profiling of artemsinin-resistant Plasmodium falciparum field isolates

status: Public on Jul 15 2014

city: Singapore

first: Sachel

last: Mok

address: 60 Nanyang Drive

country: Singapore

institute: Nanyang Technological University

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

overall_design: Refer to individual Series


title: A novel approach to identify genes that determine grain protein deviation in cereals

status: Public on Jul 04 2014

city: Harpenden

first: Artem

last: Lysenko

state: Herts

address: Rothamsted Estate

department: Computational and Systems Biology Department

country: United Kingdom

institute: Rothamsted Research

summary:
Grain yield and protein content were determined for six wheat cultivars grown over three years at multiple sites and at multiple N-fertilizer inputs. Although grain protein was negatively correlated with yield, some grain samples had higher protein contents than expected based on their yields, a trait referred to as grain protein deviation (GPD). We used novel statistical approaches to calculate GPD across environment and to correlate gene expression in the developing caryopsis with this trait. The yield and protein content were initially adjusted for nitrogen fertilizer inputs, and then adjusted for yield (to remove the negative correlation) resulting in environmental corrected GPD. The transcriptome data for all samples were subjected to Principal Component Analysis (PCA) and ANOVA to identify individual Principal Components (PCs) correlating with GPD alone. Scores of the selected PCs significantly related to cultivar differences and GPD but not to the yield or protein content were identified as reflecting a multivariate pattern of gene expression related to genetic variation in GPD. Sets of genes significant for these PCs and hence GPD were identified as candidate genes determining cultivar differences in GPD.
Microarray profiling has been used to identify the links between gene expression and grain protein content in 6 different varietes of wheat grown at 2 different sites, 3 N levels and during 3 growth seasons.

overall_design: Six UK cultivars (Istabraq , Hereward, Marksman,  Cordiale, Malacca and Xi 19)  were grown over three seasons (2008-9, 2009-10 and 2010-11) at Rothamsted . In the present publication, data from two sites are included: Rothamsted and RAGTResearch (Harpenden, UK) and at four other sites in the south-east of the UK (RAGT, Ickleton, Cambridge; Limagrain, Woolpit, Suffolk; Syngenta, Whittlesford, Cambridge; KWS-UK, Thriplow, Hertfordshire) in 2009-10 and 2010-11 only. Three replicate plots were grown at three N levels: 100kg/ha, (N100), 200kg/ha (N200) and 350 kg/ha (N350) (see Barraclough et al., 2010, Chope at al., 2014).   Developing heads (10 per plot) were tagged and caryopses were harvested from the Rothamsted (2009, 2010 and 2011) and RAGT (2010 and 2011) sites at 21 days after anthesis (mid-grain filling) to measure gene expression using Affymetrix wheat microarrays giving a total of 161 samples.  Six UK cultivars (Istabraq , Hereward, Marksman,  Cordiale, Malacca and Xi 19)  were grown over three seasons (2008-9, 2009-10 and 2010-11) at Rothamsted Research (Harpenden, UK) and at four other sites in the south-east of the UK (RAGT, Ickleton, Cambridge; Limagrain, Woolpit, Suffolk; Syngenta, Whittlesford, Cambridge; KWS-UK, Thriplow, Hertfordshire) in 2009-10 and 2010-11 only. Three replicate plots were grown at three N levels: 100kg/ha, (N100), 200kg/ha (N200) and 350 kg/ha (N350) (see Barraclough et al., 2010, Chope at al., 2014).   Developing heads (10 per plot) were tagged and caryopses were harvested from the Rothamsted (2009, 2010 and 2011) and RAGT (2010 and 2011) sites at 21 days after anthesis (mid-grain filling) to measure gene expression using Affymetrix wheat microarrays giving a total of 161 samples.

first: Ellen

last: Mosleth

first: Yongfang

last: Wan

first: Simon

last: Penson

first: Gemma

last: Chope

first: Peter

last: Shewry

first: Malcolm

last: Hawkesford


title: Keratinocyte detachment-differentiation connection

status: Public on Apr 25 2014

first: Miroslav

last: Blumenberg

address: 455 First Ave #874

department: Dermatology

institute: NYU School of Medicine

summary: Epidermis, a continuously self-renewing and differentiating organ, produces a protective stratum corneum that shields us from external chemical, physical and microbial threats. Epidermal differentiation is a multi-step process regulated by influences, some unknown, others insufficiently explored. Detachment of keratinocytes from the basement membrane is one such pro-differentiation stimulus. Here, we define the transcriptional changes during differentiation, especially those caused by detachment from the substratum. Using comprehensive transcriptional profiling, we revisited the effects of detachment as a differentiation signal to keratinocytes. We identified the genes regulated by detachment, the corresponding ontological categories and, using metaanalysis, compared the genes and categories to those regulated by other pro-differentiating stimuli. We identified 762 genes overexpressed in suspended keratinocyte, including known and novel differentiation markers, and 1427 in attached cells, including basal layer markers. Detachment induced epidermis development, cornification and desmosomal genes, but also innate immunity, proliferation inhibitors, transcription regulators and MAPKs; conversely the attached cells overexpressed cell cycle, anchoring, motility, splicing and mitochondrial genes, and both positive and negative regulators of apoptosis. Metaanalysis identified which detachment-regulated categories overlap with those induced by suprabasal location in vivo, by reaching confluency in vitro, and by inhibition of JUN kinases. Attached and in vivo basal cells shared overexpression of mitochondrial components. Interestingly, melanosome trafficking components were also overexpressed in the attached and in vivo basal keratinocytes. Reaching confluency did not affect adhesion and ECM proteins. Lipid metabolism and steroid metabolism were induced by confluency and by JNK inhibition, respectively. These results suggest that specific pro-differentiation signals induce specific features of the keratinization process, which are in vivo orchestrated into harmonious epidermal homeostasis.

overall_design: Human epidermal keratinocytes are grown in standard growth medium either attached in tissue culture plates, or suspended, in the same medium, in bacteriological plates. After 48 hrs, attached and suspended cultures were harvested and their transcriptomes compared.

first: Tomohiro

last: Banno


title: Transcriptome analysis of mvp mutant reveals important changes in global gene expression and a role of methyl-jasmonate in vernalization and flowering in wheat

status: Public on May 02 2014

city: Montreal

first: Fathey

last: Sarhan

state: Quebec

address: CP 8888, Succursale Centre-Ville

department: Biology

country: Canada

institute: University of Quebec at Montreal

summary: The maintained vegetative phase (mvp) mutant has a non-flowering phenotype caused by deletions including, but not limited to, the genes CYS, PHYC and VRN1. However the impact of these deletions on flowering genes and global gene expression is still unknown. In this study, we showed that these deletions caused the up-regulation of several pathogenesis related (PR) and jasmonate responsive genes using microarray analysis. Our results raise the hypothesis that jasmonates may be involved in flowering. To confirm this hypothesis, the methyl-jasmonate (MeJA) and jasmonic acid (JA) content in mvp and wild type plants was measured. The content of JA was comparable in all plants while the content of MeJA was higher in mvp plants.  Our transcriptomic and chemical analyses of the mvp mutants plants reveal that the deletion of the major vernalization gene TaVRN1 induces the up-regulation of the major biotic stress related genes and the accumulation of MeJA. In addition, our results demonstrate an important role of MeJA during vernalization and flowering in wheat.

overall_design: A total of 3 biological replicates (R1, R2 and R3) for each condition (wild type (control) and mvp mutant (mutant) ) were used for microarray analyses. Each biological replicate sample was obtained by pooling three wild type plants (control) or five mvp plants (mutant) from different plants harvested randomly. The different biological samples of einkorn spring wheat whole aerial part were ground in dry ice to fine powder and total RNA was extracted with trizol (Invitrogen, Burlington, ON, CA). Total RNA was cleaned using RNeasy plant mini kit (Qiagen) and integrity was determined on agarose gel and on a bioanalyser (Agilent 2100). Synthesized cDNAs were transcribed to cRNAs with the 3’IVT labelling kit (Santa Clara, CA, USA) and hybridized to the Affymetrix wheat genome array (Santa Clara, Ca, USA) at the McGill University and Génome Québec Innovation Centre (Montreal, Qc, CA). The experimental design consisted of three biological replicates for each of the two conditions, 1: The einkorn wheat  (Triticum monococcum L. 2n = 2x = 14, AmAm) wild type plants (control) and 2: the mvp plants (mutant). Thus, a total of 3 biological samples from each of the two conditions described above were used for hybridizations.

first: Diallo

last: Oury

first: Agharbaoui

last: Zahra

first: Mohamed

last: Badawi

first: Ali-Benali

middle: M

last: Ali

first: Moheb

last: Amira

first: Mario

last: Houde


title: Endocrine response in invasive lobular carcinoma is characterized by unique estrogen-mediated gene expression and de novo tamoxifen resistance

status: Public on Jan 16 2014

city: Pittsburgh

first: Uma

last: Chandran

state: PA

address: 5150 Center Ave

department: BioMedical Informatics

institute: University of Pittsburgh


title: Genome-wide analyses of GATA6 occupancy and functions provide insights into its oncogenic mechanisms in human gastric cancer (microarray)

status: Public on Dec 02 2013

first: Ramesh

last: Shivdasani

address: Dana Bldg, Room 720, 450 Brookline Ave

department: Department of Medical Oncology

institute: Dana-Farber Cancer Institute

summary: To identifiy core GATA6 functions and transcriptional targets in human gastric cancer, including additional subservient transcriptional regulators via integrative analysis of GATA6 transcription factor occupancy, gene dependency, and tumor synexpression.

overall_design: This study used Affymetrix U133A 2.0 gene chips with 2 control and 2 treated replicates for 2 cell types.

first: Rita

last: Sulahian


title: Genome wide gene-expression analysis of the spider mite Tetranychus urticae after long term host transfer from acyanogenic Phaseolus vulgaris cv. 'Prelude' bean plants to cyanogenic Phaseolus lunatus cv. '8078' bean plants

city: Ghent

first: Wannes

last: Dermauw

address: Coupure Links 653

department: Crop Protection

country: Belgium

institute: University Ghent

summary: 250 adult T. urticae females from the London strain (grown on acyanogenic P. vulgaris cv. Prelude bean plants) were transferred to cyanogenic P. lunatus cv. 8078 bean plants.  Thirty-five generations after the host transfer, total RNA was extracted from mites growing on both bean species (London and London-CYANO strain) and used in in a genome-wide gene expression microarray (Sureprint G3 microarray, Agilent) experiment to assess significantly differentially expressed genes (FC ≥ 2 and FDR-corrected p-value < 0.05) between mites grown on P. vulgaris (cv. Prelude) bean plants (London strain) and mites grown for 35 generations on P. lunatus (cv. 8078) bean plants (London-CYANO strain).

