title: ABCC5 supports osteoclast formation and promotes breast cancer metastasis to bone

status: Public on Nov 09 2012

city: Montreal

first: Sean

last: Cory

state: QC

address: 3649 Promenade Sir William Osler

department: Bioinformatics

institute: McGill University

summary: Bone is the primary site of breast cancer metastasis and complications associated with bone metastases can lead to a significantly decreased quality of life in these patients. Thus, it is essential to gain a better understanding of the molecular mechanisms that underlie the emergence and growth of breast cancer skeletal metastases. Methods: To search for novel molecular mediators that influence breast cancer bone metastasis, we generated gene expression profiles from laser capture micro-dissected trephine biopsies of both breast cancer bone metastases and primary breast tumors that metastasized to bone. Bioinformatics analysis identified genes that are differentially expressed in breast cancer bone metastases compared to primary mammary tumors. Results: ABCC5, an ATP-dependent transporter, was found to be overexpressed in breast cancer osseous metastases relative to primary mammary tumors. In addition, ABCC5 was significantly up-regulated in human and mouse breast cancer cell lines with high bone-metastatic potential. Stable knockdown of ABCC5 significant reduced bone metastatic burden and osteolytic bone destruction in mice. The decrease in osteolysis was further associated with diminished osteoclast numbers. Conclusions: Our data, for the first time, suggests that ABCC5 functions as a mediator of breast cancer skeletal metastasis. ABCC5 expression in breast cancer cells is important for the efficient bone resorption mediated by osteoclasts. Hence, ABCC5 may be a potential therapeutic target for breast cancer bone metastasis.

overall_design: primary breast tumors vs. bone trephine biopsies

first: Peter

last: Siegel

first: Anna

last: Mourskaia


title: Transcriptomic analysis of Bmi1 overexpression in NSPC.

status: Public on Nov 12 2012

city: Trieste

first: Danilo

last: Licastro

department: Genomica Funzionale

country: Italy

institute: CBM

summary: We have previously shown that conditional overexpression of Bmi1 in NSC increases their proliferation both in the developing neocortexand in the postnatal brain (Yadirgi et al. 2011). However, during embryonic development, increased and ectopic proliferation induced by overexpression of Bmi1 in progenitors committed toward a neuronal lineage triggered apoptosis, leading eventually to a reduced overall brain size (Yadirgi et al. 2011). These findings –increased proliferation of neural stem/progenitor cells (NSPC) and apoptosis of neuronal committed progenitors - could be faithfully reproduced in an in vitro assay where NSPC isolated from Nestin-Cre; STOP FloxBmi1 embryos are cultured in floating conditions in the presence of EGF and FGF2 (neurosphere assay). We isolated NSPC from Nestin-Cre;STOP FloxBmi1 E16.5 neocortices and cultured them briefly under neurosphere inducing conditions. We then analysed their transcriptome by whole-genome Illumina platform mouse v2 and compared it to the transcriptome of NSPC isolated from non-transgenic or single transgenic littermates. The objective of this analysis was to identify genes differentially expressed upon overexpression of the PcG gene Bmi1 in neural stem/progenitor cells.

overall_design: 4 samples, 2 condition with 2 biological replicates per condition

first: Silvia

middle: S

last: Marino

first: Serena

last: Acquati

middle: D


title: Gene Expression Levels in PiZ mice Compared to Wild-type (Wt)C57Bl/6

status: Public on Nov 08 2012

city: St. Louis

first: Nancy

last: Marcus

state: Missouri

address: 1100 S. Grand,Doisy Research Center

department: Pediatrics

country: USA

institute: St. Louis University

summary: Individuals expressing alpha-1-antitrypsin mutant Z protein accumulate misfolded, mutant protein in the liver and are at risk for liver diseases including cirrhosis and hepatocellular carcinoma. Transgenic PiZ mice, a model for this liver disease, display similar pathologies to humans, including inflammation, increases in proliferation, autophagy and apoptosis, accumulation of globules and develop fibrosis and hepatocellular carcinoma with age.  Microarrays were used to compare the gene expressions of PiZ mice to wild-type mice in order to identify the pathways that are altered in this disorder.

overall_design: Pooled samples from 4 mice, 3-4 months old were used for each of 4 categories. PiZ males, PiZ females, C57Bl/6 males, C57Bl/6 females

first: Jeffrey

middle: H

last: Teckman

first: David

middle: A

last: Rudnick

first: Keith

last: Blomenkamp


title: Identification of single nucleotide polymorphisms regulating peripheral blood mRNA expression with genome-wide significance: an eQTL study in the Japanese population

status: Public on Nov 27 2012

city: Kodaira

first: Daimei

last: Sasayama

address: 4-1-1 Ogawahigashi-machi

country: Japan

institute: National Center of Neurology and Psychiatry

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

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

overall_design: Refer to individual Series


title: A role for Prenylated rab acceptor 1 in vertebrate photoreceptor development

status: Public on Nov 02 2012

city: Bethesda

first: Matthew

middle: J

last: Brooks

state: MD

address: 6 Center Dr Bldg 6, Rm 303

department: NEI

institute: NIH

summary: The rd1 mouse retina is a well-studied model of retinal degeneration where rod photoreceptors undergo cell death beginning at postnatal day P10 until P21. This period coincides with photoreceptor terminal differentiation in a normal retina. We have used the rd1 retina as a model to investigate early molecular defects in developing rod photoreceptors prior to the onset of degeneration. Using a microarray approach, we performed gene profiling comparing rd1 and wild type retinas at four time points starting at P2, prior to any obvious biochemical or morphological differences, and concluding at P8, prior to the initiation of cell death. We have identified genes that are differentially regulated in the rd1 retina at early time points, which may give insights into developmental defects that precede photoreceptor cell death. This is the first report of PRA1 expression in the retina. Our data support the hypothesis that PRA1 plays an important role in vesicular trafficking between the Golgi and cilia in differentiating and mature rod photoreceptors.

overall_design: Retinal samples were harvested from both rd1/le and wt animals at postnatal days 2, 4, 6, and 8 for microarray.  Each sample included 8-14 retinas and experiments were performed in quadruplicate. Ten micrograms of total RNA was used for cDNA systhesis in target molecule production.

first: Virginia

middle: M

last: Dickison

first: Angela

last: Richmond

first: Ameair

last: Abu Irqeba

first: Joshua

middle: G

last: Martak

middle: C

last: Hoge

first: Mohammed

middle: I

last: Othman

first: Ritu

last: Khanna

first: Alan

last: Mears

first: Adnan

middle: Y

last: Chowdhury

first: Anand

last: Swaroop

first: Judith

last: Ogilvie


title: An eQTL study in the Japanese population [gene expression_2]

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

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

first: Hiroaki

last: Hori

first: Seiji

last: Nakamura

first: Ryo

last: Miyata

first: Toshiya

last: Teraishi

first: Kotaro

last: Hattori

first: Miho

last: Ota

first: Noriko

last: Yamamoto

first: Teruhiko

last: Higuchi

first: Naoji

last: Amano

first: Hiroshi

last: Kunugi


title: Genome-wide analysis of epicardial gene expression in E11.5 mouse hearts

status: Public on Nov 01 2012

city: Dallas

first: Guo

middle: N

last: Huang

state: TX

address: 6000 Harry Hines Blvd, NA8.510

department: Molecular Biology

institute: University of Texas Southwestern Medical Center

summary: Identification of epicardium-enriched genes in the embryonic heart. The epicardium encapsulates the heart and functions as a source of multipotent progenitor cells and paracrine factors essential for cardiac development and repair. Injury of the adult heart results in re-activation of a developmental gene program in the epicardium, but the transcriptional basis of epicardial gene expression has not been delineated. We established a mouse embryonic heart organ culture and gene expression system that facilitated the identification of epicardial enhancers activated during heart development and injury. Epicardial activation of these enhancers depends on a combinatorial transcriptional code centered on CCAAT/enhancer binding protein (C/EBP) transcription factors. Disruption of C/EBP signaling in the adult epicardium reduced injury-induced neutrophil infiltration and improved cardiac function. These findings reveal a transcriptional basis for epicardial activation and heart injury, providing a platform for enhancing cardiac regeneration.

overall_design: Total RNA obtained from lacZ-positive epicardial cells isolated from the E11.5 Tcf21lacZ hearts compared to total dissociated heart cells

first: Eric

last: Olson


title: Pancreatic cancer and non-malignant pancreas cell lines

city: Vancouver

first: Kelsie

middle: L

last: Thu

state: British Columbia

address: 675 West 10th Avenue

country: Canada

institute: BC Cancer Research Centre

type:
Expression profiling by array
Methylation profiling by array
Genome variation profiling by array


title: RNA expression analysis of pancreatic cancer and non-malignant pancreas cell lines

summary:
Genome wide expression profiling of 20 PDAC cell lines and an immortalized non-malignant pancreatic duct cell line (HPDE) to facilitate identification of novel tumor suppressor genes using an integrative genomics approach
Genome wide expression profiling of 20 PDAC cell lines and an immortalized non-malignant pancreatic duct cell line (HPDE) to facilitate identification of novel tumor suppressor genes using an integrative genomics approach

overall_design: RNA from the 21 samples was converted to Cy3 labeled cRNA and hybridized to the array; arrays were processed with GenePix software and median array normalization was performed

first: Wan

last: Lam


title: Transcriptional imprinting of transmigrating neutrophils on T84 intestinal epithelial cells

status: Public on Oct 31 2012

city: Aurora

last: Campbell

state: CO

address: 12700 East 19th Ave

institute: University of Colorado - Anschutz Medical Campus

summary: Neutrophil accumulation in crypt abscesses is a pathological hallmark of ulcerative colitis.  Based on recent evidence that mucosal metabolic changes influence disease outcomes, we hypothesized that transmigrating neutrophils influence the transcriptional profile of intestinal epithelia.  Microarray studies revealed a cohort of hypoxia-responsive genes regulated by neutrophil-epithelial crosstalk. Real-time O2 sensing indicated that transmigrating neutrophils rapidly deplete microenvironmental O2 sufficient enough to stabilize intestinal epithelial cell hypoxia-inducible factor (HIF). Utilizing HIF reporter mice in a TNBS colitis model, we investigated the relative contribution of neutrophils and the respiratory burst to “inflammatory hypoxia” in vivo.  Gp91phox-null mice, which mirror human chronic granulomatous disease, developed accentuated colitis compared to control with exaggerated neutrophil infiltration and diminished inflammatory hypoxia. In conclusion, transcriptional imprinting of host tissue by infiltrating neutrophils modulates the host response to inflammation. Likewise, the respiratory burst contributes fundamentally to localized O2 depletion, resultant microenvironmental hypoxia and effective inflammatory resolution.

