title: Effect of simulated microgravity on E. coli K12 MG1655 growth and gene expression

status: Public on Sep 06 2012

city: Hyderabad

first: kotakonda

last: Arunasri

state: Andhra Pradesh

address: Habsiguda

country: India

institute: Centre for Cellular and Molecular biology

summary: This study demonstrates simulated microgravity effects on E. coli K 12 MG1655 when grown on LB medium supplemented with glycerol. The results imply that E. coli readily reprograms itself to combat the multiple stresses imposed due to microgravity. Under these conditions it survives by upregulating oxidative stress protecting genes and simultaneously down regulating the membrane transporters and synthases to maintain cell homeostasis.

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: In this study, a clinostat that mimics microgravity conditions was used to investigate the effects of microgravity on E. coli grown in LB medium supplemented with glycerol to monitor the effects on growth and global gene expression using Affymetrix DNA microarrays.

last: Shivaji

first: K


title: Expression profiling of MCF7 cells upon nutlin3a treatment

status: Public on Sep 07 2012

city: Stockholm

first: Fedor

last: Nikulenkov

address: Nobels vag 16

country: Sweden

institute: Fedor Nikulenkov

summary:
The tumor suppressor p53 can induce various biological responses. Yet it is not clear whether it is p53 in vivo promoter selectivity that triggers different transcription programs leading to different outcomes. Our analysis of genome-wide chromatin occupancy by p53 using ChIP-seq (deposited in Sequence Read Archive database as SRP007261) revealed “p53 default program”, i.e. the pattern of major p53-bound sites that is similar upon p53 activation by nutlin3a, RITA or 5-FU in breast cancer cells, despite different biological outcomes triggered by these compounds. Parallel analysis of gene expression allowed identification of 280 previously unknown p53 target genes, including p53-repressed AURKA.  The consensus p53 binding motif was present more frequently in p53-induced, than in repressed targets, indicating different mechanisms of gene activation versus repression. We identified several possible cofactors of p53, and found that STAT3 antagonised p53-mediated repression of a subset of genes, including AURKA. Finally, we showed that the expression of the novel p53 targets correlates with p53 status and survival in breast cancer patients.
We used microarrays to detail the global programme of gene expression changed upon nutlin3a treatment and knocking-down of STAT3 transcription program

overall_design: MCF7 cell with or without knock-down of STAT3 were treated with nutlin3a and collected for RNA extraction and hybridization on Affymetrix microarrays.

first: Clemens

last: Spinnler

first: Hai

last: Li

first: Claudia

last: Tonelli

first: Shi

last: Yao

first: Turunen

last: Miko

first: Kivioja

last: Teemu

first: Ignatiev

last: Ilija

first: Kel

last: Alexander

first: Taipale

last: Jussi

first: Selivanova

last: Galina


title: Progressive Activation of Th2/Th22 characterizes acute and chronic atopic dermatitis

status: Public on Sep 21 2012

city: New York

first: Mayte

last: Suarez-Farinas

state: NY

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

country: USA

institute: Mount SinaiSchool of Medicine

summary: Atopic dermatitis (AD) is a common disease, with an increasing prevalence. The primary pathogenesis of the disease is still elusive, resulting in lack of specific treatments. The prevailing view is that AD is a biphasic, T-cell polarized disease, with Th2 predominating acute AD, and a switch to Th1 characterizing chronic disease. Identification of factors that participate in onset of  lesions and maintenance of chronic lesions is critical for development of targeted therapeutics. We performed global genomic, molecular and cellular profiling of paired non-lesional, acute, and chronic skin biopsies from ten AD patients. Onset of acute lesions is associated with a striking increase in a subset of terminal differentiation proteins, specifically the IL-22-modulated S100A7-9. Correspondingly, acute disease is associated with significant increases in gene expression levels of the major Th22- (IL-22) and Th2- (IL-4, IL-31) cytokines and Th17-regulated genes (CCL20, PI3/Elafin), without significant changes in IL-17. A lesser induction of Th1- (IFNγ, MX-1, CXCL9-11) associated genes was detected in acute disease. Chronic skin lesions are characterized by significantly intensified activation of Th22, Th2 and Th1. Our data establish increased expression of S100A7-9 and other epidermal genes at onset of acute AD, with parallel activation of Th2 and Th22 cytokines. Our findings suggest an absence of switch mechanism in chronic disease and instead indicate that progression to chronic lesions is associated with intensified activation of immune axes that initiate onset of acute lesions, particularly Th22 and Th2. This alters the prevailing view of pathogenesis, with important therapeutic implications.

overall_design: Acute, chronic, and non-lesional skin samples were collected from ten patients with moderate-to-severe AD that met our inclusion criteria, under an institutional review board–approved protocol. The following criteria were employed to define acute AD and distinguish true acute from “acute on chronic” skin lesions: a) new lesions of <72 hours duration, as previously defined;14 b) lack of skin lichenification; c) lack of regenerative hyperplasia, as defined by epidermal thickness ≤150μ [hematoxylin and eosin (H&E)] and basal or confluent supra-basal Keratin 16 (K16) positivity. No systemic or topical treatments were allowed for ≥4 weeks prior to biopsies. Biopsy specimens were frozen in optimal cutting temperature (OCT) for immunohistochemistry (IHC) and liquid nitrogen for RNA extraction.

last: Suárez-Fariñas

first: Emma

last: Guttman-Yasky


title: CpG Methylation by Methyl 450K  Bead Arrays from ENCODE/HAIB

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

summary:
This data was generated by ENCODE. If you have questions about the data, contact the submitting laboratory directly (Florencia Pauli mailto:fpauli@hudsonalpha.org). If you have questions about the Genome Browser track associated with this data, contact ENCODE (mailto:genome@soe.ucsc.edu).
This track is produced as part of the ENCODE project. The track displays the methylation status of specific CpG dinucleotides in the given cell types as identified by the Illumina Infinium Human Methylation 450 Bead Array platform (http://www.illumina.com/products/methylation_450_beadchip_kits.ilmn). In general, methylation of CpG sites within a promoter causes silencing of the gene associated with that promoter.
The Infinium Human Methylation 450 platform uses bisulfite treated genomic DNA to assay the methylation status of more than 450,000 CpG sites covering all designatable RefSeq genes, including promoter, 5' and 3' regions, without bias against those lacking CpG islands. Additionally, the assay includes CpG islands and shores, CpG sites outside of CpG islands, non-CpG methylated sites identified in human stem cells, differentially methylated sites identified in tumor versus normal (multiple forms of cancer) and across several tissue types, CpG islands outside of coding regions, miRNA promoter regions, and disease-associated regions identified through GWAS.
Detailed information for the CpG targets is in an CSV formatted spreadsheet in the supplemental directory (http://hgdownload-test.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibMethyl450/supplemental/).

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design:
Cells were grown according to the approved ENCODE cell culture protocols (http://hgwdev.cse.ucsc.edu/ENCODE/protocols/cell).
Genomic DNA was isolated from each cell line with the QIAGEN DNeasy Blood & Tissue Kit according to the instructions provided by the manufacturer. DNA concentrations and a level of quality of each preparation was determined by fluorescence with the Qubit Fluorometer (Invitrogen). Genomic DNA was treated with sodium bisulfite, converting unmethylated cytosines of CpG dinucleotides into uracils; methylated cytosines did not get converted. After bisulfite treatment, the methylation status of a site was assayed by single base-pair extension with a Cy3 or Cy5 labeled nucleotide on oligo-beads specific for the methylated or unmethylated state.
The bisulfite conversion reaction was done using the Zymo Research EZ-96 DNA Methylation Kit (http://www.zymoresearch.com/product/ez-96-dna-methylation-kit-d5003). One step of the protocol was modified. During the incubation, a 30 second 95oC denaturing step every hour was included to increase reaction efficiency as recommended by the Illumina Infinium Human Methylation27 protocol.
The bead arrays were run according to the protocol provided by Illumina (http://hgdownload-test.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibMethyl450/supplemental/wgEncodeHaibMethyl450IlluminaProtocol.pdf).
A beta value was calculated for each CpG target with Illumina's Bead Studio software with the Methylation Module v3.2. Beta-value = intensity value from the methylated bead type/(intensity values from the methylated + intensity value from unmethylated bead types + 100). The data was then quality-filtered using p-values. Beta values with p-value greater than 0.01 are considered to fall below the minimum intensity and threshold are displayed as "NA".
Any beta value equal to or greater than 0.6 was considered fully methylated. Any beta value equal to or less than 0.2 was considered to be fully unmethylated. Beta values between 0.2 and 0.6 were considered to be partially methylated.
Score in the bed files is beta value x 1000

first: Richard

last: Myers

first: Devin

last: Absher

first: Florencia

last: Pauli


title: Expression data from E18.5 mouse dorsal telencephalon

city: Chapel Hill

first: xiaoyan

last: li

state: NC

address: 115 Mason Farm Road

department: Neuroscience Center

institute: University of North Carolina

summary: Radial progenitors deficient in both Mek1 and Mek2 fail to transition to the gliogenic mode in late embryogenesis, and astrocyte and oligodendroglial precursors fail to appear.  In exploring mechanisms, we found the Ets transcription family member Etv5/Erm is strongly regulated by MEK. Our microarray assay showed that Erm is specifically downregulated in Mek mutant brain.

overall_design: RNA was extracted from dorsal corticies of E18.5 WT or Mek1,2\NesCre conditional mutant embryos. There were totally 4 samples: 2 WT and 2 mutants.  200 ng of total RNA was prepared for microarray hybridization according to the GeneChip® Whole Transcript (WT) Sense Target Labeling Assay user manual.

first: Xiaoyan

first: Jason

middle: M

last: Newbern

first: William

middle: D

last: Snider


title: Integrative Analysis of a series of newly diagnosed Diffuse Large B-cell Lymphomas (DLBCLs)

status: Public on Sep 12 2012

city: Boston

first: Björn

last: Chapuy

state: MA

address: 450 Brookline Ave.

department: Medical Onology

institute: Dana-Farber Cancer Institute

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

summary: Diffuse large B-cell lymphoma (DLBCL) is a clinically and biologically heterogeneous disease. We have characterized recurrent copy number alterations (CNAs) in a large series of primary DLBCLs with HD-SNP arrays and the GISTIC algromithm. We evaluated the associations between transcript abundance and the presence of specific CNAs by obtaining RNA profiles on the majority of the primary DLBCLs and integrating the gene expression profiles with the copy number data.

overall_design: High molecular weight DNA and total RNA were extracted from frozen biopsy specimens of newly diagnosed and previously untreated primary DLBCLs according to IRB-approved protocols. DLBCL diagnoses and > 80% tumor involvement were confirmed by expert hematologists. 180 primary DLBCLs and 53 normal DNA samples were profiled on Affymetrix SNP array 6.0. 169 of these primary DLBCLs were  RNA profiled, 78 on Affymetrix U133A+B and 91 on U133plus2 arrays.

first: B

first: S

last: Monti

first: M

middle: A

last: Shipp


title: Sublytic concentrations of Staphylococcus aureus Panton-Valentine leukocidin alter human polymorphonuclear leukocyte gene expression and enhance bactericidal capacity.