overall_design: 4 replicates for one comparison: mites of the London strain grown on P. lunatus for 35 generations (London-CYANO) compared to mites of the London strain grown on P. vulgaris bean plants (London)

first: Nicky

last: Wybouw

first: Thomas

last: Van Leeuwen


title: The effect of imatinib therapy on tumor associated macrophages (TAMs) in human gastrointestinal stromal tumor (GIST)

status: Public on Nov 20 2013

first: Jeffrey

last: Zhao

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

summary:
The gene expression profile of TAMs microbead isolated from freshly obtained human GISTs were compared in tumors that were untreated, responding to imatinib (sensitive), or resistant to imatinib (resistant)
The Affymetrix Human Genome U133A 2.0 platform was used

overall_design: TAMs were microbead isolated from 12 untreated, 5 sensitive, and 4 resistant tumors. Tumors were obtained freshly from the operating room from consenting patients using an IRB approved protocol. Tumors were digested using collagenase and TAMs isolated using microbead negative selection for KIT, CD3, and CD56 followed by positive selection for CD14.

first: Michael

last: Cavnar

first: Shan

last: Zeng

first: Teresa

middle: S

last: Kim

first: Eric

middle: C

last: Sorenson

first: Lee

last: Ocuin

first: Vinod

middle: P

last: Balachandran

first: Adrian

last: Seifert

first: Jonathan

last: Greer

first: Rachel

last: Popow

first: Megan

last: Crawley

first: Noah

last: Cohen

first: Benjamin

middle: L

last: Green

first: Ferdinand

last: Rossi

first: Peter

last: Besmer

first: Cristina

middle: R

last: Antonescu

first: Ronald

last: DeMatteo


title: NF-kB essential modulator (NEMO) is essential for KSHV-encoded viral FLICE inhibitory protein (vFLIP) K13- induced gene expression and its N-terminal 251 resdidues are sufficent for this process

status: Public on Mar 27 2014

city: Los Angeles

first: Vasu

last: Punj

address: Biggy Street

institute: USC

summary: We report here that  KSHV viral infection targets the NF-kB pathway which is crucial for cell survival. KSHV protein vFLIP K13 is known to directly interact with cellular protein NEMO of the NF-kB pathway. We used gene expression array to suggets that  the interaction of K13 with NEMO is important to activate NF-kB pathway.

overall_design: We employed gene array analysis followed by bioinformatics analyses  as well as biological pathways  to determine  the effect of K13  interaction with Nemo in Jurkat cell line system. Total RNA was isolated  isolated using standard RNAeasy kit protocol (Qiagen). Their gene expression profiles were obtained using the Affymetrix Human Genome U133A 2.0 Array.

first: Bhairavi

last: Tolani

first: Hittu

last: Matta

first: Ramakrishnan

last: Gopalakrishnan

first: Preet

last: Chaudhary


title: Gene expression of liver tissue from Pcyt2 mice

status: Public on Mar 06 2014

city: Guelph

first: marica

last: bakovic

state: ON

address: 50 Stone road east

department: HHNS

institute: university of Guelph

summary:
Pcyt2 defient mice has metabolic syndrome and insulin resistance. We used microarray to study the gene expression of these mice to
understand the global program of gene expression underlying the metabolic syndrome, obesity and insulin resistance.

overall_design: 2 month-old Pcyt2 deficient mice and age matched control mice liver tissues were choosen for RNA extraction and gene expression using Affymetrix microarray.

first: Marica

last: Bakovic


title: 5q- Myelodysplastic Syndrome Masquerading as Diamond Blackfan Anemia

status: Public on Nov 05 2013

city: Little Rock

first: Jason

middle: Eli

last: Farrar

state: AR

address: 1 Children's Way, #512-10

department: Pediatrics/Hematology-Oncology

institute: University of Arkansas for Medical Sciences

type:
SNP genotyping by SNP array
Expression profiling by array

summary: Diamond Blackfan anemia is a congenital bone marrow failure syndrome characterized by hypoproliferative anemia, often with associated physical abnormalities.  Perturbations of the ribosome appear critically important to the development of DBA, as alterations in 9 different ribosomal protein genes have been identified in multiple unrelated families, along with rarer abnormalities of additional ribosomal proteins.  However, presently only 50-60% of patients have an identifiable genetic lesion by ribosomal protein gene sequencing. Using genome-wide SNP array to evaluate for regions of recurrent copy variation, we identified 2 patients with mosaic loss in the region of the the chromosome 5-deleted region involved in somatically-acquired 5q- myelodysplastic syndrome.

overall_design: Samples were analyzed on Illumina HumanOmni1_Quad, HumanOmniExpress, or HumanOmniExpressExome Genotyping bead arrays; 1 patient was available for longitudinal study including assessment of mosaicism in lymphoid and myeloid-enriched cell populations before treatement with lenolidamide. Similar studies were performed while on lenoldamide therapy in peripheral blood at 3 months and in bone marrow at 20 months of treatment. One patient with mosaic deletion of 5q was available for longitudinal study including assessment of gene expression in bone marrow before and during treatment with lenalidomide.

first: Adrianna

last: Vlachos

first: Jeffrey

last: MLipton

first: David

last: MBodine


title: Expression data of A2EN cells during early stage of Chlamydia trachomatis infection

status: Public on Apr 09 2014

city: Durham

first: Raphael

last: Valdivia

state: NC

address: 207 Research drive, Jones bldg 272

department: Molecular Genetics and Microbiology

institute: Duke University

summary:
Chlamydia trachomatis is an obligate intracellular pathogen that causes trachoma and sextually transmitted disease in human. During early stage of infection, Chlamydia secreted bacterial effector proteins into host cell cytoplasm to help its entry and estabilishment of early replicated niche.
We identified a Chlamydia mutant that lack an early Effector. To address the function of this effector, we infected A2EN cells with this mutant (G1V) and its complemented counterpart (G1TEPP) to see what host gene transcriptions are affected by this effector.

overall_design: A2EN cells were mock infected, or infected with a Chlamydia mutant or its complemented counterpart for 4 hour post infection.

first: Victoria

middle: K

last: Carpenter

first: Yi-Shan

last: Chen


title: ERK Oscillation-Dependent Gene Expression Patterns and Deregulation By The Stress-Response

status: Public on Mar 13 2014

city: Richland

first: Katrina

last: Waters

state: WA

address: 902 Battelle Blvd; MSIN J4-18

department: Biological Sciences Division

institute: Pacific Northwest National Laboratory

summary:
Studies were undertaken to determine whether oscillatory behavior in the extracellular signal regulated kinase (ERK) pathway results in unique gene regulation patterns.  Microarray analysis was performed on three subcloned populations of human keratinocytes with distinct ERK signaling/oscillation phenotypes.
Microarray analysis identified 45 genes that overlapped between 2 subclones with oscillation phenotypes but not in the subclone which is non-oscillatory.  Transcription factor networks revealed a role for MED1 in mediating ERK oscillation-dependent gene expression, which was confirmed with Western blot analysis.  Further experimentation confirmed a role for p38 in the mediation of MED1 phosphorylation and ERK oscillatory behavior.

overall_design: hTERT-immortalized normal human keratinocytes (provided by Dr. Jerry Shay, The University of Texas Southwestern Medical Center) were stably transfected with ERK1-green fluorescent protein chimera and stable subclones were isolated with distinct ERK activation/oscillation patterns: Clone #1 exhibits transient ERK activation with ligand activation but does not oscillate; Clone #2 exhibits persistent ERK oscillations that are dependent on ligand activation; and Clone #3 exhibits spontaneous ERK oscillations in the absence of ligand activation.

first: Thomas

last: Weber


title: A PGC-1alpha-dependent decrease in mitochondrial oxidative metabolism in muscle of humans with inherited insulin resistance

status: Public on Feb 17 2014

city: Roskilde

first: Vibe

last: Skov

address: Koegevej 7-13

department: Hematology

country: Denmark

institute: Roskilde Hospital

summary: We used microarrays to assess gene expression profiling of 6 patients with a mutation (Arg1174Gln) in the tyrosine kinase domain of the insulin receptor gene (INSR) and 10 matched healthy controls

overall_design: Total RNA was purified from skeletal muscle and amplified to biotin-labeled aRNA and hybridized to microarray chips.

first: Skov

last: Vibe


title: Treatment of renal cell carcinoma cell line A-498 with zebularine

status: Public on Oct 24 2013

city: Berlin

first: Hans

last: Krause

address: Charitéplatz 1

department: Klinik für Urologie

country: Germany

institute: Charité - Universitätsmedizin Berlin

summary: Cultures of A-498 cells were treated for 120hours with 1000µM zebularine (SIGMA) in three independent biological experiments. Zebularine acts as a DNA methyltransferase (DNMT) inhibitor thereby upregulating genes that are inactivated by e.g. promotor hypermethylation. The experiment aimed to search for upregulated transcripts to provide new targets for biomarker development and therapeutic use. 308 candidates were upregulated more than 1.5-fold. Members of the metallothionein group (MT1G, MT1H, and MT2A) were validated in 49 clinical samples of renal cell carcinomas.

overall_design: Total RNA of treated (1000µM zebularine) and untreated A-498 cells (experiment A05-A07) was subjected to Affymetrix array analysis to detail the overall expression changes after treatment with a DNMT inhibitor. Treated cells showed no obvious signs of zebularine-induced cytotoxicity as revealed by XTT assays. Cell were split twice during the 120hour treatment period.

first: Imad

last: Al-Kamal


title: Effect of PIAS1 on gene expression

status: Public on Feb 06 2014

first: BIN

last: LIU

address: 10833 Le Conte Avenue

institute: UCLA

summary:
To study the effect of PIAS1 on transcriptional regulation, we establishedstable PIAS1 shRNA knockdown cells in breast cancer cell line MDA-MB231.
By comparing the expression profiles of control vs PIAS1 knockdown cells, we can identify potential PIAS1 target genes involved in breast tumorigenesis.

overall_design: MDA-MB231 Control shRNA and PIAS1 shRNA2 cells were cultured in DMEM plus 10% FBS (DMEM) or SCM for 30 h, and total RNA was used for microarray.

first: B

last: Liu

first: V

last: Chernishof


title: Expression data from human abdominal, subcutaneous adipose tissue

status: Public on Oct 29 2013

city: London

first: Carol

last: Shoulders

address: Charterhouse Square

department: Centre for Endocrinology

institute: QMUL

summary:
FCHL is a common, complex genetic lipid disorder with a largely unknown aetiology. Altered adipose tissue metabolism has been implicated as contributing to FCHL.
We used microarrays to investigate the mRNA profiles of FCHL patients with CHD and non-FCHL patients with CHD in comparison with non-FCHL, non-CHD patients to define a core set of genes that were differentially expressed in FCHL and to provide a reasonable launch-pad for examining the direct contribution of one of this gene set to the development of adipose tissue.

overall_design: Adipose tissue was obtained from the same anatomical site - the subcutaneous, upper abdominal region - of white British males, either at coronary artery bypass surgery (designated as: FCHL-CHD (13 individuals, subdivided on TG response to statins into Group 1 (n=4), Group 2 (n=7) and unclassified (n=2)) and non-FCHL-CHD patients (6 individuals)), or at heart valve replacement: non-FCHL, non-CHD subjects (5 individuals; controls).