overall_design: Two models were employed, direct and indirect. The “Direct” migration model entailed establishing a chemotactic gradient (using fMLP) across monolayers of T84 intestinal epithelial cells grown on the underside of permeable supports (3um pore). Neutrophils (PMN) were induced to migrate in the physiologically relevant the physiologically relevant basolateral-to-apical direction. Following migration, T84s were rested in complete media and 2hrs later harvested for RNA isolation. In the Indirect model, PMN were applied to T84s as with the direct model. After migration, conditioned supernatants were collected,  cells pelleted and supernatants filtered through 0.2um pore. Conditioned supernatants were transferred to naive T84 monolayers for 2hrs, followed by RNA harvest. Each model was exposed to neutrophils (PMN) or not. All monolayers contained chemotactic peptide fMLP on the apical side. Total of 12 samples, 4 conditions in triplicate: Direct migration without neutrophils (T84 +fMLP -PMN), Direct migration with neutrophils (T84 +fMLP +PMN), Indirect migration without neutrophils (T84 +fMLP -PMN), Indirect migration with neutrophils (T84 +fMLP +PMN)

first: Walter

last: Bruyninckx

first: Caleb

last: Kelly

first: Louise

middle: E

last: Glover

first: Eoin

last: McNamee

first: Amanda

last: Bayless

first: Brittelle

last: Bowers

first: Stefan

middle: F

last: Ehrentraut

first: Adrianne

last: Burgess

first: Lucy

last: Golden-Mason

first: John

last: Garvey

first: Amber

last: Sorensen

first: Raphael

last: Nemenoff

first: Paul

last: Jedlicka

first: Cormac

middle: T

last: Taylor

first: Douglas

last: Kominsky

first: Sean

middle: P

last: Colgan


title: STAC3 is required for myotube formation and myogenic differentiation in vertebrate skeletal muscle

status: Public on Dec 01 2012

city: St Lucia

first: Neil

last: Bower

state: Qld

address: Carmody Road

department: Institute for Molecular Bioscience

country: Australia

institute: University of Queensland

summary:
STAC3 was identified as a nutritionally regulated gene from an Atlantic salmon subtractive hybridization library with highest expression in skeletal muscle.  Salmon STAC3 mRNA was highly correlated with myogenin and myoD1a expression during differentiation of a salmon primary myogenic culture and was regulated by amino acid availability. In zebrafish embryos, STAC3 was initially expressed in myotomal adaxial cells and in fast muscle fibres post-segmentation.  Morpholino knockdown resulted in defects in myofibrillar protein assembly, particularly in slow muscle fibres, and decreased levels of the hedgehog receptor patched.  The function of STAC3 was further characterized in vitro using the mammalian C2C12 myogenic cell line.  STAC3 mRNA expression increased during the differentiation of the C2C12 myogenic cell line.  Knockdown of STAC3 by RNAi inhibited myotube formation, and microarray analysis revealed that transcripts involved in cell cycle, focal adhesion, cytoskeleton and the pro-myogenic factors IGFBP-5 and IGF2 were down regulated.  RNAi-treated cells had suppressed AKT signalling and exogenous IGF2 was unable to rescue the phenotype, however, IGF/AKT signalling was not blocked.  Overexpression of STAC3, which results in increased levels of IGFBP-5 mRNA, did not lead to increased differentiation.  In synchronized cells, STAC3 mRNA was most abundant during the G1 phase of the cell cycle.  RNAi-treated cells were smaller, had higher proliferation rates and decreased proportion of cells in G1 phase when compared to controls, suggesting a role in the G1 phase checkpoint. These results identify STAC3 as a new gene required for myogenic differentiation and myofibrillar protein assembly in vertebrates.

We identified STAC3 as being essential for myogenic differentiation. The goal of the microarray analysis was to identify genes that were up- or down-regulated in C2C12 cells when STAC3 expression was inhibited by interfering RNA (RNAi). The microarray compares the C2C12 mouse myogenic cell line between control samples to samples treated with an interfering RNA directed at STAC3.  The mouse C2C12 cell line was used at two time points: day 0, which was 24 hours after adding the RNAi, with cells growing in growth media (non-differentiating), and day 1, which was 48 hours after the interfering RNAi was added, and 24 hours after switching to differentiation media.

overall_design: RNAi-treated cells were transfected with an RNAi directed against STAC3, and control cells were transfected with a high-GC content control RNAi. Total RNA was extracted from control and RNAi-treated samples at two time points, at day 0 (24 h after treating with RNAi, while samples were still in growth media), and at day 1 (cells grown in differentiation media for 24h, 48 h after RNAi treatment). At each time point, STAC3 RNAi-treated cells were compared to controls. For the array comparison, at day 0, triplicate biological samples + one technical replicate were used for the controls, and four biological samples were used for the RNAi-treated cells.  At day 1, four biological samples and one technical replicate were used for controls and RNAi-treated cells. Technical replicate identifiers are appended by _r.

first: Ian

last: Johnston


title: Distinctive microRNA signature of medulloblastomas associated with the WNT signaling pathway

status: Public on Oct 27 2012

city: Navi Mumbai

first: Neelam

middle: V

last: Shirsat

state: Maharashtra

address: Kharghar, Sector 21

department: Shirsat Lab

country: India

institute: Advanced Centre for Treatment, Research and Education in Cancer. Tata Memorial Centre

summary:
Medulloblastoma is a malignant brain tumor that occurs predominantly in children. Current risk stratification based on the clinical parameters is inadequate for accurate prognostication. In order to get a better understanding of medulloblastoma biology, miRNA profiling of medulloblastomas was carried out in parallel with the expression profiling of protein- coding genes.
miRNA profiling of medulloblastomas was carried out using Taqman Low Density Density Aarray v 1.0 having 365 human microRNAs. In parallel, genome--wide expression profiling of protein coding genes was carried out using Affymetrix gene 1.0 ST arrays. Both the profiling studies identified four molecular subtypes of medulloblastomas. Expression levels of select protein-coding genes and miRNAs could classify an independent set of medulloblastomas. Twelve of 31 medulloblastomas were found to overexpress genes belonging to the canonical WNT signaling pathway and carry a mutation in CTNNB1 gene. A number of miRNAs like miR-193a, miR-224/miR-452 cluster, miR-182/miR-183/miR-96 cluster, and miR-148a having potential tumor/metastasis suppressive activity were found to be overexpressed in the WNT signaling associated medulloblastomas. Exogenous expression of miR-193a and miR-224, two miRNAs that have the highest WNT pathway specific upregulation, was found to inhibit proliferation, increase radiation sensitivity and reduce anchorage-independent growth of medulloblastoma cells. Expression level of tumor/metastasis suppressive miRNAs in the WNT signaling associated medulloblastomas is likely to determine their response to treatment, and thus, these miRNAs would be important biomarkers for risk stratification within the WNT signaling associated medulloblastomas.

overall_design: A total of 19 human sporadic medulloblastomas were profiled using the Affymetrix Gene 1.0 ST array

first: A

last: Gokhale

first: R

last: Kunder

last: Goel

last: Sarin

last: Moiyadi

last: Shenoy

first: C

last: Mamidipally

first: S

last: Noronha

last: Kannan

first: N


title: Exacerbated neuronal ceroid lipofuscinosos phenotype in Cln1/5 double knock-out mice

city: Helsinki

first: Tea

last: Blom

address: P.O.Box 104

department: Public Health Genomics

country: Finland

institute: National Institute for Health and Welfare

summary: Both CLN1 and CLN5 deficiency leads to severe neurodegenerative diseases of childhood, known as neuronal ceroid lipofuscinoses (NCL). The broadly similar phenotypes of NCL mouse models, and the potential for interactions between NCL proteins, raise the possibility of shared or converging disease mechanisms. To begin addressing these issues we have developed a novel mouse model lacking both Cln1 and Cln5 genes. These Cln1/5 double knock-out (Cln1/5 dko) mice were fertile, showing a slight decrease in expected Mendelian breeding ratios, as well as impaired embryoid body formation of induced pluripotent stem cells derived from Cln1/5 dko fibroblasts. Typical manifestations of the NCL diseases, seizures and motor dysfunction, were detected at the age of 3 months, earlier than in either single knock-out mouse. Pathological analyses revealed a similar exacerbation and earlier onset of disease in Cln1/5 dko mice, which exhibit a pronounced accumulation of autofluorescent storage material. Cortical demyelination and more pronounced glial activation in cortical and thalamic regions was followed by cortical neuron loss. Alterations in lipid metabolism in Cln1/5 dko showed specifically an increase in serum phospholipid transfer protein (PLTP) activity. Finally, gene expression profiling of Cln1/5 dko cortex revealed defects in myelination and immune response pathways, with a prominent downregulation of alpha-synuclein in Cln1/5 dko mouse brains. The simultaneous loss of both Cln1 and Cln5 genes may enhance the typical pathological phenotypes of these mice by disrupting down shared or convergent pathogenic pathways, which may potentially include interactions of CLN1 and CLN5.

overall_design:
Basic characterization of Cln1/5 double knock-out mouse model.
Aim was to find possible differentially expressed genes and up-or downregulated pathways in Cln1/5 double knock-out vs. wild-type mouse cortex.
Total RNA isolated from 1 month old Cln1-/-/Cln5-/- mouse cortex.


title: A mouse model of rhabdomyosarcoma originating from the adipocyte lineage

status: Public on Oct 22 2012

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

summary: Activation of Sonic Hedgehog signaling through expression of a constitutively active Smoothened allele under control of an aP2 adipocyte-restricted transgene in mice gives rise to aggressive skeletal muscle tumors that display the histologic and molecular characteristics of human embryonal rhabdomyosarcoma with high penetrance.

overall_design: Conditional mouse models of embryonal rhabdomyosarcoma were created by activation of the oncogenic SmoM2 allele by both the non-muscle aP2-Cre or myotube Myogenin-Cre.

first: Mark

last: Hatley

first: Wei

last: Tang

first: Matthew

middle: R

last: Garcia

last: Millay

first: Ning

last: Liu

first: Jonathan

last: Graff

first: Rene

last: Galindo

first: Eric

last: Olson


title: Creation of an anti-inflammatory GR cistrome by TLR4 signaling

city: Berlin

first: N. Henriette

last: Uhlenhaut

address: Robert-Roessle-Str 10

country: Germany

institute: Max Delbrueck Center

summary: An unresolved molecular paradox is how the glucocorticoid receptor (GR) activates some genes while potently repressing others. We carried out genome-wide localization and expression profiling experiments in primary bone marrow-derived mouse macrophages treated with Dexamethasone in the presence or absence of LPS. Unexpectedly, we find that the anti-inflammatory GR cistrome, which is principally composed of ‘canonical’ GREs colocalizing with NF-κB and AP-1 co-enriched with the myeloid lineage factors C/EBP and Pu.1, is shaped by TLR4-directed chromatin dynamics, suggesting that context rather than sequence may be a critical determinant of function.

overall_design: Total RNA was obtained from primary bone marrow-derived mouse macrophages treated overnight with EtOH or 1 uM Dexamethasone, unstimulated or stimulated with LPS. Two seperate experiments were performed (at 3 hr and 6 hr LPS-treatment timepoints).

