title: Gene expression in the mouse embryonic small intestine in the presence or absence of E-cadherin

status: Public on Feb 28 2012

city: Milwaukee

first: Michele

last: Battle

state: WI

address: 8701 Watertown Plank Rd

department: Cell Biology, Neurobiology, and Anatomy

institute: Medical College of Wisconsin

summary: Gene expression was compared between E18.5 E-cadherin conditional knockout (cKO) small intestine and E18.5 control mouse small intestine.

overall_design: E18.5 mouse small intestine was collected from control and E-cadherin conditional knockout mice. RNA was prepared.  Affymetrix Mouse Gene 1.0 gene arrays were used to interrogate gene expression.  Data was analyzed using dChip software.


title: Progesterone-regulated genes in immune cells: Regulation of T cell genes by progesterone

status: Public on Mar 02 2012

city: West Lafayette

first: Chang

last: Kim

state: IN

address: 725 Harrison St

department: Comparative Pathobiology

country: USA

institute: Purdue

summary: We examined the global gene expression pattern of T cells regulated by progesterone to gain further insights into the regulatory mechanisms of progesterone. We found 325-347 cord blood T cell genes up or down-regulated by P4 in the presence or absence of exogenous TGFb1. Peripheral blood T cells were relatively unresponsive with only 30-70 genes regulated by P4. IL-6 receptor (IL-6R) expression was greatly down-regulated by progesterone in cord blood, but not PB, T cells. Overall, these differences in gene expression are consistent with the differential responses of cord blood and peripheral blood T cells to progesterone. To gain insights into the differences of progesterone and control dendritic cells, we performed a microarray study and found ~180 genes regulated by progesterone in dendritic cells. The gene expression information suggests that progesterone has the potential to alter dendritic cell responses to cytokines, chemokine production, and migration which in combination would control T cell differentiation.

overall_design: The CD4+ CD25- T cells were isolated from cord blood and peripheral blood and cultured in the presence and absence of progesterone 2 ug per mL, TGFb1 150 pg/mL and IL-2 100u/mL for 5-6 days. T cells from cord blood and peripheral blood were compared.


title: The alarmin interleukin-33 drives protective antiviral CD8+ T cell responses

status: Public on Feb 27 2012

city: Geneva

first: Sandra

last: Kallert

address: 1, rue Michel-Servet

department: Pathology and Immunology

country: Switzerland

institute: University of Geneva

summary: Pathogen-associated molecular patterns decisively influence antiviral immune responses, whereas the contribution of endogenous signals of tissue damage, also known as “damage-associated molecular patterns” or “alarmins”, remains ill-defined. We show that interleukin-33 (IL-33), an alarmin released from necrotic cells, is necessary for potent CD8+ T cell (CTL) responses to replicating, prototypic RNA and DNA viruses in mice. IL-33 signaled through its receptor on activated CTLs, enhanced clonal expansion in a MyD88-dependent, CTL-intrinsic fashion, determined polyfunctional effector cell differentiation and was necessary for virus control. Moreover, recombinant IL-33 augmented vaccine-induced CTL responses. Radio-resistant cells of the splenic T cell zone produced IL-33, and efficient CTL responses required IL-33 from radio-resistant cells but not from hematopoietic cells. Thus, alarmin release by radio-resistant cells orchestrates protective antiviral CTL responses.

overall_design: 2 groups (wt vs. ST-/- P14 cells), 3 replicates per group.

first: Weldy

middle: V

last: Bonilla

first: Anja

last: Fröhlich

first: Karin

last: Senn

first: Marylise

last: Fernandez

first: Susan

last: Johnson

first: Mario

last: Kreutzfeldt

first: Ahmen

middle: N

last: Hegazy

first: Christina

last: Schrick

first: Padraic

middle: G

last: Fallon

first: Roman

last: Klemenz

first: Susumu

last: Nakae

first: Heiko

last: Adler

first: Doron

last: Merkler

first: Max

last: Löhning

first: Daniel

middle: D

last: Pinschewer


title: Transcriptome analysis of differentiating normal and leukemic erythroid progenitors

city: Bronx

first: Sandeep

middle: Nagaraj

last: Wontakal

state: NY

address: 1300 Morris Park Ave Chanin 402

department: Cell Biology

institute: Albert Einstein College of Medicine

summary: We compared the transcriptomes of differentiating cultures of ES cell derived erythroid progentor cells (ES-EP) and murine erythroleukemia (MEL) cells stably transfected with GATA-1 fused to ER.

overall_design: RNA was isolated from duplicate differntiating cultures of MEL and ES-EP using Affymetrix GeneChip Mouse Gene 1.0 ST.

first: Arthur

last: Skoultchi


title: Methylation Profiling of Blood DNA from Healthy Children (Harvard Age Study)

status: Public on Feb 24 2012

city: Atlanta

first: Benjamin

last: Barwick

state: GA

address: 1365 Clifton Rd. NE WCI-C 4th Floor Benches 36-37

department: Hematology and Medical Oncology

institute: Emory University

summary:
Analysis of the DNA methylation level in peripheral blood leukocytes from healthy children using the Illumina HumanMethylation450 BeadChip

Groupings by family membership requested but not provided by submitter

overall_design: DNA methylation association study in healthy children

first: Reid

middle: S

last: Alisch

first: Warren

middle: T

last: Stephen


title: Gene expression profiling of pediatric myelodysplastic syndrome (MDS) characterizes disease subtype and time to progression into acute myeloid leukemia (AML)

status: Public on Feb 29 2012

city: padova

first: silvia

last: bresolin

state: padova

address: via giustiniani 3

department: department of women's and children's health

country: Italy

institute: università di padova

summary: Identification of relevant subgroups in childhood MDS patients by gene expression analysis and gene involve in progression into AML

overall_design: Class comparison between different subgroups of pediatric MDS (class risk, classification subtype)

first: Silvia

last: Bresolin

first: Geertruy

last: te Kronnie


title: Expression data from untreated and ATP treated AML blasts

status: Public on Feb 25 2012

city: Modena

first: Rossella

last: Manfredini

address: Via Gottardi 100

department: Life Sciences

institute: Centre for Regenerative Medicine

summary:
In the present study, we investigated whether, and to what extent, P2Rs and their ligands are involved in the regulation of AML cells. Our findings show that AML blasts express several receptors belonging to the P2X and P2Y family. Although different samples respond differently to ATP and UTP stimulation (reflecting the variability intrinsic to the group of acute myeloid leukemias), all the tested samples appear to be responsive to purinergic signalling, as demonstrated by intracellular calcium mobilization.
GEP analysis demonstrated that ATP induced the expression of cell cycle inhibitors and negative modulators of cell motility, such as inhibitors of GTPase activity. On the contrary, ATP inhibits the expression cell-cycle related genes (cyclins and CDKs), activators of cell motility (Rho GTPases regulators, matrix degradation enzyme and cytoskeleton proteins) and adhesion molecules involved in homing and engraftment.

overall_design: Blast cells obtained from 12 AML patients (3 M0/M1; 3 M2; 3 M4; and 3 M5) were cultured for 24 h with or without 1 mM ATP. Total RNA from 106 ATP-treated and untreated cells was extracted to study variation of gene expression profile induced by ATP treatment in leukemic cells.

first: Valentina

last: Salvestrini

first: Roberta

last: Zini

first: Lara

last: Rossi

first: Sara

last: Gulinelli

first: Elisa

last: Bianchi

first: Wanda

last: Piacibello

first: Luisa

last: Caione

first: Giorgia

last: Migliardi

first: Maria

middle: R

last: Ricciardi

first: Agostino

last: Tafuri

first: Simona

last: Salati

first: Francesco

last: Di Virgilio

first: Michele

last: Baccarani

first: Davide

last: Ferrari

first: Roberto

middle: M

last: Lemoli


title: Charaterization of the initial molecular events of adipose tissue development and growth during overfeeding in humans

status: Public on Mar 05 2012

city: Pierre Bénite

first: emmanuelle

last: meugnier

address: Cens Eli Bat 2 D- Hopital Lyon Sud

country: France

summary: The adaptive mechanisms in response to excess energy supply are still poorly known in humans. Our aims were to define metabolic responses and changes in gene expression in adipose tissue of healthy volunteers during fat overfeeding.

overall_design: Healthy lean and overweight subjects were submitted to a high fat diet during 56 days. Adipose tissue biopsies were taken at Day 0, Day 14 and Day 56.

first: Maud

last: Alligier

first: Emmanuelle

last: Meugnier

first: Martine

last: Laville

first: Hubert

last: Vidal


title: Gene expression data from Wild Type and  Nlrp10 deficient dendritic cells treated with or without LPS

status: Public on Feb 23 2012

city: New Haven

first: Hailong

last: Meng

state: CT

address: 300 George Str

institute: Yale University

summary:
Nlrp10-deficient mice have a profound defect in helper T cell-driven immune responses. T cell priming is impaired due to a defect in the emigration of a dendritic cells from inflamed tissue and antigen transport to draining lymph nodes. DC chemotaxis to CCR7-dependent and independent ligands is intact in the absence of Nlrp10.
Therefore to identify novel molecules potentially involved in Nlrp10-dependent DC function we used an unbiased gene array approach on Nlrp10-deficient BMDCs treated with or without LPS.

overall_design: 8 samples were analysed. BMDCs were independantly generated from 2 WT and 2 Nlrp10 deficient mice. Samples were treated with or without LPS

first: Stephanie

middle: C

last: Eisenbarth

first: Adam

last: Williams

first: Steven

middle: H

last: Kleinstein


status: Public on Mar 03 2012

city: Columbus

first: kalpana

last: ghoshal

state: OH

address: 420 W. 12th Avenue

department: Molecular and Cellular Biochemistry

institute: The Ohio State University

summary:
Liver transcriptome profiling of liver specific miR-122 knockout (miR-122loxP/loxP Alb-Cre) and control (miR-122loxP/loxP) male mice. Expression profile of several hundred mRNAs that include miR-122 targets were altered in miR-122 KO livers.