first: Stuart

middle: D

last: Horswell

first: Dlear

last: Zindrou

first: Rossi

last: Naoumova

first: James

last: Scott


title: Endocrine response in invasive lobular carcinoma is characterized by unique estrogen-mediated gene expression and de novo tamoxifen resistance (SUM44)

first: Uma

last: Chandran

summary: Invasive lobular carcinoma (ILC) is a histological subtype of breast cancer that is frequently associated with favorable outcomes, as ~90% of ILC express the estrogen receptor (ER). However, recent retrospective analyses suggest that ILC patients receiving adjuvant endocrine therapy may not benefit from improved outcomes versus other breast cancer patients. Based on these observations, we characterized ER function and endocrine response in ILC models. The ER-positive ILC cell lines MDA MB 134VI (MM134) and SUM44PE were used to examine the ER-regulated transcriptome in vitro via gene expression microarray analyses and ER ChIP-Seq.  In parallel, estrogen response was assessed in vivo in the patient-derived ILC xenograft HCI-013. Response to endocrine therapy was also examined in ILC cell lines. We identified 915 genes that were uniquely E2-regulated in ILC cell lines versus other breast cancer cell lines, and a subset of these genes were also regulated in vivo in HCI-013. We observed that MM134 were de novo tamoxifen resistant, and were induced to grow by 4-hydroxytamoxifen, as well as other anti-estrogens, as partial agonists. Growth was accompanied by agonist activity of tamoxifen on ER-mediated gene expression. Though tamoxifen induced cell growth, MM134 cells required FGFR1 signaling to maintain viability and were sensitive to combined endocrine therapy and FGFR1 inhibition. Our observation that ER drives a unique program of gene expression in ILC cells correlates with the ability of tamoxifen to induce growth in these cells. Targeting growth factors using FGFR1 inhibitors may block survival pathways required by ILC and reverse tamoxifen resistance.

overall_design: Cells were hormone deprived by replacing growth medium with IMEM+2% charcoal stripped serum for 3 days. Following deprivation, cells were treated for 3 or 24 hours with 1nM E2 or vehicle (0.01% EtOH) in biological quadruplicate. Following treatment, cells were lysed and RNA was harvested using the Illustra RNAspin Mini kit (GE Health). cRNA synthesis and labeling was performed using the Ambion MessageAmp Premier Kit (Life Technologies), and cRNA was hybridized to U133A 2.0 arrays (Affymetrix, Santa Clara, CA). cRNA synthesis and labeling, hybridization, and scanning were performed by the University of Pittsburgh Cancer Biomarkers Facility.

first: Matthew

last: Sikora

first: Kristine

last: Cooper

first: Amir

last: Bahreini

first: Soumya

last: Luthra

first: Guoying

last: Wang

first: Nancy

last: Davidson

first: David

last: Dabbs

first: Alana

last: Welm

first: Steffi

last: Oesterreich


title: Endocrine response in invasive lobular carcinoma is characterized by unique estrogen-mediated gene expression and de novo tamoxifen resistance (MM134)

overall_design: Cells were hormone deprived by replacing growth medium with IMEM+10% charcoal stripped serum for 3 days. Following deprivation, cells were treated for 3 or 24 hours with 1nM E2 or vehicle (0.01% EtOH) in biological quadruplicate. Following treatment, cells were lysed and RNA was harvested using the Illustra RNAspin Mini kit (GE Health). cRNA synthesis and labeling was performed using the Ambion MessageAmp Premier Kit (Life Technologies), and cRNA was hybridized to U133A 2.0 arrays (Affymetrix, Santa Clara, CA). cRNA synthesis and labeling, hybridization, and scanning were performed by the University of Pittsburgh Cancer Biomarkers Facility.


title: Expression data from responders/nonresponders before/after receiving DLI for relapse of CML s/p BMT

status: Public on Sep 30 2013

first: Pavan

last: Bachireddy

state: MA

address: 77 Avenue Louis Pasteur

summary:
Increasing evidence across malignancies suggests that infiltrating T cells at the site of disease are crucial to tumor control. We hypothesized that marrow-infiltrating immune populations play a critical role in response to donor lymphocyte infusion (DLI), an established and potentially curative immune therapy whose precise mechanism remains unknown.  We therefore analyzed marrow-infiltrating immune populations in 29 patients (22 responders, 7 nonresponders) with relapsed chronic myelogenous leukemia who received CD4+ DLI in the pre-tyrosine kinase inhibitor era.
We used microarrays to detail the global programme of gene expression underlying T cell infiltration into bone marrow of responders and nonresponders to DLI.

overall_design: mRNA expression profiling of marrow-infiltrating CD3+ positively selected T cells of 4 responders compared to 2 non-responders, before and after DLI, was performed on Affymetrix microarrays.

first: Ursula

last: Hainz

first: Michael

last: Rooney

first: Nir

last: Hacohen

first: Catherine

last: Wu


title: Expression data from wheat cultivars

status: Public on Jan 30 2014

city: Hangzhou

first: shaohui

last: Li

address: Yuhangtang road

country: China

institute: Zhejiang University

summary:
To identify genes involved in susceptibility, genechip hybridization experiments were performed in order to examine genes differentially expressed upon inoculation of resistant and susceptible wheat cultivars with powdery mildew.
Some genes were identified which were just expressed in the susceptible host both after mock-inoculation and pathogen infection. Also, a total of 2693 transcripts were differentially expressed (fold change≥2) in Yumai 13 in response to powdery mildew as compared to itself, comprising 1464 and 1229 up- and down-regulated genes respectively.

overall_design: Seven-day-old wheat seedlings of susceptible cultivar Yumai 13, two resistant cultivars HY and CYC were inoculated with powdery mildew and harvested at 0, 24, 48 hpi for RNA extraction and hybridization on Affymetrix microarrays. We sought to screen some genes which have very high expression in Yumai 13, but not in CYC and HY by pairwise comparation.

first: Li

last: Shaohui

first: Hu

last: Dongwei


title: mRNA oxidation data from dry dormant and after-ripened wheat seeds

status: Public on Dec 15 2013

city: Winnipeg

first: Belay

middle: T.

last: Ayele

state: MB

address: 222 Agriculture Building

department: Plant Science

institute: University of Manitoba

summary:
After-ripening induced seed dormancy release in wheat is associated with mRNA oxidation.
We used Affymetrix GeneChip Wheat Genome Array to identify mRNAs differentially oxidized by after-ripening

overall_design: Dormant and after-ripened seeds in dry state were used for isolating oxidized mRNAs and hybridization on Affymetrix GeneChip. After-ripened seeds were generated by storing dormant seeds at room temperature for 10 months.

middle: T

first: Mark

last: Jordan

first: Feng

last: Gao


title: Transcriptional Profiling Defines the Roles of ERK and p38 Kinases in Epidermal Keratinocytes

status: Public on Sep 05 2013

city: New York

first: Miroslav

last: Blumenberg

address: 455 First Ave #874

institute: NYU School of Medicine

summary: Epidermal keratinocytes respond to extracellular influences by activating cytoplasmic signal transduction pathways that change the transcriptional profiles of affected cells. To define responses to two such pathways, p38 and ERK, we used SB203580 and PD98059 as specific inhibitors, and identified the regulated genes after 1, 4, 24 and 48 hrs, using Affymetrix’ Hu133Av2 microarrays.  Additionally, we compared genes specifically regulated by p38 and ERKs with those regulated by JNK and by all three pathways simultaneously. We find that the p38 pathway induces the expression of extracellular matrix and proliferation-associated genes, while suppressing microtubule-associated genes; the ERK pathway induces the expression of nuclear envelope and mRNA splicing proteins, while suppressing steroid synthesis and mitochondrial energy production enzymes. Both pathways promote epidermal differentiation and induce feedback inactivation of MAPK signaling. c-FOS, SRY and N-Myc appear to be the principal targets of the p38 pathway, Elk-1 SAP1 and HLH2 of ERK, while FREAC-4, ARNT and USF are common to both. The results for the first time comprehensively define the genes regulated by the p38 and ERK pathways in epidermal keratinocytes and suggest a list of targets potentially useful in therapeutic interventions.

overall_design: Human epidermal keratinocytes are grown in Keratinocyte Serum-Free Medium (Gibco) supplemented with 0.05 mg/ml bovine pituitary extract, 2.5 ng/ml epidermal growth factor, 0.09 mM CalCl2 and 1% penicillin/streptomycin (KGM). They are switched to Keratinocyte Serum Free-Media (Gibco) supplemented only with 1% penicillin/streptomycin (KBM) 24 h prior to commencing experiments. A set is left as controls, others treated with 5 uM JNK inhibitor SP600125, 15 uM p38 inhibitor SB203580, or 50 um  ERK inhibitor PD98059. Timecourse of treated and parellel control samples over a 48 hr period was performed.

first: Alix

last: Gazel

first: Rajiv

middle: I

last: Nijhawan

first: Rebecca

last: Walsh


title: Molecular Mapping of Keratinocyte Differentiation by Functional Gene Expression Profiling

city: Phoenix

first: Yoga

last: Balagurunathan

state: AZ

address: 445 N. Fifth street

institute: TGEN

summary:
Our goal was to establish a robust and reliable platform for the mapping of gene expression changes occurring during the process of keratinocyte
differentiation. We hypothesized that a functional gene expression profiling approach capable of identifying the program of gene expression over time would facilitate more focused identification of relevant genes. To achieve this, we used the confluenceinduced differentiation (CID) model, a widely used and reliable method that in many aspects recapitulates in vivo differentiation of human epidermal keratinocytes (Paragh et al, 2010; Poumay and Pittelkow, 1995).

overall_design:
Primary human keratinocytes from three donors were subjected to CID in
separate cultures and harvested at successive time points including 2 days prior to reaching confluence (D(-2)), at the point of confluence (D(0)), as well as after reaching confluence (D(1), D(2) and D(3)). In order to minimize any donor and sample effects, the RNA samples were pooled at each time point and gene expression profiling was performed (Affymetrix U133 A & B). Secondary validation study was performed with three additional time observation arrayed in Affymetrix U133A2 platform for the 3 patient pool. The time observations were: D(-3),D(-2),D(-1),D(0),D(+1),D(+2),D(+3),D(+5).

first: Aleksandar

last: Aleksandar

first: Daniel

last: Johnson

first: Yoganand

first: Sonsoles

last: Shack

first: Lalitamba

last: Alla

last: Bittner

last: Pittelkow


title: Expression data from human foreskin fibroblasts (HFFs) infected with type I strains of Toxoplasma gondii.

status: Public on Aug 20 2013

city: Cambridge

first: Ninghan

last: Yang

address: 77 Massachusetts Ave, 68-270

institute: MIT

summary: Type I strains of Toxoplasma gondii exhibit phenotypic variation, but it is uncertain how differently type I strains modulate the host cell. We determined differential host modulation by type I strains through microarray.

overall_design: HFFs were infected with RH-ERP, RH-JSR and GT1 for 24 hours. Total RNA was isolated and hybridized to Affymetrix GeneChip Human Genome U133A 2.0 arrays.