first: Ruth

last: Yu

first: Ronald

last: Evans


title: Expression data from transplanted HCmel3 mouse melanomas relapsing to adoptive T-cell therapy in vivo

status: Public on Oct 10 2012

city: Bonn

first: Michael

last: Holzel

address: Sigmund-Freud Str. 25

department: Institute of Clinical Chemistry and Clinical Pharmacology

institute: University Hospital Bonn

summary: Adoptive cell therapies (ACT) with cytotoxic T-cell targeting melanocytic antigens can achieve remissions in metastatic melanoma patients, but tumours frequently relapse. To study the underlying mechanisms of resistance we have generated a genetically engineered mouse melanoma model that faithfully recapitulates tumour regression, remission and relapse as seen in patients. HCmel3 mouse melanoma cells were injected into syngneic C57/BL6 (H-2b) mice. We performed transcriptional profiling of control, relapsed and re-transplanted relapsed tumours to characterize the changes in gene expression patterns associated with the respective treament conditions. In addition, we analysed the transcription profile of ACT relapsed melanoma cultures in vitro and the transcriptional response to the inflammatory cytokine Tnf-alpha. The study aimed to identify molecular mechanisms contributing to ACT resistance to optimize therapeutic regimens in the clinic.

overall_design: Total RNA obtained from five biological replicates (rep) of control, relapsed and re-transplanted HCmel3 mouse melanomas in vivo and two biological replicates (rep) of HCmel3 cells, HCmel3-R (relapse) cells and Tnf-alpha treated HCmel3 cells in vitro.

first: Jennifer

last: Landsberg

first: Judith

last: Kohlmeyer

first: Marcel

last: Renn

first: Tobias

last: Bald

first: Meri

last: Rogava

first: Mira

last: Cron

first: Martina

last: Fatho

first: Volker

last: Lennerz

first: Thomas

last: Wölfel

last: Hölzel

last: Tüting


title: Global gene expression analysis of Ncoa3 knockdown in mouse embryonic stem cells

status: Public on Oct 02 2012

city: Singapore

first: Vibhor

last: Kumar

address: 60 Biopolis Street, Genome, #02-01

country: Singapore

institute: Genome Institute of Singapore

summary: Orphan nuclear receptor Esrrb is vital in maintaining ES cells and like Oct4, Sox2 and Nanog is essential for self-renewal and pluripotency. Esrrb functions in somatic cells via LBD/AF-2-dependent coactivator recruitment to target genes. Here we show that in ES cells coactivator recruitment is similarly required and identify Ncoa3 as the Esrrb coactivator needed for activation of its target genes. Ncoa3 is essential for self-renewal and the induction of pluripotency in reprogramming, and genome-wide analysis of Ncoa3 binding reveals extensive overlap with Esrrb and pluripotency factors along with marks of active genes. Mechanistically, we show Ncoa3 is specifically required to bridge RNApol2 to Esrrb. We thus identify a new member of the ES pluripotency network and describe Esrrb and Ncoa3 as key factors linking core pluripotency factors to the general transcription machinery.

overall_design: Three biological replicates each for control scrambled shRNA and Ncoa3 shRNA transfected E14 mouse ESCs. The global gene expression profiles of Ncoa3 knockdown cells were compared to control scrambled shRNA knockdown cells 4 days post-transfection.

first: Michelle

last: Percharde

first: Jia

last: Chi


title: mRNA expression after siRNA-mediated knock down of Enhancer of zeste homolog 2 (Ezh2) in human umbilical vein endothelial cells

status: Public on Oct 16 2012

first: Henryk

last: Dreger

address: Charitéplatz 1

department: Cardiology and Angiology

institute: Charité - Universitätsmedizin Berlin

summary: mRNA expression after Ezh2 knock down was analyzed to identify genes regulated by Ezh2.

overall_design: Human umbilical vein endothelial cells (HUVEC) were transfected with 25 nmol/L of control small interfering RNA (siRNA) (Silencer Select Negative Control Ambion, Austin, TX) or siRNA directed against Ezh2 (s4918; Ambion) using Oligofectamine (Invitrogen). Total RNA was harvested 72 hours after transfection.

first: Antje

last: Ludwig

first: Andrea

last: Weller

first: Verena

last: Stangl

first: Gert

last: Baumann

first: Silke

last: Meiners

first: Karl


title: Hypothalamic gene expression in small litter vs control mouse (postnatal overnutrition)

status: Public on Oct 01 2012

city: Houston

first: Govindarajan

last: Kunde Ramamoorthy

state: Texas

address: 1100 Bates Street

institute: Baylor College of Medicine

summary: Gene expression microarray profiling in adult (P180) small litter vs control mice.

overall_design: Total RNA isolated from hypothalamus excised from P180 males and females; 3 mice in each sex and each group (12 total).

first: Robert

last: Waterland


title: The Role of IL-22 in Regulating Gene Expression During Recovery from Influenza Infection

status: Public on Oct 19 2012

city: Pittsburgh

first: John

last: Alcorn

state: PA

address: 4401 Penn Ave

institute: Children's Hospital of Pittsburgh

summary: Analysis of whole lung RNA expression 21 days following influenza infection in wild-type and IL-22 -/- mice.

overall_design: Total lung RNA was isolated 21 days post-infection for microarray.


title: The effect on gene expression of Smchd1 deletion in pre-B cells from E17.5 Eµ-Myc embryos

status: Public on Sep 30 2012

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

institute: Walter and Eliza Hall Institute of Medical Research

summary: Smchd1 appears to act as a tumour suppressor in the Eµ-Myc mouse B cell lymphoma model. We find a small number of gene expression differences at E17.5 in the pre-B cells, before phenotypic differences are observed.

overall_design: The microarrays compared Smchd1 null and Smchd1 wildtype E17.5 preB cell samples. All samples are on the C57BL/6 background and carry the Eµ-Myc transgene, and the Smchd1 null samples are additionally homozygous for a Smchd1 genetrap allele.

first: Huei

middle: S

last: Leong

first: Yifang

last: Hu

first: Marnie

last: Blewitt


title: Transcriptional profiling of bulge stem cells

city: Brussels

first: KHALIL

last: KASS YOUSSEF

address: 808, Route de Lennick

country: Belgium

institute: ULB-IRIBHM

summary: In adult skin, each hair follicle contains a reservoir of stem cells (the bulge), which can be mobilized to regenerate the new follicle with each hair cycle and to reepithelialize epidermis during wound repair. Here we report new methods that permit their clonal analyses and engraftment and demonstrate the two defining features of stem cells, namely self-renewal and multi-potency. We also show that, within the bulge, there are two distinct populations, one of which maintains basal lamina contact and temporally precedes the other, which is suprabasal and arises only after the start of the first postnatal hair cycle. This spatial distinction endows them with discrete transcriptional programs, but surprisingly, both populations are growth inhibited in the niche but can self-renew in vitro and make epidermis and hair when grafted. These findings suggest that the niche microenvironment imposes intrinsic “stemness” features without restricting the establishment of epithelial polarity and changes in gene expression.

overall_design: FACS was used to isolate pure populations of living total K14-GFP-actin expressing cells and K14-GFP-actin α6high CD34high cells from postnatal d49 mouse back skins for RNA extraction and hybridization on Affymetrix microarrays. By comparing the transcriptional profile of FACS-isolated GFP α6high CD34high expressing cells with FACS-isolated total GFP cells, we determined the genes differentially regulated in basal bulge stem cells in telogen stage comparing to total epidermis

first: Cedric

last: Blanpain

first: William

last: Lowry

first: Elaine

last: Fuchs


title: Gene expression in E13.5 mouse lower molar whole tooth germ and oral tissue

status: Public on Oct 06 2012

city: Boston

first: David

middle: Paul

last: Nusinow

state: MA

address: 77 Avenue Louis Pasteur

department: Division of Genetics

institute: Brigham and Women's Hospital

summary: Gene expression profiles were generated from embryonic day 13.5 CD-1 mouse mandibular first molars whole tooth and non-tooth non-bone oral tissue.

overall_design: Three biological replicates from embryonic day 13.5 CD-1 mice were generated from pooled tissues across multiple mice. The tooth germ and non-tooth oral tissues were paired from the same embryos.

first: Adam

last: Kiezun

first: Daniel

last: O'Connell

first: Joel

last: Chick

first: Yingzi

last: Yue

first: Richard

last: Maas

first: Steven

last: Gygi

first: Shamil

last: Sunyaev


title: The effect on gene expression of Smchd1 deletion in primary MEFs, transformed MEFs and MEF tumours

summary: Smchd1 appears to act as a tumour suppressor in the transformed fibroblast model. We find gene expression differences are most pronounced in the transformed MEFs. We always detect a small number of clustered genes and imprinted genes as differentially expressed, along with others involved in tumorigenesis.

overall_design: The microarrays compared Smchd1 null and Smchd1 wildtype samples from different cell types (primary MEFs, transformed MEFs, tumours derived from transformed MEFs). Wildtype mice are FVB/N and Smchd1 null mice have the MommeD1 point mutation on a FBV/N background.


title: Genome-wide expression analysis of autologous eutopic and ectopic endometrium from fertile Indian women with endometriosis

city: New Delhi

first: Meraj

middle: Alam

last: Khan

state: Delhi

address: Room No.2029

department: Physiology

institute: All India Institute of Medical Sciences

summary: Whole genome expression analyses of autologous, paired eutopic and ectopic endometrial samples obtained during proliferative and secretory phases of menstrual cycles from eighteen (n=18) fertile women suffering from  confirmed stage 3 (moderate) and stage 4 (severe) ovarian endometriosis were performed using whole human genome oligo microarray Agilent paltform (Cat. No. G4112F).

overall_design: In the present study, genome-wide expression analysis of autologous, paired eutopic and ectopic endometrial samples obtained during proliferative (n=13) and secretory (n=5) phases of menstrual cycle from fertile women (n=18) suffering from moderate (stage 3; n=8) or severe (stage 4; n=10) endometrioma was performed by using Agilent single color oligo microarray platform (G4112, 4X44K). Thus eighteen (18) eutopic (shown as EU) and eighteen (18) ectopic (shown as EC) samples from eighteen (18) subjects with confirmed menstrual phase (proliferative and secretory) and severity stages (stage 3 and stage 4) were studied.

middle: A

first: Debabrata

last: Ghosh

first: Jayasree

last: Sengupta


title: Whole genome expression profile of lung epithelial cells following chronic arsenic exposure

status: Public on Sep 26 2012

city: Morgantown

first: Todd

last: Stueckle

state: WV

address: 1095 Willowdale Road

department: Health Effects Laboratory Division

institute: National Institute for Occupational Safety and Health

summary: This study chronically exposed human lung epithelial BEAS-2B cells to low-dose arsenic trioxide in vitro to elucidate cancer promoting gene signaling networks (GSNs) associated with As-transformed (B-As) cells.  Following a six month exposure, exposed cells were assessed for enhanced cell proliferation, colony formation, invasion ability and in vivo tumor formation compared to control cell lines.   Collected mRNA was subjected to whole genome expression microarray profiling followed by in silico Ingenuity Pathway Analysis (IPA) to identify lung carcinogenesis modes of action.  B-As cells displayed significant increases in proliferation, colony formation and invasion ability compared to BEAS-2B cells.  B-As injections into nude mice resulted in development of primary and secondary metastatic tumors.   As exposure resulted in widespread up-regulation of genes associated with mitochondrial metabolism and increased ROS protection suggesting mitochondrial dysfunction.  Carcinogenic initiation via ROS and epigenetic mechanisms was further supported by altered DNA repair, histone, and ROS-sensitive signaling.  NF-κB, MAPK and NCOR1 signaling disrupted PPARα/δ-mediated lipid homeostasis.  A ‘pro-cancer’ GSN identified increased survival, proliferation, inflammation, metabolism, anti-apoptosis and mobility signaling.  IPA-ranked signaling networks identified altered p21, EF1α, Akt, MAPK, and NF-κB signaling networks promoting genetic disorder, altered cell cycle, cancer and changes in nucleic acid and energy metabolism.  In conclusion, transformed B-As cells with their whole genome GSN profile provide an in vitro As model for future lung cancer signaling research and data for chronic As exposure risk assessment.