Loss of miR-122 in the germ line resulted in significant changes in hepatic gene expression profile.  Among the upregulated genes many are direct targets of miR-122

overall_design:
GSM517838-GSM517847: Liver transcriptome profiling of liver specific miR-122 knockout and control male mice. Total liver RNA from 8 week old five control and five liver-specific miR-122 knock out male mice (C57/BL6J background)

GSM791601-GSM791604: Liver transcriptome profiling of germ-line miR-122 knockout and control male mice. Liver RNA from 5 week old control (floxed) and miR-122KO mice were analyzed by mouse whole transcriptome profiling.

first: Kalpana

last: Ghoshal

first: Huban

last: Kutay

first: Tasneem

last: Motiwala

first: Sarah

last: Warner

first: Timothy

last: Wise

first: Lianbo

last: Yu


title: TOV112D cells treated with NSC319726

status: Public on Feb 22 2012

city: New Brunswick

first: Alexei

last: Vazquez

state: NJ

address: 195 Little Albany St

institute: The Cancer Institute of New Jersey

summary:
Rescuing the function of mutant p53 protein is an attractive cancer therapeutic strategy. Using the NCI anticancer drug screen data, we identified two compounds from the thiosemicarbazone family that manifest increased growth inhibitory activity in mutant p53 cells, particularly for the p53R175 mutant.  Mechanistic studies reveal that NSC319726 restores WT structure and function to the p53R175 mutant.  This compound kills p53R172H knock-in mice with extensive apoptosis and inhibits xenograft tumor growth in a 175-allele specific mutant p53 dependent manner.  This activity depends upon the zinc ion chelating properties of the compound as well as redox changes.  These data identify NSC319726 as a p53R175 mutant reactivator and as a lead compound for p53 targeted drug development.
We utilized gene expression microarrays to examine the transcriptional activity of p53 targets in TOV112D cells after treatment with NSC319726.

overall_design: Triplicate cultures of TOV112D cells untreated, treated with NSC319726. Total RNA was extracted and hybridized to Affymetrix human U133 plus 2.0 microarrays.

first: Xin

first: Darren

last: Carpizo


title: Lung Natural Helper cells

city: Vancouver

first: Timotheus

middle: You Fu

last: Halim

state: British Columbia

address: 675 West 10th Avenue

department: Terry Fox Laboratory

country: Canada

institute: BC Cancer Research Centre

summary:
Natural Helper cells constitute a unique lineage of Th2-cytokine producting innate lymphocytes, here we characterize the gene expression profile of non-stimulated or PMA/ionomycin-stimulated Natural Helper cells from naive C57Bl/6 mouse lungs.
We used microarrays to detail the gene expression profile of stimulated and unstimulated lung Natural Helper cells in mice.

overall_design: Lineage(-)Sca-1(+)c-Kit(-/low)CD127(+)CD25(+) Lung Natural Helper cells were purified from naive 6-8 week old B6 mice by FACS.  RNA was extracted immediately from un-stimulated Natural Helper cells after FACS. Stimulated Natural Helper cells were cultured with PMA/ionomycin for 3 days followed by RNA extraction.

middle: Y

first: Fumio

last: Takei


title: Effects of Primary Osteoporosis on Human Mesenchymal Stem Cells

city: Wuerzburg

first: Peggy

last: Benisch

country: Germany

institute: Orthopedic Center for Musculoskeletal Research

summary: In the present study we analyzed the effect of primary osteoporosis on the transcriptome of human mesenchymal stem cells (hMSC; alternatively named mesenchymal stromal cells) from human bone marrow. Human MSC of elderly patients suffering from osteoporosis were isolated from femoral heads after low-energy fracture of the femoral neck. Bone marrow of age-matched, non-osteoporotic donors was obtained of femoral heads after total hip arthroplasty.

overall_design: Cells were isolated from human bone marrow according to the previously described protocol (Noth et al., 2002, J Orthop Res, 20/5, 1060-1069) under agreement of the local Ethics Committee of the University of Würzburg. Human MSC of elderly patients suffering from osteoporosis were isolated from femoral heads after low-energy fracture of the femoral neck. Additional criteria for confirming primary osteoporosis in these donors were vertebrae fractures and advanced age. Bone marrow of age-matched, non-osteoporotic donors was obtained of femoral heads after total hip arthroplasty due to osteoarthritis and/or hip dysplasia. RNA samples were taken from passage 1 or passage 2.

first: P

first: F

last: Jakob

first: R

last: Ebert


title: Effects of Cellular Senescence on Human Mesenchymal Stem Cells

summary: In the present study we analyzed the effect of cellular senescence on the transcriptome of human mesenchymal stem cells (hMSC; alternatively named mesenchymal stromal cells) from bone marrow. Human MSC were isolated from femoral heads of non-osteoporotic donors after total hip arthroplasty.

overall_design: Cells were isolated from human bone marrow according to the previously described protocol (Noth et al., 2002, J Orthop Res, 20/5, 1060-1069) under agreement of the local Ethics Committee of the University of Würzburg. Bone marrow was obtained of femoral heads after total hip arthroplasty due to osteoarthritis and/or hip dysplasia. MSC were replated after reaching 70-90% confluence until they entered state of cellular senescence.  RNA samples of control cells were taken from passage 1 or passage 2.


title: Effects of aging, primary osteoporosis, and cellular senescence on Human Mesenchymal Stem Cells

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

overall_design: Refer to individual Series


title: Effects of aging on Human Mesenchymal Stem Cells

summary: In the present study we analyzed the effect of advanced donor age on the transcriptome of human mesenchymal stem cells (hMSC; alternatively named mesenchymal stromal cells) from bone marrow. Human MSC of elderly and middle-aged patients without symptoms of osteoporosis were isolated from femoral heads after total hip arthroplasty.

overall_design: Cells were isolated from human bone marrow according to the previously described protocol (Noth et al., 2002, J Orthop Res, 20/5, 1060-1069) under agreement of the local Ethics Committee of the University of Würzburg. Bone marrow was obtained of femoral heads after total hip arthroplasty due to osteoarthritis and/or hip dysplasia. RNA samples were taken from passage 1 or passage 2.


title: Effects of resistance exercise on the transcriptome in MHC I and MHC IIa muscle fibers of young and old women

status: Public on Feb 21 2012

city: Indianapolis

first: Shawn

middle: T.

last: Estrem

address: Lilly Corporate Center

institute: Eli Lilly and Company

summary: Global microarray (HG U133 Plus 2.0) was used for the first time to investigate the effects of resistance exercise on the transcriptome in slow-twitch myosin heavy chain (MHC) I and fast-twitch MHC IIa muscle fibers of young and old women.  Vastus lateralis muscle biopsies were obtained pre and 4hrs post resistance exercise in the beginning (untrained state) and at the end (trained state) of a 12 wk progressive resistance training program.

overall_design: A total of 14 females were included in this investigation.  The participants included 8 young (23±2y) and 6 old (85±1y) females.  All subjects participated in 12 wks of progressive resistance training consisting of bilateral knee extensions with 3x10 reps at 70% of 1-RM, and 3d/wk for a total of 36 training sessions.  Vastus lateralis biopsies were obtained in conjunction with the 1st and 36th (last) training session and included a basal biopsy and another biopsy 4hrs post the resistance exercise session. From each biopsy sample, we isolated individual muscle fibers.  After myosin isoform identification of isolated fibers (SDS-PAGE), RNA extraction of 20 MHC I and 20 MHC IIa muscle fibers per biopsy sample followed.  Thus, each resulting sample contained total RNA from 20 muscle fibers of identical fiber type (MHC I or MHC IIa).  A total of 70 samples were analyzed on separate microarray chips, and samples were not pooled between subjects.  The study design allowed us to examine the acute effects of resistance exercise on the transcriptome in MHC I and MHC IIa muscle fibers in the untrained and trained state.

first: Ulrika

last: Raue

first: Todd

middle: A

last: Trappe

first: Hui-Rong

last: Qian

first: Leah

last: Helvering

first: Rosamund

last: Smith

first: Scott


title: Determination of the protein interactome of the transcription factor Sox2 in embryonic stem cells engineered for inducible expression of four reprogramming factors

status: Public on Feb 20 2012

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:
Coordinate expression of the somatic cell reprogramming factors Oct4, Sox2, Klf4 and c-Myc within embryonic stem cells preserves the self-renewal of these cells, while allowing for the expression epitope tagged Sox2. Taking advantage of this observation, we engineered embryonic stem cells (i-OSKM-ESC) to inducibly express Oct4, Klf4, c-Myc and an epitope tagged form of Sox2 from a polycistronic element, in the presence of doxycycline. We isolated Sox2 and its associated protein complexes by co-immunoprecipitation. Subsequently, we identified the Sox2-protein interactome in self-renewing embryonic stem cells using an unbiased proteomic screen (Multidimensional Protein Identification Technology [MudPIT]).
Affymetrix microarrays were used to characterize the gene expression profile of i-OSKM-ESC in the absence and presence of doxycycline.

overall_design: Mouse embryonic stem cells (KH2) were engineered to express Oct4, epitope tagged Sox2, Klf4 and c-Myc in the presence of doxycyline, to produce i-OSKM-ESC. The i-OSKM-ESC were cultured in the absence or presence of doxycyline (4 µg/mL) for 24 hours. RNA was extracted from each condition, and used for microarray analysis.

first: Zhiguang

last: Gao

first: Jesse

middle: L

last: Cox

first: Joshua

last: Gilmore

first: Briana

last: Ormsbee

first: Sunil

middle: K

last: Mallanna

first: Michael

middle: P

last: Washburn

last: Rizzino


title: Molecular Phenotypes of Acute Kidney Injury in Kidney Transplants

city: Edmonton

first: Konrad

last: Famulski

state: Alberta

address: 250 HMRC

institute: University of Alberta

summary: Microarray analysis of human kidneys with acute kidney injury (AKI) has been limited because such kidneys are seldom biopsied. However, all kidney transplants experience AKI, and early kidney transplants without rejection are an excellent model for human AKI: they are screened to exclude chronic kidney disease, frequently biopsied, and have extensive follow-up. We used histopathology and microarrays to compare indication biopsies from 28 transplants with AKI to 11 pristine protocol biopsies of stable transplants. Kidneys with AKI showed increased expression of 394 injury-repair response associated transcripts, including many known epithelial injury molecules (e.g. ITGB6, LCN2), tissue remodeling molecules (e.g. VCAN), and inflammation molecules (S100A8, ITGB3). Many other genes also predict the phenotype, depending on statistical filtering rules, including AKI biomarkers as HAVCR1 and IL18. Most mouse orthologs of the top injury-repair transcripts were increased in published mouse AKI models. Pathway analysis of the injury-repair transcripts revealed similarities to cancer, development, and cell movement. The injury-repair transcript score AKI kidneys correlated with reduced function, future recovery, brain death, and need for dialysis, but not future graft loss. In contrast, histologic features of "acute tubular injury" did not correlate with function or with the molecular changes. Thus the injury-repair associated transcripts represent a massive coordinate injury-repair response of kidney parenchyma to AKI, similar to mouse AKI models, and provide an objective measure for assessing the severity of AKI in kidney biopsies and validation for the use of many AKI biomarkers.

overall_design: AKI biopsies sample names and CEL files are from GSE21374. All consenting renal transplant patients undergoing biopsies for cause as standard of care between 09/2004 and 10/2007 at the university of Alberta or between 11/2006 and 02/2007 at the University of Illinois were included in the analysis. In addition to the cores required for standard histopathology, we collected one core for gene expression studies. the relationship between gene expression in the biopsy and subsequent graft loss was analyzed.

first: Declan

last: de Freitas

first: Philip

middle: F

last: Halloran


title: Gene expression levels in colon cancer cells with mutant K-ras under hypoxic conditions

city: Boston

first: Daniel

last: Shue

state: MA

address: 50 Blossom Street

department: GI Unit

institute: Massachusetts General Hospital

summary: The goal of this study was to identify those genes that were differentially expressed in colon cancer cells with mutant K-ras under hypoxic conditions

overall_design: DKS-5 (K-ras mutant) and DKO-3 (K-ras wild-type) were cultured in normoxic (21% O2) and 12-hour hypoxic (1% O2) conditions.  This was repeated for a total of 2 samples per condition.

last: Chung


title: Adipose tissue transcriptome in insulin resistance

city: Helsinki

first: Jarkko

last: Soronen

address: Haartmaninkatu 8

department: Institute for Molecular Medicine Finland (FIMM)

country: Finland

institute: University of Helsinki

overall_design:
5 arrays from obese insulin-resistant and lean insulin-sensitive females adipose tissue at fasting and after 3h hyperinsulinemia
FIR x 5, FIS x 5, HIR x 5, HIS x 5
F=fasting, H=hyperinsulinemia, IR=Insulin-resistant, IS=Insulin-sensitive (FIR, FIS, HIR, HIS)


title: Effects of age on the skeletal muscle transcriptome

first: Shawn

last: Estrem

summary: Global microarray (HG U133 Plus 2.0) was used to investigate the basal level skeletal muscle transcriptome profile of young and old adults.  One vastus lateralis muscle biopsy was obtained in the basal state from 36 different subjects.