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

summary: Community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) infections are often caused by strains encoding Panton-Valentine leukocidin (PVL). PVL can cause lysis of polymorphonuclear leukocytes (PMNs) and other myeloid cells in vitro, a function considered widely as the primary means by which PVL might contribute to disease. However, at sublytic concentrations PVL can function as a PMN agonist. To better understand this phenomenon, we investigated the ability of PVL to alter human PMN function.  PMNs exposed to PVL had enhanced capacity to produce superoxide in response to N-formyl-methionyl-leucyl-phenylalanine (fMLF), but unlike priming by lipopolysaccharide, this response did not require Toll-like receptor signal transduction. On the other hand, there was subcellular redistribution of NADPH oxidase components in PMNs following exposure of these cells to PVL - a finding consistent with priming.  Priming of PMNs with other agonists such as IL-8 or GM-CSF altered the ability PVL to cause formation of pores in the plasma membranes of these cells.  Microarray analysis revealed significant changes in the human PMN transcriptome following exposure to PVL, including up-regulation of molecules that regulate the inflammatory response. Consistent with the microarray data, mediators of the inflammatory response were released from PMNs after stimulation with PVL. We conclude that exposure of human PMNs to sublytic concentrations of PVL elicits a proinflammatory response that is regulated in part at the level of gene expression. We propose that PVL-mediated priming of PMNs enhances the host innate immune response.

overall_design: time series of PMN's non treated vs PVL treated vs iPVL treated

first: Shawna

middle: F

last: Graves

first: Scott

last: Kobayashi

first: Kevin

middle: R

last: Braughton

first: Adeline

last: Whitney

first: Daniel

middle: E

first: Devon

middle: L

last: Rasmussen

first: Liliya

middle: N

last: Kirpotina

first: Mark

middle: T

last: Quinn

first: Frank

last: DeLeo


title: Divergent dysregulation of gene expression in Fmr1 and Tsc2 knockout mouse models of autism spectrum disorders

first: Sek Won

last: Kong

address: 300 Longwood Avenue

department: Informatics Program

institute: Boston Children's Hospital

summary:
Fragile X syndrome and tuberous sclerosis are genetic syndromes that both have a high rate of comorbidity with autism spectrum disorder (ASD). Several lines of evidence suggest that these two monogenic disorders may converge at a molecular level through the dysfunction of activity-dependent synaptic plasticity.
To explore the characteristics of transcriptomic changes in these monogenic disorders, we profiled genome-wide gene expression levels in cerebellum and blood from murine models of fragile X syndrome and tuberous sclerosis.
Differentially expressed genes and enriched pathways were distinct for the two murine models examined, with the exception of immune response-related pathways. In the cerebellum of the Fmr1 knockout (Fmr1-KO) model, the neuroactive ligand receptor interaction pathway and gene sets associated with synaptic plasticity such as long-term potentiation, gap junction, and axon guidance were the most significantly perturbed pathways. The phosphatidylinositol signaling pathway was significantly dysregulated in both cerebellum and blood of Fmr1-KO mice. In Tsc2 heterozygous (+/−) mice, immune system-related pathways, genes encoding ribosomal proteins, and glycolipid metabolism pathways were significantly changed in both tissues.
Our data suggest that distinct molecular pathways may be involved in ASD with known but different genetic causes and that blood gene expression profiles of Fmr1-KO and Tsc2+/− mice mirror some, but not all, of the perturbed molecular pathways in the brain.

overall_design: For the Fmr1-KO model, 10 mice, consisting of 5 KO and 5 WT mice, were profiled. Thus, 10 pairs of blood and cerebella samples were profiled. Likewise, for the Tsc+/- model, 3 transgenic and 3 WT mice were sacrificed and paired blood and cerebella samples were prepared for gene expression profiling.  All samples were profiled using the Affymetrix Mouse Gene ST 1.0 ST arrays. Three factors—tissue (i.e. blood vs. cerebellum), treatment (i.e. knockout vs. wildtype), and genetic background (Fmr1-KO vs. Tsc2+/-)—were analyzed with analysis of variance (ANOVA). Subsequently, we compared blood and brain gene expression changes in Fmr1 and Tsc2 knockout mice models using WT littermates as controls using t-tests with unequal variances.  The false discovery rate (FDR) was calculated using Storey and Tibshirani’s method.

first: Sek-Won

first: Malcolm

middle: G

last: Campbell


title: Expression data for transcriptional engineering mutants capable of L-tyrosine overproduction

status: Public on Sep 04 2012

city: Cambridge

first: Christine

last: Santos

address: 77 Massachusetts Ave, 56-422

institute: Massachusetts Institute of Technology

summary: We measured transcriptional changes in four strains – P2, rpoD3, rpoA14, and rpoA27 - in an effort to understand mechanisms by which L-tyrosine production is positively influenced by the presence of mutant rpoA- and rpoD-encoded transcriptional components.

overall_design: Strains P2, rpoA14, rpoA27, and rpoD3 were grown in 50 ml MOPS minimal medium to an OD600 of approximately 0.4.  Triplicates samples of RNA (on three separate days) were then extracted for hybridization onto Affymetrix microarrays.

middle: S

first: Gregory

last: Stephanopoulos


title: ISL1 regulates PPARg activation and early adipogenesis via BMP4-dependent and -independent mechanisms

status: Public on Sep 05 2012

city: Sydney

first: xiuquan

last: ma

address: 384 Victoria Street

country: Australia

institute: Garvan Institute of Medical Research

summary: While adipogenesis is controlled by a cascade of transcription factors, the global gene expression profiles in the early phase of adipogenesis are not well defined. Using microarray analysis of gene expression in 3T3-L1 cells we have identified evidence for the activity of 2568 genes during the early phase of adipocyte differentiation. One of these, ISL1, was of interest since its expression was markedly upregulated at 1 h after initiation of differentiation with a subsequent rapid decline. Overexpression of ISL1 at early times during adipocyte differentiation, but not at later times, was found to profoundly inhibit differentiation. This was accompanied by moderate down-regulation of PPARg levels, substantial down-regulation of PPARg downstream genes and down-regulation of BMP4 levels in preadipocytes. Readdition of BMP4 overcame the inhibitory effect of ISL1 on PPARg but not aP2 expression, a downstream gene of PPARg; and BMP4 also partially rescued ISL1 inhibition of adipogenesis, an effect which is additive with rosiglitazone. These results suggest that ISL1 is intimately involved in early regulation of adipogenesis, modulating PPARg expression and activity via BMP4-dependent and -independent mechanisms. Our time course gene expression survey sets the stage for further studies to explore other early and immediate regulators.

overall_design: To explore global gene expression profiles during early adipocyte differentiation, total cellular RNA was isolated from 3T3-L1 cells at 0h, 0.5h, 1h, 2h, 4h, 8h and 48h following treatment with differentiation cocktail. At the same time, to check ISL1-regulated genes in 3T3-L1 cells, total cellular RNA was isolated from 3T3-L1 cells overexpressing Flag-ISL1 at 0h and 48h. Individual RNA from biological triplicates was used for microarray analysis.

first: Xiuquan

last: Ma

first: Pengyi

last: Yang

first: Warren

middle: H

last: Kaplan

first: Bon-Hyang

last: Lee

first: Lindsay

last: Wu

first: Yee-Hwa

first: Mayu

last: Yasunaga

first: Kenzo

last: Sato

first: Donald

middle: J

last: Chisholm

first: David

last: James


title: Structural, functional and molecular analysis of the effects of aging in the small intestine and colon of C57BL/6J mice [Colon data]

status: Public on Sep 03 2012

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

summary: By regulating digestion and absorption of nutrients and providing a barrier against the external environment the intestine provides a crucial contribution to the maintenance of health. To what extent aging-related changes in the intestinal system contribute to the impaired health of the aging body is still under debate. Young (4 months) and old (21 months) male C57BL/6J mice were fed a control low-fat (10E%) or a high-fat diet (45E%) for 2 weeks. During the intervention gross energy intake and energy excretion in the feces were measured. After sacrifice the small and large intestine were isolated whereby the small intestine was divided in three equal parts. Of each of the isolated segments Swiss rolls were prepared for histological analysis and the luminal content was isolated to examine alterations in the microflora with 16S rRNA Q-PCR. Furthermore, mucosal scrapings were isolated from each segment to determine differential gene expression by microarray analysis and global DNA methylation by pyrosequencing. Digestible energy intake was similar between the two age groups on both the control and the high-fat diet implying that macronutrient metabolism is not affected in 21-month-old mice. This observation was supported by the fact that the microarray analysis on RNA from intestinal scrapings showed no marked changes in expression of genes involved in metabolic processes. Decreased expression of Cubilin was observed in the intestine of 21-month-old mice, which might contribute to aging-induced vitamin B12 deficiency. Furthermore, microarray data analysis revealed enhanced expression of a high number of genes involved in immune response and inflammation in the colon, but not in the small intestine of the 21-month-old mice. Aging-induced global hypomethylation was observed in the colon and the distal part of the small intestine, but not in the first two sections of the small intestine. In 21-month old mice the most pronounced effects of aging was observed in the colon, limited changes were observed in the small intestine.

overall_design: Young (4M) and old (21M) wild type C57BL/6J mice were fed a low-fat diet or high-fat diet for 2 weeks. After the diet intervention period, the animals were killed and scrapings were made of the colon. Total RNA was isolated and subjected to gene expression profiling.

first: Wilma

last: Steegenga

first: Mark

last: Boekschoten

first: Nicole

last: de Wit

first: Noortje

last: IJssennagger

first: Shohreh

last: Keshtkar


title: Structural, functional and molecular analysis of the effects of aging in the small intestine and colon of C57BL/6J mice

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

overall_design: Refer to individual Series


title: Human-specific patterns of gene expression in the brain (Arrays)

city: Dallas

first: Genevieve

last: Konopka

state: TX

address: 5323 Harry Hines Blvd.

department: Neuroscience

institute: UT Southwestern Medical Center

summary: We identified human-specific gene expression patterns in the brain by comparing expression with chimpanzee and rhesus macaque

sample_organism:
Macaca mulatta
Pan troglodytes
Homo sapiens

platform_organism:
Macaca mulatta
Homo sapiens

overall_design: Comparative gene expression in human, chimpanzee, and rhesus macaque brain

first: Fying

last: Gao

first: Daniel

last: Geschwind


title: Expression data from REST knock-out versus REST wild type cells during in vitro neurogenesis

city: Basel

first: Dirk

last: Schuebeler

address: Fabrikstrasse 24

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

summary: While changes in chromatin are integral to transcriptional reprogramming during cellular differentiation, it is currently unclear how chromatin modifications are targeted to specific loci. We developed a computational model on the premise that transcription factors (TFs) direct dynamic chromatin changes during cell fate decisions. When applied to a neurogenesis paradigm, this approach predicted the TF REST as a determinant of gain of Polycomb-mediated H3K27me3 in neuronal progenitor cells. We prove this prediction experimentally by showing that the absence of REST causes loss of H3K27me3 at target promoters in trans at the same cellular state. Moreover, promoter fragments containing a REST binding site are sufficient to recruit H3K27me3 in cis, while deletion of their REST site results in loss of H3K27me3. These findings illustrate that computational modeling can systematically identify TFs that regulate chromatin dynamics genome-wide. Local determination of Polycomb activity by REST exemplifies such TF based regulation of chromatin.

