title: RNA Microarray data from embryonic mouse brains wt vs foxf2 mutant

status: Public on Mar 02 2015

city: Gothenburg

first: Ali

middle: Moussavi

last: Nik

address: Medicinaregatan 9C

department: Chemistry and Molecular Biology

institute: Gothenburg University

summary: Brain of the foxf2 mutant mouse embryo shows microvascular aneurysm, underdeveloped blood brain barrier and also significant defects in the tissue integrity. Foxf2 expresses in the pericytes of the brain and seem to play an important role in proper development of the BBB.

overall_design: Brains of E18.5  wt and foxf2 mutant mouse embryos dissected and RNA extracted from the brains using Sigma mammalian total RNA extraction kit. The RNA then been sent to th core facility for hybridization.

first: Peter

last: Carlsson

first: Azadeh

last: Reyahi


title: Expression data from cardiac CD11c+MHC II+ cells

status: Public on Mar 31 2015

city: Fukuoka

first: Yoshitomo

last: Motomura

state: Fukuoka

address: 3-1-1, Maidashi, Higashi-ku

department: Medical Institute of Bioregulation

country: Japan

institute: Kyushu University

type:
Expression profiling by array
Third-party reanalysis

summary:
We previously reported that a synthetic Nod1 ligand, FK565, induced coronary arteritis in mice similar to Kawasaki disease. However, the molecular mechanisms underlying this site-specific inflammation have remained elusive. In this study, we found that CD11c+MHC class II+ cells accumulated in the heart of FK565-treated mice prior to arteritis development.
We used microarray analysis to detail gene expression of CD11c+MHC class II+ cells.

overall_design: To obtain gene expression profile of CD11c+MHC class II+ cells, we isolated these cells from hearts of FK565-treated mice. Briefly, female mice at 8weeks age were administered 500 μg of FK565 subcutaneously at day 0 and day 3. At day6, murine hearts were removed and digested with collagenase. CD11c+MHC II+ cells were sorted as PI–CD45+Ly6G–NK1.1–CD11b+CD11c+MHC II+ using FACS Aria cell sorter (BD Biosciences). Sorted cells were subjected to RNA preparation. Two independent replicates from ten mice were made.

first: Sho

last: Yamasaki


title: Gene expression analysis of midbrain dopamine progenitors in embryonic mouse

status: Public on Feb 28 2015

city: Melbourne

first: Christopher

last: Bye

state: Victoria

address: University of Melbourne

country: Australia

institute: The Florey Institute of Neuroscience and Mental Health

summary: To improve the standardization of cell therapies for Parkinson’s disease, methods for the selection and isolation of midbrain dopaminergic progenitors for transplantation are required. To facilitate this we established an expression profile for genes selectively expressed on transplantable midbrain dopaminergic progenitors using microarray analysis.

overall_design: Expression of GFP in the ventral mesencephalon of embryonic E12.5 Ngn2-GFP mice identifies a distinct sub-population of cells containing virtually all of the midbrain dopaminergic progenitors. Gene expression profiles from 3 biological replicates of FACS isolated GFP-positive cells from mouse Ngn2-GFP ventral mesencephalon were generated using microarrays. To reduce the likelihood of identifying transcripts from non-dopaminergic progenitors, 3 biological replicates of FACS isolated GFP-negative cells from mouse Lmx1a-GFP ventral mesencephalon (definitively non-dopaminergic) were used as a reference population.

first: Chris

middle: R

first: Marie

last: Jönsson

first: Anders

last: Björklund

first: Clare

middle: L

last: Parish

first: Lachlan

middle: H

last: Thompson


title: Effects of the histone demethylase LSD1/KDM1A on the gene expression program of murine hematopoietic progenitor cells.

status: Public on Feb 20 2015

city: Shimotsuke

first: Yusuke

last: Furukawa

state: Tochigi

address: 3311-1 Yakushiji

department: Center for Molecular Medicine

institute: Jichi Medical University

summary:
We established transgenic mice overexpressing the histone demethyase LSD1/KDM1A under the control of Sca-1 promoter and investigated the global changes in gene expression in hematopoietic progenitor cells using a microarray-
based approach.

overall_design: We isolated mRNA from Sca-1-positive hematopoietic progenitor cells from two transgenic mice, Line 6 and Line 3, and subjected them to gene expression analysis using an Affimetrix GeneChip Array.

first: Taeko

last: Wada


title: Mechanical stress enhances CD9 expression in cultured podocytes

status: Public on Feb 27 2015

city: Greifswald

first: Karlhans

last: Endlich

address: Friedrich-Loeffler-Str. 23c

department: Anatomy and Cell Biology

country: Germany

institute: University Medicine Greifswald

summary:
Transcriptomes of differentiated cells of the conditionally immortalized mouse podocyte cell line SVI (Schiwek et al., Kidney Int. 66: 91-101, 2004) were determined as described in Warsow et al. (Kidney Int. 84: 104-115, 2013) after application of mechanical stress (Endlich et al., J. Am. Soc. Nephrol. 12: 413-422, 2001) as compared to control conditions.
Elevated glomerular pressure represents a high risk for the development of severe kidney diseases and causes an increase of mechanical load to podocytes. In this study we investigated whether mechanical stress alters gene expression in cultured podocytes using gene arrays. We found that tetraspanin CD9 is significantly upregulated in cultured podocytes after mechanical stress. The differential expression of CD9 was confirmed by RT-PCR and Western blot under stretched and unstretched conditions. Furthermore, mechanical stress resulted in a relocalization of CD9. To get an insight into the functional role of CD9, podocytes were transfected with pEGFP-CD9. The expression of CD9 induced the formation of substratum-attached thin arborized protrusions (TAPs). Ca2+ depletion revealed that podocytes over-expressing CD9 possess altered adhesive properties in contrast to the control transfected cells. Finally, elevated CD9 expression increased migration of podocytes in a wound assay. In summary, our results suggest that upregulation of CD9 may play an important role in podocyte morphology, adhesion and migration.

overall_design: Three independent batches were used.

first: Antje

last: Blumenthal

first: Jürgen

last: Giebel

first: Gregor

last: Warsow

first: Li

last: Li

first: Ramesh

last: Ummanni

first: Sandra

last: Schordan

first: Eric

first: Paul

last: Klemm

first: Norbert

last: Gretz

first: Nicole


title: Expression profiling of LB-22 immortalized mouse embryonic kidney cells in control and WT1 siRNA knockdown conditions

city: Boston

first: Jordan

last: Kreidberg

state: MA

address: 300 Longwood Ave

department: Medicine

country: USA

institute: Boston Children's Hospital

summary:
LB-22 is an immortalized mesenchymal cell line derived from embryonic kidneys of 'immortomice'. Immortomice ubiquitously express an interferon-inducible, temperature-sensitive SV-40 large T antigen.
LB-22 cells were selected for endogenous abundant expression of the mouse Wilms' tumor suppressor homolog WT1, an important transcription factor in kidney development. Here, we assessed changes in gene expression in response to siRNA mediated WT1 knockdown.

overall_design:
LB-22 cells were transfected either with WT1 siRNA or scramble Control siRNA. Total RNA was extracted 48 hours after transfection and Affymetrix Mouse 430.2 expression arrays were hybridized according to standard protocols.

CEL files not available for this dataset.

middle: A

first: Eunnyung

last: Bae


title: Role of Notch receptors in ozone induced lung injury in mice

status: Public on Feb 24 2015

city: Research Triangle Park

first: Dr. Steven

last: Kleeberger

state: NC

address: 111 T.W. Alexander Drive

institute: NIEHS

summary: Ozone is a highly toxic air pollutant and global health concern.  Mechanisms of genetic susceptibility to ozone-induced lung inflammation are not completely understood.  We hypothesized Notch3 and Notch4 are important determinants of susceptibility to ozone-induced lung inflammation.  Wild type (WT), Notch3 (Notch3-/-) and Notch4 (Notch4-/-) knockout mice were exposed to ozone (0.3 ppm) or filtered air for 6-72 hours.  Ozone increased bronchoalveolar lavage fluid (BALF) protein, a marker of lung permeability, in all genotypes, but significantly greater concentrations were found in Notch4-/- compared to WT and Notch3-/-.  Significantly greater mean numbers of BALF neutrophils were found in Notch3-/- and Notch4-/- mice compared to WT mice after ozone.  Expression of whole lung Tnf was significantly increased after ozone in all genotypes, and was significantly greater in Notch3-/- mice compared to WT.  Statistical analyses of the transcriptome identified differentially expressed gene networks between WT and knockout mice basally and after ozone, and included Trim30, a member of the inflammasome pathway, and Traf6, an inflammatory signaling member.  These novel findings are consistent with Notch3 and Notch4 as susceptibility genes for ozone-induced lung injury, and suggest that Notch receptors protect against innate immune inflammation.

overall_design: Wild-type, Notch3 knockout, and Notch4 knockout mice at 7-13 weeks of age were exposed continuously to air or 0.3 ppm ozone for 6, 24, or 48 hours. Three biological replicates from individual animals were included in each exposure group from each genotype and samples hybridized to the GeneChip Mouse Genome 430 2.0 array (Affymetrix).

first: Steven


title: Expression data from memory P14 transgenic T cells

status: Public on Feb 25 2015

city: Atlanta

first: Shruti

last: Subramaniam

state: GA

address: Clifton Road

institute: Emory University

summary:
Microarray analysis was used to compare differences and similarities in gene expression patterns between memory CD8+ T cells from mice infected with lymphocytic choriomeningitis virus (LCMV) or influenza virus.
Keywords: infection response

overall_design: Mice containing transferred P14 CD8+ transgenic T cells were infected with LCMV or influenza and rested for 90 days.  P14 cells were purified by cell sorting, as well as cells from unimmunized P14 mice as controls, and used for RNA extraction and hybridization on Affymetrix microarrays.


title: Identification of novel long non-coding RNAs in prostate cancers

city: Rotterdam

first: Guido

last: Jenster

department: Urology

country: Netherlands

institute: Erasmus MC

summary: Long non-coding RNAs show highly tissue and disease specific expression profiles. We analyzed prostate cancer and normal adjacent prostate samples to identify cancer-specific transcripts and found 334 candidates, of which 15 were validated by RT-PCR.

overall_design: 8 Prostate cancer samples from radical prostatectomies, 12 samples from normal adjacent prostate, 12 samples from lymph node metastasis and 10 samples from transurethral resection of the prostrate were included in this study. These samples contained more than 70% cancer and less than 30% stromal tissue.

first: René

last: Böttcher


title: The Nicotinic alpha6 Subunit Gene Determines Variability in Chronic Pain Sensitivity and Nicotine Anti- allodynia via Cross-inhibition of P2X2/3 Receptors.