first: Jeroen

last: Saeij


title: Identification of candidate genes for processing quality for good chapatti (flat unleavened bread)

status: Public on Jan 13 2014

city: Mohali

first: JOY

last: ROY

state: Punjab

address: C-127, Industrial Area, Phase 8

department: Agri-Biotech

country: India

institute: National Agri-Food Biotechnology Institute (NABI)

summary: Gene-specific two-way ANOVA analysis for identification of candidate genes for processing quality, seed development, and interaction (quality x development)

overall_design: Gene expression data of two good chapatti making varieties, C306 and Lok1 and two poor chapatti making varieties, sonalika and WH291 at three seed development stages (7, 14, and 28 days after anthesis) were analyzed using gene-specific two-way ANOVA to partition variation in gene expression due to quality, seed development, and their interaction (quality x development).

first: Joy

last: Roy

first: Anuradha

last: Singh

first: Shrikant

last: Mantri

first: Rakesh

last: Tuli


title: Alteration in transcript level in wheat alloplasmic lines

status: Public on Dec 11 2013

city: Ames

first: PLEXdb Curator

middle: Sudhansu

state: IA

address: 1023  Crop Genomes Informatics Lab (Iowa State University)

department: Virtual Reality Application Center

institute: Iowa State University

summary:
Alloplasmic lines provide a unique tool to study the nucleo-cytoplasmic interactions. Alloplasmic lines T183 and T195 were developed through the introgression of the cytoplasm from Aegilops uniaristata (T183) and Aegilops squarrosa (T195) in the nuclear background of Triticum aestivum cv. Chris. Alloplasmic line TH237 was produced introgressing the Hordeum chilense accession H7 cytoplasm into the nuclear background of Triticum aestivum accession T20. Fifty seeds for each sample in pots of 11 cm diameter and grown in controlled conditions under 600µE m-2 s–1 high light intensity in a daily regime of 12 h light at 22°C and 12 h darkness at 15°C. Plants were bulked from each pot and three biological replicate used for the transcriptomics Fully expanded second leaves were collected two weeks from sowing in the middle of the light period and used for transcriptomic analysis.

****PLEXdb (http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor,  Cristina Crosatti.  The equivalent experiment is TA49 at PLEXdb.

overall_design:
genotype: EU_T20(3-replications);
genotype: ALLO_TH237(3-replications);
genotype: EU_CHRIS(3-replications);
genotype: ALLO_183(3-replications);
genotype: ALLO_195(3-replications)

first: Cristina

last: Crosatti

first: Luigi

last: Cattivelli


title: Long-term growth under elevated CO2 differentially suppresses biotic stress genes in non-acclimated versus cold-acclimated winter wheat

status: Public on Aug 23 2013

city: Montreal

first: Khalil

last: kane

address: 2080 saint-urbain

department: Sciences biologiques

institute: University of Quebec in Montreal

summary: This study compared the photosynthetic performance and the global gene expression of the winter hardy wheat Triticum aestivum cv Norstar grown under non-acclimated (NA) or cold-acclimated (CA) condition at either ambient CO2 or elevated CO2 (EC). CA Norstar maintained comparable light saturated and CO2 saturated rates of photosynthesis but lower quantum requirements for photosystem II and non photochemical quenching relative to NA plants even at EC. Neither NA nor CA plants were sensitive to feedback inhibition of photosynthesis at EC. Global gene expression using microarray combined with bioinformatics analysis revealed that genes affected by EC were 3 times higher in NA (1022 genes) compared to CA (372 genes) Norstar. The most striking effect was the down-regulation of genes involved in the plant defense responses in NA Norstar. In contrast, cold acclimation reversed this down regulation  due to the cold  induction of genes involved in plant pathogenesis resistance, and cellular and chloroplast protection. These results suggest that EC have less impact on plant performance and productivity in cold adapted winter hardy plants in the northern climates compared to warmer environments. Selection for cereal cultivars with constitutively higher expression of biotic stress defense genes may be necessary under EC during the warm growth period and in warmer climates.

overall_design: Twelve replicate pots with 3 plants per pot were grown at either NA or CA conditions at either ambient or EC. To minimize any possible chamber effects, the 12 replicate pots at each growth condition were distributed between two growth chambers.  A total of 3 biological replicates for each condition were used for microarray analyses. Each biological replicate sample was obtained by pooling three whole fully expanded 3rd leaves from different plants harvested randomly. The different biological samples of Norstar winter wheat leaves were ground in dry ice to fine powder and total RNA was extracted with trizol (Invitrogen, Burlington, ON, CA). Total RNA was cleaned using RNeasy plant mini kit (Qiagen) and integrity was determined on agarose gel and on a bioanalyser (Agilent 2100). Synthesized cDNAs were transcribed to cRNAs with the 3’IVT labelling kit (Santa Clara, CA, USA) and hybridized to the Affymetrix wheat genome array (Santa Clara, Ca, USA) at the McGill University and Génome Québec Innovation Centre (Montreal, Qc, CA). The experimental design consisted of three biological replicates for each of the four growth conditions, 1: Non-acclimated (NA) at ambient CO2 (AC) (NAAC); 2: Cold-acclimated (CA) at ambient CO2 (AC) (CAAC); 3: Non-acclimated (NA) at elevated CO2 (EC) (NAEC); 4: Cold-acclimated (CA) at elevated CO2 (EC) (CAEC). Thus, a total of 3 biological samples from each of the 4 growth conditions described above were used for hybridizations.

last: Kane

first: Keshav

last: Dahal

first: Mohamed

last: Badawi

first: Mario

last: Houde

first: Norman

last: Hüner

first: Fathey

last: Sarhan


title: microRNAs distinguish cytogenetic subgroups in pediatric AML and contribute to complex regulatory networks in AML-relevant pathways

status: Public on Sep 11 2013

city: Düsseldorf

first: Pablo

last: Landgraf

address: Moorenstraße 5

department: Clinic of Pediatric Oncology, Hematology and Clinical Immunology

institute: Heinrich-Heine University Düsseldorf

type:
Other
Non-coding RNA profiling by array
Expression profiling by array

summary: microRNAs, important regulators of cell proliferation and apoptosis, have been shown to be involved in the pathogenesis of acute myeloid leukemia in adulthood AML. However, comprehensive studies in AML of children and adolescents are missing so far. We investigated the miRNA expression profiles of different AML subtypes from 102 pediatric patients in comparison to CD34+ cells from healthy donors and adult AML patients, in order to identify differentially expressed miRNAs. Pediatric samples with core factor binding acute myeloid leukemia and promyelocytic leukemia could be distinguished from each other and MLL rearranged AML subtypes by 9 and 18 miRNAs, respectively. miR-126, -146a, -181a/b, -100, and miR-125b were identified as highest differentially expressed with marked difference of expression between pediatric and adulthood samples of the same cytogenetic subgroup. We next isolated the miRNA targeting complex from t(8;21) and t(15;17) cell line models and comprehensively identified bound miRNAs and targeted mRNAs by a newly devised immunoprecipitation assay followed by rapid microarray detection. Our findings indicate separate binding preferences for the four human Argonaute proteins. Subsequent bioinformatic analysis revealed a concerted action of different Ago proteins in the regulation of AML-relevant pathways, providing an experimental based database of miRNA-mRNA target interaction in Argonaute proteins.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design:
Ago-associated microRNAs: Co-immunoprecipitation in the acute myeloid leukemia cell line models, KASUMI-1 and NB4, of the four human  Argonaute complexes using monoclonal antibodies and stringent washing conditions. We performed photo-activated UV cross-linking using 4’-thioruidine before cell lysis. Unspecific binding to the bead matrix and to the Fc part of the monoclonal rat antibody were recorded and corrected by empty bead controls and an antibody isotype control. Argonaute-associated miRNAs/mRNAs and unspecific bound miRNAs/mRNAs of the isotype control were identified by microarray hybridization. These experiments were performed in triplicates.
Ago-associated mRNAs: Co-immunoprecipitation in the acute myeloid leukemia cell line models, KASUMI-1 and NB4, of the four human  Argonaute complexes using monoclonal antibodies and stringent washing conditions. We performed photo-activated UV cross-linking using 4’-thioruidine before cell lysis. Unspecific binding to the bead matrix and to the Fc part of the monoclonal rat antibody were recorded and corrected by empty bead controls and an antibody isotype control. Argonaute-associated miRNAs/mRNAs and unspecific bound miRNAs/mRNAs of the isotype control were identified by microarray hybridization. These experiments were performed in triplicates.
AML-patient microRNAs: RNA extraction using the TRIzol protocol (Invitrogen), labeling of RNA with Cy3- (universal reference) and Cy5-Dyes (samples) using a truncated and mutated RNA ligase, hybridization of miRNAs over night at 42°C using miRXplore microarrays and the a-Hyb Hybridization Station (MACS molecular Miltenyi Biotec)

first: Svenja

last: Daschkey

first: Arndt

last: Borkhardt

first: Silja

last: Röttgers

first: Jutta

last: Bradtke

first: Andrea

last: Teigler-Schlegel

first: Gunter

last: Meister


title: Human foreskin fibroblasts (HFFs) infected with type I strains of Toxoplasma gondii

first: Ninghan

last: Yang

department: Biology

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

sample_organism:
Toxoplasma gondii
Homo sapiens

platform_organism:
Toxoplasma gondii
Homo sapiens

overall_design: Refer to individual Series


title: GBM response to Smo and PI3K inhibitors

status: Public on Sep 01 2013

city: Boston

first: Rosalind

middle: A

last: Segal

address: 450 Brookline Ave

department: Cancer Biology

institute: Dana Farber Cancer Institute

summary: Combination therapy with Smo and PI3K inhibitors results in a synergistic effect in reducing tumor growth in PTEN-deficient Glioblastoma. To identify  consequences of combination therapy with an Smo inhibitor and a PI3K inhibitor on a genome-wide scale, we performed Affymetrix microarrays with two different PTEN-deficient GBMs treated with single drugs or combination therapy. A small set of genes was significantly affected by combination therapy in hBT70 and/or hBT112, including several genes implicated in GBM prognosis, or identified as targets of Shh, PI3K or S6 pathways 29-33 .

overall_design: There are two different human GBM tumors (BT70 and BT112).  Both are PTEN deficient. Samples were treated with DMSO (Control), LDE225 at 1 uM for 5 days, BKM 120 100 nM for 5 days, or LDE225 1 uM and BKM 120 100 nM for 5 days (Combo).  Two biological  replicates of each condition were analyzed.

first: Mariella

last: Gruber-Olipitz


title: Microarray data from CREB inhibited and control mesothelioma cells

status: Public on Oct 21 2013

city: Burlington

first: Arti

last: Shukla

state: VT

address: 89 Beaumont Avenue

department: Pathology

institute: University of Vermont

summary: Cyclic AMP response element binding protein (CREB) is known to play important roles in growth and drug resistance of various cancers. Here we show roles of inhibition of CREB1 on gene expression profile of malignant mesothelioma (MM) cells (Hmeso and H2373/PPMMill).