overall_design: A total of 36 subjects were included in this investigation.  The young (n=15, 25±1y) participants included 7 males and 8 females.  The old (n=21, 78±1y) participants included 10 males and 11 females.  All subjects were healthy and had never been involved in any formal exercise.  Skeletal muscle biopsies were obtained from the vastus lateralis in the basal state.  The RNA integrity of all 36 samples was very good with an average RIN number of 8.2.  All samples were analyzed on a separate microarray chip, and samples were not pooled between subjects.

first: Ulrika

last: Raue

first: Todd

last: Trappe

last: Qian


title: Effects of resistance exercise and resistance training on the skeletal muscle transcriptome in young and old adults

summary: Global microarray (HG U133 Plus 2.0) was used to investigate the effects of resistance exercise and resistance training on the skeletal muscle transcriptome profile of 28 young and old adults. Vastus lateralis muscle biopsies were obtained pre and 4hrs post resistance exercise in the beginning (untrained state) and at the end (trained state) of a 12 wk progressive resistance training program.

overall_design: A total of 28 subjects were included in this investigation.  The young (n=16, 24±1y) participants included 8 males and 8 females.  The old (n=12, 84±1y) participants included 6 males and 6 females.  All subjects participated in 12 wks of progressive resistance training consisting of bilateral knee extensions with 3x10 reps at 70% of 1-RM, and 3d/wk for a total of 36 training sessions.  Vastus lateralis biopsies were obtained in conjunction with the 1st and 36th (last) training session and included a basal biopsy and another biopsy 4hrs post the resistance exercise session (for a total of 4 biopsies per subject).  The RNA integrity for all samples was very good with an average RIN number of 7.6.  All 110 samples were analyzed on a separate microarray chip, and samples were not pooled between subjects.  The study design allowed us to examine the acute effects of resistance exercise on the skeletal muscle transcriptome in the untrained and trained state.  The design also provided information on the effects of resistance training on basal level gene expression and the effects of age on basal level gene expression

first: Hui-Rong

first: Leah

last: Helvering

first: Rosamund

last: Smith


title: Exogenous Interleukin-10 versus Glucocorticoids: Effect on Gene Expression and Pro-inflammatory Cytokine Release in Polymorphonuclear Leukocytes and Monocytes of the Newborn

status: Public on Feb 16 2012

city: Manhasset

first: Dennis

last: Davidson

state: New York

address: 350 Community Dr

department: Pediatrics

institute: The Feinstein Institute for Medical Research

summary:
INTRODUCTION: Persistent lung inflammation, with an influx of polymorphonuclear leukocytes and monocytes, occurs early in bronchopulmonary dysplasia. We hypothesized that: 1) that interleukin-10, a potent anti-inflammatory cytokine, would cause a markedly different gene expression profile compared to dexamethasone in these cells, and 2) monocyte insensitivity to dexamethasone was related to glucocorticoid receptor expression.
RESULTS: For polymorphonuclear leukocytes, there were  <20% of genes changing expression in common between interleukin-10 and dexamethasone. The monocyte had 5 times the number of genes changing expression with interleukin-10 compared to the polymorphonuclear leukocyte. Dexamethasone, in the therapeutic range, had no effect on  gene expression in monocytes. The order of potency for inhibition of interleukin-8 release from monocytes was IL-10>betamethasone>> dexamethasone and hydrocortisone. Glucocorticoid potency was directly related to the degree of glucocorticoid receptor translocation to the monocyte nucleus.
DISCUSSION: Gene expression profiles by IL-10 versus dexamethasone indicates that there may be major differences in efficacy and adverse effects if interleukin-10 is used for therapy in the future. Betamethasone may be a better therapeutic choice than dexamethasone.
METHODS: Isolated cord blood cells were pre-incubated with anti-inflammatory agents prior to endotoxin stimulation. Measurements were made by microarrays, RT-qPCR, ELISA, and Western blots.

overall_design:
Isolation of cord blood polymorphonuclear leukocytes and monocytes separately from 5 subjects. Endotoxin stimulation in cell culture for 4 hours. Comparison of gene expression between endotoxin alone versus endotoxin-stimualted cells pretreated with interleukin-10 or dexamethasone (at equimolar, therapeutic levels, 10-8 M.
Cell Types : MONOs, PMNs; Treatments: LPS, LPS+IL-10, LPS+DEX

first: Veronika

last: Miskolci


title: Expression data from normal thymocytes, 24 day pre-tumor Dnmt3b-deficient thymocytes, Wild-Type Tumors, and Dnmt3b-deficient Tumors

first: Ryan

last: Hlady

state: Nebraska

department: Eppley

institute: UNMC

summary: Dnmt3b is a DNA methytransferase which is an enzyme that methylated genomic DNA which contributes to genomic stability and transcriptional regulation.

overall_design: We genetically inactivated Dnmt3b in the hematopoeitic compartment in the context of MYC overexpression and analysed the resulting thymic lymphomas.

first: Rene

last: Opavsky

first: Jana

last: Opavska

first: Slavomira

last: Novakova


title: Seminal plasma and transforming growth factor-β regulate gene expression in human Ect1 ectocervical epithelial cells

city: Adelaide

first: Sarah

middle: Anne

last: Robertson

state: SA

address: Frome Rd

department: paediatrics and Reproductive Health

country: Australia

institute: University of Adelaide

summary: In this study we examined the influence of seminal plasma on gene expression in human Ect1 ectocervical epithelial cells, and the extent to which recombinant TGFβ3 elicits comparable changes. Ect1 cells were incubated with recombinant human TGFβ3 (5 ng/ml), 10% pooled human seminal plasma (v/v), or medium alone for 10h. RNA was reverse transcribed into cDNA and hybridized to Affymetrix GeneChip® Human Genome U133 plus 2.0 microarrays (Affymetrix, Santa Clara, CA). Exposure of Ect1 cells to seminal plasma resulted in differential expression of a total of 3955 probe sets, identified using high stringency criteria with MAS 5.0 analysis. These corresponded to 1338 genes up-regulated and 1343 genes down-regulated by seminal plasma. TGFβ3 treatment of Ect1 cells resulted in differential expression of 884 probe sets, corresponding to 346 up-regulated genes and 229 down-regulated genes. The genes differentially regulated by seminal plasma included several genes associated with cytokine–cytokine receptor interaction, TGFβ signalling, JAK/STAT signalling or VEGF signalling pathways, as specified by the KEGG database. Of 47 genes in these families, 17 (36.1%) were similarly regulated by both seminal plasma and TGFβ3. These data, together with additional experiments showing all three TGFβ isoforms can regulate inflammatory cytokine expression in Ect1 cells, identify TGFβ isoforms as key agents in seminal plasma that signal induction of pro-inflammatory cytokine synthesis in cervical cells.

overall_design: RNA from each of four biological replicates, each comprising pooled material from separate sets of 4 replicate wells, was analysed for each treatment. Total RNA was reverse transcribed into cDNA and sent to the Australian Genome Research Facility (AGRF; Melbourne, Australia) for single-cycle labeling and hybridization to 12 Affymetrix GeneChip® Human Genome U133 plus 2.0 microarrays (Affymetrix, Santa Clara, CA).

first: David

middle: J

last: Sharkey

first: Anne

last: Macpherson


title: Expression data from peripheral blood mononuclear cell in patients with type 1 diabetes before and after peripheral stem cell transplantation

city: shanghai

first: lei

last: ye

address: 197#, second ruijin road

country: China

institute: ruijin hospital

summary: Autologous nonmyeloablative hematopoietic stem cell transplantation (AHST) was the first therapeutic approaches that can improveβcell function in type 1 diabetic (T1D) patients. This study was designed to investigate the potential mechanisms involved.We applied AHST to nine T1D patients diagnosed within six months and analyzed the acute response in peripheral blood  genomic expression profiling at the six-month follow-up.

overall_design: Peripheral blood mononuclear of newly diagnosed type1 diabetes patients at diagnosis and at six months post-transplantation by autologous peripheral stem cell were purified by  LymphoprepTm gradient purification according to the manufacturer’s instructions (Axis-Shield PoC AS, Oslo, Norway) for futher microarray analysis.

first: Xiaofang

last: Zhang

first: Weiqiong

last: Gu


title: Expression data from mouse livers expressing or lacking Cre recombinase during pneumonia

first: Lee

last: Quinton

address: 72 E Concord St

institute: Boston University School of Medicine

summary:
Cre-recombinase expression under control of an albumin promoter in the presence of floxed alleles is a highly effective and specific way to target gene mutations in hepatocytes.  However, some concerns have been raised regarding off-target and/or toxic effects of cre itself, possibly confounding the interpretation of studies employing this approach.  We have now used this tool to succesfully target gene deletions in hepatocytes during pneumonia, a condition which results in significant remodeling of the hepatic transcriptome.  The goal of this study was to determine what effects, if any, cre expression alone has on hepatic gene expression during bacterial pneumonia.
Mutant mice expressed CRE-recombinase under control of an albumin promoter.  Results from mutants were compared to wild-type mice on the same genetic background (C57BL/6).  Microarray analysis was performed on liver RNA collected from both genotypes of mice in the absence and presence of pneumococcal pneumonia.

overall_design: RNA from 2 separate groups of mice (3 mice per group) was analyzed: 1) Control mice infected intratracheally for 24h with 10^6 CFU of Streptococcus pneumoniae (serotype 3); and 2) Mutant mice infected intratracheally for 24h with 10^6 CFU of Streptococcus pneumoniae (serotype 3).

first: Joseph

last: Mizgerd


title: Acute expression of cyclin D1 in mouse mammary gland using the tetracycline system

status: Public on Feb 10 2012

city: PHILADELPHIA

first: Adam

last: Ertel

state: PA

address: 233 S 10TH ST

department: Cancer Biology

institute: Thomas Jefferson University

summary: Analysis of mammary glands from tet-inducible (rtTA) transgenic mice expressing cyclin D1 (Ccnd1). MMTV-rtTA transgenic mice (MMTV-Mouse Mammary Tumor Virus promoter) were cross-mated to cyclin D1 transgenic mice under the control of the tet operon. 8-week-old tetracycline-inducible cyclin D1/rtTA bi-transgenic pregnant female mice (12 days postcoitus) were treated with doxycycline through drinking water supplementation at a final concentration of 2 mg/ml. Control mice were rtTA transgenics alone and were treated in the same manner. After 7 days of doxycycline treatment, the mice were sacrificed and mammary glands taken for RNA isolation. Results provide insight into the in vivo gene expression pattern regulated by cyclin D1 through acute induction.

overall_design: Two separate control mice positive for the MMTV-rtTA transgene were compared to 3 separate cyclin D1/rtTA bi-transgenic female mice.

first: Richard

middle: G

last: Pestell

first: Mathew

last: Casimiro

first: Zuoren

last: Yu


title: Effects of Primary Osteoporosis and Advanced Age on Human Mesenchymal Stem Cells

first: Peggy

last: Benisch

summary: In the present study we analyzed the effect of primary osteoporosis and advanced donor age on the transcriptome of human mesenchymal stem cells (hMSC; alternatively named mesenchymal stromal cells) from bone marrow. Human MSC of elderly patients suffering from osteoporosis were isolated from femoral heads after low-energy fracture of the femoral neck. Control cells were obtained from bone marrow of femoral heads of middle-aged, non-osteoporotic donors after total hip arthroplasty.

overall_design: Cells were isolated from human bone marrow according to the previously described protocol (Noth et al., 2002, J Orthop Res, 20/5, 1060-1069) under agreement of the local Ethics Committee of the University of Würzburg. Human MSC of elderly patients suffering from osteoporosis were isolated from femoral heads after low-energy fracture of the femoral neck. Additional criteria for confirming primary osteoporosis in these donors were vertebrae fractures and advanced age. Bone marrow of middle-aged, non-osteoporotic donors was obtained of femoral heads after total hip arthroplasty due to osteoarthritis and/or hip dysplasia. RNA samples were taken from passage 1 or passage 2.