status: Public on Feb 18 2015

city: San Diego

first: John

last: Walker

state: CA

address: 10675 John Jay Hopkins

institute: Genomics Institute of the Novartis Research Foundation

summary:
We used microarray-based expression genomics in 25 inbred mouse strains to identify dorsal root ganglion (DRG)-expressed genetic contributors to mechanical allodynia a prominent symptom of chronic pain.
Expression genetics identifies a role for the Chrna6 (alpha 6-nicotinic receptor) gene in pain in mice and humans.

overall_design: Dorsal root ganglion tissue across multiple inbred mouse strains, both male and female

first: Jeffrey

middle: S

last: Wieskopf

first: Jayanti

last: Mathur

first: Walrati

last: Limapichat

first: Michael

last: Post

first: Mona

last: Al-Qazzaz

first: Robert

middle: E

last: Sorge

first: Loren

middle: J

last: Martin

first: Dmitri

middle: V

last: Zaykin

first: Shad

middle: B

last: Smith

first: Kelen

last: Freitas

first: Jean-Sebastien

last: Austin

first: Feng

last: Dai

first: Jie

last: Zhang

first: Jaclyn

last: Marcovitz

first: Alexander

last: Tuttle

first: Peter

middle: M

last: Slepian

first: Sarah

last: Clarke

first: Ryan

last: Drenan

first: Jeff

last: Janes

first: Shakir

last: Al Sharari

first: Samantha

middle: K

last: Segall

first: Eske

last: Aasvang

first: Weike

last: Lai

first: Reinhard

last: Bittner

first: Christopher

middle: I

last: Richards

first: Gary

middle: D

last: Slade

first: Henrik

last: Kehlet

first: Uwe

last: Maskos

first: Jean-Pierre

last: Changeux

first: Marshall

last: Devor

first: William

last: Maixner

first: Luda

last: Diatchenko

first: Inna

last: Belfer

first: Dennis

last: Dougherty

first: Andrew

last: Su

last: Lummis

first: M


title: Hydroxypropyl-β-cyclodextrin spikes local inflammation that induces Th2 and Tfh responses to the coadministered antigen

status: Public on Feb 15 2015

city: Ibaraki-shi

first: Yoshinobu

last: Igarashi

state: Osaka

address: 7-6-8 Asagi Saito

institute: National Institutes of Biomedical Innovation, Health and Nutrition

summary:
Gene expression data from mouse organs after hydroxypropyl-β-cyclodextrin injection
Cyclodextrins are commonly used as a safe excipient to enhance the solubility and bioavailability of hydrophobic pharmaceutical agents. In this study, we reprofiled hydroxypropyl-β-cyclodextrin (HP-β-CD) as a vaccine adjuvant, and found that it acts as a potent and unique adjuvant.

overall_design: C57BL/6J mice (6 week old, male, n = 3) were injected i.d. or i.p. with a total volume of 200 micro liter of 30% HP-β-CD in PBS. The vehicle-control mice (n = 3) were injected with the same volume of PBS. After 6 h, the inguinal LNs, Liver, and Spleen were removed (within one hour for all samples) and global gene expression was obtained by Affymetrix GeneChip.

first: Motoyasu

last: Onishi

first: Edward

last: Wijaya

first: Noriyuki

last: Nakatsu

first: Taiki

last: Aoshi

first: Ken

last: Ishii


title: Effects of AβPP Antisense Treatment on Hippocampal Gene Expression in Adult Mice with Memory Deficits

status: Public on Feb 13 2015

city: St. Louis

first: Harvey

last: Armbrecht

state: MO

address: #1 Jefferson Barracks Drive

department: Division of Geriatric Medicine & Department of Molecular Microbiology & Immunology

institute: St. Louis Veterans Affairs Medical Center , & Saint Louis University School of Medicine

summary:
The purpose of this study was to determine the effect of peripheral (IV) administration of AβPP antisense on hippocampal gene expression as well as on learning and memory as measured by T-maze in adult male mice aged 12 months.  The AβPP antisense treatment reversed learning and memory deficits and altered the expression of 944 hippocampal genes, which are involved in a coordinated set of signaling pathways.  Expression and pathway findings were verified at the protein and functional (phosphorylation) levels.
Global differential profiling of hippocampal gene expression (12 month old adult mice:  Control, SAMP8, SAMP8 + Random antisense, SAMP8 + AβPP antisense) was performed using Affymetrix GeneChip® Mouse Genome 430 2.0 Arrays.  The AβPP antisense reversed the memory deficits and altered expression of 944 hippocampal genes. Pathway analysis showed significant gene expression changes in 9 pathways. These include the MAPK signaling pathway (P = 0.0078) and the phosphatidylinositol signaling pathway (P = 0.043), which we have previously shown to be altered in SAMP8 mice. The changes in these pathways contributed to significant changes in the Neurotropin (P = 0.0083) and Insulin Signaling (P = 0.015) pathways, which are known to be important in learning and memory.  Changes in these pathways were accompanied by phosphorylation changes in the downstream target proteins p70S6K, GSK3β, ERK, and CREB.  These changes in hippocampal gene expression and protein phosphorylation may suggest specific new targets for antisense therapy aimed at improving memory.

overall_design: One-way ANOVA (4 conditions, n=4).  Variables were treatment (AβPP antisense, Random antisense, no treatment) and mouse strain (Control and SAMP8).  This results in 4 groups: (All 12-month-old adult male mice) NT-Control, NT_SAMP8, Random_AS-SAMP8, and AβPP_AS-SAMP8.   Each group had 4 biological replicates (4 mice).  The 'Control' mice were a 50% backcross of the SAMP8 mice with CD-1 mice (50% SAMP8 mice).  These mice were closely related to SAMP8 mice but exhibited no memory deficits at 4 or 12 months.  The SAMP8 mice had memory deficits at 12 months but not at 4 months.

first: Akbar

last: Siddiqui


title: Gene expression changes in brain vascularture in Notch3 knockout mice

city: Uppsala

first: L.

last: He

address: Dag Hammarskjölds Väg 20

country: Sweden

institute: Uppsala University

summary:
Vascular smooth muscle cells (VSMC) are important for contraction, blood flow distribution and regulation of blood vessel diameter, but to what extent they contribute to the integrity of blood vessels and blood-brain barrier function is less well understood. In this report, we explored the impact of the progressive loss of VSMC in the Notch3-/- mouse on blood vessel integrity in the central nervous system
To explore the molecular consequences of the VSMC phenotype in Notch3-/- mice, we performed genome-wide transcriptional profiling of the brain vasculature in mutants and littermate controls using Affymetrix Mouse Genome 430 2.0 Array.

overall_design: Three Notch3 knockout and three littermate control mice at age of 2 months were used to profile the transcriptomes.  Total RNA was extracted from cerebral and cerebellar microvascular fragments and hyrbridized separately on the Mouse Genome 430 2.0 Array according to standard procedures.

first: Tanya

last: Henshall

first: Annika

last: Keller

first: Liqun

first: Bengt

last: Johansson

first: Elisabet

last: Wallgard

first: Elisabeth

last: Raschperger

first: Christer

last: Betsholtz

first: Urban

last: Lendahl


title: Gene Expression in 70Z/3 pre-B cells Stably Overexpressing Individual members of the mirn23a MiRNA Cluster

status: Public on Feb 12 2015

city: South Bend

first: Richard

last: Dahl

state: IN

address: Harper Hall 227, 1234 Notre Dame Ave.

department: Microbiology and Immunology

institute: Indiana University School of Medicine, South Bend

summary: Expression of the mirn23a cluster in murine hematopoietic progenitors blocks B cell development.  Overexpressed individual cluster members miRs-23a, 24-2, and -27a in 70/3 mouse pre-B cells in order to examine changes in gene expression that would potentially reveal targets of the miRs relevant to hematopoiesis.

overall_design: Two independent 70Z/3 cell lines for each experimental group were generated (MSCV, miR-23a, miR-24-2, and miR-27a). RNA was generated and  hybridized  on Affymetrix microarrays.


title: In vivo electroporation-based conditional oncogenic activation implicates multiple distinct cellular origins for Group3 medulloblastoma

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

summary:
We examined the transformation susceptibility of different cerebellar stem/progenitors by developing several new Group3 medulloblastoma murine models using orthotopic transplantation and in utero electroporation (EP)-based in vivo gene transfer with Cre/LoxP-mediated conditional Myc gene activation and loss of Trp53 function.
We used microarrays to compared the transcriptome of these novel Group3 medulloblastoma mouse models and CPC mouse models to existing mouse models of medulloblastoma subgroups and used cross-species analysis to compare these models to human medulloblastoma subgroups

overall_design: This study aimed to compare CPC models to other orthotopic models in GSE65888. Orthotopic cell-lineage specific MYC tumors were generated by enforced Myc expression in P6 GNPs isolated from P0-1 tamoxifen treated [Atoh1-CreER;Trp53fl/-] and [Prom1-CreER;Trp53fl/-] mice followed by cortical implants in immunocompromised mice. These tumors are referred to as Atoh1ER-MYC [dka072-075], Prom1-CreER [dka077-081]. The first Group3 MB models in which tumors developed in situ were generated by electroporation of plasmids containing Myc and dominant negative Trp53 flanked by loxP sites into the fourth ventricle of E13.5 Blbp-Cre [dka081, 087, 089, 090, 091 and blm121], Gad2-IRES-Cre [blm128-130 and blm134] and Ptf1a-Cre [blm135-137] mouse embryos. The gene expression profile of these tumors were compared to our previously published Group3 MB model as well as SHH and WNT models of medulloblastoma. For SHH subgroup medulloblastoma, [dka001-005, 009, 033 and 034] and [dka050-057], spontaneous medulloblastomas from [Cdkn2c-/-; Trp53Fl/Fl; Nestin-Cre] and [Cdkn2c-/-; Ptch1+/-] (Uziel et al.,2005 Genes Dev) were used, respectively. For Group3 medulloblastomas, [dka013-16, 049 and 065-067], in which Myc was overexpressed in Cdkn2c-/-, Trp53-/- cerebellar cells and implanted into the cortices of immunocompromised nude mice prior to tumor isolation. For WNT subgroup medulloblastomas [pgr003, 016 and 066], spontaneously developed tumors from CTNNB1+/lox (ex3); BLBP-Cre; Trp53Fl/Fl (Gibson et al., 2010, Nature) were removed for RNA extraction.