overall_design: Expression profiling of REST knock-out (RESTko) versus REST wildtype (RESTwt) or REST heterozygous knock-out (RESThet) cells at three stages of in vitro neuronal differentiation.  RESTko and RESTwt/RESThet embryonic stem (ES) cells were differentiated to terminal neurons (TN) via a defined neuronal progenitor (NP) state. Three biological replicates (suffixes a to c).

first: Anne

last: Schoeler


title: Structural, functional and molecular analysis of the effects of aging in the small intestine and colon of C57BL/6J mice [Small Intestine data]

overall_design: Young (4 months) and old (21 months) C57BL/6J mice were fed a low-fat (10E%) diet or high-fat (45%E) diet for 2 weeks. After the diet intervention period, the animals were killed and scrapings were made of the proximal, middle and distal part of the small intestine. Total RNA was isolated, pooled and subjected to gene expression profiling.


title: Effects of H2be ectopic over-expression on gene expression in the main olfactory epithelium (MOE) of 5-week old mice.

status: Public on Sep 01 2012

first: Stephen

middle: W.

last: Santoro

address: 16 Divinity Ave.

department: Molecular and Cellular Biology

institute: Harvard University

summary:
We have identified a replication-independent histone variant, Hist2h2be (referred to herein as H2be), which is expressed exclusively by olfactory chemosensory neurons. Levels of H2BE are heterogeneous among olfactory neurons, but stereotyped according to the identity of the co-expressed olfactory receptor (OR). Gain- and loss-of-function experiments demonstrate that changes in H2be expression affect olfactory function and OR representation in the adult olfactory epithelium. We show that H2BE expression is reduced by sensory activity and that it promotes neuronal cell death, such that inactive olfactory neurons display higher levels of the variant and shorter life spans. Post-translational modifications (PTMs) of H2BE differ from those of the canonical H2B, consistent with a role for H2BE in altering transcription. We propose a physiological function for H2be in modulating olfactory neuron population dynamics to adapt the OR repertoire to the environment.
The objective of generating this dataset was to analyze the effects of the ectopic over-expression of H2be (expressed from an Omp-promoter-driven transgene and tagged with a FLAG epitope) on gene expression in the main olfactory epithelium of 5-week old mice.

overall_design: This dataset compares gene expression in wild type and H2be-GF main olfactory epithelium (MOE) samples. There are 6 replicates for WT and 4 replicates for H2be-GF (equal mixture of males and females).

middle: W

first: Catherine

last: Dulac


title: Effects of H2be loss of function on gene expression changes in the main olfactory epithelium (MOE) as a result of activity deprivation through unilateral naris occlusion (UNO).

summary:
We have identified a replication-independent histone variant, Hist2h2be (referred to herein as H2be), which is expressed exclusively by olfactory chemosensory neurons. Levels of H2BE are heterogeneous among olfactory neurons, but stereotyped according to the identity of the co-expressed olfactory receptor (OR). Gain- and loss-of-function experiments demonstrate that changes in H2be expression affect olfactory function and OR representation in the adult olfactory epithelium. We show that H2BE expression is reduced by sensory activity and that it promotes neuronal cell death, such that inactive olfactory neurons display higher levels of the variant and shorter life spans. Post-translational modifications (PTMs) of H2BE differ from those of the canonical H2B, consistent with a role for H2BE in altering transcription. We propose a physiological function for H2be in modulating olfactory neuron population dynamics to adapt the OR repertoire to the environment.
The objective of generating this dataset was to analyze the effects of H2be loss of function on gene expression changes in the main olfactory epithelium as a result of activity deprivation through unilateral naris occlusion (UNO).

overall_design: This dataset compares gene expression in wild type and H2be-KO main olfactory epithelium (MOE) samples from 5-week old mice that were subjected to unilateral naris occlusion (UNO) for 3 weeks starting from 2 weeks of age. Samples consist of MOE halves that were dissected and carefully removed from the medial bone. Each sample contains tissue from 2 mice (1 female and 1 male). There are three replicates for each genotype (H2be-KO or WT) and UNO side (open or closed) combination.


title: Expression data from glucocorticoid-treated ALL (CCRF-CEM-C7-14 cells)

city: Manchester

first: Daphne

last: Chen

address: Oxford Road

country: United Kingdom

institute: University of Manchester

summary:
The beneficial effects of glucocorticoids (GCs) in acute lymphoblastic leukemia (ALL) are based on their ability to induce apoptosis. Omics technologies such as DNA microarray analysis are widely used to study the changes in gene expression and have been successfully implemented in biomarker identification. In addition, time series studies of gene expression enable the identification of correlations between kinetic profiles of glucocorticoid receptor (GR) target genes and diverse modes of transcriptional regulation. This study presents a genome-wide microarray analysis of both our and published Affymetrix HG-U133 Plus 2.0 data in GCs-sensitive and -resistant ALL. GCs-sensitive CCRF-CEM-C7-14 cells were treated with dexamethasone at three time points (0 h, 2 h and 10 h). The treated samples were then compared to the control (0 h).
The published data used were as follows:
GSE2677:
GSM51674: B-ALL-24-24h
GSM51675: B-ALL-24-6h
GSM51676: B-ALL-24-0h
GSM51680: B-ALL-17-24h
GSM51681: B-ALL-17-8h
GSM51682: B-ALL-17-0h
GSM51677: B-ALL-13-24h
GSM51678: B-ALL-13-8h
GSM51679: B-ALL-13-0h
GSM51683: B-ALL-31-24h
GSM51684: B-ALL-31-6h
GSM51685: B-ALL-31-0h
GSM51686: B-ALL-32-24h
GSM51687: B-ALL-32-6h
GSM51688: B-ALL-32-0h
GSM51689: B-ALL-33-24h
GSM51690: B-ALL-33-6h
GSM51691: B-ALL-33-0h
GSM51692: B-ALL-37-24h
GSM51693: B-ALL-37-6h
GSM51694: B-ALL-37-0h
GSM51695: B-ALL-38-24h
GSM51696: B-ALL-38-6h
GSM51697: B-ALL-38-0h
GSM51698: B-ALL-40-24h
GSM51699: B-ALL-40-6h
GSM51700: B-ALL-40-0h
GSM51701: B-ALL-43-24h
GSM51702: B-ALL-43-6h
GSM51703: B-ALL-43-0h
GSM51707: T-ALL-25-24h
GSM51708: T-ALL-25-6h
GSM51709: T-ALL-25-0h
GSM51704: T-ALL-20-24h
GSM51705: T-ALL-20-8h
GSM51706: T-ALL-20-0h
GSM51710: T-ALL-2-24h
GSM51711: T-ALL-2-8h
GSM51712: T-ALL-2-0h
GSE2842
GSM60545: S-Line-PreB-6h-EtOH
GSM60546: S-Line-PreB-6h-GC
GSM60547: S-Line-PreB-24h-GC
GSM60542: S-Line-C7H2-6h-EtOH
GSM60543: S-Line-C7H2-6h-GC
GSM60544: S-Line-C7H2-24h-GC
GSM60560: R-Line-CEMC1-6h-EtOH
GSM60561: R-Line-CEMC1-6h-GC
GSM60562: R-Line-CEMC1-24h-GC
GSM60564: R-Line-C7R1-6h-EtOH
GSM60566: R-Line-C7R1-6h-GC
GSM60576: R-Line-C7R1dim-low-6h-EtOH
GSM60578: R-Line-C7R1dim-low-6h-GC
GSM60579: R-Line-C7R1dim-low-24h-GC
GSM60581: R-Line-PreB-6h-EtOH
GSM60583: R-Line-PreB-6h-GC
GSM60584: R-Line-PreB-24h-EtOH
GSM60586: R-Line-PreB-24h-GC
GSM60548: C-Line-CEMC1-ratGR-6h-EtOH
GSM60549: C-Line-CEMC1-ratGR-6h-GC
GSM60550: C-Line-CEMC1-ratGR-24h-GC
GSM60551: C-Line-C7R1dim-high-6h-EtOH
GSM60552: C-Line-C7R1dim-high-6h-GC
GSM60553: C-Line-C7R1dim-high-24h-GC

overall_design: Dexamethasone-treated CCRF-CEM-C7-14 samples were divided into 3 groups based on time points: the untreated control (0 h), 2 h and 10 h.


title: Expression data from glucocorticoid-treated ALL


title: The activity-dependent histone variant H2BE modulates the life span of olfactory neurons

type: Genome binding/occupancy profiling by genome tiling array


title: Effects of H2be loss of function on gene expression in the main olfactory epithelium (MOE) of 6-month old mice.

summary:
We have identified a replication-independent histone variant, Hist2h2be (referred to herein as H2be), which is expressed exclusively by olfactory chemosensory neurons. Levels of H2BE are heterogeneous among olfactory neurons, but stereotyped according to the identity of the co-expressed olfactory receptor (OR). Gain- and loss-of-function experiments demonstrate that changes in H2be expression affect olfactory function and OR representation in the adult olfactory epithelium. We show that H2BE expression is reduced by sensory activity and that it promotes neuronal cell death, such that inactive olfactory neurons display higher levels of the variant and shorter life spans. Post-translational modifications (PTMs) of H2BE differ from those of the canonical H2B, consistent with a role for H2BE in altering transcription. We propose a physiological function for H2be in modulating olfactory neuron population dynamics to adapt the OR repertoire to the environment.
The objective of generating this dataset was to analyze the effects of H2be loss of function on gene expression in the main olfactory epithelium of 6-month old mice.

overall_design: This dataset compares gene expression in wild type and H2be-KO main olfactory epithelium (MOE) samples. There are six replicates for each genotype (equal mixture of males and females).


title: Expression data from AJ and C3H mouse lungs exposed to NNK

city: Irvine

first: William

last: Gordon

address: 839 Health sciences way

department: Medicine

institute: University of CA Irvine

summary:
Identification of genes associated with exposure to the carcinogen Nitrosamine (NNK) in mouse lungs of susceptible (AJ) and resistant (C3H) strains.
Microarrays were used to capture all of the up and down regulated genes in two strains of mice.

overall_design: Lungs were excised and analyzed between 3-12 weeks after exposure to NNK before mature tumors had formed

first: Bogi

last: Andersen

first: Valentin

last: Galitovskiy

first: Sergei

last: Grando


title: Expression data from glucocorticoid-treated ALL (BCR-ABL patients)

overall_design: Arrays were obtained from 10 children with Philadelphia positive (Ph+) ALL treated uniformly. They were categorized as good risk if the marrow had <25% blasts after 8 days of therapy without imatinib and poor risk if the blast count was >25%. During this time they received 8 days of Dex and 1 dose each of anthracycline, vincristine and L-Asparaginase, according to the EsphALL protocol. The samples were analysed at day 17 and compared to the untreated (day 0) samples.

first: Saha

last: Vaskar


title: Gene expression data of parotid tissue from Primary Sjogren’s Syndrome and controls

city: Los Angeles

first: Steve

last: Horvath

address: 695 Charles E. Young Drive South, Box 708822

department: Human Genetics

institute: University of California, Los Angeles

summary: Primary Sjögren’s syndrome (pSS) is a chronic autoimmune disease with complex etiopathogenesis. Here we use Affymetrix U133 plus 2.0 microarray gene expression data from human parotid tissue. Parotid gland tissues were harvested from 17 pSS and 14 14 non-pSS sicca patients and 18 controls. The data were used in the following article:  Nazmul-Hossain ANM, Pollard RPE, Kroese FGM, Vissink A, Kallenberg CGM, Spijkervet FKL, Bootsma H, Michie SA, Gorr SU, Peck AB, Cai C, Zhou H, Horvath S, Wong DTW (2012) Systems Analysis of Primary Sjögren’s Syndrome Pathogenesis in Salivary Glands: Comparative Pathways and Molecular Events in Humans and a Mouse Model.