overall_design: Stably transfected HMESO or H2373/PPMMill cells with either shControl or shCREB1 plasmids were used. Microarrays were performed on samples from 2 independent experiments. Each sample was analyzed on a separate array (2 independent biological replicates).


title: A mutation in the c-Fos gene associated with congenital generalized lipodystrophy

status: Public on Aug 07 2013

city: Duesseldorf

first: Birgit

last: Knebel

address: Auf'm Hennekamp 65

department: Cinical Biochemistry and Pathobiochemistry

institute: German Diabetes Center

summary:
Lipodystrophies resemble syndromes of disturbed adipocyte biology or development and severe congenital forms (CGL) lack adipose tissue. The ubiquitous immediate-early gene c-fos is one essential transcription factor to initiate adipocyte differentiation. In a CGL patient we identified a single homozygous point mutation in the promoter of c-fos gene. The mutation facilitates the formation of a novel specific protein/ DNA complex and ubiquitously reduces basal and inducible c-fos transcription activity.
We used microarrays to determine differences in gene expression due to a repressive c-fos promoter mutation in a patient with CGL.

overall_design: Cultued fibroblasts of non diabetic controls and a patient with c-fos promoter mutation were analyzed at identical passage number and growth conditions without further additional treatment.

first: Jorg

last: Kotzka

first: Dirk

last: Muller-Wieland


title: Analyses of a deactivation genetic variation in Ha-Ras proto oncogene identified in a patient wit premature aging and insulin resistance

summary:
Inherited genetic variants of insulin receptor induced cellular signaling have long been suspected to contribute to the development of type-2- diabetes mellitus. In this report we discuss a heterozygous mutation in the first coding exon of the proto-oncogene Ha-Ras (Ha-RasA11P) that we have identified in a patient with familial premature aging syndrome. The patient has atopic sklerodermic skin alterations, insulin resistance as well as disturbances in lipid metabolism. In vitro analyzes have shown that this mutation disrupted not only the signal transduction of the insulin receptor but also other receptor tyrosine kinases, such as IGF-1, EGF, PDGF. These results demonstrate that HA-Ras has a significant role in insulin sensitivity in humans.
We used microarrays to determine differences in gene expression due to a deactivating Ha-Ras mutation reducing c-fos expression in a patient with lipodystrophy and a Werner-like syndrome.

overall_design: Cultued fibroblasts of non diabetic controls and a patient with deactivating Ha-Ras mutation were analyzed at identical passage number and growth conditions without further additional treatment.


title: Gene Expression Signature of Human Polynucleotide Phosphorylase (hPNPaseold-35) in Melanoma

status: Public on Jul 30 2013

city: Jacksonville

first: Catherine

last: Dumur

state: FL

address: 5008 Mustang Rd

department: Anatomic Pathology

institute: Sonic Healthcare USA

summary:
Human Polynucleotide Phosphorylase (hPNPaseold-35) is an evolutionarily conserved 3’→5’ exoribonuclease implicated in the regulation of numerous physiological processes like maintenance of mitochondrial homeostasis, mtRNA import and aging-associated inflammation.
From an RNase perspective, little is known about the RNA or miRNA species it targets for degradation or whose expression it regulates; except for c-myc and miR-221.

overall_design: To further elucidate the functional implications of hPNPaseold-35 in cellular physiology, we knocked-down and overexpressed hPNPaseold-35 in melanoma cells and performed gene expression analyses to identify differentially expressed transcripts. Biological triplicates were run on microarrays.

first: Paul

last: Fisher

first: Upneet

last: Sokhi


title: The Demethylase JMJD2C/KDM4C Localizes to H3K4me3 Positive Transcription Start Sites (Affymetrix microarray analysis)

status: Public on Jan 09 2014

city: Copenhagen N

first: Marianne

middle: Terndrup

last: Pedersen

address: Ole Maaloes Vej 5

department: University of Copenhagen

institute: BRIC

summary: We have mapped transcriptional changes after depletion of the histone demethylases JMJD2C/GASC1/KDM4C and JMJD2A/KDM4A alone or in combination in the esophageal squamous carcinoma cell line, KYSE150. The KYSE150 cell line contains an amplification of the JMJD2C locus.

overall_design: RNA was extracted from KYSE150 cells transfected with shRNAs targeting JMJD2C and/or JMJD2A. The experiment was performed in triplicates and expression levels analyzed using Affymetrix microarrays.


title: Integrative genomics of gene and metabolic regulation by estrogen receptors α and β and coregulators [expression]

status: Public on Jul 05 2013

city: Urbana

first: Zeynep

last: Madak Erdogan

state: IL

address: 1201 S Goodwin Ave

department: FSHN

institute: UIUC

summary:
The closely related transcription factors (TFs), estrogen receptors ERα and ERβ, regulate divergent gene expression programs and proliferative outcomes in breast cancer. Utilizing MCF-7 breast cancer cells with ERα, ERβ, or both receptors as a model system to define the basis of differing response specification by related TFs, we show that these TFs and their key coregulators, SRC3 and RIP140, generate overlapping as well as unique chromatin-binding and transcription-regulating modules.
Cistrome and transcriptome analyses and use of clustering algorithms delineated 11 clusters representing different chromatin-bound receptor and coregulator assemblies that could be functionally associated through enrichment analysis with distinct patterns of gene regulation and preferential coregulator usage, RIP140 with ERβ and SRC3 with ERα. The receptors modified each other’s transcriptional effect, and ERβ countered the proliferative drive of ERα through several novel mechanisms associated with specific binding site clusters. Our findings delineate distinct TF-coregulator assemblies that function as control nodes specifying precise patterns of gene regulation, proliferation, and metabolism, as exemplified by two of the most important nuclear hormone receptors in human breast cancer.

overall_design:
MCF-7 cells expressing endogenous ERalpha were infected with adenovirus carrying either estrogen receptor beta (AdERb) or no insert (Ad) at multiplicity of infection (moi) of 50. ERβ only cells were generated from these cells by knockdown of ERα in parental cells using the following siERα sequences from Dharmacon: forward, 5’-UCAUCGCAUUCCUUGCAAAdTdT-3’, and reverse, 5’-UUUGCAAGGAAUGCGAUGAdTdT-3’. siRNA experiments were performed as previously described, and resulted in knocknown of ERα mRNA and protein by greater than 95% (GSE4006, PMID 16809442). Briefly, cells were transfected with 20 nM siCtrl [GSE4006] or siERα for 48 h after infection. Then cells were treated with 0.1% EtOH (Veh) or 10 nM E2 (Sigma-Aldrich) for 24h. All experiments were conducted with two replicates.
key words; Adenovirus infection,siRNA knock-down, ligand treatment

last: Erdogan

first: Benita

last: Katzenellenbogen


title: A functional liaison between E2F and the aberrant ETS oncogene EWS/FLI1 in Ewing's sarcoma

status: Public on Jul 01 2013

city: Vienna

first: Maximilian

last: Kauer

address: Zimmermannplatz 10

department: Molecular Biology

country: Austria

institute: CCRI, St.Anna Children Cancer Research Institute

summary: Translocations of ETS transcription factors are driver mutations in diverse cancers. We investigated the genomic network of the ETS fusion EWS/FLI1 in Ewing's sarcoma (ESFT) as a model of ETS-driven tumorigenesis. ChIP-Seq and transcriptional analysis identified E2F3 as a principle co-factor of EWSFLI1 defining functionally distinct gene sets. While EWS/FLI1 binding independent of E2F3 predominantly associated with repressed differentiation genes, significant co-localization with E2F3 was discovered at proximal promoters of activated growth-related genes. Thus, EWS/FLI1 promotes oncogenesis by simultaneously perturbing differentiation state and augmenting the expression of genes co-regulated by E2F3. Integration of additional E2F3 and ERG localization data from prostate cancer containing TMPRSS2/ERG verified that the ETS-E2F module is also found in prostate cancer and may be of general relevance to ETS driven cancers.

overall_design: Timecourse with 6 timepoints of a doxicyclin inducible EWS-FLI1 knockdown in the A673 Ewing's Sarcoma celline

first: Sven

last: Bilke

first: Raphaela

last: Schwentner

first: Fan

first: Robert

last: Walker

first: Heinrich

last: Kovar

last: Meltzer


title: Expression data from mesenchymal stem cells of ossifying fibroma

status: Public on Jul 24 2013

city: Los Angeles

first: Cunye

last: Qu

address: 2250 Alcazar st., CSA103

institute: University of Southern California

summary: Ossifying fibroma (OF) is a common benign fibro-osseous neoplasm of orofacial bones, showing progressive enlargement of the affected jaw with deficiency in bone formation. Our aim is to discover the molecular difference between mesenchymal stem cells from OF and normal jaw bone to provide basis for development of clinical therapy. Global gene expression comparison and gene ontology analysis found that several singaling pathways are involved in the process, including TGFb signaling and Notch signaling. Inhibition of  TGFb signaling in mesenchymal stem cells of OF can increase the osteogenesis and decrease proliferation, shedding light on developing strategies for therapy.

overall_design: RNA from mesenchymal stem cells of OF is compared to that of normal jaw bone.

first: Songtao

last: Shi


status: Public on Dec 01 2013

first: Darrell

middle: Jiro

last: Yamashiro

state: NY

address: 1130 St. Nicholas Ave, Room 924A

department: Pediatrics

institute: Columbia University

summary: We asked whether combining Notch and VEGF blockade would enhance suppression of tumor angiogenesis and growth, using the NGP neuroblastoma model. NGP tumors were engineered to express a Notch1 decoy construct (N1D), which restricts Notch signaling, and then treated with either the anti-VEGF antibody bevacizumab or vehicle. Combining Notch and VEGF blockade led to blood vessel regression, increasing endothelial cell apoptosis and disrupting pericyte coverage of endothelial cells. Combined Notch and VEGF blockade did not affect tumor weight, but did additively reduce tumor viability. Our results indicate that Notch and VEGF pathways play distinct but complementary roles in tumor angiogenesis, and show that concurrent blockade disrupts primary tumor vasculature and viability further than inhibition of either pathway alone.

overall_design: 6 neuroblastoma tumors were transfected with Notch1 decoy, 6 with Notch1 decoy and treated with bevacizumab, 6 tumors treated with bevacizumab, and 6 control tumors were profiled by human 133A 2.0 arrays

first: S

last: Hernandez

first: D

last: Banerjee

first: A

last: Garcia

first: T

last: Kangsamaksin

first: W

last: Cheng

first: Y

last: Funahashi

first: C

middle: J

last: Shawber

first: J

last: Kitajewski

last: Kandel


title: Expression data wheat Flag Leaf at anthesis

city: St. Lucia

first: Maarten

last: Kooiker

state: QLD

address: 306 Carmody Road

country: Australia

institute: CSIRO Plant Industry

summary:
TaMYB13 is a transcription factor that has been associated with fructan accumulation in previous studies in wheat (Xue et al. 2011 Plant journal 68: 857 - 870). In this study we aimed to find genes regulated by TaMYB13, through overexpression of this transcription factor in wheat and perform expression analysis by making use of Affymetrix genechip assays.
Expression of control plants was compared to transgenic lines, and total RNA was extracted from Flag leaves at anthesis.