first: Daisuke

last: Kawauchi

first: Robert

last: Ogg

first: Li

last: Liu

last: Shih

first: Brian

last: Murphy

first: Jerold

last: Rehg

first: Andrey

last: Korshunov

first: Christopher

last: Calabrese

first: Frederique

last: Zindy

first: Timothy

last: Phoenix

first: Yoshiya

last: Kawaguchi

first: Jan

last: Gronych

last: Gilbertson

first: Peter

last: Lichter

first: Amar

last: Gajjar

first: Marcel

last: Kool

first: Paul

last: Northcott

first: Stefan

last: Pfister

first: Martine

middle: F

last: Roussel


title: Plasticity of Hopx+ Type I alveolar cells to regenerate Type II cells in the lung

status: Public on Feb 10 2015

city: Philadelphia

first: Rajan

last: Jain

address: 3400 Civic Center Blvd

department: Cell and Developmental Biology

institute: University of Pennsylvania

summary: Hopx is a transcription co-factor expressed during lung development and we wanted to profile Hopx +/+ and -/- embyonic lungs. Results inform the role of Hopx in embryonic lung development

overall_design: We used microarrays to profile the transcriptome of Hopx -/- lungs compared to Hopx +/+ lungs. Lungs were microdissected and three biological replicates were used for each genotype.

first: Jonathan

last: Epstein

first: Chinmay

last: Trivedi


title: Differential expression of mouse Grem1+ Vs. Grem1- bone-marrow cells

city: New York

middle: Cragin

last: Wang

state: NY

address: 1130 St. Nicholas Ave

department: Medicine- Liver and Digestive Diseases

institute: Columbia University Medical Center

summary:
The gene expression of bone marrow cells of mice enriched for
Gremlin1 vs control was measured (n=3).
It is not known if endogenous adult mesenchymal stem cells
(MSCs) exist.Following culture,perisinusoidal mesenchymal
cells can clonally recapitulate the skeletal microenvironment,
but this fails to confirm their endogenous lineage
repertoire. Multipotential MSCs in vitro may be
fate-restricted in vivo and specific perisinusoidal
recombination does not trace bone or cartilage
Reconciling in vitro MSCs with their in vivo
potential has been challenging and remains
untested outside of the bone. We prove
that expression of the bone morphogenetic
protein (BMP)-antagonist gremlin 1 (Grem1)
identifies a population of self-renewing,
multipotent bone, cartilage and stromal-primed
MSCs in both health and healing that are
completely distinct from the established
Nes-GFP niche-supporting mesenchymal cells.
Grem1 recombination also identifies small
intestinal MSCs (siMSCs) that can be
transplanted and clonally trace the
self-renewing, multilineage periepithelial
mesenchymal sheath. Our findings prove the
existence of adult MSCs that are regionally
and functionally distinct from perisinusoidal
Nes-GFP cells. We also established that the
mesenchyme undergoes ordered turnover outside
of the bone and may help to preserve regional
niches. Grem1 MSCs provide a new focus for
investigating mesenchymal renewal and repair.

overall_design:
a.Adult (6-8 weeks) Grem1;TdTomato mice were induced by oral tamoxifen and their bone marrow harvested by digestion sorted for Non-recombined CD45/CD31/Ter-119 triple negative bone marrow cells (n=3).
b.Adult (6-8 weeks) Grem1;TdTomato mice were induced by oral tamoxifen and their bone marrow harvested by digestion sorted for Grem1 (n=3). Same mice as in a so that samples are matched.

first: Daniel

last: Worthley

first: Michael

last: Churchill

first: Jocelyn

middle: T

last: Compton

first: Yagnesh

last: Tailor

first: Meenakshi

last: Ra

first: Yiling

last: Si

last: Levin

first: Aysu

last: Uygur

first: Matthew

last: Schwartz

first: Stefanie

last: Gross

first: Wanda

last: Setlik

first: Xiaowei

last: Chen

first: Ashley

middle: N

last: Martinez

first: Saqib

last: Nizami

first: Jon-Michael

last: Caldwell

first: Bernhard

middle: W

last: Renz

first: Samuel

last: Asfaha

first: C

last: Westphalen

first: Yoku

last: Hayakawa

first: Guangchun

last: Jin

first: Karan

last: Nagar

first: Hongshan

first: Alka

last: Kolhe

first: Jared

last: Carpenter

first: Mark

last: Glaire

first: Abhinav

last: Nair

first: Ashlesha

last: Muley

first: Nicholas

last: Manieri

first: Sureshkumar

last: Muthupalani

first: James

last: Fox

first: Maximillian

last: Reichart

first: Andrew

last: Giraud

first: Robert

last: Schwabe

first: Jean-Phillipe

last: Pradere

first: Deborah

last: Gumucio

first: Anil

last: Rustgi

first: Thaddeus

last: Stappenbeck

first: Richard

last: Friedman

last: Gershon

first: Tracy

last: Grikscheit

first: Francis

middle: Y

last: Lee

first: Lei


title: HMGA1:  A master regulator of tumor progression in triple-negative breast cancer cells

city: Baltimore

first: Linda

last: Resar

state: MD

address: 720 Rutland Ave

department: Hematology

institute: Johns Hopkins University

summary: Emerging evidence suggests that tumor cells metastasize by co-opting stem cell transcriptional networks, although the molecular underpinnings of this process are poorly understood.  Here, we show for the first time that the high mobility group A1 (HMGA1) gene drives metastatic progression in triple negative breast cancer cells (MDA-MB-231) by reprogramming cancer cells to a stem-like state.  We  discovered an HMGA1 signature in triple negative breast cancer cells that is highly enriched in embryonic stem cells.  Together, these findings indicate that HMGA1 is a master regulator of tumor progression in breast cancer by reprogramming cancer cells through stem cell transcriptional networks.  Future studies are needed to determine how to target HMGA1 in therapy.

overall_design: HMGA1 was knocked-down in MDA-MB-231 cells using siRNA as we previously described (Tesfaye A 2007). RNA from three independent knockdown experiements along with 3 control populations were collected by Rneasy miniprep (Qiagen) and analyzed by Affymetrix Human Exon 1.0 ST platform.

first: Sandeep

last: Shah

first: Leslie

last: Cope

first: Weijie

last: Poh

first: Amy

last: Belton

first: Sujayita

last: Roy

first: C

middle: C

last: Talbot Jr.

first: Saraswati

last: Sukumar

first: David

middle: L

last: Huso

first: L


title: Gene expression of resting memory, resting naive and in vitro activated memory CD8+CD127+ T cells from spleen and bone marrow (BM)

status: Public on Feb 05 2015

city: Berlin

first: Pawel

last: Durek

address: Charitéplatz 1

institute: Deutsches Rheuma-Forschungszentrum

summary: To understand differences between resting and activated memory CD8+ T cells, we compared the global gene expression of ex vivo isolated naive and spleen and BM memory cells to in vitro activated spleen and BM memory cells.

overall_design: Single cell suspension from the spleen and bones of aged C57BL/6 mice were prepared. Naive (CD44-CD127+) and memory (CD44+CD127+) CD8+CD3+ T cells were then cytometrically sorted. Sorted cells were either immediately processed for RNA preparation or were activated with anti-CD3 and anti-CD28 for 42-44 hours. Total RNA was extracted using the NucleoSpin RNA (Macherey-Nagel). The integrity and amount of isolated RNA was assessed for each sample using an Agilent 2100 Bioanalyzer (Agilent, Waldbronn, Germany) and a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE). Double-stranded complementary RNA was synthesized from 1 µg total RNA using Message AmpII Biotin (Ambion, USA). Fifteen micrograms of fragmented cRNA of each sample were hybridized to MG_U430_2 GeneChips (Affymetrix) in triplicates. Hybridization was performed in a Hybridization Oven 640, and chips were washed and stained in the Fluidics Station 400 (both Affymetrix). Finally, the arrays were scanned with a GeneChip Scanner 3000 using the GCOS software, version 1.4, both Affymetrix. All relevant GCOS data of quality checked microarrays were analyzed with High Performance Chip Data Analysis (HPCDA, unpublished), using the BioRetis database (www.bioretis-analysis.de), as described and validated previously.

first: Özen

last: Sercan-Alp

first: Sibel

last: Durlanik

first: Daniel

last: Schulz

first: Mairi

last: McGrath

first: Joachim

middle: R

last: Grün

first: Marcus

last: Bardua

first: Koichi

last: Ikuta

first: Evridiki

last: Sgouroudis

first: René

last: Riedel

first: Sandra

last: Zehentmeier

first: Anja

last: Hauser

first: Motokazu

last: Tsuneto

first: Fritz

last: Melchers

first: Koji

last: Tokoyoda

first: Hyun-Dong

last: Chang

first: Andreas

last: Thiel

last: Radbruch


title: Gene expression data from livers of 3-month-old HNF4alpha knockout mice

status: Public on Feb 01 2015

city: Kansas City

first: Udayan

last: Apte

state: KS

address: 3901 Rainbow Blvd, MS1018

department: Pharmacology

institute: University of Kansas Medical Center

summary: HNF4alpha is a master regulator of hepatic differentiation. In this study, HNF4alpha was deleted in adult mice using a Cre-LoxP system where Cre recombinase was delivered using an AAV8 virus.

overall_design: Total RNA was isolated from the livers of HNF4alpha-floxed mice (mixed backgournd) treated with either Control Virus or Cre-carrying virus at 3 months of age.


title: Gene expression profiles of PBMC in CRPC patients receiving persornalized peptide vaccination

city: Fukuoka

first: Hiromitsu

last: Araki

address: 744 Motooka Nishi-Ku

institute: Kyushu University

summary: Personalized peptide vaccination (PPV) is one of the attractive immunotherapy with high immune-boosting effects. However, as with most therapeutic agents, PPV does not elicit beneficial immune and/or clinical responses in all of the treated cancer patients. To identify prognostic biomarker for the selection of patients most likely to benefit from PPV, we conducted whole genome gene expression analysis of prevaccination peripheral blood mononuclear cells (PBMCs) of 112 castration-resistant prostate cancer (CRPC) patients.

overall_design: Total RNA obtained from prevaccination PBMCs in 112 CRPC patients

first: Nobukazu

last: Komatsu

first: Tetsuro

last: Sasada

first: Masanori

last: Noguchi

first: Kyogo

last: Itoh

first: Kosuke

last: Tashiro

first: Satoru

last: Kuhara


title: Comparison of the tarnscriptome of 4T1 control cells versus shRNA NFAT1 transduced cells (mouse)

status: Public on Feb 07 2015

city: Orsay

first: Jacques

last: GHYSDAEL

address: Centre Universitaire, Bat 110

country: France

institute: Institut Curie

summary: 4T1 is a mammary tumor cell line to which the NFAT1 transcription factor is essential for tumorigenesis and metastasis.

overall_design: control or shRNA transduced 4T1 cells growing in culture were collected and RNA was extracted from each sample and processed for hybridization to Affymetrix arrays.