first: P

first: F

last: Jakob

first: R

last: Ebert


status: Public on Feb 11 2012

city: Paris

first: Franck

last: Tirode

address: 26 Rue d'Ulm

department: Inserm U830

institute: Institut Curie

summary:
Expression profiling of Ewing sarcoma samples in the frame of the CIT program from the french Ligue Nationale Contre le Cancer (http://cit.ligue-cancer.net).
Ewing sarcoma a rare pediatric tumor characterized by EWSR1-ETS fusions, is predominantly observed in populations of European ancestry. A genome-wide association study of at least 401 French ES patients compared to either 684 French or 3668 US self-described Caucasian controls consistently revealed candidate loci at chromosomes 1 and 10 (p<10-6). These loci were further replicated in two independent sets of cases and controls. Joint analysis identified rs9430161 (p=1.4x10-20; OR=2.2, CI99=1.8-2.7) 25kb upstream to TARDBP (1p36.22) and rs224278 (p=4.0x10-17 OR=1.7, CI99=1.4-1.9) 5kb upstream to EGR2 (10q21). The frequency of the major risk haplotypes in the European population were observed to be less prevalent in the African population, suggesting that variants at these loci could contribute to the differences in ES incidence observed between continents. TARDBP shares structural similarities with EWSR1 and FUS (TLS) EGR2 is an EWSR1-ETS target gene. Variants at both loci were associated with expression levels of TARDBP, ADO and EGR2.

overall_design: 117 Ewing sarcoma samples were profiled using affymetrix hgu133Plus2 arrays.

first: Olivier

last: Delattre

first: Oliver

last: Greiner

first: Gaelle

last: Pierron

first: Stephanie

last: Reynaud


title: Mouse livers during pneumonia

overall_design: Refer to individual Series


title: Expression data from mouse livers lacking STAT3 and RelA during pneumonia

summary:
A common response to physiological duress is the hepatic acute phase response, a process during which the expression of many genes is altered in the liver.  Amongst these transcripts are those encoding acute phase proteins, defined as circulating proteins with significantly changed concentrations during an acute phase response.  The goal of this study was to determine the influence of two transcription factors, STAT3 and NF-kappaB p65 (RelA), on hepatic gene changes including but not limited to acute phase proteins during bacterial pneumonia.
Using the Cre-LoxP system, mice were generated with combined functional deletions of both STAT3 and RelA in hepatocytes.  In mutant mice, Cre-recombinase was expressed under transcriptional control of an albumin promoter in the presence of homozygous floxed alleles for both STAT3 and RelA.  Wild-type control mice lacked the Cre-recombinase transgene.  Microarray analysis was performed on liver RNA collected from both genotypes of mice in the absence and presence of pneumococcal pneumonia.

overall_design: RNA from 4 separate groups of mice (3 mice per group) was analyzed: 1) Uninfected wild-type control mice; 2) Uninfected mutant mice lacking liver STAT3 and RelA; 3) Control mice infected intratracheally for 24h with 10^6 CFU of Streptococcus pneumoniae (serotype 3); and 4) Mutant mice infected intratracheally for 24h with 10^6 CFU of Streptococcus pneumoniae (serotype 3).


title: Expression data from mouse livers lacking NF-kappaB RelA (p65) during pneumonia

summary:
A common response to physiological duress is the hepatic acute phase response, a process during which the expression of many genes is altered in the liver.  Amongst these transcripts are those encoding acute phase proteins, defined as circulating proteins with significantly changed concentrations during an acute phase response.  The goal of this study was to determine the influence of NF-kappaB RelA (p65) on hepatic gene changes including but not limited to acute phase proteins during bacterial pneumonia.
Using the Cre-LoxP system, mice were generated with functional deletion of NF-kappaB RelA (p65) in hepatocytes.  In mutant mice, Cre-recombinase was expressed under transcriptional control of an albumin promoter in the presence of homozygous floxed alleles for RelA.  Wild-type control mice lacked the Cre-recombinase transgene.  Microarray analysis was performed on liver RNA collected from both genotypes of mice in the absence and presence of pneumococcal pneumonia.


title: Expression data from mouse livers lacking STAT3 during pneumonia

summary:
A common response to physiological duress is the hepatic acute phase response, a process during which the expression of many genes is altered in the liver.  Amongst these transcripts are those encoding acute phase proteins, defined as circulating proteins with significantly changed concentrations during an acute phase response.  The goal of this study was to determine the influence of STAT3 on hepatic gene changes including but not limited to acute phase proteins during bacterial pneumonia.
Using the Cre-LoxP system, mice were generated with functional deletion of STAT3 in hepatocytes.  In mutant mice, Cre-recombinase was expressed under transcriptional control of an albumin promoter in the presence of homozygous floxed alleles for STAT3.  Wild-type control mice lacked the Cre-recombinase transgene.  Microarray analysis was performed on liver RNA collected from both genotypes of mice in the absence and presence of pneumococcal pneumonia.


title: Calcitriol supplementation effects on Ki67 expression and transcriptional profile of breast cancer specimens from post-menopausal patients

status: Public on Feb 18 2012

city: São Paulo

first: Maria Lucia

middle: Hirata

last: Katayama

state: São Paulo

address: Av Dr Arnaldo

department: Radiology and Oncology

country: Brazil

institute: Faculty of Medicine University São Paulo

summary: Background: Breast cancer patients present lower 1,25(OH)2D3 or 25(OH)D3 serum levels than unaffected women. Although 1,25(OH)2D3 pharmacological concentrations of 1,25(OH)2D3 may exert antiproliferative effects in breast cancer cell lines, much uncertainty remains about the effects of calcitriol supplementation in tumor specimens in vivo. We have evaluated tumor dimension (ultrassonography), proliferative index (Ki67 expression), 25(OH)D3 serum concentration and gene expression profile, before and after a short term calcitriol supplementation (dose to prevent osteoporosis) to post-menopausal patients. Results: Thirty three patients with operable disease had tumor samples evaluated. Most of them (87.5%) presented 25(OH)D3 insufficiency (<30 ng/mL). Median period of calcitriol supplementation was 30 days. Although tumor dimension did not vary, Ki67 immunoexpression decreased after supplementation. Transcriptional analysis of 15 matched pre/post-supplementation samples using U133 Plus 2.0 GeneChip (Affymetrix) revealed 18 genes over-expressed in post-supplementation tumors. As a technical validation procedure, expression of four genes was also determined by RT-qPCR and a direct correlation was observed between both methods (microarray vs PCR). To further explore the effects of near physiological concentrations of calcitriol on breast cancer samples, an ex vivo model of fresh tumor slices was utilized. Tumor samples from another 12 post-menopausal patients were sliced and treated in vitro with slightly high concentrations of calcitriol (0.5nM), that can be attained in vivo, for 24 hours In this model, expression of PBEF1, EGR1, ATF3, FOS and RGS1 was not induced after a short exposure to calcitriol. Conclusions: In our work, most post-menopausal breast cancer patients presented at least 25(OH)D3 insufficiency. In these patients, a short period of calcitriol supplementation may prevent tumor growth and reduce Ki67 expression, probably associated with discrete transcriptional changes. This observation deserves further investigation to better clarify calcitriol effects in tumor behavior under physiological conditions.

overall_design: Post-menopausal patients with early stage breast cancer, in the absence of distant metastasis, were invited to take part in the study. This protocol was approved by the Institutional Ethics Committee, and a written informed consent was signed by all participants. Patients had blood and tumor samples collected during biopsy, and were prescribed calcitriol supplementation, (Rocaltrol)TM 0.50 ug/day PO, as recommended for osteoporosis prevention. Tumor specimens obtained during biopsy (pre-supplementation) or breast surgery (post-supplementation) were hand dissected and samples with at least 70% tumor cells were further processed. Breast surgery followed in about one month

first: Maria-Lucia

first: Maria-Aparecida

last: Folgueira


title: Expression data from embryonic mouse pleuroperitoneal folds and diaphragms

first: Meaghan

middle: Kathleen

last: Russell

address: 185 Cambridge Street

summary:
Microarray data from this study represent the first global transcriptional survey of gene expression during early compared to late diaphragm formation.
Based on the assumption that Congenital diaphragmatic hernia (CDH) candidate genes will have similar temporal expression trends and will be part of the same biological pathways as those already implicated in CDH, we used known CDH-associated genes as “baits” to filter expression microarray data sets (GSEA and STEM) to identify a list of novel CDH candidate genes.

overall_design: Laser-capture microdissected C57BL/6J mouse embryonic diaphragm tissues were studied at three key time-points during normal development. We studied the primordial diaphragm’s pleuroperitoneal folds at E11.5 and E12.5, and the muscularized mature diaphragm at E16.5 to identify genes and pathways that characterize important stages in diaphragm morphogenesis.

first: Patricia

last: Donahoe


title: Overexpression of BglJ and LeuO in Escherichia coli K12

status: Public on Feb 08 2012

city: Cologne

first: Karin

last: Schnetz

address: Zuelpicher Str. 47a

department: Institute for Genetics

institute: University of Cologne

summary: The only target locus of transcription factor BglJ known to date is the bgl operon, and activation of bgl by BglJ requires RcsB. Transcription factor LeuO is involved in stress responses and known as antagonist of H-NS. To identifiy novel targets of BglJ, we overexpressed BglJ in Escherichia coli K12 and measured differential gene expression by performing DNA microarray analysis. Moreover, to analyze whether all targets of BglJ require RcsB, we overexpressed BglJ in an rcsB deletion background. In addition, we overexpressed LeuO to identifiy targets of LeuO.

overall_design: We expressed BglJ from plasmid pKETS1 in Δ(yjjP-yjjQ-bglJ) strain T75 (sample group 1), LeuO from plasmid pKEDR13 (sample group 3) and used empty vector pKESK22 as control (sample group 2). To study dependence of BglJ on RcsB, we expressed BglJ from pKETS1 in Δ(yjjP-yjjQ-bglJ) ΔrcsB strain T175 (sample group 4) and used pKESK22 as control (sample group 5). Additionally, we expressed BglJ from pKETS1 in Δ(yjjP-yjjQ-bglJ) ΔleuO strain T177 (sample group 6) and used pKESK22 as control (sample group 7). For each sample group, four independent biological replicates were analyzed. We interpreted the expression values as follows: comparing expression pattern of sample group 1 with group 2 gives all loci expressed dfferentially in presence of BglJ, comparing group 3 with group 2 gives all loci expressed differentially in presence of LeuO. Comparing group 4 with group 5 gives all RcsB-independent target loci of BglJ. Comparing group 6 with group 7 gives all LeuO-independent target loci of BglJ.

first: Thomas

last: Stratmann

first: Peter

last: Frommolt

last: Nürnberg


title: Comparison of hepatic gene expression between short-term calorie restricted wild-type and Dgat1 deficient middle-aged female mice

status: Public on Feb 09 2012

city: Cincinnati

first: Nathan

last: Salomonis

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

summary:
Leanness is associated with increased lifespan and is linked to favorable metabolic conditions promoting life extension.
We show here that deficiency of the lipid synthesis enzyme acyl CoA:diacylglycerol acyltransferase 1 (DGAT1), which reduces body fat in mice, promotes longevity. Female DGAT1-deficient mice were protected from age-related increases in body fat, non-adipose tissue triglycerides, and markers of inflammation in white adipose tissue. These metabolic changes were accompanied by an increased mean and maximal lifespan of ~25% and ~10%, respectively. The gene expression profile of DGAT1-deficient mice was not highly correlated with calorie restriction of sex and age matched wild-type littermates. Our findings indicate that loss of DGAT1-mediated lipid synthesis results in leanness, protects against age-related metabolic consequences, and thus extends longevity.