overall_design: Parotid gland tissues were harvested from 17 pSS and 14 non-pSS sicca patients and 18 controls.

first: David

last: Wong


title: Transcriptional Signatures as a Disease-Specific and Predictive Inflammatory Biomarker for Type 1 Diabetes [Pneu_S3S24_10Pneu_4HC]

city: Milwaukee

first: Martin

last: Hessner

state: WI

address: 8701 Watertown Plank Road

department: Pediatrics

institute: Medical College of Wisconsin

summary: The complex milieu of inflammatory mediators associated with many diseases is often too dilute to directly measure in the periphery, necessitating development of more sensitive measurements suitable for mechanistic studies, earlier diagnosis, guiding selection of therapy, and monitoring interventions.  Previously, we determined that plasma of recent-onset (RO) Type 1 diabetes (T1D) patients induce a proinflammatory transcriptional signature in fresh peripheral blood mononuclear cells (PBMC) relative to that of unrelated healthy controls (HC).  Here, using an optimized cryopreserved PBMC-based protocol, we compared the signature found between unrelated healthy controls and patients with bacterial pneumonia.

overall_design: UPN727 cells were stimulated with either plasma from unrelated healthy controls (n=18) or plasma from patients with bacterial pneumonia (n=10). Gene expression analysis was perfromed in order to evaluate the transcriptional signature associated with bacterial pneumonia.

first: Hara

last: Levy

first: Xujing

last: Wang

first: Mary

last: Kaldunski

first: Shuang

last: Jia

first: Joanna

last: Kramer

first: Scott

last: Pavletich

first: Melissa

last: Reske

first: Mike

last: Quasney

middle: K

last: Dahmer

first: Jack

last: Gorski


title: Gene expression profiles of induced pluripotent stem cells from centenarians

city: Tokyo

first: Takuya

last: Yagi

address: 35-Shinanomachi Shinjuku-ku

country: Japan

institute: Keio University

summary: We established induced pluripotent stem cells (iPSC) from centrenarians by retroviral transduction of primary human fibroblasts. To show the similarity between 201B7 iPSC and 100-1 #16 iPSC (induced pluripotent stem cells from centenarian),  this experiment was designed.

overall_design: Undifferentiated  201B7 iPSC, and 100-1 #16 iPSCs were collected. Then, they were applied in this experiment.

first: Daisuke

last: Ito


title: Gene expression profiling of miR-regulated genes in proliferating C2C12

city: Milan

first: Gabriele

last: Bucci

address: Via Olgettina 60

department: Center of Translational Genomics and Bioinformatics

country: Italy

institute: Università vita e Salute Ospedale San Raffaele

summary: We used microarrays to detail the global programme of gene expression upon the over-expression of seven different differentiation-associated, E1A-regulated microRNAs.

overall_design: seven different microRNAs (miR-1, miR-34a, miR-22, miR-365, miR-29a, miR-145 and Let-7b) and a negative control (AllStar, Qiagen) were over-expressed at 50nM for 36hrs in proliferating myoblasts. Three independent biological experiments were performed.

first: Matteo

last: Marzi

first: Davide

last: Cittaro

first: Francesco

last: Nicassio


title: Transcriptional Signatures as a Disease-Specific and Predictive Inflammatory Biomarker for Type 1 Diabetes [H1N1_S5_5Pre_5D0]

last: Hessner

summary: The complex milieu of inflammatory mediators associated with many diseases is often too dilute to directly measure in the periphery, necessitating development of more sensitive measurements suitable for mechanistic studies, earlier diagnosis, guiding selection of therapy, and monitoring interventions.  Previously we determined that plasma of recent-onset (RO) Type 1 diabetes (T1D) patients induce a proinflammatory transcriptional signature in fresh peripheral blood mononuclear cells (PBMC) relative to that of unrelated healthy controls (HC).  Here, using an optimized cryopreserved PBMC-based protocol, we compared the signature found in pre H1N1 samples to the signature associated with active H1N1 flu.

overall_design: UPN727 cells were stimulated with plasma that was collected pre-H1N1 (healthy) or during active-H1N1 from 5 different individuals. Gene expression analysis was perfromed in order to evaluate the transcriptional signature associated with the H1N1 influenza virus.


title: Expression data from infected with Neisseria gonorrhoeae (GC) and uninfected bone marrow derived macrophages from wild type (C67BL/6) and Nod2 knock out mice

first: Nikolaos

last: Mavrogiorgos

address: 650 Albany street, EBRC building, room 610

institute: Boston University

summary: In this dataset we include the data obtained from 3 hour stimulation with Neisseria gonorrhoeae (GC) of bone marrow macrophages(BMDM) from wild type (C57BL/6) and Nod2 knock out mice (in C57BL/6 background).

overall_design:
Murine BMDM from C57BL/6 mice or NOD2 deficient mice on C57BL/6 background, plated in 6 well plates, were infected with GC at MOI 10:1 or left uninfected. At 3 hrs after infection, cells lysates were made and RNA was isolated. All conditions were done in triplicates(3 wells per condition. The experiment was done once). Whole genome microarray analysis was carried out using the Affymetrix GeneChip Gene 1.0 ST Array System. A 2-way ANOVA was applied to analyze the effects of genotype and infection by GC as well as the interaction between genotype and infection by GC.  Raw affinity data was normalized using a Robust Multichip Analysis (RMA) method at probe level
Microarray Core, Boston University Medical Center

first: N

first: R

last: Ingalls


title: Genes regulated by has-mir-31 in glioma cell line

city: HangZhou

first: Biaoyang

last: Lin

address: 866 Yu Hang Tang Road Zi Jin Gang Campus Zhejiang University.

department: ZCNI

country: China

institute: ZheJiang University

summary: Overexpression of miR-31 inhibits the migration and invasion ability of glioma cell. We sought to obtain the genes regulated by mir-31 in glioma cell line.

overall_design: The gene expression of U251-mir-31 (U251 over expressing mir-31) and U251-control. U251-Control and U251-mir-31 cells were cultured in DMEM cell culture media for RNA extraction and hybridization on Affymetrix.GeneChip.HG-U133_Plus_2.

first: Dasong

last: Hua


title: Transcriptional Signatures as a Disease-Specific and Predictive Inflammatory Biomarker for Type 1 Diabetes [CF_S1S3_5Auto_20CF_10HC]

first: Martin

summary: The complex milieu of inflammatory mediators associated with many diseases is often too dilute to directly measure in the periphery, necessitating development of more sensitive measurements suitable for mechanistic studies, earlier diagnosis, guiding selection of therapy, and monitoring interventions.  Previously, we determined that plasma of recent-onset (RO) Type 1 diabetes (T1D) patients induce a proinflammatory transcriptional signature in fresh peripheral blood mononuclear cells (PBMC) relative to that of unrelated healthy controls (HC).  Here, using an optimized cryopreserved PBMC-based protocol, we compared the signature found between unrelated healthy controls and non-diabetic cystic fibrosis patients possessing Pseudomonas aeruginosa pulmonary tract infection.

overall_design: UPN727 cells were stimulated with autologous plasma (n=5), unrelated healthy control plasma (n=24), or plasma from patients with cystic fibrosis possessing Psuedomonas aeruginosa pulmonary tract infection (n=20). Gene expression analysis was perfromed in order to evaluate the transcriptional signature associated with cystic fibrosis.

first: Hara

last: Levy

first: Xujing

last: Wang

first: Mary

last: Kaldunski

first: Shuang

last: Jia

last: Kramer


title: Expression data of Human Gastric Adenocarcinoma

city: São Paulo

first: Fatima

middle: Solange

last: Pasini

state: São Paulo

address: Av. Dr. Arnaldo, 455 sala 4115

department: Departamento de Radiologia e Oncologia

country: Brazil

institute: Faculdade de Medicina da USP

summary:
Anatomical staging is a critical, although imperfect, instrument to assess gastric cancer prognosis and define indication for surgery and adjuvant therapy. Despite recent advances, treatment results, as a whole, remain less than satisfactory. Thus, biomarkers are sorely needed to improve risk categorization and define new molecular targets for therapy.
We used microarrays to identify genes differentially expressed according to prognosis of the patients.

overall_design: A cohort of 15 patients was prospectively identified with a histological diagnosis of gastric adenocarcinoma, submitted to surgery with curative intent. Two prognostic patient groups were defined, according to overall survival (short x long), with a 24 month cut-off. These groups were matched by known prognostic factors: TNM staging, histological subtype (intestinal/diffuse) and gender.

first: Rosimeire

last: Roela

first: Roger

last: Chammas


title: Expression data of mouse mucinous lung tumors

status: Public on Aug 31 2012

city: Cincinnati

first: Yutaka

last: Maeda

state: OH

address: 3333 Burnet Avenue

department: Pulmonary Biology

institute: Cincinnati Children's Hospital

summary:
Transgenic mice (Scgb1a1-rtTA/[tetO]-KRAS.G12D/Nkx2-1+/-) develop mucinous lung tumors.  Gene expression analysis was performed using mRNAs from the whole lungs of the mice compared to that of the control mice.
We used microarrays to detail the global program of gene expression underlying development of mucinous lung tumors and identified distinct classes of up-regulated genes during this process.

overall_design: mRNAs were isolated from the whole lungs of the transgenic mice (Scgb1a1-rtTA/[tetO]-KRAS.G12D/Nkx2-1+/-) after 2 months doxycycline administration and hybridized on Affymetrix microarrays.  We sought to identify genes induced in mucinous lung tumors.

first: Jeffrey

last: Whitsett


title: Expression data from post natal mouse aortic heart valves treated with all-trans retinoic acid or a retinoic acid receptor antagonist (LE540) relative to DMSO treated controls

first: Joy

last: Lincoln

summary:
Our lab has previously shown that treatment of murine heart valve explants with ATRA promotes calcification in vitro. In order to fully explore gene expression changes in the valve in response to ATRA or LE540, a high throughput microarray was performed.
In this data set, we include expression data from dissected murine post natal aortic valve explants treated with ATRA or DMSO as a vehicle control. These data are used to obtain 432 probe sets that are differentially expressed in response to ATRA treatment, with 118 being downregulated and 314 increased.

overall_design: A total of 9 samples were analyzed; 3 DMSO treated controls, 3 LE540 and 3 ATRA treated experimental samples. Differential expression of probe sets were ranked based on false discovery rate (<0.1) and fold change (>2).

first: Danielle

last: Huk

first: Harriet

last: Hammond


title: Expression data from normal human fibroblasts expressing prelamin A or progerin, untreated or treated with farnesyltransferase inhibitor (FTI)

first: Lucio

last: Comai

address: 2250 Alcazar Street

institute: University of Southern California

summary: We compared the transcriptomes of isogenic diploid fibroblasts expressing progerin or elevated levels of wild-type prelamin A with that of wild-type fibroblasts. We subsequently used the reversion towards normal of two phenotypes, reduced cell growth and dismorphic nuclei, by treatment with farnesyltransferase inhibitor (FTI) or overexpression of ZMPSTE24, as a filtering strategy to identify genes linked to the onset of these two phenotypes.