first: J

last: Ghysdael


title: The glucosinolate metabolite 1-methoxy-3-indolylmethyl alcohol induces a gene expression profile in mouse liver similar to the expression signature caused by known genotoxic hepatocarcinogens

first: Anke

last: Ehlers

address: Max-Dohrn-Straße 8-10

department: Department of Food Safety

institute: Federal Institute for Risk Assessment

summary: Breakdown products of some glucosinolates – defense chemicals of Brassicales – induce detoxifying enzymes and demonstrate preventive activities against chemically induced tumorigenesis in animal models. However, other breakdown products are genotoxic. 1-Methoxy-3-indolylmethyl alcohol (1-MIM-OH) is mutagenic in bacterial and mammalian cells upon activation by sulphotransferases and forms DNA adducts in mouse tissues. This effect was enhanced in mice transgenic for human sulphotransferases 1A1/2 (FVB/N-hSULT1A1/2). In this study we explored gene expression changes induced by 1-MIM-OH in mouse liver.  FVB/N-hSULT1A1/2 mice were orally treated with 1-MIM-OH for 21 or 90 days, leading to high levels of hepatic 1-MIM-DNA adducts. Genome-wide expression analyzes in this tissue demonstrated no influence on detoxifying enzymes, but up-regulation of many mediators of the tumour suppressor p53 and down-regulation of Fhit and other long genes.  In conclusion, 1-MIM-OH did not induce protective enzymes, but formed high levels of DNA adducts, which were recognized by affected cells as reflected by p53 activation. While this p53 response might aim to protection, it was unable to prevent the accumulation of DNA adducts. However, various epdemiological studies reported inverse associations between the intake of cruciferous vegetables and cancer. This association might be due to the presence of other glucosinolates with tumour-preventing influences possibly outweighing adverse effects of some metabolites.    Nevertheless, 1-MIM-OH is a genotoxic substance inducing a gene expression profile similar to the expression signature caused by known genotoxic hepatocarcinogens.

overall_design:
Male FVB/N-SULT1A1/2 mice were orally treated with 1-MIM-OH, trice per week, 26 mg/kg body mass per treatment. Control animals only received the vehicle (glyceryl trioctanoate) over the same period. Animals were killed after 10 and 40 treatments (over a period of 21 and 90 d, respectively), always 24 h after the last treatment (6 treated and 6 control mice, respectively). Organs were weighed, shock-frozen in liquid nitrogen and stored for a few days at -80°C until further processing. Liver organs were ground in a Tissuelyser ball mill (Qiagen, Hilden, Germany) under cooling with liquid nitrogen. The frozen liver tissue was crushed and total RNA was isolated using the RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions. For genome-wide microarray analysis quality of RNA was controlled using the BioAnalyzer (Agilent, Santa Clara, CA, USA).
Affymetrix GeneChip hybridization (GeneChip MouseGenome 430 2.0) was performed with 1 µg total RNA according to the manufacturer’s recommendations. RNA from six individual animals per group (21-day and 90-day treatments with 1-MIM-OH or the vehicle only) was analyzed. For the analysis one hybridized GeneChip (mouse 6 [treated for 21 days with 1-MIM-OH]) was excluded due to hybridization artefacts.

first: Simone

last: Florian

first: Fabian

last: Schumacher

first: Walter

last: Meinl

first: Dido

last: Lenze

first: Michael

last: Hummel

first: Tanja

last: Heise

first: Albrecht

last: Seidel

first: Hansruedi

last: Glatt

first: Alfonso

last: Lampen


title: Transcriptome changes following loss of Apc in the intestine

status: Public on Jan 31 2015

city: Cardiff

first: Karen

middle: Ruth

last: Reed

address: Maindy Road

country: United Kingdom

institute: ECSCRI, Cardiff University

summary: Nearly all colorectal cancers have dysregulated Wnt signalling, predominantly through the mutation of the Apc (Adenomatous Polyposis Coli) gene. Therefore it is of vital importance to elucidate the key Wnt target genes in intestinal cells in vivo. We have used a novel inducible cre-lox based murine system (designated ApcFlox) to investigate the consequences of perturbation of Wnt signalling following inactivation of Apc in vivo within 100% of the intestinal epithelium. We have employed microarray analysis at 3 time points within our ApcFlox system (Day 3 prior to the onset of phenotype, day 4 the establishment of the phenotype and day 5 gross phenotype of altered proliferation, differentiation and migration) and from adenomas arising in the ApcMin/+ background allowing us characterise Wnt/beta-catenin target genes based on their expression profiles during different stages of intestinal tumourigenesis. Furthermore, we have employed microarray analysis using livers from our ApcFlox system and have demonstrated that there is very little overlap in the Wnt target genes induced by Apc loss in the liver and the intestine. More importantly, we have been able to determine a novel set of putative Wnt/beta-catenin target genes which are upregulated at both early and late stages of tumourigenesis in the intestine and may represent novel therapeutic targets in colon cancer.

overall_design: Samples were collected from Genetcially modified mice of the genotypes indicated on the sample records. Where appropriate, gene recombination was induced using IP administration of beta-napthoflavone. Cohorts of samples were used to compare the affects of APC loss in the small intestine at three time points (and compared to matched control samples in which the gene was not recombined).  Furthermore, these samples were compared to colonic polyps (and normal colon) taken from the Apcmin Mouse.

first: Owen

last: Sansom

first: Alan

last: Clarke


title: B-catenin deficiency, but not c-Myc deletion, suppresses the immediate phenotypes of Apc loss in the liver

summary: Dysregulated Wnt signalling is seen in approximately 30% of hepatocellular cancers, thus finding pathways downstream of activation of Wnt signalling is key. Using cre lox technology we have deleted the the adenomatous polyposis coli tumour suppressor protein (Apc) within the adult mouse liver and observed a rapid increase in nuclear beta-catenin and C-Myc. This is associated with an induction of proliferation leading to hepatomegally within 4 days of gene deletion. To investigate the downstream pathways responsible for these phenotypes we analysed the impact of inactivating Apc in the context of deficiency of the potentially key effectors beta-catenin and c-Myc. beta-catenin loss rescues both the proliferation and hepatomegally phenotypes following Apc loss. However c-Myc deletion, which rescues the phenotypes of Apc loss in the intestine, had no effect on the phenotypes of Apc loss. The consequences of deregulation the Wnt pathway within the liver are therefore strikingly different to those observed within the intestine, with the vast majority of Wnt targets beta-catenin dependent but c-Myc independent in the liver.

overall_design: Samples were collected from Genetcially modified mice of the genotypes indicated in the characteristics field. Gene recombination was induced using IP administration of beta-napthoflavone. Cohorts of samples were used to compare the affects of APC loss, cMYC loss and combined APC and cMYC loss in the liver (and compared to matched control samples in which the genes were not recombined).

first: Valerie

last: Meniel


title: Expression data from mouse embryo

status: Public on Jan 28 2015

city: Suita

first: Kenji

last: Hata

address: 1-8 Yamadaoka

department: Biochemistry

institute: Osaka University graduate school of dentistry

summary: To understand the molecular mechanism by which regulate skeletal development, we attempted to identify transcription factors that were highly expressed in developing cartilage during the embryonic stage.

overall_design: Col2a1-Venus-Tg mice in which chondrocytes were fluorescently labelled with the GFP-modified Venus gene. We purified total RNA from Venus-negative and Venus-positive cells and performed microarray analysis using an Affymetrix Mouse Genome 430 2.0 Array.


title: Identification of IL-22 regulated genes in the ileum after infection with Toxoplasma gondii

city: South San Francisco

first: Jason

middle: A

last: Hackney

address: 1 DNA Way

department: Department of Bioinformatics and Computational Biology

institute: Genentech, Inc.

summary:
IL-22 acts on epithelial cells and has been shown to induce tissue protective and wound healing responses in these cells. But it has recently been decribed that IL-22 exacerbates ileatis after infection with T. gondii.
The goal of the study is to identify the IL-22-dependent genes during T. gondii infection in order to understand why IL-22 is pathogenic in this context.

overall_design: one experimental condition, 5 mice per group, 2 groups: WT and IL-22 KO animals

first: Melba

last: Munoz

first: Celine

last: Eidenschenk

first: Oliver

last: Liesenfeld

first: Wenjun

last: Ouyang


title: The forced expression of Nanog or Esrrb allows preserve ESC status in the absence of nucleostemin expression

status: Public on Jan 30 2015

city: Hidaka

first: Akihiko

last: Okuda

state: Saitama

address: 1397-1 Yamane

department: Research Center for Genomic Medicine

institute: Saitama Medical University

summary: Nucleostemin (NS) gene is known to be expressed in stem cells in general including embryonic stem cells (ESCs). Previous knockdown and knockout studies have demonstrated that NS is important for the preservation of their self-renewality and high levels of pluripotent marker gene expression in mouse ESCs. In this study, we demonstrate that the forced expression of Nanog or Esrrb, but not other pluripotency factors, made NS expression dispensable in mouse ESCs. DNA microarray data deposited here underscored the notion that both Nanog and Esrrb could rather faithfully counteract the alteration of gene expression profile caused by NS expression ablation in ESCs.

overall_design: NS tet off ESCs (Stem Cells 27, 1066-1076, 2009) in which NS gene was homozygously disrupted, but NS cDNA was introduced in ROSA26 gene locus together with tetracycline-off system were used as parental ESCs to examine the effect of NS expression ablation in ESCs. In this study, how alteration of gene expression profile change associated with NS expression ablation was modulated by the forced expression of either constitutively active Stat3 (Stat3mut), Nanog or Esrrb. Effect obtained by the exposure to 2i condition (medium containing 2 kinase inhibitors against MEK and GSK3b) was also examined

first: Miyuki

last: Katano

first: Yutaka

last: Nakachi

first: Yosuke

last: Mizuno

first: Yasushi

last: Okazaki


title: Gene expression profile of Dicer knockout in mouse DP thymocytes

city: London

first: Gopuraja

last: Dharmalingam

address: Faculty of Medicine, Imperial College, Hammersmith Hospital Campus

department: Epigenetics section

institute: MRC London Institute of Medical Sciences

summary: The RNase III enzyme dicer is essential for the processing of microRNAs (miRNAs) and small interfering RNAs (siRNAs) from double-stranded RNA precursors. miRNAs and siRNAs regulate chromatin structure, gene transcription, mRNA stability and translation in a wide range of organisms. To provide a model system to explore the role of dicer-generated RNAs in the differentiation of mammalian cells in vivo, we have generated a conditional dicer allele. Deletion of dicer at an early stage of T cell development compromised the survival of αβ lineage cells, while the numbers of γδ-expressing thymocytes were not affected. In developing thymocytes, dicer was not required for the maintenance of transcriptional silencing at pericentromeric satellite sequences (constitutive heterochromatin), the maintenance of cytosine DNA methylation and X chromosome inactivation in female cells (facultative heterochromatin) and the stable shutdown of a developmentally regulated gene (developmentally regulated gene silencing). Most remarkably, given that one-third of mammalian mRNAs are putative miRNA targets, dicer appears to be dispensable for CD4/8 lineage commitment, a process where epigenetic regulation of lineage choice has been well documented. Thus, although dicer appears critical for the development of the early embryo, it may have limited impact on the implementation of lineage-specific gene expression programs.