overall_design: Liver gene expression profiles between short-term calorie restricted wild-type (WTCR) and Dgat1 deficient (KO) middle-aged (15-16 mo) female mice were compared to determine if calorie restriction and Dgat1 deficiency rely on common regulatory pathways for the promotion of longevity. Both CR and KO were compared to middle-aged wild-type female littermates fed a standard chow diet ad libitum (WTAL).

first: Carrie

last: Grueter

first: Robert

middle: V

last: Farese


title: Microarray analysis of wildtype and Klf3 KO E14.5 fetal liver cells (TER119- and TER119+)

status: Public on Feb 07 2012

city: University of NSW

first: Alister

last: Funnell

address: School of Biotechnology and Biomolecular Sciences

institute: University of NSW

summary:
The aim of this experiment was to investigate the role of KLF3 in regulating gene expression at different stages throughout the erythroid maturation process.
Affymetrix microarrays were performed on fetal liver cells (both TER119- progenitor cells and TER119+ erythroblast cells) from E14.5 wildtype and Klf3 KO mice.

overall_design: Four wildtype TER119- replicates, four Klf3 KO TER119- replicates, four wildtype TER119+ replicates, three Klf3 KO TER119+ replicates. All are from E14.5 fetal liver.

first: Merlin

last: Crossley


title: Gene-expression profiling of ZNF217-overexpressing MDA-MB-231 cells

status: Public on Feb 06 2012

city: Lyon

first: Julie

last: Vendrell

state: Select a State or Province

address: 8 avenue Rockefeller

department: INSERM U1052

institute: ISPBL - Faculté de Pharmacie de Lyon

summary: To obtain an overview of the cellular functions regulated by ZNF217 signaling in breast-cancer cell lines, we performed global gene-expression profiling on MDA-MB-231-pcDNA6 and MDA-MB-231-ZNF217 cells

overall_design: Two independent cell-culture replicates from the total population of MDA-MB-231-pcDNA6 and MDA-MB-231-ZNF217 stable transfectants were used to generate total RNA. Total RNA was extracted from cell culture using a Qiagen RNA extraction kit and RNA quality was assessed using the BioAnalyzer 2100™ (Agilent Technologies). Complex probes were produced from these RNA, then hybridized to Human genome U133 Plus 2.0 array according to the manufacturer’s recommendations (Affymetrix).

first: P

last: Cohen


title: Microarray analysis of wildtype and Klf1-/- E13.5 fetal liver

summary:
The aim of this experiment was to investigate the role of KLF1 in the fetal liver
Affymetrix microarrays were performed on fetal liver cells from E13.5 wildtype and Klf1-/- mice.

overall_design: Three wildtype replicates and three Klf1-/- replicates, all from E13.5 fetal liver.

first: Laura

last: Norton


title: Wildtype vs. CENPF knockout heart comparison

status: Public on Feb 01 2012

city: Nashville

first: David

last: Bader

address: Pierce

institute: Vanderbilt

summary: We are comparing differential gene expression in WT vs. CENPF knockout hearts

overall_design: RNA was extracted from WT and CENPF knockout mouse hearts at 12 months and submitted to Vanderbilt Microarray core for processing

first: Paul

middle: M

last: Miller

first: Ellen

last: Dees

first: Cristi

last: Galindo


title: Uropathogenic E. coli UTI89 cells in the presence of dimethyl sulfoxide or ethanol

status: Public on Feb 15 2012

city: Stanford

first: JI YOUN

last: Lim

state: CA

address: 380 Roth way, KECK 359

department: Chemistry

institute: Stanford University

summary: The expression levels of uropathogenic E. coli (UPEC) UTI89 cells in YESCA broth with and without 4% dimehtyl sulfoxide (DMSO) and 2% ethanol (EtOH) were studied.

overall_design: To determine the up- or down-regulated expression profile in the presence of dimethyl sulfoxide (DMSO) and ethanol (EtOH),  UPEC UTI89 were grown in YESCA broth with 4% dimethyl sulfoxide (DMSO) or 2% ethanol (EtOH) or no comound at 26°C with 200 rpm shaking for 24 hours were used for RNA extraction and hybridization on Affymetrix microarrays.

first: JIYOUN

last: LIM

first: LYNETTE

last: CEGELSKI


title: Characterization of colon cancer cells: a functional approach characterizing CD133 as a potential stem cell marker

status: Public on Feb 02 2012

city: Freiburg

first: Jaga

last: Virayah

address: Am Flughafen 12-14

institute: Oncotest GmbH

summary:
Background: Isolation and characterization of tumourigenic colon cancer initiating cells may help to develop novel diagnostic and therapeutic procedures.   Methods: We characterized a panel of fourteen human colon carcinoma cell lines and their corresponding xenografts for the surface expression of different potential stem cell markers: CD133, CD24, CD44, CDCP1 and CXCR4. In five cell lines and nine xenografts mRNA expression of the investigated markers was determined. Tumour growth behaviour of CD133+, CD133- and unsorted SW620 cells was evaluated in vivo.   Results: All surface markers showed distinct expression patterns in the examined tumours. Analyses of the corresponding xenografts revealed a significant reduction of cell numbers expressing the investigated markers. CD44 and CXCR4 mRNA expression correlated within the cell line panel and CD44 and CDCP1 within the xenograft panel, respectively. Small subpopulations of double and triple positive cells could be described. SW620 showed significantly higher take rates and shorter doubling times in vivo when sorted for CD133 positivity.  Conclusion: Our data support the hypothesis of a small subset of cells with stem cell-like properties characterized by a distinct surface marker profile. In vivo growth kinetics give strong relevance for an important role of CD133 within the mentioned surface marker profile.
Key words: colon cancer, tumour stem cell, CD133

overall_design: Affymetrix® HG-U133 Plus 2.0 mRNA expression arrays were used to determine the expression. CEL result files were pre-processed using the gc-RMA  (Zhijin Wu and Rafael A, 2004) algorithm. This microarray analysis was performed for a distinct colon cancer panel including 9 of the 11 xenografts evaluated for stem cell marker expression and 5 of the above mentioned cell lines.

first: Meike

last: Schneider

first: Johannes

last: Huber

first: Boris

last: Hadaschik

first: Gabrielle

last: Siegers

first: Heinz

last: Fiebig

first: Julia

last: Schüler


title: Expression data from bone marrow cultures treated with adiponectin - evidence for lipopolysaccharide contamination

city: Auckland

first: Dorit

last: Naot

address: Private Bag 92019

department: Medicine

country: New Zealand

institute: University of Auckland

summary:
The adipocyte-derived hormone adiponectin potently inhibits osteoclast formation in vitro.
Gene expression profiling of murine bone marrow cells treated with adiponectin was used to identify candidate genes that mediate the effect of adiponectin to inhibit osteoclastogenesis in these cultures. However, we found that contamination by lipopolysaccharide confounds the study of adiponectin activity.

overall_design: Bone marrow cells were cultured for up to five days and RNA was extratced from cells treated with adiponectin and from untreated controls at different time points.

first: Greg

middle: D

last: Gamble

first: Garry

last: Williams


title: Expression profiles of a panel of MSS and MSI colon cancer cell lines

city: Heidelberg

first: John

last: Mariadason

state: Victoria

address: 145-163 Studley Road

department: Austin Health

institute: Ludwig Institute for Cancer Reserach

summary: Expression profiling was used to identify genes differentially expressed in MSS (microsatellite stable) and MSI (microsatellite unstable) colon cancer cell lines.  Data submitted in support of manuscript entitled Villin expression is frequently lost in poorly differentiated colon cancer, Diego Arango, Sheren Al-Obaidi, David S. Williams, Jose Dopeso, Rocco Mazzolini, Georgia Corner, Do-Sun Byun, Carmel Murone, Lars Tögel, Nikolajs Zeps, Lauri A. Aaltonen, Barry Iacopetta and John M. Mariadason, American Journal of Pathology, 2012.

overall_design: 5 microsatellite stable (MSS) and 5 microsatellite unstable (MSI) colon cancer cell lines profiled.  Each cell line grown and arrayed in duplicate, and the duplicates averaged for each cell line before calculating means for MSS and MSI lines.


title: Expression profiling of prostate cancer VCaP and VCS2

city: Toronto

first: Housheng

middle: Hansen

last: He

state: Ontario

address: 101 College Street, PMCRT 11-305

department: Medical Biophysics

institute: UNIVERSITY HEALTH NETWORK

summary: Microarray experiments were performed for VCaP and VCS2 cells with and without androgen stimulation

overall_design: The RNA samples were extracted from VCaP and VCS2 cells treated with Ethanol or 10nM DHT for 24 hours. RNA was submitted to Dana-Farber Cancer Institute Microarray Core Facility for hybridyzation.

first: Changmeng

last: Cai

middle: H

first: Myles

last: Brown

first: Steven

last: Bulk


title: mRNA expression profiling of human immune cell subset (Roche)

status: Public on Jan 31 2012

city: Nutley

first: Donavan

last: Cheng

address: 340 Kingsland Ave

department: Translational Research Sciences

institute: Hoffmann-LaRoche

summary: Blood consists of different cell populations with distinct functions and correspondingly, distinct gene expression profiles. In this study, global miRNA expression profiling was performed across a panel of nine human immune cell subsets (neutrophils, eosinophils, monocytes, B cells, NK cells, CD4 T cells, CD8 T cells, mDCs and pDCs) to identify cell-type specific miRNAs.  mRNA expression profiling was performed on the same samples, to determine if miRNAs specific to certain cell types down-regulated expression levels of their target genes.  Six cell-type specific miRNAs (miR-143; neutrophil specific, miR-125; T cells and neutrophil specific, miR-500; monocytes and pDC specific, miR-150; lymphoid cells specific, miR-652 and miR-223; both myeloid cells specific) were negatively correlated with expression of their predicted target genes.  These results were further validated using an independent cohort where similar immune cell subsets were isolated and profiled for both miRNA and mRNA expression. miRNAs negatively correlated with target gene expression in both cohorts were identified as candidates for miRNA-mRNA regulatory pairs and were used to construct a cell-type specific regulatory network.  miRNA-mRNA pairs formed two distinct clusters in the network corresponding to myeloid (nine miRNAs) and lymphoid lineages (two miRNAs). Several myeloid specific miRNAs targeted common genes including ABL2, EIF4A2, EPC1 and INO80D; these common targets were enriched for genes involved in the regulation of gene expression (p < 9.0E-7). Those miRNA might therefore have significant further effect on gene expression by repressing the expression of genes involved in transcriptional regulation. The miRNA and mRNA expression profiles reported in this study form a comprehensive transcriptome database of various human blood cells and serve as a valuable resource for elucidating the role of miRNA mediated regulation in the establishment of immune cell identity.

overall_design: Nine cell subsets (CD16+CD66b+ Neutrophils, CD16-CD66b+ Eosinophils, CD14+ Monocytes, CD4+ T cells, CD8+ T cells, CD56+ NK cells, CD19+ B cells, CD123+ pDCs and CD11c+ mDCs) were isolated from healthy human blood and assessed for cell type purity by flow cytometry.  Cell types were isolated from 5 pools of 5 healthy donors each, with the exception for monocytes, where 10 pools were used.  RNA obtained from these purified populations were subsequently used for miRNA and mRNA expression profiling by Affymetrix GeneChip miRNA and HG-U133Plus2.0 microarrays.