overall_design: In this experiment the genome wide gene expression was assessed from wheat flag leaf material harvested at anthesis. Control plants (BW43,BW44,BW45) were compared with transgenic lines that overexpress TaMYB13 (a20, b2, b36).

first: Gang-Ping

last: Xue


title: The Bromodomain protein Brd4 Insulates Chromatin from DNA Damage Signaling through Acetyl-Lysine Binding

status: Public on Jul 14 2013

first: Charles

middle: Arthur

last: Whittaker

institute: Koch Institute

summary: DNA damage activates a complex signaling network in cells that blocks cell cycle progression, recruits factors involved in DNA repair, and/or triggers programs that control senescence or programmed cell death. Alterations in chromatin structure are known to be important for the initiation and propagation of the DNA damage response, although the molecular details are unclear. We investigated the role of chromatin structure in the DNA damage response by monitoring multiple timedependent checkpoint signaling and response events with a high-content multiplex image-based RNAi screen of chromatin modifying and interacting genes. We discovered that Brd4, a double bromodomain-containing protein, functions as an endogenous inhibitor of DNA damage signaling by binding to acetylated histones at sites of open chromatin and altering chromatin accessibility. Loss of Brd4 or disruption of acetyl-lysine binding results in an increase in both the number and size of radiation-induced !H2AX nuclear foci while overexpression of a Brd4 splice isoform completely suppresses !H2AX formation, despite equivalent double strand break formation. Brd4 knock-down cells displayed altered chromatin structure, prolonged cell cycle checkpoint arrest and enhanced survival after irradiation, while overexpression of Brd4 isoform B results in enhanced radiationinduced lethality. Brd4 is the target of the t(15;19) chromosomal translocation in a rare form of cancer, NUT Midline Carcinoma. Acetyl lysine-bromodomain interactions of the Brd4-NUT fusion protein suppresses !H2AX foci in discrete nuclear compartments, rendering cells more radiosensitive, mimicking overexpression of Brd4 isoform B. NUT Midline Carcinoma is sensitive to radiotherapy, however tumor material from this rare cancer is scarce. We therefore investigated Brd4 expression in another human cancer commonly treated with radiotherapy, glioblastoma multiforme, and found that expression of Brd4 isoform B correlated specifically with treatment response to radiotherapy. These data implicate Brd4 as an endogenous insulator of DNA damage signaling through recognition of epigenetic modifications in chromatin and suggest that expression of the Brd4 in human cancer can modulate the clinical response to DNA-damaging cancer therapy.

overall_design: Two replicates each of U2OS cells expressing either Brd4 shRNA or a control shRNA

last: Floyd

first: M

middle: E

last: Pacold

middle: M

last: Clarke

first: E

last: Blake

last: Fydrych

first: R

last: Ho

last: Lee

last: Root

last: Carpenter

last: Sabatini

last: French

last: Bradner

last: Chen

middle: B

last: Yaffe


title: Gene expression profiles of human kidneys

status: Public on Jul 18 2013

city: Philadelphia

first: Yi-An

last: Ko

state: Pennsylvania

address: 415 curie blvd

department: Genetics & Gene Regulation

institute: UPeenn

summary: The association of cytosine methylation and gene expression in the human kidneys is yet to be determined, here we have 25 pairs of the methylation and gene expression profile.

overall_design: We sought to decrease the cell type heterogeneity of kidney tissues to increase the resolution of expression profiles. To that end, microdissected human kidney tissue are used for RNA extraction and hybridization on Affymetrix microarrays.

first: Davoud

last: Mohtat

first: Masako

last: Suzuki

first: Ae

middle: S

last: Park

first: Maria

middle: C

last: Izquierdo

first: Sang

middle: Y

last: Han

first: Hyun

last: Kang

first: Han

last: Si

first: Thomas

last: Hostetter

first: James

last: Pullman

first: Melissa

last: Fazzari

first: Amit

last: Verma

first: Deyou

last: Zheng

first: John

last: Greally

first: Katalin

last: Susztak


title: Gene expression changes in human peripheral blood mononuclear cells after 3 diet interventions, TMD enriched with olive oil, TMD enriched with nuts and Low fat diet.

status: Public on Jun 30 2013

city: Barcelona

first: Olga

last: Castaner

address: Aiguader 88

department: Nutrition and cardiovascular risk department

country: Spain

institute: IMIM

summary: Despite the benefits associated with healthy diets, data on the mechanisms by which these benefits are promoted are scarce. Our aim was to explore the global transcriptomic response of biological pathways related to cardiovascular disease associated with traditional Mediterranean diet (TMD) intervention. The PREDIMED study is a large on-going, parallel, multicentre, randomised, controlled trial aimed at assessing the TMD effect on primary cardiovascular prevention. High cardiovascular risk participants were recruited and assigned to one of the following interventions: 1) TMD plus virgin olive oil (VOO); 2) TMD plus mixed nuts; or 3) low-fat diet (control group). In a sub sample of 30 volunteers of the PREDIMED- Barcelona Sur Centre, gene expression changes in peripheral mononuclear cells, after 3 months of intervention, were assessed by microarray analysis.

overall_design: A parallel study comparing three diet interventions: We analyzed 65 arrays which belonged to 34 patients, 31 microarrays at baseline (11 baseline group 1; 11 baseline group 2; 9 baseline group 3) and 34 microarrays after the 3 month intervention (11 for group 1; 11 for group 2; and 12 for group 3). The three interventions were: Group 1: 3-month Traditional Mediterranean Diet enriched with virgin olive oil; Group 2: 3-month Traditional Mediterranean Diet enriched with nuts; and Group 3: 3-month Low Fat Diet.

first: Montserrat

last: Fito

first: Mariaisabel

last: Covas

first: Dolores

last: Corella

last: Portoles


title: Expression data from human pancreatic cells PANC-1 infected with oncolytic vaccinia virus GLV-1h153

status: Public on Jun 20 2013

city: New York

first: Dana

last: Hadadd

address: 410 E 69th st 4th floor

department: Surgery

institute: Memorial Sloan-Kettering Cancer Center

summary:
Pancreatic cancer is a fatal disease associated with resistance to conventional therapies. GLV-1h153 is an oncolytic virus which has shown promise for the targeted treatment of cancer, and is engineered to carry the human sodium iodide symporter (hNIS) for the imaging of viral replication within tumors via enhanced uptake of several radionuclide probes.
We used microarrays to determine changes in gene expression patterns over time associated with infection and susceptibility of pancreatic cancer cells to GLV-1h153. Understanding into the molecular mechanisms associated with PANC-1 sensitivity to GLV-1h153 may enable identification of cancers resistant to viral therapy, avoid undesirable side effects associated with the need for higher doses of viral treatment, and development of safer and more efficacious oncolytic virotherapies.

overall_design: PANC-1 cells were infected with GLV-1h153. Zero (T0), 6 (T6) and 24 (T24) hours after infection, 3 samples of each time point were harvested and gene expression patterns assessed using HG-U133A cDNA microarray chips as compared to uninfected control (T0).

first: D

last: Haddad

first: A

last: Szalay

first: Y

last: Fong


title: Expression data for MALT1-responsive genes

status: Public on Jun 18 2013

city: Tokyo

first: Kazushi

last: Imai

address: 1-9-20 Fujimi, Chiyoda-ku

department: Biochemistry

country: Japan

institute: Nippon Dental Universty

summary:
In lymphocyte lineages, mucosa-associated lymphoid tissue 1 (MALT1) mediates the nuclear factor-κB activation signal that stimulates progression of malignant tumors.  However, its expression is inactivated in oral carcinoma patients with worse prognosis.  Unveiling genes under the control of MALT1 will provide valuable information for understanding of the mechanism of carcinoma progression.
We profiled gene datasets altered in response to MALT1 in oral carcinoma cells by the microarray analysis.  Totally, 2,933 genes with a fold change ≥ ±2.0 and P < 0.05 were identified.

overall_design: HSC2 oral carcinoma cells  were used for RNA extraction and hybridization on Affimetrix microarrays.  We sought to obtain homogenous populations of MALT1-resonsive genes in order to increase the resolution of expression profiles.  To this end, we used HSC2 cells stably expressing MALT1 (n=3) and vector alone (n=3) for the analysis.

first: Tadashige

last: Chiba


title: Genome-wide expression profiling and functional characterization of SCA28 lymphoblastoid cell lines.

status: Public on Jun 21 2013

city: Trieste

first: Paola

last: Roncaglia

state: TS

address: via Bonomea 265

department: Neurobiology

country: Italy

institute: SISSA/ISAS (International School for Advanced Studies)

summary: To identify altered pathways in SCA28 LCLs, we performed a whole genome expression profiling, based on Affymetrix Human Genome U133A 2.0 Chip Array, on LCLs from four unrelated patients, each carrying a different AFG3L2 mutation.

overall_design: Gene expression profiling of 4 patients and 6 healthy controls

first: Cecilia

last: Mancini

first: Stefano

last: Gustincich

first: Alfredo

last: Brusco


title: EWI-2 regulates melanoma growth and lung metastasis in a TGF-β1-dependent manner

status: Public on Jun 15 2013

city: Clayton

first: Konstantin

last: Knoblich

state: VIC

address: 15 Innovation Walk

department: Biochemistry and Molecular Biology

institute: Monash University

summary: EWI-2 (IgSF8) plays a novel, bifunctional role in melanoma cells. EWI-2 inhibits migration, metastasis, EMT-like changes, and CD271-dependent invasion in multiple melanoma cell lines. On the other hand, EWI-2 supports melanoma cell proliferation, survival, and xenograft growth. Consistent with these results, EWI-2 levels were elevated in human malignant melanoma, but not in metastatic melanoma samples. Altered melanoma cell functions, caused by EWI-2 ablation, are almost entirely dependent on enhanced TRF-β1 signaling, and also require contributions from tetraspanin proteins CD9 and CD81. In melanoma cells lacking EWI-2, tetraspanins CD9 and CD81 enhance TRF-β1 signaling by facilitating TβR-2−TβR-1 receptor complex formation. When EWI-2 is present, CD9 and CD81 are diverted into EWI-2 complexes, and thus TRF-β1 signaling is inhibited.

overall_design: 4 samples = 2 Control + 2 EWI-2 KD.

first: Hong-Xing

last: Wang

first: Chandan

last: Sharma

first: Scott

middle: R

last: Granter

first: Martin

last: Hemler


title: Multiplexed activation of endogenous genes by CRISPR-on, an RNA-guided transcriptional activator system

status: Public on Aug 10 2013

city: Cambridge

first: Albert

middle: W

last: Cheng

address: Room 453, 9 Cambridge Center

institute: Whitehead Institute

summary: Technologies allowing for specific regulation of endogenous genes are valuable for the study of gene functions and have great potential in therapeutics. We created the CRISPR-on system, a two-component transcriptional activator consisting of a nuclease-dead Cas9 (dCas9) protein fused with a transcriptional activation domain and single guide RNAs (sgRNAs) with complementary sequence to gene promoters. We demonstrate that CRISPR-on can efficiently activate exogenous reporter genes in both human and mouse cells in a tunable manner. In addition, we show that robust reporter gene activation in vivo can be achieved by injecting the system components into mouse zygotes. Furthermore we show that CRISPR-on can activate the endogenous IL1RN, SOX2, and OCT4 genes. The most efficient gene activation was achieved by clusters of 3 to 4 sgRNAs binding to the proximal promoters suggesting their synergistic action in gene induction. Significantly, when sgRNAs targeting multiple genes were simultaneously introduced into cells, robust multiplexed endogenous gene activation was achieved. Genome-wide expression profiling demonstrated high specificity of the system.

overall_design: We used microarray to assay the gene expression changes after transfection of dCas9VP160 with the different sgRNAs

first: Rudolf

last: Jaenisch


title: Freeze resistance basis of winter wheat mutant lines

city: Brookings

first: Xijin

last: Ge

state: SD

address: SDSU box 2220C

department: Mathematics and Statistics

institute: South Dakota State University

summary:
Two azide mutagenized lines Freeze Resistance (FR, 75% survival) and Freeze Susceptible (FS, 30% survival) were compared with and without 4°C ± 1.5 cold acclimation of crown tissue to identify genes responsible for the difference in freeze resistance.