overall_design: LckCre was used to delete a floxed Dicer1 allele from developing thymocytes (Cobb BS, Nesterova TB, Thompson E, Hertweck A, O'Connor E, Godwin J, Wilson CB, Brockdorff N, Fisher AG, Smale ST and Merkenschlager M. T cell lineage choice and differentiation in the absence of the RNAse III enzyme dicer. J. Exp. Med. 2005 201: 1367-1373). Thymocytes were stained for CD4 and CD8, and double-positive (DP) thymocytes were sorted by flow cytometry. Three biological replicates of Dicer lox/lox control samples and LckCre Dicer lox/lox KO samples were analysed.

first: B

middle: S

last: Cobb

first: Matthias

last: Merkenschlager


title: Splenic B cells from Hymenolepis diminuta-infected mice ameliorate colitis independent of T cells and via cooperation with macrophages

city: Calgary

first: Jose

last: Reyes

state: Alberta

address: 3330 Hospital Dr. NW

department: Physiology and Pharmacology

country: Canada

institute: The University of Calgary

summary: Mouse infection with the tapeworm Hymenolepis diminuta leads to a less severe DNBS-colitis. Increased Th2 and regulatory cytokine production in the spleen is a hallmark of Hymenolepis diminuta infection, therefore we hypothesized that given this microenvironment, splenic  adaptive cells acquire an anti-inflammatory phenotype. We tested the ability of putative splenic regulatory B cells generated by  Hymenolepis diminuta infection to down-regulate intestinal inflammation. We found that unlike splenic B cells from uninfected mice, splenic B cells from Hymenolepis diminuta -infected animals ameliorated chemically-induced colitis.

overall_design: Splenic B cells were magnetically isolated and also purified by cell sorting from 7 days-infected animals and  B cells from uninfected animals were used as control.

first: J

first: M

last: Sigvardsson

first: D

last: McKay


title: Time course of prion infected (RML) and globular domain ligands (POM1) in cultured organotypic cerebellar slices (COCS)

status: Public on Jan 22 2015

city: Zurich

first: Ulrich

last: Wagner

address: Schmelzbergstrasse 12

country: Switzerland

institute: Uiversity Hospital Zurich

summary: Cultured organotypic cerebellar slices were exposed for different time points with either prions (RML) versus non-infectious brain homogenate (NBH) or ligands to the globular domain of the prion protein (POM1) vs IgG

overall_design: We used microarrays to characterize the temporal response of two inducers prion protein dependent cell death: COCS were exposed to RML prions or Non-infectious brain homogenate (NBH) and harvested after 14d, 25d, 38d and 45d (4 replicates each condition). COCS were exposed to POM1 or IgG and harvested after 8h, 1d, 3d, 7d, 10d (4 replicates each condition).

first: Uli

last: Herrmann

first: Tiziana

last: Sonati

first: Jeppe

last: Falsig

first: Regina

last: Reimann

first: Paolo

last: Dametto

first: Tracy

last: O'Connor

first: Bei

last: Li

first: Agnes

last: Lau

first: Simone

last: Hornemann

first: Silvia

last: Sorce

first: Despina

last: Sanoudou

first: Adriano

last: Aguzzi


title: Pregnancy-associated alterations in DNA methylation patterns of mammary epithelial stem cells [reproductive stages]

city: Cambridge

first: Kendell

last: Clement

address: 7 Divinity Ave.

institute: Harvard University

summary: Mammary gland development and luminal differentiation occur largely postnatally during puberty and pregnancy. We found that pregnancy had the most significant effects on stem cells, inducing a distinct epigenetic state that remained stable through life.

overall_design: Mammary glands were collected from different reproductive stages to purify different epithelium cell types, which were used for RNA extraction and hybridization on Affymetrix microarrays.

first: Sung

middle: J

last: Huh

first: Patrick

last: Boyle

first: Alexander

last: Meissner

first: Kornelia

last: Polyak


title: Global gene expression analysis of human iPSC-derived Neural Stem Cells (NSC) from LCA patients and unaffected persons

status: Public on Jan 21 2015

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

institute: GenoSplice technology

summary: Our purpose was to investigate genes and molecular mechanisms involved in patients with Leber congenital amaurosis (LCA). Fibroblasts from two unrelated clinically-identified patients (Coriell) were reprogrammed to pluripotency by retroviral transduction. These human induced Pluripotent Stem Cells (hiPSCs) were differentiated into neural stem cells (NSC) that mimicked the neural tube stage and retinal pigmented epithelial (RPE) cells that could be targeted by the disease. A genome wide transcriptome analysis was performed with Affymetrix Exon Array GeneChip®, comparing LCA-hiPSCs derivatives to controls. The aim was to identify differentially expressed genes which may be associated with early developmental defect before the establishment of mature retinal circuitry.

overall_design: We analyzed iPSC-derived neural stem cells from LCA patient's fibroblast (n=2) and iPSC-derived neural stem cells from healthy people fibroblast (n=2). A total of 21 samples were analyzed : 9 NSC derived from iPSC LCA and 12 NSC derived from wild-type iPSC.

first: Celine

last: Lustremant

first: Christelle

last: Monville


title: Transcriptome profiling of mouse Gata1- megakaryocyte-erythroid progenitors (G1MEs) expressing one of the two isoforms of GATA1: full-length (GATA1fl) or an amino-truncated form of GATA1 (GATA1s).

status: Public on Jan 26 2015

city: University Park

first: Ross

last: Hardison

state: PA

address: 303 Wartik Lab

institute: Pennsylvania State University

summary: We transduced mouse Gata1- megakaryocyte-erythroid progenitors with MIGRI-GFP vector expressing GATA1fl or GATA1s cDNAs. GFP-positive cells expressing one of the two isoforms of GATA1 were isolated by FACS 42 hours following transduction and used for microarray transcriptome analysis. At this time point, there was no apparent difference in the cell surface phenotypes between GATA1fl and GATA1s-expressing cells. Transcriptome data for G1ME/GATA1fl at 42h were deposited previously under GSE14980 (GSM374049, GSM374050, GSM374051), whereas G1ME/GATA1s at 42h are deposited here.

overall_design: We performed differential expression analysis comparing mean expression levels of genes in G1ME cells at 42 hours after transduction with GATA1fl (3 replicates deposited previously under GSE14980: GSM374049, GSM374050, GSM374051) or GATA1s (3 replicates deposited here). All 6 samples were prepared the same way and analyzed on the same platform, Affymetrix Mouse Genome 420 2.0.

first: Marta

last: Byrska-Bishop

first: Daniel

last: VanDorn

first: Amy

last: Campbell

first: Marisol

last: Betensky

first: Philip

last: Arca

first: Yu

last: Yao

first: Paul

last: Gadue

first: Fernando

last: Costa

first: Richard

last: Nemiroff

first: Gerd

last: Blobel

first: Deborah

last: French

first: Mitchell

last: Weiss

first: Stella

last: Chou


title: Global gene expression analysis of human iPSC-derived Retinal Pigmented Epithelial (RPE) cells from LCA patients and unaffected persons

first: Pierre

last: de la Grange

overall_design: We analyzed iPSC-derived retinal pigmented epithelial (RPE) cells from LCA patient's fibroblast (n=2) and iPSC-derivedretinal pigmented epithelial (RPE) cells from healthy people fibroblast (n=2). A total of 13 samples were analyzed : 9 RPE cells derived from iPSC LCA and 4 RPE cells derived from wild-type iPSC.


title: Gene expression of T follicular helper (TFH) cells 6 h after ICOS-L blockade

status: Public on Jan 19 2015

first: Pawel

last: Durek

summary: The maintenance of the TFH phenotype depends on continuous signals via ICOS. For a global assessment of differences in gene expression after interruption of the ICOS pathway a genome wide transcriptome analysis was performed. We used the OT-II adoptive transfer system to isolate antigen-specific TFH cells (day 6 after immunization) after short-term (6 hours) blockade of the ICOS pathway using a monoclonal antibody against ICOS-L.

overall_design: Gene expression profiles of TFH cells with or without ICOS-L blockade. Affymetrix MG 430 2.0 whole genome arrays were performed in duplicates for the control and blockade group (4 arrays in total). To obtain genes significantly regulated upon ICOS L blockade, the expression profiles of TFH cells treated with an isotype control or anti-ICOS-L antibody were compared to each other. After total RNA extraction, reverse transcription, cDNA extraction, the biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized in duplicates for each of the two groups to the 4 GeneChip arrays: Group1 TFH cells control, Group2 TFH cells ICOS-L blockade.

first: Randi

last: Franke

first: Jan

middle: P

last: Weber

first: Franziska

last: Fuhrmann

first: Maysun

last: Al Baz

first: Dana

last: Vu Van

first: Joachim

last: Grün

first: Hans-Werner

last: Mages

last: Kroczek

first: Mir-Farzin

last: Mashreghi

first: Andreas

last: Radbruch

last: Hutloff


title: Human induced pluripotent stem cells reveal early developmental molecular correlates with a probable Leber congenital amaurosis type I

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

overall_design: Refer to individual Series


title: Identification of genes suppressed by miR-483-5p and miR-551a in a colon cancer cell-line

status: Public on Jan 16 2015

first: Jia Min

last: Loo

address: 1230 York Avenue #342

institute: The Rockefeller University

summary: miR-483-5p and miR-551a were over-expressed in a colon cancer cell-line LvM3b to identify genes that are down-regulated by the miRNAs over-expression.

overall_design: Total RNA was isolated from miR-483-5p or miR-551a over-expressing LvM3b cells as well as control LvM3b cells.

first: Jiamin


title: Role of the Transcription Factor, Erg, in Chondrocyte Fate Determination during Knee Joint Formation

status: Public on Jan 20 2015

city: london

first: mark

middle: christopher

last: howard

address: charterhouse Square

department: Endocrinology

institute: QMUL

summary: Objective: Joint formation begins with the establishment of an interzone within the cartilaginous anlagen of the future skeleton and both Gdf5 and Erg are proposed as regulators of chondrocyte differentiation during and post interzone formation. The aim of this study was to examine the relationship between Gdf5 and Erg expression and downstream effects on chondrocyte gene expression.  Design: Erg expression was identified in mouse knee joints at E13.5. Expression and microarray analyses were performed using micromass cultures of murine C3H10T1/2 mesenchymal cells undergoing induced chondrogenesis in the presence of absence of Gdf5 and Erg.  Results: At E13.5, Erg expression was found to surround epiphyseal chondrocytes and span the interzone up to the intermediate zone. Erg splice forms were expressed in micromass cultures, and their expression profile was altered by the addition of recombinant Gdf5 depending on the stage of differentiation. Overexpression of Erg-010 resulted in a downregulation of Col2a1 and Col10a1. Microarray analysis following Erg-010 overexpression identified two potential downstream targets, Ube2b and Osr2, which were also differentially regulated by Gdf5.  Conclusion: Erg regulation by Gdf5 in mesenchymal cells in vitro is dependent on the stage of chondrogenesis, and its expression in vivo demarcates chondrocytes that are not destined to be consumed by endochondral ossification.  Functionally, Erg expression causes downregulation of Col2a1 and Col10a1 expression and this effect is potentially mediated by Osr2, which is a known regulator of chondrocyte differentiation. The identification of Ube2b as a putative downstream target of Erg-010 suggests that it may contribute to the regulation of the ubiquitination pathway and thereby BMP2 signaling, which is essential for normal knee joint development.