overall_design: We carried out microarray analyses of gene expression profiling in isogenic fibroblasts lines to identify the subset of genes whose expression patterns are strongly altered upon expression of progerin or elevated levels of wild-type lamin A. A filtering strategy was then used to identify potential key effectors. We searched for genes whose expression was reverted towards normal by treatment  with farnesyl transferase inibitors (FTI) in both cell lines for 48 hours,  or by overexpression of ZMPSTE24 in cells with elevated levels of prelamin A, conditions that improve cell proliferation and leads to a significant decrease in nuclear membrane abnormalities.

first: Jose

last: Candelario


title: Transcriptional Signatures as a Disease-Specific and Predictive Inflammatory Biomarker for Type 1 Diabetes

last: Hessner

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

overall_design: Refer to individual Series


title: Gene expression profiling of microdissected HRS cells is correlated with primary treatment outcome

city: Vancouver

first: Christian

last: Steidl

state: BC

address: 675 West 10th Avenue

department: Pathology

country: Canada

institute: BC Cancer Agency

summary: Hodgkin lymphoma is derived from germinal center / post-germinal center B cells.

overall_design: Gene expression profilies of micodissected Hodkin Reed Sternberg cells (n=29) were dichotomized into primary treatment failure (n=14) and primary treatment succeses (n=15). Treament failure was defined as refractory disease or progression at any time after ABVD chemotherapy.


title: Gene expression profiling of Hodgkin lymphoma cell lines

overall_design: Gene expression profilies of the Hodgkin lymphoma cell lines were compared to 5 samples of CD77+ centroblasts derived from reactive tonsils


title: Spheroid model system

city: Uppsala

first: Mårten

last: Fryknäs

address: Akademiska sjh ingång 61

department: Medical sciencies

institute: Uppsala university

summary: Microarray based mRNA profiling was used to charactarize and compare the gene expression in cells grown as monolayer or spheroids.

first: Marten

last: Fryknas


title: Transcriptome Analysis of Exercise Ancestry

status: Public on Aug 30 2012

city: College Park

first: Stephen

last: Roth

state: MD

address: 2309 SPH Building

department: Kinesiology

institute: University of Maryland

summary:
Transcriptome analysis of gastrocnemius muscle RNA samples from exercise and sedentary ancestries
Early life and pre-conception environmental stimuli can affect adult health-related phenotypes. Exercise training is an environmental stimulus affecting many systems throughout the body and appears to alter offspring phenotypes. The aim of this study was to examine the influence of parental exercise training, or “exercise ancestry,” on morphological and metabolic phenotypes in multiple generations of mouse offspring. F0 C57BL/6 mice were exposed to voluntary exercise or sedentary lifestyle and bred with like-exposed mates to produce an F1 generation. F1 mice of both ancestries were sedentary and sacrificed at 8 wk or bred with littermates to produce an F2 generation, which was also sedentary and sacrificed at 8 wk. Small, but broad generation- and sex-specific effects of exercise ancestry were observed for body mass, fat and muscle mass, serum insulin, glucose tolerance, and muscle gene expression. F1 EX females were heavier than F1 SED females, but F1 SED females had higher absolute tibialis anterior and omental fat masses. Serum insulin was lower in F1 SED females compared to F1 EX females. F2 EX females had impaired glucose tolerance compared to F2 SED females. Analysis of skeletal muscle mRNA levels revealed several generation- and sex-specific differences in mRNA levels for multiple genes, especially those related to metabolic genes (e.g., F1 EX males had lower mRNA levels of Hk2, Ppard, Ppargc1α, Adipoq, and Scd1 than F1 SED males). These results provide preliminary evidence that parental exercise training can influence health-related phenotypes in mouse offspring.

overall_design: We analyzed RNA from 10 males each from exercise and sedentary ancestries over 2 generations of offspring (F1 and F2)

first: Lisa

middle: M

last: Guth

first: Andrew

last: Ludlow

first: Sarah

last: Witkowski

first: Mallory

last: Marshall

first: Laila

middle: C

last: Lima

last: Venezia

first: Tao

last: Xiao

first: Mei-Ling

last: Lee

first: Espen

last: Spangenburg


title: The PARN deadenylase targets a discrete set of mRNAs for decay and regulates cell motility in mouse myoblasts

city: Newark

first: Ju Youn

state: NJ

address: 185 South Orange Ave. MSB-E501

department: Biochemistry

institute: UMDNJ-New Jersey Medical School

summary: Almost all cellular mRNAs terminate in a 3’ poly(A) tail, the removal of which can induce both translational silencing and mRNA decay.  Mammalian cells encode many poly(A)-specific exoribonucleases but their individual roles are poorly understood.  Here, we undertook an analysis of the role of PARN deadenylase in mouse myoblasts using global measurements of mRNA decay rates.  Our results reveal that a discrete set of mRNAs exhibit altered mRNA decay as a result of PARN depletion and that stabilization is associated with increased poly(A) tail length and translation.  We determined that stabilization of mRNAs does not generally result in their increased abundance supporting the idea that mRNA decay is coupled to transcription.   Importantly, PARN knockdown has wide ranging effects on gene expression that specifically impact the extracellular matrix and cell migration.  Finally, although PARN has its own unique target transcripts it also influences some genes whose expression is modulated by other deadenylases.

overall_design:
In order to investigate the role of PARN deadenyl on mRNA decay in mouse muscle cells , C2C12 cells were transfected by shRNA knockdown of PARN and treated with actinomycin D to inhibit transcription. Total RNA was isolated from three replicates at 0, 15, 30, 60, 120 and 240 minutes.
The CTRL cell line stably transfected with LKO1 vector was described previously (GSE21233).

first: Jerome

first: Ju-Youn

first: Jarrett

last: Trembly

first: Jeffrey

last: Wilusz

first: Bin

last: Tian

first: Carol


title: Expression data from Sip1 cKO and control mice spinal cord

first: Qing

middle: Richard

last: Lu

address: 5323 Harry Hines Boulevard

institute: UT southwestern medical center

summary: Myelination by oligodendrocytes in the central nervous system (CNS) is essential for proper brain function, yet the molecular determinants that control this process remain poorly understood. The basic helix-loop-helix transcription factors Olig1 and Olig2 promote myelination, whereas bone morphogenetic protein (BMP) and Wnt/β-catenin signaling inhibit myelination. Here we show that these opposing regulators of myelination are functionally linked by the Olig1/2 common target Smad-interacting protein-1 (Sip1). We demonstrate that Sip1 is an essential modulator of CNS myelination. Sip1 represses differentiation inhibitory signals by antagonizing BMP receptor-activated Smad activity while activating crucial oligodendrocyte-promoting factors. Importantly, a key Sip1-activated target, Smad7, is required for oligodendrocyte differentiation and partially rescues differentiation defects caused by Sip1 loss. Smad7 promotes myelination by blocking the BMP- and β-catenin-negative regulatory pathways. Thus, our findings reveal that Sip1-mediated antagonism of inhibitory signaling is critical for promoting CNS myelination and point to new mediators for myelin repair.

overall_design: We carried out microarray profiling analysis in the Sip1 conditional KO (cKO) mouse spinal cord to detail the change of global gene expression. Sip1 c/c;Olig1-Cre mouse spinal cord was collected at P14 for RNA extraction and Affymetrix microarray analysis. Sip1 c/+;Olig1-Cre littermate spinal cord was used as the control.


title: Gene expression profiles from the hepatocellular carcinoma (HCC) tissues

city: Kwei-Shan Tao-Yuan

first: Yi

last: Huang

address: 259 Wen-Hwa 1st Road

country: Taiwan

institute: Chang Guang University

summary: To explore the molecular functions targeted by these miRNAs, we classified genes differentially expressed in clinical HCC samples into six functional clusters based on their functional similarity.

overall_design: 3-paired HCC tissue samples and adjacent normal liver tissues were obtained from patients undergoing surgery and were frozen immediately after surgical resection.

first: Shu-Jen

last: Chen


title: Nanog-dependent feedback loops regulate murine embryonic stem cell heterogeneity

city: Barcelona

first: Ana

last: Sevilla

state: Barcelona

address: Avda Diagonal 643. Edificio Malagef 4rd Floor, Faculty of Biology

department: Departamento de Biologia Celular, Fisiologia e Inmunologia

country: Spain

institute: Universidad de Barcelona

summary: A number of key regulators of mouse embryonic stem (ES) cell identity, including the transcription factor Nanog, show strong expression fluctuations at the single cell level. The molecular basis for these fluctuations is unknown. Here we used a genetic complementation strategy to investigate expression changes during transient periods of Nanog downregulation. Employing an integrated approach, that includes high-throughput single cell transcriptional profiling and mathematical modelling, we found that early molecular changes subsequent to Nanog loss are stochastic and reversible. However, analysis also revealed that Nanog loss severely compromises the self-sustaining feedback structure of the ES cell regulatory network. Consequently, these nascent changes soon become consolidated to committed fate decisions in the prolonged absence of Nanog. Consistent with this, we found that exogenous regulation of Nanog-dependent feedback control mechanisms produced more a homogeneous ES cell population. Taken together our results indicate that Nanog-dependent feedback loops play a role in controlling both ES cell fate decisions and population variability.

overall_design:
Total of 30 samples, 10 conditions in triplicates; Cell samples were harvested at day0 (Dox present, Nanog expressing, NgR day0 +Dox), and at days 1,3 and 5 days after dox withdrawal (NgR day1 -Dox, NgR day3 -Dox and NgR day5 -Dox respectively). Additionally, at each time-point a set of samples was further treated with a twelve-hour pulse of dox before being harvested (NgR day1+ 12h Dox, NgR day3+12h Dox and NgR day5+12h Dox) and compared with untreated control samples harvested at the same time (NgR day1- 12h Dox, NgR day3-12h Dox and NgR day5-12h Dox) . All time points were performed in triplicates. We performed Affymetrix GeneChip® Mouse Gene 1.0 ST arrays analyses of mouse embryonic stem cell gene expression profiles at each time point.
BD MacArthur and A Sevilla contributed equally to this study

first: Ben

middle: D

last: MacArthur

first: Michel

last: Lenz

first: Franz-Josef

last: Müller

first: Berhard

last: Schuldt

first: Andreas

middle: A

last: Schuppert

first: Sonya

last: Ridden

first: Patrick

last: Stumpf

first: Miguel

last: Fidalgo

first: Avi

last: Ma’ayan

first: Jianlong

last: Wang

first: Ihor

last: Lemischka


title: Stabilization of OCT4 synthetic mRNA in adult human skin cells using small molecules

status: Public on Aug 29 2012

city: Beaverton

first: James

middle: Anthony

last: Byrne

state: OR

address: 505 NW 185th Ave

department: Reproductive Sciences

institute: ONPRC

summary: The OCT4 transcription factor is involved in many cellular processes, including development, reprogramming, maintaining pluripotency and differentiation. Synthetic OCT4 mRNA was recently used (in conjunction with other reprogramming factors) to generate human induced pluripotent stem cells. Here, we discovered that BAY 11-7082 (BAY11) could significantly increase the expression of OCT4 following transfection of synthetic mRNA (synRNA) into adult human skin cells. Importantly, the increased levels of OCT4 resulted in significantly increased expression of genes downstream of OCT4, including the previously identified SPP1, DUSP4 and GADD45G. We also identified a novel OCT4 downstream target gene SLC16A9 which demonstrated significantly increased expression following elevation of OCT4 levels. This small molecule-based stabilization of synthetic mRNA expression may have multiple applications for future cell-based research and therapeutics.