overall_design: Whole genome expression profiling was conducted on arsenic (III) oxide-exposed human immortalized lung epithelial cells (BEAS-2B) following 6 month in vitro chronic exposure.  As2O3 exposed cells (B-As) gene expression were compared to unexposed, passage control (B-Control) cell gene expression.  Three B-As and four B-Control biological replicate cDNA samples were analyzed.  One technical replicate was performed per biological sample.

first: Yon

last: Rojanasakul


title: The effect on gene expression of Smchd1 deletion in various cell types

first: Gordon

last: Smyth

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

overall_design:
Refer to the individual subSeries.
NOTE: all the cell types need to be analyzed separately.


title: Whole-genome expression analysis of immortalized murine E10.5 anterior and posterior limb cell lines

status: Public on Sep 18 2012

city: Edinburgh

first: Iain

last: Williamson

address: Crewe Road

department: Chromosomes and Gene Expression

country: United Kingdom

institute: IGMM MRC Human Genetics Unit

summary: The transcriptomes of immortalized anterior and posterior limb cell lines derived from E10.5 embryos were compared.

overall_design: Total RNA extracted from three E10.5 anterior and posterior limb cell line samples were compared.

first: Graeme

last: Grimes

first: Wendy

last: Bickmore


title: Transcriptomics in response to cigarette smoking in humans

city: Maastricht

first: Danitsja

middle: Maria

last: van Leeuwen

address: PO Box 616

department: Health Risk Analysis and Toxicology

country: Netherlands

institute: Maastricht University

summary: Transcriptomic analysis of the effects of cigarette smoking on the gene expression in blood in humans

overall_design: Analysis of gene expression in blood from 22 smokers and 22 non-smokers

first: D

middle: M


title: The effect on gene expression of Smchd1 deletion in premalignant pre-B cells

summary: Smchd1 appears to act as a tumour suppressor in the Eµ-Myc B cell lymphoma model. We find gene expression differences are most pronounced in premalignant cells. We always detect a small number of clustered genes and imprinted genes as differentially expressed, along with others involved in tumorigenesis.

overall_design: The microarrays compared Smchd1 null and Smchd1 wildtype samples from premalignant pre-B cells. All samples are on the C57BL/6 background, and carry the Eµ-Myc transgene. Smchd1 null samples are additionally homozygous for a Smchd1 genetrap allele.

first: Huei

last: Leong

first: Yifang

last: Hu

first: Marnie

last: Blewitt


title: The NIH Human Pluripotent Stem Cell Database (Agilent, mRNA)

city: Bethesda

first: Kory

last: Johnson

address: 10/3B01, 9000 Rockville Pike

department: DIR IT & Bioinformatics

institute: NINDS/NIH

summary: To better understand the extent to which induced pluripotent stem cells (iPSCs) faithfully recapitulate the characteristics of embryonic stem cells (ESCs) under (undiff)erentiated condition, KSR condition and FBS condition and how both compare to somatic tissues under these conditions, we employed whole-genome transcriptome analysis on all twenty one hESC lines available on the pre-2008 NIH Human Pluripotent Stem Cell Registry, eight human iPSCs derived at NIH by retroviral transduction of human fibroblasts and twenty human somatic tissues.  One standard culture protocol was used in conjunction with rigorous quality control.  Expanded description of methods used and are available at: http://stemcelldb.nih.gov.

overall_design: 230 samples:  44 human ESC (UNDIFF), 16 human iPSC (UNDIFF) 44 human ESC (KSR), 15 human iPSC (KSR), 44 human ESC (FBS), 15 human iPSC (FBS), 1 human Brain, 1 human Placenta, 1 human Skeletal Muscle, 1 human Heart, 1 human Liver, 1 human Lung, 1 human Kidney, 1 human Esophagus, 1 human Ovary, 1 human Testes, 1 human Spleen, 1 human Adipose, 1 human Thyroid, 1 human Thymus, 1 human Small Intestine, 1 human Prostate, 1 human Cervix, 1 human Colon, 1 human Bladder, 1 human Trachea) and 32 processing controls (UniRef).

first: Barbara

last: Mallon

first: Josh

middle: G

last: Chenoweth

first: Rebecca

last: Hamilton

first: Paul

middle: J

last: Tesar

first: Amarendra

last: Yavatkar

first: Leonard

last: Tyson

first: Yang

middle: C

last: Fann

first: Kye

last: Park

first: Kevin

last: Chen

first: Ronald

middle: D

last: McKay


title: ICL010 - Infection of Calu-3 cells with H1N1 influenza virus A/Netherlands/602/2009

status: Public on Sep 13 2012

city: Seattle

first: Michael

last: Katze

state: WA

address: Rosen Building 960 Republican St.

department: Microbiology

institute: University of Washington

summary: Differential expression was determined in Calu-3 cells between mock infected and infected with H1N1 influenza virus A/Netherlands/602/2009 at nine time points post-infection. As a comparison, cells were also infected with A/CA/04/2009 H1N1 influenza virus at 4 time points post-infection.

overall_design: Cells were infected at an MOI of 3.0. For the A/Netherlands/602/09-infected and mock-infected cells, samples were collected at 0, 3, 7, 12, 18, 24, 30, 36, and 48 hours post-infection (h.p.i.). For the A/California/04/2009-infected cells, samples were collected at 0, 12, 24, and 48 h.p.i. Samples were collected in triplicate.

first: Amy

last: Ellis

first: Yoshi

last: Kawaoka

first: Amie

last: Eisfeld

first: G

middle: L

last: Law

first: Jean

middle: H

last: Chang


title: Genome-wide analysis of  gene expression in Non-small Cell Lung Cancer

status: Public on Sep 16 2012

city: Zhoushan

first: lina

last: ma

address: Renmin North Road No.238

country: China

institute: Zhoushan Hospital

summary:
Analysis of NSCLC development at gene expression level.  Results shows that obvious activation of cell cycle pathway, and significant repression of cell-cell communication pathways.
Illumina HumanHT-12 V4.0 expression beadchip

overall_design: Total RNA obtained from 6 paired NSCLC cancer tissue and the adjacent normal tissue.

first: Lina

last: Ma

first: Xiaoguang

last: Liu


title: A549 expression profile induced by high levels of extracellular GPBP-1

status: Public on Sep 14 2012

city: Valencia

first: Fernando

last: Revert

state: Valencia

address: Autopista del Saler 16

country: Spain

institute: Centro de Investigación Príncipe Felipe

summary: Patients undergoing immune complex-mediated GN display increased levels of circulating GPBP-1 (cGPBP-1). To assess the relationship between high levels of cGPBP-1 and the onset of these diseases we incubated A549 cells with 200 ng/mL of recombinant extracellular GPBP-1 or with buffer (control). After 3 hours cells were lysed and total RNA extracted and assessed the mRNA expression. The functional analysis of  data provide evidence that high levels of circulating GPBP-1 correlate with a lupus-prone cellular response.

overall_design: A549 cells were seeded in 6-well plates, grown for 18 hours and treated with 200 ng/mL of recombinant extracellular GPBP-1 or buffer (TBS). After three hours of incubation, cells were lysed, total RNA extracted and mRNA expression analysed following Agilent's recommendations.

first: Jesús

last: Macías

first: Juan

last: Saus


title: MGMT modulates glioblastoma angiogenesis and response to the tyrosine kinase inhibitor sunitinib

status: Public on Sep 11 2012

city: Edmonton

first: Kathryn

last: Graham

state: Alberta

address: 11560 University Ave

department: Oncology

institute: University of Alberta

summary: Angiogenesis inhibitors, such as sunitinib, represent a promising strategy to improve glioblastoma (GBM) tumor response. In this study, we used the O6-methylguanine methyltransferase (MGMT)-negative GBM cell line U87MG stably transfected with MGMT (U87/MGMT) to assess whether MGMT expression affects the response to sunitinib. We showed that the addition of sunitinib to standard therapy (temozolomide [TMZ] and radiation therapy [RT]) significantly improved the response of MGMT positive but not of MGMT-negative cells. Gene expression profiling revealed alterations in the angiogenic profile, as well as differential expression of several receptor tyrosine kinases targeted by sunitinib. MGMT-positive cells displayed higher levels of vascular endothelial growth factor receptor 1 (VEGFR-1) compared with U87/EV cells, whereas they displayed decreased levels of VEGFR-2. Depleting MGMT using O6-benzylguanine suggested that the expression of these receptors was directly related to the MGMT status. Also, we showed that MGMT expression was associated with a dramatic increase in the soluble VEGFR-1/VEGFA ratio, thereby suggesting a decrease in bioactive VEGFA and a shift towards an antiangiogenic profile. The reduced angiogenic potential of MGMT-positive cells is supported by: (i) the decreased ability of their secreted factors to induce endothelial tube formation in vitro and (ii) their low tumorigenicity in vivo compared with the MGMT-negative cells. Our study is the first to show a direct link between MGMT expression and decreased angiogenicity and tumorigenicity of GBM cells and suggests the combination of sunitinib and standard therapy as an alternative strategy for GBM patients with MGMT-positive tumors.

overall_design: RNA was isolated from parental U87 (U87_EV) and MGMT-transfected U87 (U87_MGMT) triplicate. Pairwise gene expression differences were compared between the two cell lines.  Features selected had more than 2-fold up-or down-regulated (P values of >05, unpaired Student’s  t-test with Bonferroni multiple testing correction) were identified. Database for annotation, visualization, and integrated discovery23 was used to identify enriched gene ontology (GO) biological themes.24 The GO data mining was conducted at a term specificity level 3.25 The EASE score was set at 0.05 and the minimum number of genes in a category was 5.

first: Manik

last: Chahal

first: Siham

last: Sabri

first: Bassam

last: Abdulkarim


title: Genome-wide analysis of Bcl11a regulation genes in bone marrow derived pro-B cells

city: Frederick

first: Jack

last: Chen

address: SAIC-Frederick Miller Dr

institute: NIH

summary: To investigate the role of Bcl11a in pro-B cells, we performed global gene epxression in Bcl11a-deficient pro-B cells and Bcl2-rescued Bcl11a-deficient pro-B cells and compared it to that of the wild typle control pro B cells.

overall_design: Total RNA obtained from 3 batch of cultured pro-B cells of Bcl11a-deficient pro-B cells, Bcl2-rescued Bcl11a-deficient pro-B cells and control pro-B cells respectively.

first: Yong

last: Yu

first: Peng

last: Li


title: Comparison of gene expression profilling between iPS vs SSEA-1 positive or SSEA-1/3 negative sorted N417 cell line

city: Kitakyushu

first: Mitsuhiro

last: Suzuki

state: Fukuoka

address: 1-1 Iseigaoka, Yahatanisi-ku

department: Biochemistry

institute: University of Occupational and Environmental Health, Japan

summary: To prove that hypoxia generates Cancer stem cells (CSCs) from non-CSCs, we needed to separate out already existing tumorigenic cells from the cell population. To identify CSCs, we used ES cell-specific cell surface antigens (SSEA-1, -3, -4, and Tra1-81) on the assumption that the immature cell fraction would be rich in CSCs. We analyzed the expression levels of such embryonic antigens and stemness genes in cells exposed to hypoxia.