overall_design: RNA from overexpression experiments was extracted as described above. Total RNA quality was confirmed using a Bioanalyzer 2100 (Agilent). Labelled targets were generated from total RNA and hybridized to GeneChip Mouse Genome 430 2.0 arrays (Affymatrix) (Genomics Centre, University of Manchester). The raw fluorescence intensity values were normalized using a Robust Multi-array Average approach using dChip (V2005)

first: Mark

last: Howard

first: Gillian

last: Wallis

first: Rocky

last: Tuan


title: Alternatively processed  and compiled RNA-Sequencing and clinical data for thousands of samples from The Cancer Genome Atlas

status: Public on Jan 27 2015

city: Salt Lake City

first: Mumtahena

last: Rahman

state: UT

address: 20 South 2030 East, Rm 420

department: Biomedical Informatics

institute: University of Utah

type: Expression profiling by high throughput sequencing

summary: We reprocessed RNA-Seq data for 9264 tumor samples and 741 normal samples across 24 cancer types from The Cancer Genome Atlas with "Rsubread". Rsubread is an open source R package that has shown high concordance with other existing methods of alignment and summarization, but is simple to use and takes significantly less time to process data. Additionally, we provide clinical variables publicly available as of May 20, 2015 for the tumor samples where the TCGA ids are matched.

overall_design:
Using Rsubread version 1.14.2 R package, we aligned the fastq files downloaded from Cghub. First, the reads were aligned with align() function to the UCSC hg19 reference genome. Second, featureCounts() function was used to summarize the gene level expression values as integer number. Third, these summarized gene values were normalized to FPKM and TPM values. In addition, we downloaded clinical data for all tumor samples. We collated this data into a matrix and matched the ids reported in RNA-Seq data. A supplemental file showing the cancer type of each sample is included for the users.
Please note that
[1] All 9264 tumor samples have been combined to create the processed matrix files for tumor samples
[2] All 741 normal samples have been combined to create the processed matrix files for normal samples
[3] The TCGA_24_CancerType_Samples.txt and TCGA_24_Normal_CancerType_Samples.txt  files list each sample tumor type for tumor samples and normal samples respectively.
[4] 548 clinical variables for each sample are provided in the TCGA_24_548_Clinical_Variables_9264_Samples.txt
[5] Raw data mRNA sequence can be downloaded from CGHub (https://cghub.ucsc.edu/) with an access key and processed with pipeline available from https://github.com/srp33/TCGA_RNASeq_Clinical.

first: Stephen

last: Piccolo


title: Expression data from aortic smooth muscle cells (AoSMC) and myofibroblasts (FB) isolated respectively from the ascending aortas and the aortic valves of bicuspid (BAV) and tricuspid aortic valve (TAV) patients

status: Public on Jan 15 2015

city: Stockholm

first: Jesper

middle: Robert

last: Gådin

address: CMM, L8:02 Karolinska Universitetessjukhuset, Solna

department: Department of Medicine

institute: Karolinska Institutet

summary:
AoSMC and FB were cultured and exposed to transforming growth factor beta1 (TGFb1) prior to the exon array analysis
The objective was to study the TGFb responsivness, at the gene expression level, in AoSMC and FB form BAV and TAV patients

overall_design: 54 samples in total were generated from biopsies obtained from 23 different individuals. We performed paired analyses to compare the un-treated (c) versus the TGFb1 (t1) treated cells, for each patient

first: Valentina

last: Paloschi

first: Shaukat

last: Khan

first: Hanna

middle: M

last: Björck

first: Lei

last: Du

first: Shohreh

last: Maleki

first: Joy

last: Roy

middle: H

last: Lindeman

first: Salah

last: Mohamed

first: Takeshi

last: Tsuda

first: Anders

last: Franco-Cereceda

first: Per

last: Eriksson


title: Knockout mice lacking MG56

status: Public on Jan 14 2015

city: Kyoto city

first: Atsuhiko

last: Ichimura

state: Kyoto

address: 46-29, Yoshida Shimoadachi-cho, Sakyo-ku

department: Department of Biological Chemistry

institute: Kyoto University

summary: To survey altered gene expression in MG56-knockout muscle, total RNA preparations from mouse hindlimb muscle and hearts were subjected to gene microarray analysis. Results exhibit the effects of MG56 deficiency on overall transcription, and may further imply the biological role of MG56.

overall_design: Total RNA samples were preparated from Tibialis-anterior (TA) muscle and hearts of three P9 MG56-knockout mice and the corresponding wild-type mice were mixed and then subjected to Affymetrix Mus musculus microarrays.

first: Hiroshi

last: Takeshima


title: Expression data from mouse proprioceptive sensory neuron subclasses.

city: New York

first: Joriene

last: de Nooij

address: 650 West 168th Street

department: Neurology

institute: Columbia University

summary:
Proprioception relies on two main classes of proprioceptive sensory neurons (pSNs). These neurons innervate two distinct peripheral receptors in muscle, muscle spindles (MSs) or Golgi tendon organs (GTOs), and synapse onto different sets of spinal targets, but the molecular basis of their distinct pSN subtype identity remains unknown.
We used microarray analysis to compare gene expression profiles between MS- and GTO- innervating proprioceptors.

overall_design: We generated transgenic mice in which MS and GTO pSNs are labelled with different fluorescent proteins (see de Nooij et al., 2015 for details). We used Fluorescent Activated Cell Sorting (FACS) to isolate the MS and GTO pSN subsets from dissociated DRG from p7-10 transgenic mice. Neurons from multiple FACS experiments were pooled into three samples each for the MS and GTO pSN subset.

first: Thomas

last: Jessell


title: Identification of genes suppressed by miR-483-5p and miR-551a in a colon cancer cell-line (study 2)

first: Jia Min

last: Loo

first: Jiamin


title: Identification of miRNAs that regulate Colorectal Cancer Metastasis

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


title: The Microbial Metabolite Deoxycholic Acid Modulates Cholesterol Metabolism in the Germ-Free Mouse

status: Public on Jan 08 2015

city: San Diego

first: John

last: Walker

address: 10675 John Jay Hopkins

institute: Genomics Institute of the Novartis Research Foundation

summary: Deoxycholic acid (DCA) is a secondary bile acid produced by a small number of commensal species of bacteria present in the mammalian gut.  Elevated DCA concentration correlates with disease states including colon cancer and cholesterol gallstones, but the associated mechanisms are not fully understood. Both primary and secondary bile acids are also capable of affecting gene expression through nuclear receptors such as FXR.  To better understand the impact of a commensal-derived secondary bile acid on host metabolism we fed DCA to germ-free (GF) mice, which normally lack DCA, and compared the hepatic transcriptomes of bile acid fed GF mice to GF mice receiving a control diet, as well as to those of conventionally housed control animals.  Interestingly, the feeding of DCA to GF mice, but not the feeding of cholic acid (CA) from which DCA is derived, results in an up-regulation of genes of cholesterol biosynthetic pathways.  GF mice normally have elevated hepatic cholesterol compared to conventionally housed mice. Despite increase in the expression of cholesterol biosynthetic genes, the DCA fed GF mice showed a markedly decreased level of hepatic cholesterol equivalent to the hepatic cholesterol concentration of conventionally colonized animals.  Total cholesterol in the serum was unaffected by DCA, but there was a decrease in the HDL lipoprotein fraction as well as an increase in the non-HDL lipoprotein fraction of the serum cholesterol.  DCA, but not CA, is sufficient to modulate host lipoprotein metabolism.  Taken together, these results suggests that a minor component of the gut microbiome has a significant impact on cholesterol homeostasis through secondary metabolism of bile acids and suggests a possible therapeutic intervention route through  the microbial metabolic pathways.

overall_design: two mouse strains, three diets, one time point

last: Hollenbeck

first: Andrew

last: Anfora

first: Ganes

last: Bhat

first: Van

last: Nguyen-Tran

first: Eric

last: Peters

first: Sanjay

last: Agarwalla

first: Scott

last: Lesley


title: Gene expression data from transgenic and knockout mice

first: Feng

last: He

address: 423 E23rd Street

institute: New York University

summary:
Activation of oncogenic ras pathway accounts for up to 90% low-grade superficial urothelial carcinomas of bladder, and p53 deficiency is very common in high-grade muscle invasive carcinomas. These two pathways in bladder urothelial tumorigenesis used to be considered divergent and their potential collaboration has not been illustrated.
We did laser capture micro-dissection (LCM) to separate the tumor cells from the whole bladder tissues from H-ras transgenic and p53 knockout mice, as well as normal urothelial cells as control. Microarray was then performed to identify distinct classes of up-regulated genes during tumorigenesis and progression.

overall_design: In order to get the gene expression profiles of carcinoma in situ (CIS), muscle invasive tumors and normal cells, we used LCM to purify the cells from mixture of different types of cells, and then extracted RNA for microarray. There are three groups applied in microarray, which are normal cells as control, CIS (tumor genesis) and invasive tumors (tumor progression).

first: Xue-Ru

last: Wu


title: Track normalization and averaging of H3K4me3 ChIP-seq data across various cell and tissue types.

city: Bethesda

first: Ian

last: Fingerman

address: 45 Center Dr.

department: NCBI Epigenomics

institute: National Institutes of Health

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Data tracks from chromatin immunoprecipitation followed by high throughput sequencing (ChIP-seq) experiments were sorted by tissue or cell types and processed using an in-house algorithm that provides normalization functionality followed by generation of a track average.

overall_design: Re-analysis of Roadmap Epigenomics H3K4me3 ChIP-seq datasets using an in-house algorithm to create an average data track.