first: Florence

last: Allantaz

first: Tobias

last: Bergauer

first: Palanikumar

last: Ravindran

first: Michel

last: Rossier

first: Martin

last: Ebeling

first: Laura

last: Badi

first: Bernhard

last: Reis

first: Hans

last: Bitter

first: Matilde

last: D'Asaro

first: Alberto

last: Chiappe

first: Sriram

last: Sridhar

first: Gonzalo

last: Duran Pacheco

first: Michael

middle: E

last: Burczynski

first: Denis

last: Hochstrasser

first: Jacky

last: Vonderscher

first: Thomas

last: Matthes


title: Analysis of A375 and A375 clones that acquired resistance to GSK2118436 after treatment with GSK2118436 (GSK436), GSK1120212 (GSK212), or the combination of GSK2118436 and GSK1120212 for 24 hour

city: Collegeville

first: Vivian

last: Zhang

address: 1250 S. Collegeville Rd

department: Oncology Translational Research

institute: GlaxoSmithKline

summary:
In an effort to understand the mechanisms of acquired resistance to BRAF inhibitors, we isolated clones that acquired resistance to the BRAF inhibitor GSK2118436 derived from the A375 BRAF V600E mutant melanoma cell line. This resistance clones acquired mutations in NRAS and MEK1. One clones, 16R6-4, acquired two mutations in NRAS – Q61K and A146T. Proliferation and western blot analyses demonstrated that these clones were insensitive to single agent GSK2118436 or GSK1120212 (an allosteric MEK inhibitor) but were sensitive to the combination of GSK2118436 and GSK1120212. To further characterize this combination, global transcriptomic analysis was performed in A375 and 16R6-4 after 24 hour treatment with GSK2118436, GSK1120212 or the combination of GSK2118436 and GSK1120212.
This data set was published in Molecular Cancer Therapeutics with the title “Combined inhibition of BRAF and MEK, BRAF and PI3K/mTOR, or MEK and PI3K/mTOR overcomes acquired resistance to the BRAF inhibitor GSK2118436, mediated by NRAS or MEK mutations” by Greger, J.G., et.al.

overall_design: A375 and 16R6-4 (an A375 derived GSK2118436 resistance clone) were treated for 24 hours with 0.1 micromolar GSK2118436, 1 micromolar GSK2118436, 0.01 micromolar GSK1120212, 0.1 micromolar GSK2118436 + 0.01 micromolar GSK1120212, or 1 micromolar GSK2118436 + 0.01 micromolar GSK1120212.

first: James

last: Greger


title: Expression data from furfural-tolerant E. coli strain and wild type under furfural stress

status: Public on Jan 28 2012

city: Beijing

first: Jianqing

last: Wang

state: Beijing

address: One Tsinghua Graden Road

department: Chemical Engineering

institute: Tsinghua University

summary:
Cellular tolerance toward furfural is a complex phenotype involved many genes, and hard to be improved by manipulating individual genes. We previously established exogenous global regulator IrrE mutants that confer Escherichia coli with significantly enhanced tolerance to furfural stress.
In order to elucidate the mechanism for enhancement of furfural tolerance in the mutants and to identify new genes and pathways that can be possible targets for engineering of furfural tolerance, we carried out comparative transcriptomic with the representative strains F1-37 and WT (harboring the furfural-tolerant mutant F1-37 of IrrE and the wild type IrrE, respectively). The data from transcriptome analyses were deposited here.

overall_design: Cells of furfural-tolerant mutant F1-37 and wild-type strain WT were grown in LB medium supplemented with furfural, and the cells were harvested in the exponential phase. The samples for both of these two strains were prepared in triplicate with biological replicates.

first: Zhanglin

last: Lin


title: Genome-wide transcription analysis of Escherichia coli in response to extremely low-frequency magnetic fields

city: Leipzig

first: Simona

middle: Gabriele

last: Huwiler

address: Bruederstr. 34

department: Institute of Biochemistry

institute: University of Leipzig

summary: The widespread use of electricity raises the question of whether or not 50 Hz (power line frequency in Europe) magnetic fields (MFs) affect organisms. We investigated the transcription of Escherichia coli K-12 MG1655 in response to extremely low-frequency (ELF) MFs. Fields generated by three signal types (sinusoidal continuous, sinusoidal intermittent, and power line intermittent; all at 50 Hz, 1 mT), were applied and gene expression was monitored at the transcript level using an Affymetrix whole-genome microarray. Bacterial cells were grown continuously in a chemostat (dilution rate D = 0.4 h-1) fed with glucose-limited minimal medium and exposed to 50 Hz MFs with a homogenous flux density of 1 mT. For all three types of MFs investigated, neither bacterial growth (determined using optical density) nor culturable counts were affected. Likewise, no statistically significant change (fold-change > 2, P ≤ 0.01) in the expression of 4,358 genes and 714 intergenic regions represented on the gene chip was detected after MF exposure for 2.5 h (1.4 generations) or 15 h (8.7 generations). Moreover, short-term exposure (8 min) to the sinusoidal continuous and power line intermittent signal neither affected bacterial growth nor showed evidence for reliable changes in transcription. In conclusion, our experiments did not indicate that the different tested MFs (50 Hz, 1 mT) affected the transcription of E. coli.

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

overall_design: A total of 60 chips are included in this study. Each comparison (treated vs. sham-treated cultures; untreated negative control cultures) consists of three replicates. The three magnetic field test conditions include sinusoidal continous, sinusoidal intermittent (2 min on, 4 min off) and power line intermittent (2 min on, 4 min off). Exposure periods were 8 min, 2.5 h, or 15 h. The response control consists of E. coli cells treated for 10 min with 1 mM H2O2 or the equivalent water volume. The negative control comprises samples taken from cultures grown with the exposure chambers swiched off.

first: Christian

last: Beyer

first: Jürg

last: Fröhlich

first: Hauke

last: Hennecke

last: Egli

first: David

last: Schürmann

first: Hubert

last: Rehrauer

first: Hans-Martin

last: Fischer


title: Gene expression profiles of p53 depleted human mammary epithelial cells with their Ras-infected epithelial and mesenchymal derivatives

first: stéphane

last: ansieau

address: 28 rue Laennec

department: Centre Léon Bérard

institute: Inserm U590

summary: The epithelial-mesenchymal transition (EMT) is an embryonic transdiffrentiation program which consists of the conversion of polarized epithelial cells into a motile mesenchymal phenotype. EMT is aberrantly reactivated during tumor progression, promoting metastatic dissemination. Herein, we demonstrate that EMT permissive conditions also favor tumor initiation by minimizing the number of events required for neoplastic transformation. We further demonstrated that even partial commitment of human mammary epithelial cells into an EMT program is sufficient to confer malignant properties, suggesting that the reactivation of embryonic EMT inducers participate to the primary tumor growth long before the initiation of the invasion-metastasis cascade.

overall_design: Human mammary epithelial cells (HMEC) were sequentially depleted in p53 through RNA interference (shp53), transduced with H-RasG12V and immortalized by hTert. Two different Tert/shp53/Ras cell population emerge that display either an epithelial (Epi) or a mesenchymal (Mes) phenotype. Gene expression profiles of the Tert/shp53 control cells and of tert/shp53/Ras/Epi and Tert/shp53/Ras/Mes were analyzed.

first: MOREL

last: Anne-Pierre

first: ANSIEAU

last: Stéphane


title: Reprogramming of prostate cancer-associated stromal cells

city: Seattle

first: Alvin

middle: Y

last: Liu

state: WA

address: 815 Mercer Street Box 358056

department: Urology

institute: University of Washington

summary: CD90+ prostate cancer-associated (CP) stromal cells represent a disease cell type found only in tumor tissue. Genetic reprogramming by induced pluripotent stem (iPS) cell technology might be used to “normal gene expression of diseased cells thereby providing a cure. The resultant iPS cells would no longer express the disease program, and, like stem cells, might respond to normal differentiative signaling. Thus, CP stromal cells, isolated from tumor tissue and cultured in vitro, were transfected with POU5F1/LIN28/NANOG/SOX2 lentiviral vectors. iPS cells were obtained at a frequency of 10^4. Transcriptome analysis showed an almost complete match in gene expression between the iPS cells and human embryonic stem cells. Genes of CP stromal cells were fully inactivated.

overall_design: CP stromal cells were isolated from tissue, cultured and transfected with lentiviral vectors containing NANOG, SOX2, POU5F1, LIN28. The resultant induced pluripotent cells were analyzed by DNA microarrays.


title: Progesterone inhibits epithelial-to-mesenchymal transition in endometrial cancer: patient data

status: Public on Jan 26 2012

city: Rotterdam

first: Paul

last: van der Horst

address: PO box 2040

department: Obstetrics & Gynaecology

country: Netherlands

institute: Erasmus University Medical Center

summary: Every year more than 42,000 women die of endometrial cancer, mainly due to recurrent or metastatic disease. The presence of tumor infiltrating lymphocytes (TILs) as well as progesterone receptor (PR) positivity has been correlated with improved prognosis. This study describes two mechanisms by which progesterone inhibits metastatic spread of endometrial cancer: by stimulating T-cell infiltration and by inhibiting epithelial-to-mesenchymal cell transition (EMT). Paraffin sections from patients with (n=9) or without (n=10) progressive endometrial cancer (recurrent or metastatic disease) were assessed for the presence of CD4+ (helper), CD8+ (cytotoxic) and Foxp3+ (regulatory) T-lymphocytes and PR expression. Progressive disease was observed to be associated with significant loss of TILs and loss of PR expression. Frozen tumor samples, used for genome-wide expression analysis, showed significant regulation of pathways involved in immunosurveillance, EMT and metastasis. For a number of genes, such as CXCL14, DKK1, DKK4 and WIF1, quantitive RT-PCR was performed to verify down regulation in progressive disease. To corroborate the role of progesterone in regulating invasion, Ishikawa (IK) endometrial cancer cell lines stably transfected with PRA (IKPRA), PRB (IKPRB) and PRA+PRB (IKPRAB) were cultured in the presence/absence of progesterone (MPA) and used for genome-wide expression analysis, Boyden- and wound healing migration assays, and IHC for known EMT makers. IKPRB and IKPRAB cell lines showed MPA induced inhibition of migration and loss of the mesenchymal marker vimentin at the invasive front of the wound healing assay. Furthermore, pathway analysis of significantly MPA-regulated genes showed significant down regulation of important pathways involved in EMT, immunesuppression and metastasis: such as IL6-, TGF-β and Wnt/β-catenin signalling. Intact progesterone signaling in non-progressive endometrial cancer seems to be an important factor stimulating immunosurveillance and inhibiting transition from an epithelial to a more mesenchymal, more invasive phenotype.

overall_design: From 4 non-progressive and 4 progressive patients, snap-frozen endometrial cancer tumor specimens were used for microarray analysis. Gene expression data of progressive disease was compared with non-progressive disease.

first: Yongyi

first: Ingrid

last: Vandenput

first: Liesbeth

middle: C

last: Kühne

first: Patricia

last: Ewing

first: Wilfred

last: van IJcken

first: Marten

last: van der Zee

first: Frederic

last: Amant

first: Curt

middle: W

last: Burger

first: Leen

last: Blok


title: aNOF vs. CAF

status: Public on Jan 27 2012

city: Chicago

first: Youjia

last: Hua

state: IL

address: 303 East Superior Street, Lurie 6-220

institute: Northwestern University

summary: Compare the difference between pairwise aNOF and CAF samples for two patients

overall_design:
patient #225: aNOF #225 vs CAF #225
patient #248: aNOF #248 vs CAF #248

first: Anirban

middle: K

last: Mitra

first: Marion

middle: R

last: Zillhaldt

first: Papal

last: Tiwari

first: Marcus

last: Peter

first: Ernst

last: Lengyel


title: Progesterone inhibits epithelial-to-mesenchymal transition in endometrial cancer