overall_design: iPS (253G1), SSEA-1 positive-N417 3 of SSEA-1/3 double negative-N417, each condition is represented by 3 biological replicates

first: Hajime

last: Iida


title: The effect on gene expression of Smchd1 deletion in end stage lymphomas

first: Gordon

last: Smyth

department: Bioinformatics

summary: Smchd1 appears to act as a tumour suppressor in the Eµ-Myc B cell lymphoma model. We find gene expression differences are most pronounced in the premalignant cells, and observe more variability in end stage lymphomas. We always detect a small number of clustered genes and imprinted genes as differentially expressed, along with others involved in tumorigenesis.

overall_design: The microarrays compared Smchd1 null and Smchd1 wildtype samples from end stage lymphomas. All lymphomas are on the C57BL/6 background and carry the Eµ-Myc transgene, and Smchd1 null samples are additionally homozygous for a Smchd1 genetrap allele.

first: Huei

last: Leong

first: Yifang

last: Hu

first: Marnie

middle: E

last: Blewitt


title: Genome wide analysis of germinal center MYC positive B-cells

city: Berlin

first: Dinis

middle: Pedro

last: Calado

state: Buch

address: Robert-Rössle-Str. 10

institute: Max-Delbrück-Centrum für Molekulare Medizin (MDC)

summary: Analysis of the gene expression profile between MYC positive and MYC negative germinal center B-cells.

overall_design: Total RNA isolated from MYC positive and MYC negative GC B-cells, isolated by FACS from 10 day sheep red blood cell immunized mice MycEGFP (a Myc reporter allele, in which a MYC-EGFP fusion protein (MYCEGFP) is expressed from the endogenous Myc locus, Huan, CY et al Eur J Immunol 2008)

middle: P


title: Expression data from CD34+ hematopoietic cells transduced with control or anti-HCLS1 shRNA

status: Public on Sep 09 2012

city: Hannover

first: Siarhei

last: Kandabarau

address: Carl-Neuberg-Str 1

institute: Hannover Medical School

summary: Knockdown of HCLS1 mRNA in CD34+ hematopoietic cells resulted in a severe diminished in vitro myeloid differentiation which was in line with downregulation of a set of genes, e.g., of Wnt or PI3K/Akt signaling cascades. We performed microarrays to evaluate specific genes and signaling systems regulated by HCLS1 in hematopoietic cells.

overall_design: CD34+ hematopoietic cells were isolated from the bone marrow of healthy individuals, transduced with lenitvirus-based RFP-expressed shRNA constructs targeting HCLS1 mRNA (two different shRNA constructs were used simultaneously) or scrambled control shRNA. After 4 days of the transductions, RFP+ cells were sorted, and total RNA of sorted cells was isolated and used for Affymetrix Exome arrays.

first: Julia

last: Skokowa

first: Karl

last: Welte


title: Cytosolic DNA stimulated gene regulation

status: Public on Jan 15 2013

city: Miami

first: Tianli

last: Xia

state: FL

address: 1550 NW 10th Ave

institute: University of Miami

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series

first: Glen

last: Barber


title: Distinct roles for IL-27 and IFN-g in the development of T-bet+ Treg required to limit infection-induced pathology

status: Public on Sep 07 2012

city: Philadelphia

first: daniel

last: beiting

address: 380 S. University Ave

department: Pathobiology

institute: University of Pennsylvania

summary: IL-27 is a potent antagonist of TH1-mediated inflammation, but the basis for this effect is not fully understood. Recent studies identified a population of T-bet+ CXCR3+ Treg that limit TH1-mediated immune pathology. The studies presented here demonstrate that IL-27-mediated STAT1 activation promotes Treg expression of T-bet and CXCR3. Infection with Toxoplasma gondii induced a similar Treg population that limits T cell responses and this population at mucosal sites is IL-27-dependent. Furthermore, transfer of Treg ameliorated the infection-induced CD4+ T cell-mediated pathology observed in IL-27p28-/- mice. Although IFN-γ promoted a similar population of cells in the periphery, it did not compensate for the absence of IL-27 at mucosal sites and microarray analysis revealed that Treg exposed to either cytokine have distinct transcriptional profiles. These findings suggest that IFN-γ and IL-27 have different roles in Treg biology but define IL-27 as a key cytokine that promotes the development of Treg specialized to control TH1 immunity.

overall_design: Three conditions were analyzed across two timepoints.  Inducible regulatory T cells (iTreg) were generated in vitro in the presence of IL-27, IFNg or under 'Neutral' conditions as a control.  Samples were collected at 10 hours and 2 days during the culture period.  Three biological replicates were used for each condition.

first: Daniel

last: Beiting

first: Aisling

last: O'Hara

first: Christopher

last: Hunter


title: Genome-wide analysis of tumor regression upon K-RAS inactivation

status: Public on Sep 06 2012

city: Dallas

first: Kimberly

last: Batten

state: TX

address: 5323 Harry Hines Blvd

department: Cell biology

institute: UT Southwestern Medical Center

summary: We performed expression profiling on micro-dissected lung tumors derived from a doxycycline-inducible K-RAS mouse model in order to gain mechanistic insight into K-RAS-mediated tumor maintenance. In this model, the tumors were induced with doxycycline for 11 weeks (in order to obtain lung tumors). At this point the doxycyline was withrawn from the food of the mice and consequently K-RAS inactivated. Thus, the genome-wide analysis was performed on tumors at timepoints 0, 24h and 48h after K-RAS inactivation.

overall_design: Total RNA obtained from mouse lung tumors at time 0 and 24h or 48h after K-RAS inactivation.

first: Pier

last: Scaglioni

first: Georgia

last: Konstantinidou

first: Chendong

last: Yang

first: Katja

last: Schuster

first: Jerry

middle: W

last: Shay

first: Ralph

last: DeBerardinis


title: Regulating type 1 IFN effects in CD8 T cells during viral infections: changing STAT4 and STAT1 expression for function

city: Providence

first: M. Pilar

last: Gil

state: Rhode Island

address: 75 Waterman St

institute: Brown University

summary: Type 1 IFNs can conditionally activate all of the signal transducers and activators of transcription molecules (STATs), including STAT4. The best-characterized signaling pathways use STAT1, however, and type 1 IFN inhibition of cell proliferation is STAT1 dependent. We report that type 1 IFNs can basally stimulate STAT1- and STAT4- dependent effects in CD8 T cells, but that CD8 T cells responding to infections of mice with lymphocytic choriomenigitis virus have elevated STAT4 and lower STAT1 expression with significant consequences for modifying the effects of type 1 IFN exposure. The phenotype was associated with preferential type 1 IFN activation of STAT4 as compared to STAT1. Stimulation through the TCR induced elevated STAT4 expression, and STAT4 was required for peak expansion of antigen-specific CD8 T cells, low STAT1 levels, and resistance to type 1 IFN-mediated inhibition of proliferation. Thus, a mechanism is discovered for regulating the consequences of type 1 IFN exposure in CD8 T cells, with STAT4 acting as a key molecule in driving optimal antigen-specific responses and overcoming STAT1-dependent inhibition of proliferation.

overall_design: CD8 T cells were purified from uninfected WT, STAT1-deficient and STAT4-deficient mice or from D8 LCMV-infected WT mice and either control treated or treated with 1x104 U mouse IFNalpha for 90 minutes.

first: M

first: Christine

last: Biron


title: Gene expression and epigenetic profiling of CD34+ hematopoietic progenitor cells in multiple sclerosis patients

status: Public on Sep 05 2012

city: Hamburg

first: Christian

last: Schulze

address: Falkenried 94

institute: ZMNH

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

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


title: Gene expression and epigenetic profiling of CD34+ hematopoietic progenitor cells in multiple sclerosis patients (expression)

summary: Intense immunosuppression followed by autologous hematopoietic stem cell transplantation (aHSCT) is a potential treatment for patients suffering from aggressive multiple sclerosis (MS). However it remains unresolved whether autologous CD34+ hematopoietic progenitor cells of MS patients show gene expression differences prior to aHSCT that indicate a preset proinflammatory state, which would then also predispose to or predetermine recurrence of the autoimmune disease. To approach this key point we compared the gene expression signature of CD34+ and CD34- cells collected from MS patients and healthy donors (HD). Whole genome gene expression of CD34+ and CD34- cells was analysed with the Human 4x44K Design Array (Agilent-Technologies). As main observation we found only minor differences in the gene expression signature of MS patients compared to HD. Only a single gene, troponin-type-1 (TNNT1), reached statistical significance after correction for multiple comparisons (logFC=3.1, p<0.01). There was a decreased expression of several protease genes, myeloperoxidase (MPO), neutrophil-elastase (ELA2), cathepsin-G (CTSG) and serine-protease 21 (PRSS21) in HPCs of MS patients, albeit not reaching statistical significance. In summary we did not detect substantial alterations in the gene expression profile of CD34+ HPCs in MS. Our data support the use of autologous hematopoietic stem cell transplantation for treatment of an autoimmune disease.

overall_design: Samples of CD34+ cells were obtained from 4 female MS patients and 4 age matched  healthy donors (3 female) mobilized by G-CSF (2x5μg/kg/day) and 4 MS patients (2 female) mobilized by G-CSF (5μg/kg/day) plus Cyclophosphamide (Cy, 4g/m2). White blood cells, containing the CD34+ cell fraction, were collected by leucocytapheresis from peripheral blood, frozen and stored in liquid nitrogen. All samples were thawed and processed at one center and CD34+ HPCs purified by magnetic bead separation using the autoMACS system (Miltenyi). Purity and viability of CD34+ cells was analyzed by Fluorescence Activated Cell Sorter (FACS). Total cellular RNA were extracted with TRIzol reagent and analyzed with the Human 4x44K Design Array (Agilent-Technologies).

first: Andreas

last: Lutterotti

first: Ilijas

last: Jelcic

first: Sven

last: Schippling

first: Petra

last: Breiden

first: Benedetta

last: Mazzanti

first: Stefanie

last: Reinhard

first: Massimo

last: DiGioia

first: Annamaria

last: Repice

first: Luca

last: Massacesi

last: Sputtek

first: Gabriela

last: Salinas-Riester

first: Nicolaus

last: Kroeger

first: Mireia

last: Sospedra

first: Riccardo

last: Saccardi

first: Axel

last: Zander

first: Roland

last: Martin


title: The downstream molecules of Notch signaling in vascular endothelial cell senescence

status: Public on Aug 28 2012

city: Chiba

first: Yohko

last: Yoshida

address: 1-8-1, Inohana, Chuo-ku

institute: Chiba University Graduate school of medicine

summary: To further investigate the mechanism how the decline in Notch signaling induces premature senescence in endothelial cells, we performed microarray analysis and identified Id1 nd DUSP1 as the downstream molecules of Notch pathway. In quantitative PCR and western blot analyses, the expression level of Id1 and DUSP1 increased in Notch1 over-expressing endothelial cells and decreased in knockdown similar to the result of microarray.