title: Lung expression data from highly pathogenic H5N1 virus infected and uninfected mice

city: St Louis

first: Adrianus

middle: Cornelis Maria

last: Boon

state: Missouri

address: 660 Euclid Avenue

institute: Washington University School of Medicine

summary:
Susceptible and Resistant mouse strain, e.g. DBA/2J and C57BL/6J respectively, were inoculated with a highly pathogenic H5N1 influenza A virus (A/Hong Kong/213/2003) for 72 hours.
Differences in expression were analyzed and use to identify candidate genes and pathways that contributed to the difference in H5N1 pathogenesis in these two strains. Recombinant inbred BXD strains are derived from the DBA/2J and C57BL/6 parent and were used to identify genetic loci associated with resistant to H5N1 infection.

overall_design: Female 6-8 weeks old animals were inoculated with H5N1 virus or not and 72 hours later the lungs were obtained and immediately homogenized in Trizol. The extracted RNA was submitted for Affymetrix Gene expression arrays. Differences in gene-expression were determined and used to identify candidate genes and pathways that are important for disease severity and susceptiblity to H5N1 virus.

first: Richard

last: Webby


title: microRNA profiling of normal testes and testicular germ cell tumors using deep sequencing approach

first: Deniz

middle: Mahmut

last: Ozata

address: CCK R8:04

department: Oncology-pathology

institute: Karolinska University Hospital, Karolinska Institutet

type: Non-coding RNA profiling by high throughput sequencing

summary: Several observations have pointed a link between small RNA pathway and testicular germ cell tumorigenesis. Yet, the role of small RNAs in testicular germ cell tumors (TGCTs) is still not completely understood. In this study, we characterized the expression profiles of sRNAs in 9 primary sporadic TGCTs and 2 normal testes (NTs) using a sequencing approach. Our data show comprehensive coverage of microRNAs (miRNAs) expressed in human TGCT tissues and NTs, including the identification of 29 candidate novel miRNAs. We identified the differentially expression of miR-506~514 cluster and miR-21, miR-223 in the TGCTs compared to NTs. Functionally, we showed that miR-514a-3p positively regulates apoptosis through directly regulating PEG3. We further demonstrate that PEG3 activates NF-kappa B pathway in human testicular germ cell tumors.

overall_design: 11 snap frozen tissues, including 2 Normal Testes (NTs) and 9 Testicular germ tumors (TGCTs), were subjected to small RNA sequencing using  Solexa/Illumina sequencing platform (Illumina 1G Genome Analyzer)

first: Weng-Onn

last: Lui


title: TSLP Expression: Analysis with a ZsGreen TSLP Reporter Mouse

status: Public on Jan 06 2015

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

summary: Thymic stromal lymphopoietin (TSLP) is a type I cytokine that plays a central role in induction of allergic inflammatory responses.  Its principal targets have been reported to be dendritic cells and / or CD4 T cells; epithelial cells are a principal source.  We report here the development of a reporter mouse (TSLP-ZsG) in which a ZsGreen (ZsG)-encoding construct has been inserted by recombineering into a bacterial artificial chromosome (BAC) immediately at the translation initiating ATG of TSLP.  The expression of ZsG by mice transgenic for the recombinant BAC appears to be a faithful surrogate for TSLP expression, particularly in keratinocytes and medullary thymic epithelials cells (mTECs).  A comparison of gene expression in ZsG expressing and ZsG negative mTECs and cortical thymic epithelial cells, which are all ZsG negative, revealed that all three populations can be distinguished from one another.  In particular ZsG (and TSLP) expressing mTECs and ZsG- mTECs are separable populations based on gene expression profiling.   Little or no expression of ZsG is observed in bone marrow-derived mast cells or basophils or in CD45+ cells infiltrating TSLP/ZsG-expressing skin. Using the TSLP-ZsG reporter mouse, we show that TNFa and IL-4/IL-13 are potent inducers of TSLP expression by keratinocytes and that local activation of Th2 and Th1 cells induces keratinocyte TSLP expression. We suggest that the capacity of TSLP to both induce Th2 differentiation and to be induced by activated Th2 cells raises the possibility that TSLP may be involved in a positive feedback loop to enhance allergic inflammatory conditions.

overall_design: comparison of reporter mouse construct types ZsG-cTEC, ZsG-mTEC and ZsG+

first: Cedric

last: Dewas

first: Xi

last: Chen

first: Tetsuya

last: Honda

first: Ilkka

last: Junttila

first: Jay

last: Linton

first: Mark

last: Udey

first: Lionel

last: Feigenbaum

first: Lily

last: Koo

first: Joy

last: Williams

first: William

middle: E

last: Paul


title: Identification of genes affected by Wnt3a in primary mouse myoblasts

city: PALO ALTO

first: Thomas

last: Rando

address: 3801 Miranda Ave

institute: STANFORD UNIVERSITY SCHOOL OF MEDICINE

summary: In order to gain insight into the molecular events operating downstream of canonical wnt-signaling in myoblasts, we compared by microarray analysis the transcriptome of myoblast cultured for 4 hours in the presence and absence of Wnt3a.

overall_design: Primary myoblasts isolated from newborn mice were treated for 4 hours in DMEM 2% horse serum in presence or in absence of Wnt3a (100ng/ml)

first: Stefano

last: Biressi


title: Gene expression profiling in proximal versus distal mouse colon

status: Public on Jan 01 2015

city: HERAKLION

first: ARISTIDES

last: ELIOPOULOS

state: CRETE

address: UNIVERSITY CAMPUS

department: MEDICAL SCHOOL

country: Greece

institute: UNIVERSITY OF CRETE

summary: Analysis of gene expression in proximal versus distal part of the mouse large intestine.

overall_design: Three (3) animals (biological replicates) were used to isolate tissue from proximal and distal areas of the large intestine.

first: Aristides

middle: G

last: Eliopoulos

first: George

last: Pavlopoulos


title: Akt-Induced Mitochondrial Dysfunction in the Heart

status: Public on Jan 05 2015

city: Birmingham

first: Adam

last: Wende

state: AL

address: PBMR Rm 506 901 19th Street South

department: Pathology

institute: University of Alabama at Birmingham

summary: Sustained Akt activation induces cardiac hypertrophy (LVH), which may lead to heart failure. This study tested the hypothesis that Akt activation contributes to mitochondrial dysfunction in pathological LVH. Akt activation induced LVH and progressive repression of mitochondrial fatty acid oxidation (FAO) pathways. Preventing LVH by inhibiting mTOR failed to prevent the decline in mitochondrial function but glucose utilization was maintained. Akt activation represses expression of mitochondrial regulatory, FAO, and oxidative phosphorylation genes in vivo that correlate with the duration of Akt activation in part by reducing FOXO-mediated transcriptional activation of mitochondrial-targeted nuclear genes in concert with reduced signaling via PPARα/PGC-1α and other transcriptional regulators. In cultured myocytes Akt activation disrupted mitochondrial bioenergetics, which could be partially reversed by maintaining nuclear FOXO, but not by increasing PGC-1α. Thus, although short-term Akt activation may be cardioprotective during ischemia by reducing mitochondrial metabolism and increasing glycolysis, long-term Akt activation in the adult heart contributes to pathological LVH in part by reducing mitochondrial oxidative capacity.

overall_design: Three samples per group of 8-week-old wild-type or transgenic mice with cardiac-specific constitutive expression of an activated Akt (caAkt) in the heart at 8 weeks of age were used. Mice have been previously described in depth (Shioi T, McMullen JR, Kang PM, Douglas PS, Obata T, Franke TF, Cantley LC, Izumo S. 2002. Akt/protein kinase B promotes organ growth in transgenic mice. Mol. Cell. Biol. 22:2799-2809.). After hearts were removed total myocardial RNA was labeled and processed as described below for microarray analysis to detail the global changes in gene expression underlying development of heart failure in this mouse model.

first: Brian

middle: T

last: O'Neill

first: Heiko

last: Bugger

first: Bart

last: Weimer

first: E

middle: D

last: Abel


title: Expression data from polarized macrophages: effect of p53

city: Singapore

first: Ling

last: Li

address: 8A Biomedical Grove

country: Singapore

institute: Agency for Science Technology and Research, Singapore

summary:
p53 is critically important in preventing oncogenesis but its role in non-cancer biology remains unclear.  Macrophages exist as two subtypes (M1 and M2). Nutlin-3a (p53 activator) inhibits M2 gene expression and phenotype. p53 acts by suppressing transcription of c-Myc and thence regulates expression of a subset of M2 markers. This work has implications for our understanding of the mechanisms that regulate plasticity of macrophages in health and disease.
We used microarrays to study the global programme of gene expression in nutlin-3a and 10058F4 (C-myc inhibitor) treated polarised mouse macrophages

overall_design: 5 groups of cultured mouse macrophages: (i) M0 (untreated), (ii) M1, (iii) M2, (iv) M2+nutlin-3a, (v) M2+MYC inhibitor (10058F4). 3 biological replicates per treatment group.

first: M

last: Champ


title: Gene expression changes induced by overexpression of MN1 and MN1VP16  in murine bone marrow cells

city: Hannover

first: Adrian

last: Schwarzer

address: Carl-Neuberg-Str. 1

department: Experimental Hematology

institute: Hannover Medical School

summary: Myeloid differentiation is blocked in acute myeloid leukemia (AML), but the molecular mechanisms are not well characterized. MN1 is overexpressed in some AML patients and confers resistance to all-trans retinoic acid (ATRA)-induced differentiation. To understand the role of MN1 as a transcriptional regulator in myeloid differentiation, we fused transcriptional activation (VP16) or repression (M33) domains with MN1 and characterized these cells in vivo. Transcriptional activation of MN1 target genes induced myeloproliferative disease with long latency and differentiation potential to mature neutrophils. A large proportion of differentially expressed genes between leukemic MN1 and differentiation-permissive MN1VP16 cells belonged to the immune response pathway like Irf8 and Ccl9. As MN1 is a co-factor of MEIS1 and RARA, we compared chromatin occupancy between MN1, MEIS1 and RARA. Immune response genes that were upregulated in MN1VP16 cells were co-targeted by MN1 and MEIS1, but not RARA, suggesting that myeloid differentiation is blocked through transcriptional repression of shared target genes of MN1 and MEIS1. Constitutive expression of  Irf8 or its target gene Ccl9 identified these genes as potent inhibitors of MN1-induced leukemia. Our data show that MN1 prevents activation of the immune response pathway, and suggest that restoration of Irf8 signalling as a novel therapeutic target in AML.