overall_design: 4 samples (untreated H9 hESCs, untreated HUF1 skin fibroblasts, HUF1 cells treated with OCT4 synthetic mRNA, HUF1 cells treated with OCT4 synthetic mRNA and BAY11) were analyzed with 2 biological replicates per sample.


title: Expression data regulated by hMOF in non-small cell lung cancer (NSCLC) cell lines

city: Beijing

first: Lei

last: Zhao

address: School of Medicine,Tsinghua University

institute: Tsinghua University

summary: A549 and H1299 cell lines were transfected with hMOF specific siRNA or control siRNA, and Affymetrix oligonucleotide microarray was conducted to systematically determine downstream targets regulated by hMOF.

overall_design: Two NSCLC cell lines (four samples) transfected with hMOF specific siRNA or control siRNA

first: Da-liang


title: Molecular signature of brain resident memory CD8+ T cells

city: Parkville

first: Gordon

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

institute: Walter and Eliza Hall Institute of Medical Research

summary: Tissue resident memory (Trm) represent a newly described memory T cell population. We have previously characterized a population of Trm that persists within the brain following acute virus infection. Although capable of providing marked protection against a subsequent local challenge, brain Trm do not undergo recall expansion following dissociation from the tissue. Furthermore, these Trm do not depend on the same survival factors as the circulating memory T cell pool as assessed either in vivo or in vitro. To gain greater insight into this population of cells we compared the gene-expression profiles of Trm isolated from the brain to circulating memory T cells isolated from the spleen following an acute virus infection. Trm displayed altered expression of genes involved in chemotaxis, expressed a distinct set of transcription factors and overexpressed several inhibitory receptors. Cumulatively, these data indicates that Trm are a distinct memory T cell population disconnected from the circulating memory T cell pool and displaying a unique molecular signature which likely results in optimal survival and function within their local environment.

overall_design: 13 samples were analyzed: 5 replicates of memory OT-I CD8+.CD103-  T cells isolated from the spleen of mice on day 20 p.i. with VSV-OVA. 5 replicates of memory OT-I CD8+CD103+ T cells isolated from the brain of mice on day 20 p.i. with VSV-OVA; and 3 replicates of memory OT-I.CD8+ CD103- T cells isolated from the brain of mice on day 20 p.i. with VSV-OVA

first: Linda

last: Wakim

first: Amanda

last: Woodward-Davis

first: Ruijie

last: Liu

first: Yifang

last: Hu

first: Michael

last: Bevan


title: Guthrie card methylomics identifies temporally stable epialleles that are present at birth in humans (Methylation BeadChip)

status: Public on Aug 27 2012

city: Cambridge

first: Thomas

last: Down

address: Tennis Court Road

department: WT/CRUK Gurdon Institute

institute: University of Cambridge

summary: A major concern in common disease epigenomics is distinguishing causal from consequential epigenetic variation. One means of addressing this issue is to identify the temporal origins of epigenetic variants via longitudinal analyses. However, prospective birth-cohort studies are expensive and time-consuming. Here we report DNA methylomics of archived Guthrie cards for the retrospective longitudinal analyses of in utero-derived DNA methylation variation. We first validate two methodologies for generating comprehensive DNA methylomes from Guthrie cards. Then, using an integrated epigenomic/genomic analysis of Guthrie cards and follow-up samplings, we identify inter-individual DNA methylation variation that is present both at birth and three years later. These findings suggest that disease-relevant epigenetic variation could be detected at birth i.e. before overt clinical disease. Guthrie card methylomics offers a potentially powerful and cost-effective strategy for studying the dynamics of inter-individual epigenomic variation in a range of common human diseases.

overall_design: Bisulphite converted DNA was hybridised to the Illumina Infinium 450k Human Methylation Beadchip

first: H

last: Beyan

first: T

first: S

middle: V

last: Ramagopalan

first: K

last: Uvebrant

first: A

last: Nilsson

first: M

middle: L

last: Holland

first: C

last: Gemma

first: G

last: Giovannoni

first: B

middle: O

last: Boehm

last: Ebers

last: Lernmark

last: Cilio

first: R

last: Leslie

first: V

last: Rakyan


title: An integrated genomic and expression analysis of 7q deletion in splenic marginal zone lymphoma (Affymetrix HG-U133plus2 gene expression microarray)

first: Alan

last: Watkins

address: Addenbrooke's Hospital

summary: Splenic marginal zone lymphoma (SMZL) is an indolent B-cell lymphoproliferative disorder characterised by 7q32 deletion, but the target genes of this deletion remain unknown. In order to elucidate the genetic target of this deletion, we performed an integrative analysis of the genetic, epigenetic, transcriptomic and miRNomic data. High resolution array comparative genomic hybridization of 56 cases of SMZL delineated a minimally deleted region (2.8Mb) at 7q32, but showed no evidence of any cryptic homozygous deletion or recurrent breakpoint in this region. Integrative transcriptomic analysis confirmed significant under-expression of a number of genes in this region in cases of SMZL with deletion, several of which showed hypermethylation. In addition, a cluster of 8 miRNA in this region showed under-expression in cases with the deletion, and three (miR-182/96/183) were also significantly under-expressed (P <0.05) in SMZL relative to other lymphomas. Genomic sequencing of these miRNA and IRF5, a strong candidate gene, did not show any evidence of somatic mutation in SMZL.

overall_design: For gene expression microarrays. A total of 48 cases of SMZL (including 15 with 7q deletion) were analysed using the Affymetrix HG-U133 Plus 2.0 platform (Affymetrix, Santa Clara, California, USA). 14 SMZL and 10 FL/MCL are included in this submission. The other Samples are part of GSE35348. Arrays were performed according to the manufacturer’s instructions. Briefly, RNA was extracted from snap frozen tissues with >70% tumour cells using the RNEasy extraction kit (Qiagen) and subjected to DNAse treatment (Turbo DNAse kit, Ambion). RNA integrity was assessed using an Agilent 2100 Bioanalyzer. cDNA synthesis was carried out with 2ug RNA using the GeneChip® One-Cycle cDNA Synthesis Kit (Affymetrix), followed by in vitro transcription with biotin-labelled nucleotides using GeneChip® IVT Labeling Kit. Biotinylated cRNA was purified and hybridized to the Affymetrix HG-U133 Plus 2.0 chips in a GeneChip® Hybridisation Oven 640 at 45oC for 14 hours. The arrays were then washed and stained using the Fluidics station 450 system (Affymetrix). The arrays were scanned using the Affymetrix GeneArray® Scanner 3000. Hybridisation and labelling controls were included according to the manufacturer’s instructions, and quality control analysis of microarrays was performed to published standards.

first: Rifat

last: Hamoudi

first: Naiyan

last: Zeng

first: Qingguo

last: Yan

first: Yuanxue

last: Huang

first: Hongxiang

last: Liu

first: Jianzhong

last: Zhang

first: Esteban

last: Braggio

first: Rafael

last: Fonseca

first: Laurence

last: de Leval

first: Peter

middle: G

last: Isaacson

first: Andrew

last: Wotherspoon

first: Ellen

last: McPhail

first: Ahmet

last: Dogan

first: Ming

middle: Q

last: Du


title: Expression data from either growing IMR90 human fibroblasts or senescent IMR90 cells with Ras expression and indicated hairpins

status: Public on Aug 25 2012

city: New York

first: Ozlem

last: Aksoy

address: 415 East 68th Street

department: Watson School of Biological Sciences

institute: CSHL

summary: Oncogene-induced senescence is an anti-proliferative stress response program that acts as a fail-safe mechanism to  limit oncogenic transformation and is regulated by the retinoblastoma protein (RB) and p53 tumor suppressor  pathways. We identify the atypical E2F family member E2F7 as the only E2F transcription factor potently upregulated  during oncogene-induced senescence, a setting where it acts in response to p53 as a direct transcriptional  target. Once induced, E2F7 binds and represses a series of E2F target genes and cooperates with RB to efficiently  promote cell cycle arrest and limit oncogenic transformation. Disruption of RB triggers a further increase in E2F7,  which induces a second cell cycle checkpoint that prevents unconstrained cell division despite aberrant DNA  replication. Mechanistically, E2F7 compensates for the loss of RB in repressing mitotic E2F target genes.

overall_design: To understand the contribution of different genes, especially E2F7 to the expression profile of senescent cells, we infected human IMR90 cells with Ras and different hairpins. The infected population was selected using first with 2 ug/ml puromycin (Sigma) for 2 days, then 100 ug/ml hygromycin B (Roche) for 3 days. RNA was isolated 7 days after the puromycin selection and hybridized to Affymetrix microarrays. We tried to understand the effect of E2F7 in the transcription profile of senescent cells.

first: Agustin

last: Chicas

first: Scott

last: Lowe

first: Xiaowo

last: Wang

first: Tianying


title: Stem cell therapy of murine liver cirrhosis

status: Public on Aug 28 2012

city: Kanazawa

first: Yoshio

last: Sakai

state: Ishikawa

address: 13-1 Takara-machi

department: Department of Gastroenterology

institute: Kanazawa University

summary: Gene expression profiles of the liver and hepatic inflammatory cells in murine non-alcoholic steatohepatitis models by treatment with adipose tissue derived stem cells

overall_design: Cirrhotic C57Bl/6 female mice fed by atherogenic high fat diet for 40 weeks were treated with adipose tissue-derived stem cells twice every two weeks. Two weeks later, gene expression of the liver and intrahepatic inflammatory cells were examined by DNA microarray.

first: Akihiro

last: Seki


title: Musashi2 is required for the self-renewal and pluripotency of embryonic stem cells

city: Omaha

first: Angie

last: Rizzinio

state: NE

address: 986805 Nebraska Medical Center

department: Eppley Institute for Research in Cancer and Allied Diseases

institute: University of Nebraska Medical Center

summary:
Recent studies have shown that the RNA binding protein Musashi 2 (Msi2) plays prominent roles during development and leukemia. Additionally, in embryonic stem cells (ESC) undergoing the early stages of differentiation, Msi2 has been shown to associate with Sox2, which is required for the self-renewal of ESC. These findings led us to examine the effects of Msi2 on the behavior of ESC. Using an shRNA sequence that targets Msi2 and a scrambled shRNA sequence, we determined that knockdown of Msi2 disrupts the self-renewal of ESC and promotes their differentiation. Collectively, our findings argue that Msi2 is required to support the self-renewal and pluripotency of ESC.
We used microarrays to better understand global changes in ESC gene expression following the knockdown of the RNA-binding protein Msi2 as compared to control ESC expressing a scrambled shRNA.

overall_design: Mouse embryonic stem cells (D3) were treated with lentivirus engineered for the expression of a Msi2 targeting shRNA sequence or scrambled (control) shRNA sequence. Following selection for infected cells with puromycin, cells were subcultured at low density and allowed to grow for 4 days (see treatment protocol) before RNA was extracted. RNA was collected and analyzed one time for each of the two samples.