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

overall_design: Refer to individual Series


title: Gene expression from Mouse Embryonic Fibroblasts

city: Barcelona

first: Jose

last: Aramburu

address: Carrer Doctor Aiguader 88

department: Experimental and Health Sciences

country: Spain

institute: Universitat Pompeu Fabra

summary:
Gene expression from Wild-type and NFAT5 knock-out Mouse Embryonic Fibroblasts
keywords: Mouse Embryonic Fibroblasts

overall_design: We analyzed 3 arrays from each condition: isotonic wild-type MEFs, hypertonic treated wild-type MEFs , isotonic wild-type MEFs pretreated for 1 hour with 100 nM Torin1, hypertonic treated wild-type MEFs pretreated for 1 hour with 100 nM Torin1, isotonic knock-out MEFs and hypertonic treated knock-out MEFs.

first: Mari

last: Ortells


title: NOF vs. iCAF 4d

summary: Compare the difference between pairwise NOF and iCAF (4d) tissues for one patient

overall_design: patient #626: NOF #626 vs iCAF #626


title: NOF vs. coCAF 7d

summary: Campare the difference between pairwise NOF and coCAF tissues for three patients

overall_design:
patient #603: NOF #603 vs coCAF #603
patient #609: NOF #609 vs coCAF #609
patient #612: NOF #612 vs coCAF #612


title: mRNA expression profiling of human immune cell subsets (HUG)

first: Donavan

last: Cheng

state: NJ

first: Florence

last: Allantaz

first: Tobias

last: Bergauer

first: Palanikumar

last: Ravindran

first: Michel

middle: F

last: Rossier

first: Martin

last: Ebeling

first: Laura

last: Badi

first: Bernhard

last: Reis

first: Hans

last: Bitter

first: Matilde

last: D'Asaro

first: Alberto

last: Chiappe

first: Sriram

last: Sridhar

first: Gonzalo

last: Duran Pacheco

first: Michael

last: Burczynski

first: Denis

last: Hochstrasser

first: Jacky

last: Vonderscher

first: Thomas

last: Matthes


title: Cancer-associated fibroblast transfected with miR-155, anti-miR-31 and anti-miR-214

first: Youjia

last: Hua


title: Genome-wide maps of chromatin state in mouse erythroid cells.

status: Public on Jan 30 2012

city: Oxford

first: Monika

middle: S

last: Kowalczyk

state: Oxfordshire

address: Headley Way

department: MRC Molecular Haematology Unit

country: United Kingdom

institute: Weatherall Institute of Molecular Medicine, University of Oxford

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We generated genome-wide chromatin state and RNA Polymerase II binding maps in mouse erythroid cells by ChIP-Seq.

overall_design: Examination of 4 different histone modifications (H3K4me3, H3K4me1, H3K27me3, H3K27ac) and RNA Polymerase II (RNAP2) binding in mouse erythroid cells  (Ter119+).

first: Magnus

last: Lynch

first: Jim

last: Hughes

first: Douglas

last: Higgs


title: NOF vs. iCAF 2d

summary: Compare the difference between pairwise NOF and iCAF (2d) tissues for one patient

overall_design: patient #474: NOF #474 vs iCAF #474

first: Anirban

last: Mitra

first: Marion

last: Zillhaldt

first: Papal

last: Tiwari

first: Marcus

last: Peter

first: Ernst

last: Lengyel


title: Genome-wide analysis of gene expression in isoflavone and 3,3’-diindolylmethane treated C4-2B prostate cancer cells

status: Public on Jan 25 2012

city: Detroit

first: Fazlul

middle: H.

last: Sarkar

state: MI

address: 4100 John R

department: Pathology

institute: Wayne State University School of Medicine

summary: Expression profiling of isoflavone and 3,3’-diindolylmethane treated C4-2B prostate cancer cells was conducted using Affymetrix Human Genome U133 Plus 2.0. Array

overall_design: C4-2B prostate cancer cells were treated with isoflavone and B-DIM for 6 hours or longer up to 72 hours. Gene expression profiling was conducted


title: Progesterone inhibits epithelial-to-mesenchymal transition in endometrial cancer: cell line data

first: Paul

last: van der Horst

overall_design: The PRA- and PRB-expressing Ishikawa endometrial cancer cell line (IKPRAB36) was cultured for 48h in the absence or presence of 1nM MPA (n = 3). The RNA was isolated and used for hybridization on Affymetrix microarrays. Cells cultured in the presence of MPA were compared with cells cultured in the absence of MPA.

first: Yongyi

last: Wang

first: Ingrid

last: Vandenput

first: Liesbeth

last: Kühne

first: Patricia

last: Ewing

first: Wilfred

last: van Ijcken

first: Marten

last: van der Zee

first: Frederic

last: Amant

first: Curt

last: Burger

first: Leen

middle: J

last: Blok


title: Expression data from human cord blood CD161++/CD161+/CD161- CD8+ T cell subsets

first: Natasha

last: Sahgal

address: Old Road Campus

department: Ludwig Institute of Cancer Research

institute: University of Oxford

summary: We used microarray to compare gene expression between CD161++/CD161+/CD161-CD8+ T cells from human cord blood.

overall_design: Lymphocytes from freshly obtained human cord blood samples were isolated by Ficoll density centrifugation. CD8+ T cells were purified by negative selection using magnetic beads and subsequently labelled with fluorescent antibodies prior to sorting using MoFlo MLS cell sorter (Dako).

first: Lucy

last: Walker

first: Yu-Hoi

last: Kang

first: Matthew

middle: O

last: Smith

first: Hannah

last: Tharmalingham

first: Narayan

last: Ramamurthy

first: Vicki

last: Fleming

first: Alistair

last: Leslie

first: Ye

last: Oo

first: Alessandra

last: Geremia

first: Thomas

last: Scriba

first: Willem

middle: A

last: Hanekom

first: Georg

last: Lauer

first: Olivier

last: Lantz

first: David

last: Adams

first: Fiona

last: Powrie

first: Eleanor

last: Barnes

last: Klenerman


title: Expression data from healthy human CD161++CD8aa and CD161++CD8ab T cells

first: Natasha

last: Sahgal

summary: We used microarrays to compare gene expression between healthy human CD161++CD8aa and CD161++CD8ab T cells.

overall_design: We sorted freshly obtained peripheral blood mononucleocytes from healthy controls by first using magnetic beads to negatively select for CD8a+ T cells, fluorescently labelling isolated cells with antibodies and subsequent sorting using MoFlow MLS cell sorter (DAKO). Sorted samples were snap frozen. RNA was later extracted from the sorted populations prior to hybridization to Affymetrix arrays.

last: Walker

middle: M

first: Paul


title: Human MAIT and CD8++ cell development


title: Expression levels in strained vs. non-strained Calu-3 lung epithelial cells

status: Public on Jan 24 2012

city: Aurora

first: Michael

last: Koeppen

institute: Univeristy of Colorado - Anschutz Medical Campus

summary: Ventilator induced lung injury can lead to serious conditions like ARDS which are associated with a high mortality (around 30%, Stapleton et al., Chest, 2005). We hypothesized that changes of expression levels of different genes would lead us to the identification of critical target genes, which might influence the inflammation and outcome associated with this condition.  We used human whole genome U133 Plus 2.0 microarrays to detail the changes of gene expression and identified distinct classes of up-regulated genes during this process.

overall_design: Confluent non strained and strained human Calu-3 cells were selected for RNA extraction and hybridization on Affymetrix microarrays.

first: K

last: Brodsky

first: H

last: Eltzschig


title: Expression data from Bone-Marrow Mesenchymal Stromal Cells (BM-MSC) from Follicular Lymphoma patient (FL) or Healthy Donor (HD).

city: Rennes

first: Delphine

last: Rossille

address: 2 avenue du Pr. Léon Bernard

institute: INSERM U1236-MOBIDIC

summary:
Human bone marrow mesenchymal stromal cells (BM-MSC) could be committed toward a functional lymphoid-like stroma by a combination of TNFalpha (TNF) and Lymphotoxin alpha1/beta2 (LT) (Amé-Thomas et al Blood 2007).
Bone marrow and lymph node stromal cells support FL malignant cell recruitment and growth in particular after comittment to a lymphoid-like differentiation in vitro.
In addition, more than 70% of FL patients exhibit a bone marrow involvment at diagnosis.
We delineate using Affymetrix U133+2.0 microarrays the gene expression profile of BM-MSC obtained  from FL patients (FL-MSC) and age-matched healthy donors (HD-MSC) in order to identify a specific FL-MSC signature.
In addition, we used Affymetrix microarrays to define the gene expression signature of lymphoid-like stromal cells obtained from HD-MSC by treatment with TNF/LT in vitro. This TNF/LT signature was then used to interpret the gene expression profile of FL-MSC.

overall_design: GEP was performed on 10 BM-MSC from FL patients and 6 from healthy donors, treated or not with TNF(10 ng/mL)/LT(100ng/mL)

first: Fabien

last: Guilloton

first: Karin

last: Tarte


title: Prognostic Significance and Gene Expression Profiles of p53 Mutations in Microsatellite Stable Stage III Colorectal Adenocarcinoma

city: Birmingham

first: Dongquan

last: Chen

state: AL

address: 1717 11th Ave South

institute: Univ of Alabama at Birmingham

summary:
Clinical Significance: Understanding the differences in colorectal cancer (CRC) aggressiveness and clinical outcomes in relation to tumor stage and different molecular subsets is at most important for designing treatment regimens. However, molecular signatures for specific phenotypic subsets that predict the aggressiveness and clinical outcomes of CRC, specifically in advanced disease stage are lacking. Therefore, for the first time, the current study has identified a set of molecular markers that are associated with aggressive Stage III CRCs that exhibited microsatellite stable and mutant p53 phenotypic features. These findings might aid in designing aggressive treatment regimens and help to provide insights into the development of novel therapeutic targets.
Results: Increased incidence of p53 mutations in MSS CRCs (58%) was associated with higher CRC-specific mortality than MSS-p53 wild-type phenotypes (log-rank, P=0.025; and hazard ratio, 2.52; 95% confidence interval, 1.25-5.08). Of 49 down-regulated genes, LPAR6, PDLIM3 and PLAT and of 35 up-regulated genes, TRIM29, FUT3, IQGAP3, and SLC6A8, were confirmed by qNPA, qRT-PCR, and IHC platforms.  Conclusions: p53 mutations are associated with poor prognosis of Stage III microsatellite stable CRCs.

overall_design: p53 wild type vs. mutant tumor samples

first: Upender

last: Manne


title: Silencing of HAI-1 in a human oral squamous cell carcinoma cell line, SAS

city: Miyazaki

first: Tsuyoshi

last: Fukushima

address: 5200 Kihara, Kiyotake

country: Japan

institute: University of Miyazaki

summary:
To examine the role of hepatpcyte growth factor activator inhibitor type 1 (HAI-1) in cancer, we analyzed effect of HAI-1 silencing on gene expression profiles of human oral squamous cell carcinoma cell line, SAS. We used short hairpin RNA (shRNA) directed against HAI-1 mRNA. We constructed retroviral vectors which showed stable and significant silencing effects on HAI-1 genes of SAS.
Microarray data of the expression profiles of duplicated experiments of HAI-1-knockdown SAS with that from the control cell are shown.

overall_design: HAI-1-knockdown SAS and the control cell were proceeded to RNA extraction and hybridization on Affymetrix microarrays. The experiment was repeated respectively  (HAI-1KD_1, HAI-1KD_2, HAI-1con_1, and HAI-1con_2).