overall_design: The gene expression of human unbilical endothelial vein cells (HUVEC) infected with retroviral vectors encoding Jagged1, Jagged1-shRNA, or Notch1-shRNA. HUVEC infected with empty vector was used as a control. In each genotypes, three independent lines at passage 8 were performed.

first: Masakatsu

last: Yamashita

first: Kazuhiro

last: Sato


title: Bromodomain-dependent stage-specific male genome programming by Brdt [Illumina BeadArray]

status: Public on Aug 30 2012

city: La Tronche

first: Sophie

last: Rousseaux

address: Bd de la Chantourne

department: IAB

country: France

institute: INSERM-UGA

summary: Male germ cell differentiation is a highly regulated multistep process initiated by the commitment of progenitor cells into meiosis and characterized by major chromatin reorganizations in haploid spermatids. We report here that a single member of the double bromodomain BET factors, Brdt, is a master regulator of both meiotic divisions and post-meiotic genome repackaging. Upon its activation at the onset of meiosis, Brdt drives and determines the developmental timing of a testis-specific gene expression program. In meiotic cells, Brdt initiates a genuine histone acetylation-guided programming of the genome by activating essential meiotic genes and repressing a “progenitor cells” gene expression program, while “priming” a post-meiotic gene group for further activation. At post-meiotic stages, a global chromatin hyperacetylation gives the signal for Brdt’s first bromodomain to direct the genome-wide replacement of histones by transition proteins. Brdt is therefore a unique and essential regulator of male germ cell differentiation, which, by using various domains in a developmentally controlled manner, first drives a specific spermatogenic gene expression program, and later controls the tight packaging of the male genome.

overall_design: Total RNA obtained from testes from prepuberal mice at 17dpp and at 20dpp were compared between Brdt-/- and Brdt+/- (17dpp), between Brdt-/- and Brdt +/+ (20dpp) and between BrdtBD1del and Brdt wt mice (20dpp). In each experiments, 6 replicates of each genotype and condition were used.

first: Saadi

last: Khochbin

first: Jonathan

last: Gaucher

first: Philippe

last: Guardiola


title: Gene expression in primary isolated human myoblast during proliferation, G0 arrest, reactivation and differentiation

status: Public on Sep 01 2012

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

institute: Genotypic Technology

summary: A microarray study including two primary isolated human myoblast cell cultures ( samples A and B) was designed in order to detect the differences in global gene expression during four different culture conditions, two actively proliferating and two non-proliferating. Myoblasts were kept long term proliferating (BG0, before G0) followed by G0 arrest (G0), reactivation (AG0, after G0) and finally they were differentiated (Dif). The samples BG0 and AG0 were harvested when cells reached 70-80% confluence. The raw data from gene arrays were normalized, sample A and B were paired and the mean expression value used for further analyses. The four samples were compared to each other in order to detect differences in gene expression between the samples.

overall_design: Primary isolated human myoblast cells were cultured through four different culture, BG0, G0, AG0 and Dif. Two independent studies were made with primary isolated myoblasts from two different individuals for each of the four culture condition. Thus the number of samples for microarray analyses was 8.

first: Jeeva

last: Sellathurai

first: Sirisha

last: Cheedipudi

first: Jyotsna

last: Dhawan

first: Henrik

last: Schroeder


title: Lack of local vitamin D synthesis accelerates breast cancer development after Cyp27B1 gene ablation in mammary epithelium

status: Public on Aug 25 2012

city: Montréal

first: greg

last: VOISIN

state: QC

address: 3840 Saint-Urbain

department: Département de Médecine, Centre de Recherche

institute: Centre Hospitalier de l'Université de Montréal Hôtel Dieu

summary: The ablated Cyp27b1 mice showed no difference in mammary development but tumorigenesis was significantly accelerated. Cell proliferation, angiogenesis, cell cycle progression and survival markers were upregulated by Cyp27b1 ablation, a pattern confirmed by microarray analysis.

overall_design: Triplicate samples each of control mice and Cyp27b1 knockout mice.

first: Richard

last: Kremer

first: Jiarong

last: Li


title: Gene expression profiling of mouse uterine tissue from progesterone receptor-Cre knockout of Dicer

status: Public on Aug 15 2012

city: Houston

first: Chad

last: Creighton

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

summary: Epithelial-stromal interactions in the uterus are required for normal uterine functions such as pregnancy, and multiple signaling pathways are essential for this process. Although Dicer and microRNAs (miRNA) have been implicated in several reproductive processes, the specific role of Dicer and miRNA in uterine development is not known. To address the roles of miRNA in the regulation of these key uterine pathways, we generated a conditional knockout (cKO) of Dicer in the postnatal uterine epithelium and stroma using progesterone receptor (PR)-Cre. These Dicer cKO are sterile with small uteri, which demonstrate significant defects including absence of glandular epithelium and enhanced stromal apoptosis, beginning at postnatal day 15 with expression of Cre and deletion of Dicer. Although these mice had normal serum steroid hormone levels, critical uterine signaling pathways, including progesterone-responsive genes, Indian hedgehog signaling, and the Wnt/Beta-catenin canonical pathway, were dysregulated at the mRNA level.

overall_design:
Gene expression profiling data from pools of Dicer cKO and control uteri groups, at 15 days.
two group comparison

first: Shannon

last: Hawkins

first: Franco

last: Demayo

first: Marty

last: Matzuk


title: The new multi-targeted agent Curaxin-137 suppresses mammary tumorigenesis in Her2/neu transgenic mice

city: buffalo

first: Dan

last: Wang

state: NY

address: Elm & Carlton Streets

institute: RPCI

summary: Global gene expression profiles in liver and spleen between Curaxin-treated and control mice

overall_design: Gene expression profiles of samples isolated from 2 mice in each treatment group, control (plain water), and treated 0.1 and 0.2 mg/ml of Curaxin-137 from 4 to 14 weeks of age. Liver and spleen RNAs were analyzed

first: Igor

last: Koman

first: Mairead

last: Commane

first: Song

last: Liu

first: Andrei

last: Gudkov

first: Katerina

last: Gurova


title: Promoter DNA methylation couples genome-defense mechanisms to epigenetic reprogramming in the mouse germline

status: Public on Aug 01 2012

city: Cambridge

first: Jamie

last: Hackett

address: Tennis Court Road

institute: Gurdon Institue


title: Testis Gene Expression Changes after JQ1 treatment

status: Public on Aug 16 2012

city: College Station

first: Qinglei

address: 4458 TAMU

institute: Texas A&M University

summary: JQ1 is a small-molecule (BET family) bromodomain inhibitor that causes a contraceptive effect in mice by blocking spermatogenesis and reducing sperm motility.

overall_design: Genome-wide Illumina gene expression analysis of male mice treated with 50 mg/kg JQ1(treated) or vehicle (control) daily for 6 weeks (6-12 weeks of age).

first: Martin

first: Michael

middle: R

last: McKeown

first: Panagis

last: Filippakopoulos

first: Lang

last: Ma

first: Julio

last: Agno

first: Madeleine

last: Lemieux

first: Sarah

last: Picaud

middle: N

last: Yu

first: Jun

last: Qi

first: Stefan

last: Knapp

first: James

last: Bradner


title: Microarray analysis of genes activated by mouse CAR and human CAR in vivo.

first: Scott

middle: Andrew

last: Ochsner

address: One Baylor Plaza

department: Molecular and Cellular Biology

summary: This dataset is a four-ligand x three-genotype Affymetrix microarray analysis of the regulation of liver genes in the mouse by the constitutive androstane receptor (CAR).

overall_design: 24 female mice of mixed background (C57BL/6x129Sv) were divided into three groups:  wild-type (contains only mouse CAR; mCAR), CAR.KO = knockout mice (mice ablated for mCAR gene; mCAR -/-), and  CAR.AH= contains human CAR transgene under the control of the mouse albumin promoter in the mCAR -/- background.  Each of the three groups underwent four different treatment regimens:  CO = corn oil vehicle control, PB = phenobarbitol (100 mg/kg/day), an anti-convulsant agent which can translocate both mCAR and hCAR into the nucleus to turn on target gene expression, TC = TCPOBOP, a potent non-metabolized ligand of mCAR (3 mg/kg), CITCO = a hCAR specific ligand (30 mg/kg/day).  Two mice were used per treatment group and each mouse RNA was used for one chip.

first: Steven

middle: S

last: Chua

first: David

last: Moore


title: Gene expression profiling of human peripheral T cell lymphoma cases vs. reactive lymph nodes

city: Madrid

first: Esperanza

last: Martín-Sánchez

address: Melchor Fernandez Almagro 3

institute: Spanish National Cancer Research Centre (CNIO)

summary: Peripheral T cell lymphoma (PTCL) is a very aggressive disease which currently lacks efficient targeted therapy. New therapeutic strategies are needed to improve the very poor outcome of these patients. However, little is known about the molecular pathogenesis of this disease. In this study, we performed a gene expression profiling analysis of a series of 38 PTCL cases in order to find deregulated pathways or genes that could become therapeutic agents for PTCL patients.

overall_design: 38 PTCL cases and 6 reactive lymph nodes were hybridized with the Universal Human Reference RNA (Stratagene, La Jolla, CA), which served as the reference sample.

first: Magdalena

middle: B

last: Wozniak

first: Socorro

last: Rodríguez-Pinilla

first: Miguel

middle: A

last: Piris


title: Development of gene expression signatures for latent and clinical tuberculosis (TB)

status: Public on Aug 07 2012

city: beijing

first: hyk

last: liu

address: beijing

institute: IPB

summary: For further identify the differentiation between latent and clinical tuberculosis (TB), we employed whole genome microarray expression profiling to study genes with significant expression change in peripheral CD4+T cells between healthy control, latent tuberculosis (LTB) and clinical tuberculosis (TB). Our experiment included 4 groups: healthy donor (HD), latent TB1 (LTB1) with low IFN-gamma release level, latent TB2 (LTB2) with high IFN-gamma release level, and tuberculosis (TB) with high IFN-gamma release level. Human peripheral blood mononuclear cells were collected, from which CD4+T cells were isolated. Total RNA of each individuals of each group was extracted from peripheral CD4+T cells. One μg of RNA mixture, pooled equivalently by each individual total RNA of each group, was administrated microarray test. Compared with HD, through analyzing enriched-Gene Ontology (GO) terms and KEGG pathways of each group, we found peripheral CD4+T cells might had different ability for mycobacterium tuberculosis infection in  LTB1, LTB2 and TB. Finally we detected that TNFSF13/APRIL and TNFSF13B/BAFF was significant up-regulation in both CD4+T cells and serum of TB by real time PCR and ELISA, respectively.

overall_design: Peripheral CD4+ T cells were purified by positive selection using magnetic beads (BD IMagTM anti-human CD4 Particles-DM, BD Biosciences). Total RNA was extracted from CD4+ T cells (CD4-RNA) of LTB1, LTB2 and TB patients and healthy controls by RNeasy Mini Kit (QIAGEN).Then, RNA quality was checked and mixed with an equal quantity of each individual. The number of included-individuals in each group was 11 for HD, 11 for LTB1, 12 for LTB2 and 11 for TB.