first: Erin

last: Wuebben

first: Sunil

last: Mallanna

first: Jesse

last: Cox

last: Rizzino


title: GPI-anchored Timp1 protein

status: Public on Aug 23 2012

city: München

first: Carsten

last: Jäckel

address: Schillerstr 42

department: Klinische Biochemie

country: Germany

institute: Klinikum der Universität München, Klinische Biochemie

summary:
Tissue inhibitor of metalloproteinase 1 (TIMP-1) controls matrix metalloproteinase (MMP) activity through 1:1 stochiometric binding. Human TIMP-1 fused to a glycosylphosphatidylinositol (GPI) anchor (TIMP-1-GPI) shifts the activity of TIMP-1 from the extracellular matrix to the cell surface. TIMP-1-GPI treated renal cell carcinoma cells (RCC) show increased apoptosis and reduced proliferation. Transcriptomic profiling and regulatory pathway mapping were used to identify potential mechanisms driving these effects. Significant changes in inhibitor of DNA binding (IDs), TGF-β1/SMAD and BMP pathways resulted from TIMP-1-GPI treatment. These events were linked to reduced TGF-β1 signaling mediated by inhibition of proteolytic processing of latent TGF-β1 by TIMP-1-GPI.
Activity of TIMP-1 from the extracellular matrix to the cell surface. TIMP-1-GPI treated renal cell carcinoma cells (RCC) show increased apoptosis and reduced proliferation. Transcriptomic profiling and regulatory pathway mapping were used to identify potential mechanisms driving these effects. Significant changes in inhibitor of DNA binding (IDs), TGF-β1/SMAD and BMP pathways resulted from TIMP-1-GPI treatment. These events were linked to reduced TGF-β1 signaling mediated by inhibition of proteolytic processing of latent TGF-β1 by TIMP-1-GPI.

overall_design: Renal cell carcinoma cells were transfected with empty vector, rhTimp1 and 2 concentrations of Timp1-GPI fusion protein

first: P

last: Nelson

first: S

last: Notohamiprodjo

first: R

last: Djafarzadeh

first: N

last: Rieth

first: M

last: Hofstetter

first: C

last: Jaeckel


title: Kruppel like factor 7 overexpression suppresses hematopoietic stem and progenitor cell function

status: Public on Aug 24 2012

city: Saint Louis

first: laura

last: schuettpelz

state: MO

address: 660 S. Euclid

institute: washington university

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

overall_design: Refer to individual Series


title: HSC expression array

summary:
Increased expression of Kruppel like factor 7 (KLF7) is an independent predictor of poor outcome in pediatric acute lymphoblastic leukemia. The contribution of KLF7 to hematopoiesis has not been previously described. Herein, we characterized the effect on murine hematopoiesis of the loss of KLF7 and enforced expression of KLF7. Long-term multilineage engraftment of Klf7-/- cells was comparable to control cells, and self-renewal, as assessed by serial transplantation, was not affected.  Enforced expression of KLF7 results in a marked suppression of myeloid progenitor cell growth and a loss of short- and long-term repopulating activity.  Interestingly, enforced expression of KLF7, while resulting in multi-lineage growth suppression that extended to hematopoietic stem cells and common lymphoid progenitors, spared T cells and enhanced the survival of early thymocytes.  RNA expression profiling of KLF7-overexpressing hematopoietic progenitors identified several potential target genes mediating these effects. Notably, the known KLF7 target Cdkn1a (p21Cip1/Waf1) was not induced by KLF7, and loss of CDKN1A does not rescue the repopulating defect. These results suggest that KLF7 is not required for normal hematopoietic stem and progenitor (HSPC) function, but increased expression, as seen in a subset of lymphoid leukemia, inhibits myeloid cell proliferation and promotes early thymocyte survival.

HSC expression array: Lin- c-Kit+ Sca-1+ CD150+ CD48- CD41- cells were sorted from wild-type C57Bl/6 mice and RNA expression analyzed. RNA expression in KLS SLAM cells.

overall_design: KLS-SLAM cells were sorted from 6-10 week old C57Bl/6 mice

first: Laura

last: Schuettpelz

first: Daniel

last: Link


summary:
Increased expression of Kruppel like factor 7 (KLF7) is an independent predictor of poor outcome in pediatric acute lymphoblastic leukemia. The contribution of KLF7 to hematopoiesis has not been previously described. Herein, we characterized the effect on murine hematopoiesis of the loss of KLF7 and enforced expression of KLF7. Long-term multilineage engraftment of Klf7-/- cells was comparable to control cells, and self-renewal, as assessed by serial transplantation, was not affected.  Enforced expression of KLF7 results in a marked suppression of myeloid progenitor cell growth and a loss of short- and long-term repopulating activity.  Interestingly, enforced expression of KLF7, while resulting in multi-lineage growth suppression that extended to hematopoietic stem cells and common lymphoid progenitors, spared T cells and enhanced the survival of early thymocytes.  RNA expression profiling of KLF7-overexpressing hematopoietic progenitors identified several potential target genes mediating these effects. Notably, the known KLF7 target Cdkn1a (p21Cip1/Waf1) was not induced by KLF7, and loss of CDKN1A does not rescue the repopulating defect. These results suggest that KLF7 is not required for normal hematopoietic stem and progenitor (HSPC) function, but increased expression, as seen in a subset of lymphoid leukemia, inhibits myeloid cell proliferation and promotes early thymocyte survival.

KLF7 overexpression in HSPCs expression array: Lin- c-Kit+ Sca-1+ cells transduced with a KLF7 expressing or control (empty vector) lentivirus. Expression profiles of KLF7 overexpressing vs controls HSPCs.

overall_design: Cells were harvested 72 hrs post-transduction to compare expression profiles of control vs KLF7 overexpressing HSPCs


title: KLF7 KO vs WT HSPC expression array

summary:
Increased expression of Kruppel like factor 7 (KLF7) is an independent predictor of poor outcome in pediatric acute lymphoblastic leukemia. The contribution of KLF7 to hematopoiesis has not been previously described. Herein, we characterized the effect on murine hematopoiesis of the loss of KLF7 and enforced expression of KLF7. Long-term multilineage engraftment of Klf7-/- cells was comparable to control cells, and self-renewal, as assessed by serial transplantation, was not affected.  Enforced expression of KLF7 results in a marked suppression of myeloid progenitor cell growth and a loss of short- and long-term repopulating activity.  Interestingly, enforced expression of KLF7, while resulting in multi-lineage growth suppression that extended to hematopoietic stem cells and common lymphoid progenitors, spared T cells and enhanced the survival of early thymocytes.  RNA expression profiling of KLF7-overexpressing hematopoietic progenitors identified several potential target genes mediating these effects. Notably, the known KLF7 target Cdkn1a (p21Cip1/Waf1) was not induced by KLF7, and loss of CDKN1A does not rescue the repopulating defect. These results suggest that KLF7 is not required for normal hematopoietic stem and progenitor (HSPC) function, but increased expression, as seen in a subset of lymphoid leukemia, inhibits myeloid cell proliferation and promotes early thymocyte survival.

KLF7 KO vs WT HSPC expression array: KLS (lineage- c-Kit+ Sca-1+) cells were sorted from the bone marrow of Klf7-/- chimeras at 12 weeks post-transplant.

overall_design: Fetal liver cells were used to establish chimeric mice (C57Bl/6 background) containing a mixture of Klf7+/+ and Klf7-/- bone marrow cells.


title: Gene expression profiling in Treg cells deficient or mutant in candidate FoxP3 cofactors

city: Boston

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary: The transcription factor FoxP3 partakes dominantly in the specification and function of FoxP3+ CD4+ T regulatory cells (Tregs), but is neither strictly necessary nor sufficient to determine the characteristic Treg transcriptional signature. Computational network inference and experimental testing assessed the contribution of several other transcription factors (TFs). Enforced expression of Helios or Xbp1 elicited specific signatures, but Eos, Irf4, Satb1, Lef1 and Gata1 elicited exactly the same outcome, synergizing with FoxP3 to activate most of the Treg signature, including key TFs, and enhancing FoxP3 occupancy at its genomic targets. Conversely, the Treg signature was robust to inactivation of any single cofactor. A redundant genetic switch thus locks-in the Treg phenotype, a model which accounts for several aspects of Treg physiology, differentiation and stability.

overall_design: To study the impact of deficiency of candidate FoxP3 cofactors (Xbp1, Eos, Gata1) on the expression of the Treg transcriptional signature, gene expression profiles were generated from purified splenic CD4+CD25hi Tregs of these mutant or knockout mice and their wildtype littermates.

first: Jonathan

last: Hill

first: Diane

last: Mathis

first: Christophe

last: Benoist


title: Gene profiling data of CD4+ T cells doubly transduced with EOS+LEF1 or GATA1+SATB1

overall_design: To study the impact of the combination of two transcription factors on the expression of the Treg transcriptional signature, CD4+ Tconv cells activated with anti-CD3+CD28 beads were retrovirally transduced with cDNAs encoding EOS and LEF1, or GATA1 and SATB1. The cells were then sorted into Trizol, and RNA was purified, labeled and hybridized to Affymetrix arrays.

first: Wenxian

last: Fu


title: Gene profiling data of CD4+ T cells transduced with FOXP3 and GATA1, then sorted into different fractions, based on the expression of Thy1.1 (FOXP3)

overall_design: To study the impact of FOXP3 alone or together with GATA1 on the expression of the Treg transcriptional signature, we sorted and profiled matched bins of FOXP3-transduced cells bearing various levels of FOXP3, alone or co-transduced with GATA1, chosen as a representative of the quintet factors.


title: Gene expression profiling of microdissected HRS cells

first: Christian

last: Steidl

address: 675 West 10th Avenue

institute: BC Cancer Agency

summary: Hodgkin lymphoma is derived from germinal center / post-germinal center B cells.

overall_design: Gene expression profilies of micodissected Hodkin Reed Sternberg cells (n=29) were compared to microdissected germinal centers (n=5)


title: Targeted disruption of the BCL9/beta-catenin complex in cancer

city: Plantagenet

first: Madeleine

middle: E.

last: Lemieux

state: ON

address: 275 Main St., Suite 252

institute: Bioinfo

summary: Stabilized Alpha-Helix peptides of BCL9 HD2 (SAH-BCL9) block BCL9 and B9L interactions with beta-catenin and specifically downregulate Wnt target gene expression.

overall_design: RNA from triplicate SAH-BCL9B- and vehicle-treated DLD1 samples (10 µM each for 12 hours) was hybridized to Affymetrix Human U133 Plus 2.0 arrays to asses global gene expression changes.

middle: E


title: ASXL1 Knock Down in Normal CD34+ Cord Blood and UKE1 Cell Lines

status: Public on Aug 21 2012

first: Omar

last: Abdel-Wahab

state: NY

address: 1275 York Ave.

department: HOPP

institute: Memorial Sloan-Kettering Cancer Center

summary: Gene expression analysis of Normal CD34+ Cord Blood and UKE1 cell lines treated with hairpins targeting ASXL1.

overall_design: Two independent studies where 1) CD34+ cord blood from normal donors were treated with either A) GFP Vector or B) ASXL1 specific short hairpin and 2) UKE1 cell lines treated with either A) GFP Vector or B) ASXL1 specific short hairpin.

first: O

last: Levine


title: BW25113 GhoS for RNase activity

city: State College

first: Thomas

middle: K.