first: Takashi

last: Baba

first: Hiroaki

last: Kataoka


title: Combination of a novel gene expression signature with a clinical nomogram improves the prediction of survival in high-risk bladder cancer

status: Public on Jan 23 2012

city: Boston

first: Markus

last: Riester

state: MA

address: 3 Blackfan Circle

department: Biostatistics & Computational Biology

institute: Dana-Farber Cancer Institute

summary: Urothelial carcinoma of the bladder is characterized by significant variability in clinical outcomes depending on stage and grade. The addition of molecular information may improve our understanding of such heterogeneity and enhance prognostic prediction. The purpose of this study was to validate and improve published prognostic signatures for high-risk bladder cancer.

overall_design: We evaluated microarray data from 93 bladder cancer patients managed by radical cystectomy to determine gene expression patterns associated with clinical and prognostic variables.


title: Expression data from 30do mouse spermatid [Affymetrix]

status: Public on Jan 20 2012

city: Canberra

first: Rohan

last: Williams

state: ACT

address: Garran Rd ACTON

institute: ANU

summary:
Chromatin performs numerous functions during cellular differentiation, and therefore it must be capable of adopting a multitude of different structures. How these various structures are established is poorly understood, but we propose that specific histone H2A variants will have a key role in remodelling chromatin during differentiation. Structurally, we show here that the gain of just a single acidic amino acid residue has generated a new mouse ‘H2A.Bbd-like’ histone variant, H2A.Lap1, and that when incorporated into nucleosomal arrays imparts on them unique biophysical properties that are distinct from arrays containing either H2A or human H2A.Bbd. Functionally, we identify H2A.Lap1 as a novel chromatin component of active genes that are expressed during spermatogenesis, and in combination with H2A.Z create a unique chromatin landscape at the start site of transcription. During round spermatid differentiation, H2A.Lap1 dramatically loads onto the inactive X chromosome enabling a subset of its genes to be transcriptionally activated.
We used microarrays together with ChIP-seq data in order to see distribution of Lap1 and expression level of the Lap1 associated genes

overall_design: Total RNA was isolated using TRIzol (Invitrogen) and the RNeasy Mini Kit (Qiagen). Samples were DNase I treated (Roche) and reverse transcribed using Superscript II reverse transcriptase following the manufacturer’s recommendations (Invitrogen). DNA was either analysed by semi–quantitative PCR, real-time qPCR using SYBR Green PCR master mix (Applied Biosystems), or subjected to DNA microarray analysis (in triplicate) using the GeneChip Mouse Gene 1.0 ST Array (Affymetrix). Robust Multichip Average (RMA) correction and probe set summaries were obtained using Affymetrix Power Tools software annotation (Affymetrix) based on the mm9 mouse genome. Unless otherwise stated, all subsequent expression analyses (see Supplementary Methods) were performed in the R statistical computing environment (version 2.11.1).

first: Tatiana

last: Soboleva


title: Kras-induced ikk2/nf-kappaB activation by IL-1 alpha and p62 freedforward loops is required for development of pancreatic ductal adenocarcinoma

city: Houston

last: Chiao

state: Texas

address: 1515 Holcombe Blvd

department: Department of Molecular and Cellular Oncology

institute: The University of Texas M. D. Anderson Cancer Center


title: Congenic dissection of a major QTL for methamphetamine sensitivity implicates epistasis

status: Public on Jan 18 2012

first: Camron

middle: D

last: Bryant

address: 920 E. 58th Street, CLSC 501

department: Human Genetics

institute: The University of Chicago

summary:
We identified a congenic mouse with an introgressed region from the A/J donor inbred strain on an inbred C57BL/6J background that showed a reduced locomotor stimulant response to methamphetamine.   We conducted microarray analysis of the striatum from drug-naive female and male mice that were 6-9 weeks old.   The congenic region is on chromosome 11 and spans approximately 84-96 Mb.  There were two groups of mice used in the analysis:  B6 control mice versus congenic mice.  Congenic mice were collapsed across heterozygous and homozygous genotypes.
All mice are on a C57BL/6J background.  Congenic mice differ only on chromosome 11 where they contain the introgressed A/J alleles from 84-96 Mb.

overall_design: 14 C57BL/6J wildtype mice and 14 B6.A/J congenic mice (84-96 Mb region from A/J strain) were examined for gene expression differences using striatal tissue (left and right punches pooled).  All mice were drug-naïve and were 6-9 weeks old at the time of sacrifice.

first: Loren

last: Kole

last: Guido

first: Greta

last: Sokoloff

first: Abraham

last: Palmer


title: Bisulphite sequencing of native LNCaP and PrEC DNA [methylation array]

city: Zuerich

first: Mark

last: Robinson

address: Winterthurerstrasse 190

department: Institute of Molecular Life Sciences

institute: University of Zuerich

type: Methylation profiling by genome tiling array

summary: As a reference dataset to compare BisChIP-seq and other methylated DNA capture experiments against, we have collected Illumina 450k to profile CpG methylation status on native DNA.

overall_design: Illumina 450k array for LNCaP and PrEC cell lines


title: Sex differences during  acute myocarditis against coxsackievirus B3 (CVB3)-induced myocarditis (10 dpi) and  chronic myocarditis/dilated cardiomyopathy (DCM) against CVB3-induced myocarditis (90 dpi)

status: Public on Jan 19 2012

city: Baltimore

first: DeLisa

last: Fairweather

state: MD

address: 615 N Wolfe St

department: Environmental Health Sciences

institute: Johns Hopkins University

summary: Men are at an increased risk of dying from heart failure caused by inflammatory heart diseases such as atherosclerosis, myocarditis and dilated cardiomyopathy (DCM). We previously showed that immune responses in the heart are phenotypically distinct in male compared to female mice 10 days after infection resulting in severe DCM in males.

overall_design: Groups consisted of Infected Males, Infected Females, Uninfected Males and Uninfected females. There are 3 mice per group. A total of 12 samples were analyzed in this experiment (12 for 10 dpi and 12 for 90 dpi).

first: Michael

last: Coronado

first: Adriana

last: Bucek

first: Djahida

last: Bedja

first: Eric

last: Abston

first: Kathleen

middle: L

last: Gabrielson


title: RNA immunoprecipitation (RIP)-Chip analysis for EWS-bound mRNA

status: Public on Jan 16 2012

city: Aomori

first: Yuji

last: Nakai

state: Aomori

address: 2-1-1, Yanagawa

department: Institute of Regional Innovation

institute: Hirosaki University

summary: Although EWS/FLI-1 fusion protein is responsible for most Ewing’s sarcoma family tumors (ESFT), the function of native EWS remains largely unknown. Here, we first showed that EWS repressed protein expression in a tethering assay. mRNAs bound to EWS were determined by RNA-immunoprecipitation Chip assay, and one of them, proline-rich Akt substrate of 40 kDa (PRAS40) mRNA, directly interacted with EWS. The inhibitor of AKT, API-2, repressed ESFT cell proliferation. We demonstrate that EWS negatively regulated PRAS40 protein expression through binding to PRAS40 3’UTR. Furthermore, PRAS40 knockdown inhibited the proliferation and metastatic potential of ESFT cells.

overall_design: Cytoplasmic lysates or whole cell lysates were prepared from HeLa S3 cells transfected with pFLAG-EWS , and incubated with anti-FLAG M2 Affinity Gel (Sigma) at 4°C for 2 h. RNAs from lysates and immunoprecipitates were analysed using GeneChip Human Genome U133 Plus 2.0 Array (Affymetrix).

first: Lin

last: Huang

first: Iku

last: Kuwahara

first: Ken

last: Matsumoto


title: Gene expression profiles of germ cells, supporting cells, interstitial cells (including steroidogenic precursors), and endothelial cells in the developing testis and ovary at 11.5, 12.5, and 13.5 dpc. (GUDMAP Series ID: 43)

city: Edinburgh

first: GUDMAP

last: Developers

address: Crewe Road

institute: IGMM MRC Human Genetics Unit

summary: The goal of this study is to determine the complete gene expression profile for each cell type of the developing gonad during the critical window in which it adopts the testis or ovarian fate.

overall_design: Transgenic mice with cell type specific fluorescent markers were used to isolate germ cells, supporting cells, interstitial cells (including steroidogenic precursors), and endothelial cells in the developing testis and ovary.  The gonads were dissociated in trypsin, and the fluorescent cells were isolated by FACS.  The RNA was collected from the isolated cells and their gene expression profiles were determined by microarray analysis.

first: Blanche

last: Capel

first: Samantha

last: Jameson


title: Gene expression data from thalamic regions of MPTP-intoxicated mouse brain by acupuncture

city: Seoul

first: Sabina

last: Lim

address: #1 Hoegi-dong Dongdaemoon-gu

country: South Korea

institute: East-West Medical Research Institute, Kyung Hee University

summary:
Acupuncture stimulations at GB34 and LR3 inhibit the reduction of tyrosine hydroxylase in the nigrostriatal dopaminergic neurons in the parkinsonism animal models. Especially, behavioral tests showed that acupuncture stimulations improved the motor dysfunction in a previous study. The thalamus is a crucial area for the motor circuit and has been identified as one of the most markedly damaged areas in Parkinson’s disease (PD), so acupuncture stimulations might also have an effect on the thalamic damage.
We investigated gene expression profile changes in the thalamic region of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-induced parkinsonism models after acupuncture at the acupoints GB34 and LR3

overall_design: C57BL/6 mice were divided into four experimental groups; ① C: Control, ② M: MPTP-treatment only, ③ MA: MPTP- and acupuncture-treatment at acupoints GB34 and LR3, ④ MNA: MPTP- and acupuncture-treatment at non-acupoints. Total RNA was isolated from two brains' thalamic regions of each experimental group (4 experimental group × 2 samples of each experimental group = total 8 samples).

first: Sujung

last: Yeo

first: Yeong-Gon

last: Choi

first: Yeon-Mi

last: Hong


title: miRNA and mRNA expression profiling of human immune cell subsets

city: Nutley

first: Donavan

last: Cheng

address: 340 Kingsland Ave

department: Translational Research Sciences

institute: Hoffmann-LaRoche

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

summary:
Blood consists of different cell populations with distinct functions and correspondingly, distinct gene expression profiles. In this study, global miRNA expression profiling was performed across a panel of nine human immune cell subsets (neutrophils, eosinophils, monocytes, B cells, NK cells, CD4 T cells, CD8 T cells, mDCs and pDCs) to identify cell-type specific miRNAs.  mRNA expression profiling was performed on the same samples, to determine if miRNAs specific to certain cell types down-regulated expression levels of their target genes.  Six cell-type specific miRNAs (miR-143; neutrophil specific, miR-125; T cells and neutrophil specific, miR-500; monocytes and pDC specific, miR-150; lymphoid cells specific, miR-652 and miR-223; both myeloid cells specific) were negatively correlated with expression of their predicted target genes.  These results were further validated using an independent cohort where similar immune cell subsets were isolated and profiled for both miRNA and mRNA expression. miRNAs negatively correlated with target gene expression in both cohorts were identified as candidates for miRNA-mRNA regulatory pairs and were used to construct a cell-type specific regulatory network.  miRNA-mRNA pairs formed two distinct clusters in the network corresponding to myeloid (nine miRNAs) and lymphoid lineages (two miRNAs). Several myeloid specific miRNAs targeted common genes including ABL2, EIF4A2, EPC1 and INO80D; these common targets were enriched for genes involved in the regulation of gene expression (p < 9.0E-7). Those miRNA might therefore have significant further effect on gene expression by repressing the expression of genes involved in transcriptional regulation. The miRNA and mRNA expression profiles reported in this study form a comprehensive transcriptome database of various human blood cells and serve as a valuable resource for elucidating the role of miRNA mediated regulation in the establishment of immune cell identity.

This SuperSeries is composed of the SubSeries listed below.

platform_organism:
Homo sapiens
synthetic construct

overall_design: Refer to individual Series

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