first: Kai

last: Liu

first: Yan

last: Zhang

first: Qianting

last: Yang

first: Yang

first: Shizong

last: Hu

first: Xinchun

last: Chen

first: Haiying

first: Qi

last: Jin


title: Xenobiotics and loss of cell adhesion drives distinct transcriptional outcomes by Aryl hydrocarbon Receptor (AhR) signaling.

status: Public on Aug 10 2012

city: Singapore

first: Kian Leong

last: LEE

state: Singapore

address: #07-21, 8 College Road

department: Duke-NUS Medical School

institute: National University of Singapore (NUS)

summary:
The Aryl hydrocarbon Receptor (AhR) is a signal regulated transcription factor, which is canonically activated by the direct binding of xenobiotics. In addition, switching cells from adherent to suspension culture also activates the AhR, representing a non-xenobiotic, physiological activation of AhR signaling. Here, we show that the AhR is recruited to target gene enhancers in both ligand (YH439) treated and suspension cells, suggesting a common mechanism of target gene induction between these two routes of AhR activation. However, gene expression profiles critically differ between xenobiotic and suspension activated AhR signaling. Por, and Cldnd1 were regulated predominately by ligand treatments, while in contrast, ApoER2 and Ganc were regulated predominately by the suspension condition. Classic xenobiotic metabolizing AhR targets such as Cyp1a1, Cyp1b1, and Nqo1 were regulated by both ligand and suspension conditions. Temporal expression patterns of AhR target genes were also found to vary, with examples of transient activation, transient repression, or sustained alterations in expression. Furthermore, sequence analysis coupled with ChIP assays and reporter gene analysis identified a functional XRE (xenobiotic response element) within the mouse Tiparp gene that features a concatemer of 4 XRE cores (GCGTG) residing in the first intron ~1.2kb downstream of the Tiparp transcription start site. Our data suggest that this XRE concatemer site concurrently regulates the expression of both Tiparp gene and its cis anti-sense non-coding RNA following ligand or suspension induced AhR activation. This work lends novel insights into how AhR signaling drives different transcriptional programs via the ligand versus suspension modes of activation.
Reference: Murray IA et al. (2005) Evidence that ligand binding is a key determinant of Ah receptor-mediated transcriptional activity. Arch Biochem Biophys 442(1):59-71.
Reference: Monk SA et al. (2001) Transient expression of CYP1A1 in rat epithelial cells cultured in suspension. Arch Biochem Biophys 393(1):154-162.
Reference: Chua SW et atl. (2006) A novel normalization method for effective removal of systematic variation in microarray data. Nucleic acids research 34(5):e38.

overall_design: 18 microarray samples consisting of AhR null and reconstituted hepatocytes subjected to 10μM YH439, 0.1% DMSO carrier control or grown in suspension culture for 8 hours in 3 biologial replicates.

last: Hao

first: Kian

last: Lee

first: Sebastian

last: Furness

first: Lorenz

last: Poellinger

first: Murray

last: Whitelaw


title: Proteo-Genomic Characterization and Mapping of Nucleosomes Decoded by Brd and HP1 Proteins (expression data)

status: Public on Jul 31 2012

city: Cincinnati

first: Iouri

last: Chepelev

state: OH

address: 3200 Vine St

institute: US Department of Veterans Affairs Medical Center

summary:
Background: Histone post-translational modifications (PTMs) constitute a branch of epigenetic mechanisms that can control the expression of eukaryotic genes in a heritable manner. Recent studies have identified several PTM-binding proteins containing diverse specialized domains whose recognition of specific PTM sites leads to gene activation or repression. Here, we present a high-throughput proteogenomic platform designed to characterize the nucleosomal make-up of chromatin enriched with a set of histone PTM-binding proteins known as histone PTM readers. We support our findings with gene expression data correlating to PTM distribution.

Results: We isolated human mononucleosomes bound by the bromodomain-containing proteins Brd2, Brd3 and Brd4, and by the chromodomain-containing heterochromatin proteins HP1alpha and HP1beta. Histone PTMs were quantified by mass spectrometry (ChIP-qMS), and their associated DNAs were mapped using deep sequencing. Our results reveal that Brd- and HP1-bound nucleosomes are enriched in histone PTMs consistent with actively transcribed euchromatin and silent heterochromatin, respectively. Data collected using RNA-Seq (GSM301568) show that Brd-bound sites correlate with highly expressed genes. In particular, Brd3 and Brd4 are most enriched on nucleosomes located within HOX gene clusters, whose expression is reduced upon Brd4 depletion by shRNA.

Conclusions: Proteogenomic mapping of histone PTM readers, alongside the characterization of their local chromatin environments and transcriptional information, should prove useful for determining how histone PTMs are bound by these readers and how they contribute to distinct transcriptional states.

overall_design: Comparison of Brd2 and HP1b shRNA knockdown HEK293 cells to control knockdown HEK293 cells.

first: Gary

last: LeRoy

first: Peter

last: DiMaggio

first: Mario

last: Blanco

first: Barry

middle: M

last: Zee

first: Keji

last: Zhao

first: Benjamin

last: Garcia


title: Gene expression profiles for hyperglycemia induced tumors and mammary glands compared to those in euglycemia

status: Public on Aug 24 2012

first: Thomas

middle: Nathan

last: Person

state: Texas

department: Clinical Sciences

institute: UT Southwestern

summary: Analysis of hyperglycemia-induced tumor progression at gene expression level. The hypothesis tested in the present study was that hyperglycemia contributes to tumor growth and metastasis. Results provide important information of the response of hyperglycemia, such as specific NRG1 pathways, HER2-3 pathways, NF-kB pathways and anti-apoptotic related genes, up- or down-regulated.

overall_design: Total RNA obtained from tumor tissues of 10-week-old PyMT/PANIC and PyMT mice as well as mammary glands of 10-week-old PANIC-ATTAC and WT mice.

first: Jiyoung

last: Park


title: Gene expression profiles for Endotropin-transgenic mice in the background of MMTV-PyMT

status: Public on Jul 28 2012

summary: Analysis of endotrophin-induced tumor progression at gene expression level. The hypothesis tested in the present study was that endotrophin contributes to tumor growth and metastasis. Results provide important information of the response of endotrophin, such as specific immune response, cell cycle regulation and EMT related genes, up- or down-regulated.

overall_design: Total RNA obtained from tumor tissues of 12-week-old PyMT/Endotrophin and PyMT mice.


title: Comparing control and IL17A treated A2780-derived ovarian cancer stem cell

city: chongqing

first: tong

last: xiang

address: xinqiao

institute: xinqiao hospital

summary: A2780-derived ovarian cancer stem cells were  in vitro cultured in the presence of 10 ng/mL basic fibroblast growth factor , 20 ng/mL epidermal growth factor , 5 μg/mL insulin, 0.4% bovine serum albumin. Then ovarian cancer stem cells were stimulated  for  4 and 6 hours in the presence or absence of 250ng/ml IL17A. Total RNA was isolated and processed according to the Agilentmanufacturer’s standard protocols

overall_design: Gene expression in ovarian cancer stem cells from A2780 cell line was measured at IL17A stmulated (4 and 6 hours) and un-stmulated.

first: Tong


title: Promoter DNA methylation couples genome-defense mechanisms to epigenetic reprogramming in the mouse germline (part 1)

first: Jamie

last: Hackett

summary: Mouse primordial germ cells (PGCs) erase global DNA methylation (5mC) as part of the comprehensive epigenetic reprogramming that occurs during PGC development. 5mC plays an important role in maintaining stable gene silencing and repression of transposable elements (TE) but it is not clear how the extensive loss of DNA methylation impacts on gene expression and TE repression in developing PGCs. Using a novel epigenetic disruption and recovery screen and genetic analyses, we identified a core set of germline-specific genes that are dependent exclusively on promoter DNA methylation for initiation and maintenance of developmental silencing. These gene promoters appear to possess a specialised chromatin environment that does not acquire any of the repressive H3K27me3, H3K9me2, H3K9me3 or H4K20me3 histone modifications when silenced by DNA methylation. Intriguingly, this methylation-dependent subset is highly enriched in genes with roles in suppressing TE activity in germ cells. We show that the mechanism for developmental regulation of the germline genome-defence genes involves DNMT3B-dependent de novo DNA methylation. These genes are then activated by lineage-specific promoter demethylation during distinct global epigenetic reprogramming events in migratory (~E8.5) and post-migratory (E10.5-E11.5) PGCs. We propose that genes involved in genome defence are developmentally regulated exclusively by promoter DNA methylation as a sensory mechanism that is coupled to the potential for TE activation during global 5mC erasure, thereby acting as a failsafe to ensure TE suppression and maintain genomic integrity in the germline.

overall_design: Total RNA isolated from duplicate independent experiments of NIH/3T3 cells, NIH/3T3 cells exposed to 1uM 5aza-dC, and NIH/3T3 after 14 days recovery after drug withdrawal


title: Global changes in gene expression in primary keratinocytes after KLF9 overexpression

first: Florian

last: Spoerl

address: Unnastr. 48

department: Aged Skin

institute: Beiersdorf AG

summary: To identify putative target genes of the transcription factor Klf9 in primary keratinocytes we over-expressed Klf9 in these cells using a lentiviral delivery system. We detected several hundred genes that show differential expression levels following ectopic Klf9 expression including several genes that are involved in proliferation and cell cycle control. These results allow insights into the mechanisms by which Klf9 regulates proliferation in primary keratinocytes.

overall_design: Primary human neonatal foreskin keratinocytes were infected with equal viral titers of a GFP and KLF9 expression construct, respectively. Cells were harvested 2,4 and 7 days after infection and total RNA was used to perform whole genome microarray analysis.


title: NHD13 vs wild type LK cells

status: Public on Jul 27 2012

city: Melbourne

first: Chris

last: Slape

address: 99 Commercial Rd

department: ACBD

institute: Monash University

summary: Investigation of differences in gene expression between NHD13 mice with myelodysplastic syndrome and wild type littermates.

overall_design: RNA was harvested from Lineage negative Kit positive cells purified from mice transgenic for NHD13 or wild type littermates. Samples were pooled in groups of 3. 3 replicates were performed for each genotype.


title: Detection of circadian gene expression in human epidermal suction blister samples

summary: To detect time of day dependent gene expression in human epidermis suction blister samples from 20 healthy subjects were obtained at three different time points throughout the day. RNA from 20 subjects were used to perform whole genome microarray analysis. Microarrays from 19 subjects showed sufficient quality to perform analysis for differential gene expression. We detected significant differential expression levels for several canonical clock genes such as Per1, Per2, Per3, Bmal1 and Rev-Erb_alpha throughout the day. In total we identified 294 genes that showed significant circadian gene expression including several transcription factors and rate limiting enzymes. To our knowledge this is the first study to investigate genome wide circadian gene expression in human epidermis.

overall_design: Suction blisters of human epidermis were obtained by applying a vacuum for approximately 2.5 h. Suction blisters for each subject (19 subjects in total) were harvested at 9.30 am, 2.30 pm and 7.30 pm.


title: Novel players in myogenesis identified by target validation for muscle specific microRNAs in C2C12 myoblasts

status: Public on Jul 23 2012

city: Oxford

first: Helio

last: Pais

address: Jonh Radcliffe Hospital

department: Weatherall Institute of Molecular Medicine

institute: University of Oxford

summary:
Search of novel miR-206 target genes in C2C12 cells, based on differential expression of transcripts containing putative miR-206 binding sites.
miR-206 candidate target genes were hpothesized to be upregulated in AM206 vs Day2 sample and downregulated in siRNA vs Day 1 sample.