last: Wood

state: PA

address: Room 161 Fenske Laboratory, University Park

department: Chemical Engineering & Biochemistry and Molecular Biology

institute: Pennsylvania State University

summary: To provide more evidence of the specificity of the RNase activity of GhoS, we performed a whole-transcriptome study for the production of GhoS vs. an empty plasmid so that we could investigate all of the cell’s transcripts for cleavage with GhoS, in vivo (i.e., BW25113/pCA24N-ghoS vs. BW25113/pCA24N with 1 mM IPTG induction of ghoS for 90 min).  Under these conditions, only 20 genes were found to be repressed by more than 4-fold; there were no induced genes. These GhoS-repressed genes were all involved in the biosynthesis/transport of purines and pyrimidines; among them, pyrI was most highly repressed (-20 fold). These results suggest that GhoS selectively cleaves only a few cellular targets.

overall_design: Overnight cultures of E. coli strains BW25113-pCA24N-ghoS and BW25113-pCA24N (emtpy plasmid) were inoculated into fresh LB medium to a turbidity of 0.05 at 600 nm and grown at 37°C. IPTG (1 mM) induction was performed when turbidity reached 0.2 and continued for 90 min. Total RNAs were isolated from the cultures and converted to cDNA for the application on E. coli genome 2.0 array.

first: Hsin-Yao

last: Cheng

first: SeokHoon

last: Hong

first: Devon

last: Osbourne


title: Gene expression changes in the septum: possible implications for microRNAs in sculpting the maternal brain.

status: Public on Aug 22 2012

city: Bar Harbor

first: Michael

middle: C.

last: Saul

state: ME

address: 600 Main St

institute: The Jackson Laboratory

summary: The transition from the non-maternal to the maternal state is characterized by a variety of CNS alterations that support the care of offspring. The septum (including lateral and medial portions) is a brain region previously linked to various emotional and motivational processes, including maternal care. In this study, we used microarrays (PLIER algorithm) to examine gene expression changes in the septum of postpartum mice and employed gene set enrichment analysis (GSEA) to identify possible regulators of altered gene expression. Genes of interest identified as differentially regulated with microarray analysis were validated with quantitative real-time PCR. We found that fatty acid binding protein 7 (Fabp7) and galanin (Gal) were downregulated, whereas insulin-like growth factor binding protein 3 (Igfbp3) was upregulated in postpartum mice compared to virgin females. These genes were previously found to be differentially regulated in other brain regions during lactation. We also identified altered expression of novel genes not previously linked to maternal behavior, but that could play a role in postpartum processes, including glutamate-ammonia ligase (Glul) and somatostatin receptor 1 (Sstr1) (both upregulated in postpartum). Genes implicated in metabolism, cell differentiation, or proliferation also exhibited altered expression. Unexpectedly, enrichment analysis revealed a high number of microRNAs, transcription factors, or conserved binding sites (177 with corrected P-value <0.05) that were significantly linked to maternal upregulated genes, while none were linked to downregulated genes. MicroRNAs have been linked to placenta and mammary gland development, but this is the first indication they may also play a key role in sculpting the maternal brain. Together, this study provides new insights into genes (along with possible mechanisms for their regulation) that are involved in septum-mediated adaptations during the postpartum period.

overall_design: In total, 12 total RNA samples derived from microdissected lateral septum were used for microarray analysis: 6 samples from virgin mice and 6 samples from age-matched lactating maternal mice. All samples are biological replicates.

first: Changjiu

last: Zhao

first: Terri

last: Driessen

first: Stephen

last: Gammie


title: Gene profiling data of CD4+ T cells transduced with FOXP3 and candidate cofactors

first: CBDM

last: Lab

state: MA

overall_design: To study the impact of FoxP3 and its candidate cofactors (Eos, Gata1, Helios, Irf4, Lef1, Satb1, Xbp1) on the expression of the Treg transcriptional signature, CD4+ conventional T cells (Tconv) activated with anti-CD3+CD28 beads were retrovirally transduced with cDNAs encoding FOXP3, candidate TFs, or a combination of FOXP3 and candidate TFs. After 3 days in culture, the transduced cells were sorted into Trizol, and RNA was purified, labeled and hybridized to Affymetrix arrays.


title: Expression data of AI4 CD8 T cells from AI4 and Rip-B7xAI4 mice

city: Bronx

first: Juan

last: Lin

address: 1300 Morris Park Ave.

institute: Albert Einstein College of Medicine

summary: B7x (B7-H4 or B7S1) is the seventh member of the B7 family and the in vivo function remains largely unknown. Despite new genetic data linking the B7x gene with autoimmune diseases, how exactly it contributes to peripheral tolerance and autoimmunity is unclear. Here we showed that B7x protein was not detected on antigen-presenting cells or T cells in both human and mice, which is unique in the B7 family. As B7x protein is expressed in some peripheral cells such as pancreatic b cells, we utilized a CD8 T cell-mediated diabetes model (AI4ab) in which CD8 T cells recognize an endogenous self-antigen, and found that mice lacking B7x developed more severe diabetes than control AI4ab mice. Conversely, mice overexpressing B7x in the b cells (Rip-B7xAI4ab) were diabetes free. Furthermore, adoptive transfer of effector AI4ab CD8 T cells induced diabetes in control mice, but not in Rip-B7xAI4ab mice. Mechanistic studies revealed that pathogenic effector CD8 T cells were capable of migrating to the pancreas but failed to robustly destroy tissue when encountering local B7x in Rip-B7xAI4ab mice. Although AI4ab CD8 T cells in Rip-B7xAI4ab mice and AI4ab mice showed similar cytotoxic function, cell death, and global gene expression profiles, these cells had greater proliferation in AI4ab mice than in RIP-B7xAI4ab mice. These results suggest that B7x in nonlymphoid organs prevents peripheral autoimmunity partially through inhibiting proliferation of tissue-specific CD8 T cells and that local overexpression of B7x on pancreatic b cells is sufficient to abolish CD8 T cell-induced diabetes.

overall_design:
AI4 mice developed T1D and Rip-B7x AI4 mice were resistant to T1D.
Total RNA was collected and gene expression compared between AI4 CD8 T cells from AI4 and Rip-B7xAI4 mice.

first: Xingxing

last: Zang

first: Jun

middle: S

last: Lee


title: Genomic Multivariate Predictors of Response to Adjuvant Chemotherapy in Ovarian Carcinoma: Predicting Platinum Resistance

city: Tampa

first: Youngchul

last: Kim

address: 12902 Magnolia Dr

institute: H. Lee Moffitt Cancer Center

summary:
Purpose:  Despite advances in radical surgery and chemotherapy delivery, ovarian cancer is the most lethal gynecologic malignancy.  Most of these patients are treated with platinum-based chemotherapies, but there is no biomarker model to guide their responses to these therapeutic agents.   We have developed and independently tested our novel multivariate molecular predictors for forecasting patients' responses to individual drugs on a cohort of 58 ovarian cancer patients.
Experimental Design:  We adapted and applied the previously-published COXEN algorithm to develop molecular predictors for therapeutic responses of patients' tumors based on expression signatures derived from the NCI-60 in vitro drug activities and genomic expression data. Genome-wide candidate biomarkers were first triaged by examining expression patterns of frozen and formalin-fixed paraffin embedded (FFPE) tissue samples.  We then identify initial drug sensitivity biomarkers for carboplatin and paclitaxel, respectively. These biomarkers  were further narrowed by examining concordant expression patterns between cell lines and a historical set of ovarian cancer patients. Multivariate predictors were obtained from the NCI-60 cell lines and refined using historical patient cohorts. To independent validate these molecular predictors,  we performed genome-wide profiling on FFPE samples of 58 ovarian cancer patients obtained prior to adjuvant chemotherapy.
Results: Carboplatin predictor significantly stratified platinum sensitive and resistant patients (p = 0.019) with sensitivity = 93%, specificity = 33%, PPV = 65%, and NPV = 78%. Paclitaxel predictor also significantly stratified patients' responses (p = 0.033) with sensitivity = 96%, specificity = 26%, PPV = 61%, and NPV = 86%.  The combination predictor for platinum-taxane combination demonstrated a significant survival difference between the predicted responders and nonresponders with median survival of 12.9 months vs. 8.1 months (p = 0.045).
Conclusions: COXEN predictors successfully stratified  platinum resistance and taxane response in this retrospective cohort, especially based on their FFPE tumor samples. Accurate prediction of chemotherapeutic response, especially to platinum agents is highly clinically relevant and could alter primary management of ovarian cancer.

overall_design: Gene expression data from 58 stage III-IV ovarian cancer patients treated with Carboplatin and Taxol agents

first: Jae

middle: K


title: Transcriptional environment and chromatin modifications interplay decides globin expression patterns.

status: Public on Aug 19 2012

city: Seattle

first: James

middle: William

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

summary: Background: Developmental stage-specific globin expression is a complex phenomenon that involves both trans- and cis-acting elements. While functional analyses ensuing recent genome-wide association studies have highlighted the important roles of trans-factors in regulating hemoglobin expression, these factors can not exert their functions without permissive chromatin domains. By transferring thoroughly profiled beta globin locus of undifferentiated human embryonic stem cells (hESCs) or hESC-derived erythroid cells into an adult erythroid transcriptional environment, we studied the influences of histone modifications on the globin expression decision within a fixed transcriptional environment. Shortly after the locus transfer, embryonic epsilon globin was not expressed regardless of original chromatin states, whereas fetal gamma globin was either expressed or not activated depending on original chromatin configurations, and the originally silent adult beta globin either remained silent or became activated depending on the expression status of gamma globin. These data suggest the interplay between transcriptional environment and the chromatin modifications determine the outcome of globin expression. As the ultimate silencing of gamma globin from hESC-derived erythroid cells in the adult transcriptional environment occurred after months-long cell proliferation, our work also has implications on attempts to generate beta globin expressing erythroid cells from hESCs or induced pluripotent stem cells.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: hESC line H1 (NIH code WA01, WiCell, Madison, WI) and adeno-associated virus (AAV)-targeted lines, were maintained and differentiated as previously described.12 (Details can be found in the supplemental information.) The expression of stem cell markers including SSEA-3, SSEA-4, TRA-1-60, and TRA-1-61 was detected by flow cytometry. To determine whether AAV-targeted lines retained their hematopoietic differentiation potential, confluent hESCs were harvested off the feeder layers and transferred to ultra-low attachment plates to allow for the formation of embryoid bodies (EBs). Day-14 EBs were dissociated into single cells and the expression of surface markers including CD34, CD71, CD45, CD31, CD41 and glycophorin-A was determined by flow cytometry. To induce erythroid differentiation, day-7 EBs were made into single cell suspension and cultured in erythroid-inducing medium for 14 days. Primers for real time PCR analysis of beta locus globin mRNA expression are provided in the supplemental information.

first: Richard

middle: P

last: Beyer

first: Kai-Hsin

last: Chang

first: Thalia

last: Papayannopoulou

first: Andy

last: Huang

first: Hemei

last: Han

first: Xiangdong

last: Fang

first: Chao-Zhong

last: Song

first: Hao

last: Wang

first: Qiliang

last: Li

first: John

last: Stamatoyannopoulos

first: George


title: Pacreatic Cell Line Transcriptomics

status: Public on Aug 15 2012

city: Rochester

first: Eric

middle: W

last: Klee

state: MN

address: 200 1st St SW

department: Health Sciences Research

institute: Mayo Clinic -Rochester, MN

summary: Analyzed the gene expression level in 5 pancreatic cell lines

overall_design: 5 samples; 1 array per sample

first: Chari

last: Suresh