Keywords: Wheat cold acclimation, stress response, cold, low temperature

overall_design:
Experiment design (8 hybridizations):
Genotype: SD16029 (FR) or SD16169 (FS)
Temperature: 25°C or 4°C

first: Fedora

last: Sutton

first: Din

last: Chen

first: Don

last: Kenefick


title: Microarray approach to investigate gene expression in human ovarian tissue after xenografting

status: Public on Jun 01 2013

city: Woluwé-St-Lambert

first: Jérôme

last: Ambroise

address: 30, Chapelle-aux-Champs (box B1.30.24)

department: Institut de Recherche Expérimentale et Clinique (IREC)

institute: Université catholique de Louvain

summary:
Cryobanking and transplantation of ovarian tissue is a promising approach to restore fertility in cancer patients. However, ischemic stress following avascular ovarian cortex grafting is known to induce stromal tissue fibrosis and alteration in follicular development.
The aim of the study is to analyse the impact of freezing-thawing and grafting procedures on gene expression in human ovarian tissue. Frozen-thawed ovarian tissue from 4 patients was xenografted for 7 days in nude mice and one non-grafted fragment was used as control.
Immediately after recovery, grafts were processed for RNA extraction and histological analysis. Their expression profile was screened by whole-genome oligonucleotide array (n=4) and validated by reverse-transcriptase polymerase chain analysis (n=10).
84 of the transcripts were significantly altered after 7 days of grafting including matrix metalloproteinase-9 and -14 and angiogenic factors such as Placental growth factor and C-X-C chemokine receptor type 4 (CXCR4). Major biological processes were related to tissue remodelling including secretory processes, cellular adhesion and response to chemical and hormone stimuli.
Angiopoietin signaling, interleukin-8 pathway and peroxisome proliferator-activated receptors activation were shown to be differentially regulated. On day 7, overexpression was confirmed by PCR for interleukin-8, transforming growth factor-beta 1, matrix metalloproteinase-14 and CXCR4 compared to the nongrafted control.
In conclusion, new as well as known genes involved in tissue restructuration and angiogenesis were identified after human ovarian tissue transplantation.  This will facilitate the development of strategies to optimize grafting techniques.

overall_design: In this study, ovarian tissue was obtained from 4 patients. Each biopsy was divided into 2 fragments. One fragment was frozen/thawed and placed in TRIzol reagent (Invitrogen) for RNA extraction. The other fragment was frozen-thawed and grafted in the intraperitoneal cavity of a nude mice. After 7 days graft were recovered and total RNA was extracted.

first: J

first: B

last: Bearzatto

first: A

last: Van Langendonckt

first: L

last: Romeu

first: CA

last: Amorim

middle: L

last: Gala

last: Donnez

first: M

last: Dolmans


title: Transcriptome analysis during seed germination of elite Chinese bread wheat cultivar Jimai 20

status: Public on Aug 14 2013

city: Beijing

first: Yonglong

last: Yu

address: 105 Xisanhuan North Road

institute: College of Life Science, Capital Normal University

summary:
Wheat seed germination is highly related to seedling survival rate and subsequent vegetative growth,and therefore directly affects the conformation of wheat yield and quality. So wheat seed germination is not only important to itself, but the whole human society. However, due to the large genome size, many studies related to wheat seed are very complex and uncompleted. Transcriptome analysis of elite Chinese bread wheat cultivar Jimai 20 may provides a comprehensive understanding of wheat seed germination.
Seed germination involves in the regulation of large number of genes, whether these genes are normal activated  or not is very important to seed germination. We performed microarray analysis using the Affymetrix Gene Chip to reveal the gene expression profiles in five phases of wheat cultivar Jimai 20 seed germination. Our results provide a new insights into the thoroughly metabolic changes of seed germination as well as the relationship between some significant genes.

overall_design: The five groups including germinating seeds were harvest at five successive phases, which were 0 (P0), 12 (P1), 24 (P2), 36 (P3), 48 (P4) hour after imbibition respectively. Three independent experiments were performed for each group.

first: Guangfang

last: Guo


title: Effect of MWCNT on Lung Fibroblast gene expression

status: Public on May 29 2013

city: Raleigh

first: Stan

last: Martin

address: 1404 Crete Dr.

institute: Science Apps, L3C

summary: Multi-walled carbon nanotubes (MWCNT) cause lung fibrosis in rodents and exacerbate airway fibrosis in the mouse ovalbumin model of allergic asthma.  Interleukin 13 (IL-13) is a key cytokine secreted by T helper type 2 (Th2) cells. IL-13 is up-regulated in human asthma and animal models that activate pro-fibrotic and pro-proliferative cell signaling cascades in human lung fibroblasts (HLF).  This study tested the hypothesis that IL-13 alters the gene expression profile of HLF exposed to MWCNT. Carbon black nanoparticles (CBNP) were also compared to MWCNT as they are relatively inert nanoparticles that do not cause fibrosis.  Confluent, quiescent cultures of HLF were treated with 10 ng/ml IL-13 or serum-free defined medium (vehicle) for 24 hours prior to treatment with 10 µg/cm2  MWCNT or CBNP. At 4, 24, or 48 hours following nanoparticle exposure, total RNA was isolated and gene expression was measured using the Affymetrix Human Genome U133A2.0 Array. The data were analyzed using the JMP Genomics statistical platform. IL-13 and MWCNT each caused changes in the expression of distinct gene subsets over the time-course investigated. The combination of IL-13 and MWCNT resulted in a gene expression profile that was distinct from patterns induced or suppressed by either IL-13 or MWCNT alone. CBNP caused changes in gene expression that were distinct from IL-13 or MWCNT. Interestingly, the combination of IL-13 and MWCNT increased the expression of IL-17A and increased collagen (Col1A1), while MWCNT alone increased interferon-inducible protein-27 (IFI27), suggesting that  Th2 microenvironment containing IL-13 shifts MWCNT-induced gene expression from a Th1 to a Th17 gene expression profile.  These data provide insight into the mechanisms by which MWCNT alter the biology of fibroblasts during normal and allergic inflammatory conditions.

overall_design: Adult Lung Fibroblasts were treated with 10 µg/cm2 MWCNT, CBNP, or vehicle with or without IL-13 for 4 hours, 24 hours, or 48 hours.

first: Stanton

first: Jessica

middle: P

last: Ryman-Rasmussen

first: Elizabeth

last: Thompson

first: Kelly

last: Shipkowski

first: Alexia

last: Taylor

first: Linda

last: Pluta

first: Russell

last: Thomas

first: James

last: Bonner


title: Biological control of Wheat take-all disease by earthworms

city: Créteil

first: Ruben

last: Puga-Freitas

address: 61 Avenue du Général de Gaulle

country: France

institute: Université Paris-Est Créteil

summary:
The take-all disease caused by the soilborne fungus Gaeumannomyces graminis var tritici (Ggt) is one of the most-studied and widespread root diseases worldwide.
Here, we investigated the ability of the earthworm Aporrectodea caliginosa to induce take-all disease tolerance in Triticum aestivum.

overall_design: In a greenhouse experiment, plants were grown in a sandy soil. Plants were inoculated or not with Ggt and in the presence or absence of earthworms. There was 4 levels of treatment (plants only, inoculated with Ggt, inoculated with earthworms or inoculated with earthworms and Ggt), and 2-3 plants per treatments.

first: R

last: Belkacem

first: S

last: Barot

first: J

last: Roger-Estrade

last: Bertrand

last: Blouin


title: Genotypic differences in water soluble carbohydrate metabolism in Triticum aestivum leaves

status: Public on Apr 30 2013

city: Brisbane

first: Gang-Ping

last: Xue

state: Qld

address: 306 Carmody Rd., St Lucia

department: Plant Industry

institute: CSIRO

summary: Fructans represent the major component of water soluble carbohydrates (WSCs) in the maturing stem of temperate cereals and are an important temporary carbon reserve for grain filling. Theoretically, genotypic variation in carbon reserve accumulation is determined by relative carbon availability and demand at the whole plant level. To evaluate the importance of source carbon availability in fructan accumulation and its associated molecular mechanisms, we performed comparative analyses of individual WSC components and the expression profiles of genes involved in major carbohydrate metabolism and photosynthesis in flag leaves of recombinant inbred lines derived from a cross between wheat cultivars Seri M82 and Babax (SB lines). High sucrose levels in the mature flag leaf (source carbon organ) were found to be positively associated with WSC and fructan concentrations in both the leaf and stem of SB lines in several field trials. Analysis of Affymetrix expression array data revealed that high leaf sucrose lines grown in abiotic-stress-prone environments had high expression levels of a number of genes in the leaf involved in the sucrose synthetic pathway and photosynthesis, such as Calvin cycle genes, antioxidant genes involved in the removal of chloroplast H2O2 and genes involved in energy dissipation.  The expression of the majority of genes involved in fructan and starch synthetic pathways were positively correlated with sucrose levels in the leaves of these SB lines.

overall_design: 8 genotypes of recombinant inbred lines Seri M82 x Babax with 2 biological replicates per genotype. Grown in the field under irrigated conditions.

first: Janneke

last: Drenth

first: Donna

last: Glassop

first: Maarten

last: Kooiker

first: Lynne

last: McIntyre


title: Caco-2 cell gene expression following co-culture with Lactobacillus casei and Bifidobacterium breve

status: Public on Apr 09 2013

city: Paris

first: Thierry

last: Pedron

address: 28 rue du Docteur Roux

department: Biologie cellulaire et Infection

institute: Pasteur Institute

summary:
To characterize how symbiotic bacteria affect the lolecular and cellular mechanisms of epithelial homeostasis, human colonic Caco-2 cells
were co-culture with Lactobacillus casei and Bifidobacterium breve.