overall_design: total RNA extracted from various differentiation stages of C2C12 cells, as well as cells treated with miR-206 mimic or miR-206 inhibitor

first: Katarzyna

last: Goljanek-Whysall

first: Vincent

last: Moulton

first: Tamas

last: Dalmay

first: Andrea

last: Munsterberg


title: Blimp1/Prdm1 governs terminal differentiation of endovascular trophoblast giant cells and defines multipotent progenitors in the developing placenta

status: Public on Jul 24 2012

first: Arne

middle: Wyndham

last: Mould

state: Oxfordshire

address: Warneford Hospital

department: Psychiatry

institute: Oxford University

summary: Expression profiling of Prdm1 mutant E9.5 placenta was performed using Illumina whole genome V2 arrays. The hypothesis tested in the present study was that Blimp1 regulates the transcription of key genes involved in trophoblast differentiation. We demonstrate that the invading SpA-TGCs display robust Blimp1 expression and Blimp1 functional loss selectively disrupts specification of this discrete TGC sub-type.  Transcriptional profiling experiments identified additional  SpA-TGC lineage restricted marker genes that potentially regulate placental morphogenesis.

overall_design: Prdm1BEH/+ (Vincent et al., 2005) animals were intercrossed to generate null placental tissue. Total RNA obtained from 10 Prdm1+/+ and 11 Prdm1-/- E9.5 placenta samples was hybridized to Illumina WG6_V2 beadchips.

first: Marc

last: Morgan

first: Li

last: Li

first: Elizabeth

last: Bikoff

last: Robertson


title: B-Raf activation cooperates with PTEN loss to drive c-Myc expression in advanced prostate cancer

status: Public on Jul 19 2012

city: Newark

first: Antonina

last: Mitrofanova

state: NJ

address: 65 Bergen Street, Rm 923B

institute: Rutgers University

summary: Anaysis of the response to different therapeutic agents at the transcriptional level. The design of the experiment allows to determine how the comnination target therapy (Rapamycin + PD0325901) treatment shifted the transcriptome towards a less aggressive or even a wild type phenotype. It also allows exploring the molecular changes involved in the transition from a non metastatic to a metastatic prostate cancer mouse model.

overall_design: Total RNA obtained form vehicle treated Nkx3.1CE2/+; Ptenf/f; BrafCA/+ (n=3), combinatorial Rapamycin and PD0325901 treated Nkx3.1CE2/+; Ptenf/f; BrafCA/+ (n=3) and vehicle treated intact Nkx3.1CE2/+; Ptenf/f (n = 6) prostate. Please contact Cory Abate-Shen (cabateshen@columbia.edu) and Jingqiang Wang (jw2639@columbia.edu) for questions about the submission.

first: Jingqiang

last: Wang

first: Takashi

last: Kobayashi

first: Nicolas

last: Floch

first: Carolyn

last: Kinkade

first: Alvaro

last: Aytes

first: David

last: Dankort

first: Celine

last: Lefebvre

first: Robert

last: Cardiff

first: Martin

last: McMahon

last: Califano

first: Michael

last: Shen

first: Cory

last: Abate-Shen


title: AT13148 is a novel, oral multi-AGC kinase inhibitor with potent pharmacodynamic and antitumor activity

status: Public on Jul 20 2012

city: Sutton

middle: te

last: Poele

state: Surrey

address: 15 Cotswold Road

department: Cancer Reserach UK Unit for Cancer Therapeutics

institute: The Institute of Cancer Research

summary: Purpose:  Deregulated phosphatidylinositol 3-kinase pathway signaling through AGC kinases including AKT, p70S6 kinase, PKA, SGK and Rho kinase, is a key driver of multiple cancers. The simultaneous inhibition of multiple AGC kinases may increase antitumor activity and minimize clinical resistance compared with a single pathway component.  Experimental Design:  We investigated the detailed pharmacology and antitumor activity of the novel clinical drug candidate AT13148, an oral ATP-competitive multi-AGC kinase inhibitor. Gene expression microarray studies were undertaken to characterize the molecular mechanisms of action of AT13148.  Results:  AT13148 caused substantial blockade of AKT, p70S6K, PKA, ROCK and SGK substrate phosphorylation and induced apoptosis in a concentration and time-dependent manner in cancer cells with clinically relevant genetic defects in vitro and in vivo. Antitumor efficacy in HER2-positive, PIK3CA-mutant BT474 breast, PTEN-deficient PC3 human prostate cancer and PTEN-deficient MES-SA uterine tumor xenografts was demonstrated. We show for the first time that induction of AKT phosphorylation at serine 473 by AT13148, as reported for other ATP-competitive inhibitors of AKT, is not a therapeutically relevant reactivation step. Gene expression studies showed that AT13148 has a predominant effect on apoptosis genes, whereas the selective AKT inhibitor CCT128930 modulates cell cycle genes. Induction of upstream regulators including IRS2 and PIK3IP1 due to compensatory feedback loops was observed.  Conclusions:  The clinical candidate AT13148 is a novel oral multi-AGC kinase inhibitor with potent pharmacodynamic and antitumor activity, which demonstrates a distinct mechanism of action from other AKT inhibitors. AT13148 will now be assessed in a first-in-human Phase I trial.

overall_design: The PTEN-deficient U87MG glioblastoma cell line was treated for 6 hours with vehicle control (DMSO) or to different concentrations of AT13148 and CCT128930 (0.1uM, 1xGI50 and 3XGI50).

first: Timothy

last: Yap

middle: I

last: Walton

first: Kyla

last: Grimshaw

last: te Poele

first: Paul

last: Eve

first: Melanie

last: Valenti

first: Alexis

last: De Haven Brandon

first: Vanessa

last: Martins

first: Anna

last: Zetterlund

first: Simon

last: Heaton

first: Kathrin

last: Heinzmann

last: Jones

first: Ruth

last: Feltell

first: Matthias

last: Reule

first: Steven

middle: J

last: Woodhead

first: Thomas

middle: G

last: Davies

first: John

middle: F

last: Lyons

first: Florence

last: Raynaud

first: Suzanne

last: Eccles

last: Workman

first: Neil

middle: T

last: Thompson

first: Michelle

last: Garrett


title: Investigations on the role of Blimp1 in pluripotency and reprogramming

status: Public on Jul 21 2012

first: Harry

last: Leitch

institute: University of Cambridge

summary: Blimp1 (Prdm1), the key determinant of primordial germ cells (PGC), plays a combinatorial role with Prdm14 during PGC specification from postimplantation epiblast cells. They together initiate epigenetic reprogramming in early germ cells towards an underlying pluripotent state, which is equivalent to embryonic stem cells (ESC). Whereas Prdm14 alone can promote reprogramming and is important for the propagation of the pluripotent state, it is not known if Blimp1 is similarly involved. Using a genetic approach, we demonstrate that Blimp1 is dispensable for the derivation and maintenance of ESC and postimplantation epiblast stem cells (EpiSC).  Notably, Blimp1 is also dispensable for reprogramming EpiSC to ESC. Thus, while Blimp1 is obligatory for PGC specification, it is not required for the reversion of EpiSC to ESC, and for their maintenance thereafter. This study suggests that reprogramming, including that of somatic cells to ESC, may not entail an obligatory route through Blimp1 positive PGC-like state.

overall_design: Comparison of gene expression between Blimp1 null and heterozygous ESC, EpiSC and rESC (plus ESC grown in 2i/LIF conditions)

first: Siqin

last: Bao

first: Azim

last: Surani


title: Genome-wide analysis of mRNA expression alterations of sorted LysM-KI LSK cells versus control LSK cells

status: Public on Jul 22 2012

city: Toronto

first: carl

last: virtanen

state: Ontario

address: 101 College St

department: Princess Margaret Genomics Centre

institute: University Health Network

summary: Microarrays were used to examine gene expression changes between bone marrow isolated  haematopoeietic cell populations (LSK cells: Lin-Sca1+cKit+) populations of control and mutant (LysM-KI) mice.   The LysM-KI mouse is a murine model which expresses an Idh1 (isocitrate dehydrogenase 1) mutation (Idh1-R132H) in cells of the myeloid lineage.  Mutations in IDH1 (and IDH2) in humans are commonly found in cytogenetically normal acute myeloid leukemia as well as glioblastomas. The current study was initiated to understand how these mutations may affect leukemogenesis and myeloid cell development.

overall_design: Total RNA obtained from bone marrow sorted LSK cells of mutant LysM-KI and control individual mice.

first: Christiane

last: Knobbe

first: Masato

last: Sasaki

first: Carl

last: Virtanen

first: Tak

last: Mak


title: Subgroup specific somatic copy number aberrations in the medulloblastoma genome [mRNA]

city: HEIDELBERG

first: Paul

middle: A.

last: Northcott

address: Im Neuenheimer Feld 280

institute: German Cancer Research Center (DKFZ)

summary: Affymetrix Human Gene 1.1 ST Array profiling of 285 primary medulloblastoma samples.

overall_design: Total RNA was extracted from primary medulloblastoma samples and hybridized to Affymetrix Human Gene 1.1 ST Arrays (24-Array Plates) according to the manufacturer's instructions.

first: David

last: Shih


title: Effects of maternal choline intake on placental gene expression

status: Public on Jul 13 2012

city: Ithaca

first: Xinyin

last: Jiang

address: 241 Kinzelberg Hall, Cornell University

department: Nutritional Sciences

institute: Cornell University

summary: To explore the influence of maternal choline intake on placental gene expression, we employed whole genome microarray expression profiling to identify genes that were differentially expressed in placental tissues obtained from  women consuming two different doses (480 vs. 930 mg/d) of choline throughout the third trimester of pregnancy. Healthy third trimester (gestational week 26-29) pregnant women were randomized to a 12-week choline controlled feeding study. The participants consumed either 480 (n=6) or 930 (n=6) mg choline/d. Full thickness placental samples were collected at delivery to extract RNA and perform the arrays.

overall_design: Healthy third trimester (gestational week 26-29) pregnant women were randomized to a 12-week choline controlled feeding study. The participants consumed either 480 (n=6) or 930 (n=6) mg choline/d for 12 weeks. Placental samples were obtained at delivery

first: Marie

last: Caudill

first: Haim

middle: Y

last: Bar

first: Jian

last: Yan

first: Allyson

last: West

first: Cydne

last: Perry


title: MiR-374a Promotes Epithelial-Mesenchymal Transition (EMT) and Metastasis of Breast Cancer (mRNA dataset)

status: Public on Jul 14 2012

city: Guangzhou

first: Mengfeng

last: Li

state: Guangdong

address: 74# zhongshan 2 Rd.

department: Zhongshan school of medicine

institute: Sun Yat-sen University

summary: This experiment is designed to evaluate gene expression alterations following miR-374a transduction in breast cancer cells. We find a significant elevation of Wnt/β-catenin signaling transcriptional targets.

overall_design: Total RNA were extracted from MCF-7 breast cancer cells stably transduced with miR-374a precursor or vector control. Two biological replications for each treatment.

first: Junchao

last: Cai