overall_design: 3 biological replicates were hybridized on Affymetrix HG-U133A

last: PEDRON


title: Response to Fusarium in near-isogenic lines harboring resistance QTLs Fhb1 and Qfhs.ifa-5A

status: Public on May 17 2013

city: Ames

first: PLEXdb Curator

address: 1023  Crop Genomes Informatics Lab (Iowa State University)

department: Virtual Reality Application Center

institute: Iowa State University

summary: Resistance mechanisms of wheat to Fusarium graminearum are still poorly understood. Multiple reports have investigated transcriptomic differences between resistant and susceptible genotypes. To investigate the genetic determinants underlying the two major contributor QTL Fhb1 and Qfhs.ifa-5A, we generated a set of near-isogenic lines, that we have used for transcriptomic studies using the Affymetrix wheat GeneChip®:  4 near-isogenic lines (BC5F2) derived from a cross of CM82036 and cv Remus (susceptible recurrent parent) and the resistant parent CM82036 have been inoculated with Fusarium spore suspension or water as control at anthesis. Samples have been taken at 3 timepoints 8, 24 and 72 hours after inoculation. Five wheat heads per condition were pooled into one sample, that has been used for RNA preparation. Including 3 replicates a total of 90 microarrays have been hybridized.  Our results identify a wide variety of genes (631 transcripts) that are differentially regulated for Fusarium graminearum in all genotypes after 72 h and 339 genes that are upregulated only in lines without Qfhs.ifa.5A. Few genes were found differentially regulated for Fusarium and QTL. Many interesting candidates emerge from the set of QTL-specific genes that are constitutively expressed when comparing water-treated samples.   ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor,  Wolfgang Schweiger.  The equivalent experiment is TA41 at PLEXdb.]

overall_design: genotype: NIL1 (resistant, Fhb1, Qfhs.ifa-5A) - treatment: Fusarium graminearum strain IFA-65 - time: 8 hai(3-replications);  genotype: NIL1 (resistant, Fhb1, Qfhs.ifa-5A) - treatment: Fusarium graminearum strain IFA-65 - time: 24 hai(3-replications);  genotype: NIL1 (resistant, Fhb1, Qfhs.ifa-5A) - treatment: Fusarium graminearum strain IFA-65 - time: 72 hai(3-replications);  genotype: NIL1 (resistant, Fhb1, Qfhs.ifa-5A) - treatment: water - time: 8 hai(3-replications);  genotype: NIL1 (resistant, Fhb1, Qfhs.ifa-5A) - treatment: water - time: 24 hai(3-replications);  genotype: NIL1 (resistant, Fhb1, Qfhs.ifa-5A) - treatment: water - time: 72 hai(3-replications);  genotype: NIL2 (moderately resistant, Fhb1) - treatment: Fusarium graminearum strain IFA-65 - time: 8 hai(3-replications);  genotype: NIL2 (moderately resistant, Fhb1) - treatment: Fusarium graminearum strain IFA-65 - time: 24 hai(3-replications);  genotype: NIL2 (moderately resistant, Fhb1) - treatment: Fusarium graminearum strain IFA-65 - time: 72 hai(3-replications);  genotype: NIL2 (moderately resistant, Fhb1) - treatment: water - time: 8 hai(3-replications);  genotype: NIL2 (moderately resistant, Fhb1) - treatment: water - time: 24 hai(3-replications);  genotype: NIL2 (moderately resistant, Fhb1) - treatment: water - time: 72 hai(3-replications);  genotype: NIL3 (moderately resistant, Qfhs.ifa-5A) - treatment: Fusarium graminearum strain IFA-65 - time: 8 hai(3-replications);  genotype: NIL3 (moderately resistant, Qfhs.ifa-5A) - treatment: Fusarium graminearum strain IFA-65 - time: 24 hai(3-replications);  genotype: NIL3 (moderately resistant, Qfhs.ifa-5A) - treatment: Fusarium graminearum strain IFA-65 - time: 72 hai(3-replications);  genotype: NIL3 (moderately resistant, Qfhs.ifa-5A) - treatment: water - time: 8 hai(3-replications);  genotype: NIL3 (moderately resistant, Qfhs.ifa-5A) - treatment: water - time: 24 hai(3-replications);  genotype: NIL3 (moderately resistant, Qfhs.ifa-5A) - treatment: water - time: 72 hai(3-replications);  genotype: NIL4 (susceptible) - treatment: Fusarium graminearum strain IFA-65 - time: 8 hai(3-replications);  genotype: NIL4 (susceptible) - treatment: Fusarium graminearum strain IFA-65 - time: 24 hai(3-replications);  genotype: NIL4 (susceptible) - treatment: Fusarium graminearum strain IFA-65 - time: 72 hai(3-replications);  genotype: NIL4 (susceptible) - treatment: water - time: 8 hai(3-replications);  genotype: NIL4 (susceptible) - treatment: water - time: 24 hai(3-replications);  genotype: NIL4 (susceptible) - treatment: water - time: 72 hai(3-replications);  genotype: CM82036 (resistant) - treatment: Fusarium graminearum strain IFA-65 - time: 8 hai(3-replications);  genotype: CM82036 (resistant) - treatment: Fusarium graminearum strain IFA-65 - time: 24 hai(3-replications);  genotype: CM82036 (resistant) - treatment: Fusarium graminearum strain IFA-65 - time: 72 hai(3-replications);  genotype: CM82036 (resistant) - treatment: water - time: 8 hai(3-replications);  genotype: CM82036 (resistant) - treatment: water - time: 24 hai(3-replications);  genotype: CM82036 (resistant) - treatment: water - time: 72 hai(3-replications)

first: Wolfgang

last: Schweiger

first: Hermann

last: Buerstmayr


title: Wheat drought responses

status: Public on May 03 2013

city: Lincoln

first: Harkamal

last: Walia

state: NE

address: Agronomy and Horticulture

institute: University of Nebraska

summary: Three wheat genotypes were exposed to water stress and root tissue collected for expression analysis

overall_design: 12 samples, Pavon76, Pavon-TL, Null Control are the three genotypes samples under well watered and water stress conditions


title: The coregulator, repressor of Estrogen Receptor Activity (REA), is a crucial regulator of the timing and magnitude of uterine decidualization.

status: Public on Apr 04 2013

city: Urbana

first: Yuechao

last: Zhao

address: 407 S. Goodwin Ave

institute: University of Illinois

summary:
Our findings establish a key role for the coregulator, Repressor of Estrogen receptor Activity (REA), in controlling the timing and magnitude of decidualization in human endometrial stromal cells in vitro and in the mouse uterus in vivo, and suggest that REA functions to synchronize uterine differentiation with concurrent embryo development, which is essential for optimal implantation and fertility.
The findings highlight that REA physiologically restrains endometrial stromal cell decidualization, controlling the timing and magnitude of decidualization to enable proper synchronization of uterine differentiation with concurrent embryo development that is essential for implantation and optimal fertility.

overall_design:
Human endometrial stromal cells (hESCs) were isolated from biopsies taken from the early proliferative stage endometrium of regularly cycling women on no hormonal medications. Cells were cultured in DMEM/F-12 mediumcontaining 5% charcoal stripped fetal bovine serum. To induce in vitro decidualization, hESCs were treated with a hormone cocktail containing 10 nM estradiol (E2), 1 μM progesterone (P4) and 0.5 uM 8-bromo-cAMP for up to 10 days, and media were changed every 48 h. For siRNA experiments, hESCs were transfected with REA siRNA or GL3 luciferase control siRNA  following the Silent-Fect kit protocol. After 48 h of transfection, hESCs were exposed to the hormone cocktail for 24 hours or 96 hours of differentiation.
key words; siRNA knock-down, hormone cocktail treatment

first: Benita

last: Katzenellenbogen


title: Expression Data from 24 orthotopic tumors grown in the pancreas of mice +/- MEK inhibitor PD0325901

city: San Francisco

first: Stephan

middle: Christoph

last: Gysin

state: California

address: 1450 3rd Street

department: HDFCCC

institute: UCSF

summary:
Analysis of mRNA profiles after MEK1/2 inhibition in human pancreatic cancer cell lines reveals pathways involved in drug sensitivity.
We used microarrays to find gene expression patterns associated with drug response and also identified genes regulated by the MAP kinase pathway

overall_design: 6 pancreatic cell lines were injected into the pancreas of nude mice and treated either with vehicle control or PD0325901 for 12 plus 12 hours.

first: Jesse

last: Paquette

first: Martin

last: McMahon


title: Expression Data from 22 human pancreatic cancer cell lines grown in triplicates +/- MEK inhibitor CI-1040

overall_design: 22 pancreatic cell lines were grown in culture media containing serum and either treated with vehicle control or CI-1040 for 24 hours


title: Expression data from SND1 knockdown clones of human HCC cell line QGY-7703

status: Public on Apr 01 2013

city: Richmond

first: Myrna

last: Serrano

state: VA

address: 1101 East Marshall St

institute: Virginia Commonwealth University

summary: Staphylococcal nuclease domain-containing protein 1 (SND1) is overexpressed in human hepatocellular carcinoma (HCC) and positively regulates development and progression of HCC. We established stable clones expressing SND1 shRNA in QGY-7703 cells and analyzed the gene expression profiles of a control clone and two SND1 knockdown clones to check what genes are regulated by SND1.

overall_design: Steady-state proliferating cells were collected for RNA extraction and Affymetrix microarray hybridization. Three biological replicates each of a control clone and 2 SND1 knockdown clones.

first: Devanand

last: Sarkar


title: Expression data from Human Tax transfected HeLa cell

status: Public on Mar 21 2013

city: Wako

first: Yoko

last: Aida

state: Saitama

address: 2-1 Hirosawa

department: Advanced Science Institute

institute: RIKEN

summary: Human T cell leukemia virus type 1 (HTLV-1) Tax is potent activator of viral and cellular gene expression that interacts with a number of cellular proteins. In this study, a large-scale host cell signaling events related to cellular proliferation were used to identify genes involved in Tax-mediated cell signaling events related to cellular proliferation and apoptosis.

overall_design: HeLa cell transiently transfected with with pCAGGS vector for control sample was compared with HeLa cell transiently transfected with with pCAGGS-Tax-FLAG vector. These cells were incubated for 30h after transfection and were used for total RNA isolation.

first: Mariluz

last: Arainga-Ramirez

first: Keisuke

last: Fukumoto


title: Gene expression levels in immortalized B cells from 95 unrelated CEPH-Utah individuals treated with 10Gy of ionizing radiation

status: Public on Mar 28 2013

city: Philadelphia

first: Renuka

last: Nayak

state: PA

address: 3516 Civic Center Blvd

institute: HHMI, University of Pennsylvania

summary: We used microarrays to examine gene expression levels from 95 unrelated CEPH-Utah individuals 0, 2 or 6 hours after treatment with 10Gy of ionizing radiation.

overall_design: We measured gene expression levels in immortalized B cells from 95 unrelated CEPH-Utah individuals.  Each individual was treated with 10Gy of ionizing radiation and expression was measured 0, 2 and 6 hour after treatment.

first: Michael

last: Kearns

first: Vivian

middle: G

last: Cheung