overall_design: C57BL/6J  bone marrow cells were harvested from mice treated for 4 days with 150 mg 5-fluorouracil/kg  and stimulated for 48 hours in DMEM supplemented with 15% FBS, 10 ng/mL hIL6, 6ng/mL mIL3, and 20ng/mL mSCF. The cells were infected with MN1 or  MN1VP16 retroviral constructs by cocultivation with irradiated  E86 viral producer cells in the presence of 5μg/mL protamine sulfate (Sigma) for 48 hours and then transplanted into lethally irradiated syngeneic recipient mice. 4 weeks after transplantation MN1, MN1VP16 GFP+ cells and Gr1+/CD11b+ bone marrow cells were FACS-sorted and analyzed by  Affymetrix GeneChip Mouse 430 2.0 (43.000 probes) microarrays

first: Michael

last: Heuser


title: Gene expression changes induced by expression of MN1 deletion mutants in murine bone marrow cells

summary: Extensive molecular profiling of leukemias and preleukemic diseases has revealed that distinct clinical entities, like acute myeloid (AML) and T-lymphoblastic leukemia, share the same pathogenetic mutations. It is not well understood how the cell of origin, accompanying mutations, extracellular signals or structural differences in a mutated gene determine the phenotypic identity of the malignant disease. We studied the relationship of different protein domains of the MN1 oncogene and their effect on the leukemic phenotype, building on the ability of MN1 to induce leukemia without accompanying mutations. We found that the most C-terminal domain of MN1 was required to block myeloid differentiation at an early stage, and deletion of an extended C-terminal domain resulted in loss of myeloid identity and cell differentiation along the T-cell lineage in vivo. Megakaryocytic/erythroid lineage differentiation was blocked by the most N-terminal domain. In addition, the N-terminus was required for proliferation and leukemogenesis in vitro and in vivo through upregulation of HoxA9, HoxA10 and Meis2. Our results provide evidence that a single oncogene can modulate cellular identity of leukemic cells based on its active domains. It is therefore likely that different mutations in the same oncogene may impact cell fate decisions and phenotypic appearance of malignant diseases.

overall_design: C57BL/6J bone marrow cells were harvested from mice treated for 4 days with 150 mg 5-fluorouracil/kg and stimulated for 48 hours in DMEM supplemented with 15% FBS, 10 ng/mL hIL6, 6ng/mL mIL3, and 20ng/mL mSCF. The cells were infected with MN1, MN1Δ1, and MN1Δ7 retroviral constructs by cocultivation with irradiated E86 viral producer cells in the presence of 5μg/mL protamine sulfate (Sigma) for 48 hours and then transplanted into lethally irradiated syngeneic recipient mice. 4 weeks after transplantation, MN1, MN1Δ1, and MN1Δ7 leukemia cells and Gr1+/CD11b+ bone marrow cells were FACS-sorted and analyzed by Affymetrix GeneChip Mouse 430 2.0 (43,000 probes) microarray.


title: Scl specifies hemogenic endothelium and inhibits cardiogenesis via primed enhancers [expression]

city: Tartu

first: Tõnis

last: Org

address: Riia 23

department: Institute of Molecular and Cell Biology

country: Estonia

institute: University of Tartu

summary: Scl/Tal1 confers hemogenic competence and prevents cardiomyogenesis in embryonic endothelium. Here we show that Scl both directly activates a broad gene regulatory network required for hematopoietic stem/progenitor cell (HS/PC) development, and represses transcriptional regulators required for cardiogenesis. Cardiac repression occurs during a short developmental window through Scl binding to distant cardiac enhancers that harbor H3K4me1 at this stage. Scl binding to hematopoietic regulators extends throughout HS/PC and erythroid development and spreads from distant enhancers to promoters. Surprisingly, Scl complex partners Gata 1 and 2 are dispensable for hematopoietic versus cardiac specification and Scl binding to the majority of its target genes. Nevertheless, Gata factors co-operate with Scl to activate selected transcription factors to facilitate HS/PC emergence from hemogenic endothelium. These results uncover a dual function for Scl in dictating hematopoietic versus cardiac fate choice and suggest a mechanism by which lineage-specific bHLH factors direct the divergence of competing fates.

overall_design: Examination of Scl target genes in ES cell derived day4 EB (embryoid body) Flk+ mesodermal cells

first: Tonis

first: Dan

last: Duan

first: Roberto

last: Ferrari

first: Amelie

last: Montel-Hagen

first: Ben

last: Van Handel

first: Marc

last: Kerényi

first: Rajkumar

last: Sasidharan

first: Ludmilla

last: Rubbi

first: Yuko

last: Fujiwara

first: Matteo

last: Pellegrini

first: Stuart

last: Orkin

first: Siavash

middle: K

last: Kurdistani

first: Hanna

last: Mikkola


title: The effect of XKA on gene expression profile in KKAy mice

status: Public on Dec 31 2014

city: hangzhou

first: zhenzhong

last: yang

address: Yuhangtang 866

country: China

institute: zhejiang univ.

summary:
Xiao-Ke-An (XKA) is a Chinese medicine for T2D. However, the therapeutic mechanisms of XKA remain to be systematically elucidated. In this study, the therapeutic mechanisms of XKA were investigated.
Male KKAy mice were administered with XKA for 32 days while the model and normal group was treated with distilled water.

overall_design: The KKAy mice were administered orally once daily with either distilled water (model group) or XKA (1.5 g/kg) for 32 days. And the C57BL/6J mice were gavaged with distilled water as normal group. Livers from normal, model and XKA (1.5 g/kg) treatment groups were used for further microarray experiment.

first: Zhenzhong

last: Yang


title: In vitro differentiation protocol of Paraxial mesoderm from mouse embryonic stem cells (mESCs)

city: ILLKIRCH

first: philippe

last: moncuquet

address: 1 rue laurent fries

institute: IGBMC

summary: Stem cell-derived tissues have wide potential for modelling developmental and pathological processes as well as cell-based therapy. However, it has proven difficult to generate several key cell types in vitro, including skeletal muscle. In vertebrates, skeletal muscles derive during embryogenesis from the presomitic mesoderm (PSM). Using PSM development as a guide, we establish conditions for the differentiation of monolayer cultures of mouse embryonic stem (ES) cells into PSM-like cells without the introduction of transgenes or cell sorting. We differentiated mouse ESCs in a medium supplemented with Rspo3, DMSO and the Bmp inhibitor Noggin. In vivo, the PSM cells are first expressing Msgn1 (posterior PSM marker) . After 3 and 4 days of differentiation of mESCs, Msgn1-positive cells were FACS-sorted and their transcriptome analyzed.

overall_design:
mESCs were differentiated in vitro as monolayer in a media containing DMSO, R-spondin, and Noggin for 3 and 4 days. Cells expressing Msgn1 were sorted

and analyzed by microarrays.

first: Philippe

last: Moncuquet

first: Miyanari

last: Ayako

first: Gobert

last: Benedicte

first: Chal

last: Jerome


title: Distinct biological and transcriptional features of FLT3-ITD variants in vitro and in vivo

city: Berlin

first: Lars

last: Bullinger

address: Augustenburger Platz 1

department: Hematology, Oncology and Tumorimmunology

institute: Charité

summary: Treatment of FLT3-ITD mutated AML remains a clinical challenge as this subset of patients show high incidence of relapse, even after allogeneic stem cell transplantation. Recently, we defined a molecular subset of FLT3-ITD mutations, located in the FLT3-tyrosine kinase domain 1 (TKD1). In multivariable analyses, insertion of ITD variants in the beta1-sheet (TKD1) was identified as an unfavorable prognostic factor for achievement of a complete remission relapse-free survival and overall survival independently of other prognostic factors such as allelic ratio. In the presented analysis we characterize ITD variants located in the TKD1. While transforming capacity and activation of downstream signaling nodes appears comparable to ‘classical’ ITD mutations located in the JM-domain, TKD1-ITDs reveal a distinct gene expression profile and confer decreased sensitivity to kinase inhibitor therapy in vitro and in vivo. This knowledge may impact clinical decisions in regard to TKI therapy versus allogeneic stem cell transplantation.

overall_design: RNA was isolated from 32D cells transduced with the respective FLT3-ITD constructs using TRIzol (Life Technologies). Total RNA was converted into double-stranded cDNA by reverse transcription using the 3' IVT Express Kit from Affymetrix and samples were hybridized to Affymetrix GeneChip Mouse Genome 430 2.0 Arrays according to the manufacturer’s recommendations (Affymetrix).

first: Florian

last: Heidel

first: Thomas

last: Fischer


title: Transcriptome of Irradiated Microglia

city: Stanford

first: Matthew

last: Li

address: 265 Campus Dr.

institute: Stanford University

summary:
Whole brain irradiation remains important in the management of brain tumors. Although necessary for improving survival outcomes, cranial irradiation also results in cognitive decline in long-term survivors. A chronic inflammatory state characterized by microglial activation has been implicated in radiation-induced brain injury, and here we present a comprehensive transcriptional profile of irradiated microglia.
Fluorescence-activated cell sorting (FACS) was used to isolate CD11b+ microglia from the hippocampi of C57BL/6 and Balb/c mice 1 month after 10Gy cranial irradiation. Affymetrix gene expression profiles were evaluated using linear modeling and rank product analyses. A conserved signature of irradiation was identified across strains, and gene set enrichment analysis was employed to functionally compare our signature to publically available mouse and human datasets.

overall_design: FACS-sorted microglia samples from three mice were analyzed from each of four groups: sham irradiated C57BL/6 mice, 10 Gy irradiated C57BL/6 mice, sham irradiated Balb/c mice, 10 Gy irradiated Balb/c mice (12 total samples analyzed). All mice were analyzed 1 month after sham or 10 Gy irradiation.

first: Terry

middle: C

last: Burns

first: Alexander

last: Morgan

first: Theo

last: Palmer


title: Expression data from mature 3T3-L1 adipocytes under berberine treatment

city: shanghai

first: Ying

address: 197 Ruijin Road II, Shanghai 200025, China

institute: Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiaotong University School of Medicine

summary: We used microarrays to detail the global program of gene expression under berberine treatment in 3T3-L1 adipocytes

overall_design: 3T3-L1 cells were induced into differentiated adipocytes and then treated with 5μM berberine for 3h, 6h or 12h for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain the change of gene expressions under such treatment.


title: Transforming pluripotency: an exon-level study of malignancy-specific transcripts in human embryonal carcinoma and embryonic stem cells

city: Oslo

first: Sharmini

last: Alagaratnam

address: Radiumhospitalet, Montebello

department: Institute for Cancer Research

country: Norway

institute: Oslo University Hospital

summary:
Exon-level transcriptome analysis of embryonal carcinoma (EC) and embryonic stem (ES) cell lines.
To circumvent difficulties of isolating pure populations of cancer stem cells for the purpose of identifying malignancy-specific gene expression, we have compared exon-resolution transcriptomic profiles of five embryonal carcinoma (EC) cell lines, a histological subtype of germ cell tumour, to their non-malignant caricature, specifically six human embryonic stem (ES) cell lines. Both cell types are readily accessible, and were purified for undifferentiated cells only. We identified a set of 28 differentially expressed genes, many of which had cancer and stemness roles. Overexpression of the recently discovered pluripotency gene NR5A2 in malignant EC cells revealed an intriguing indication of how WNT-mediated dysregulation of pluripotency is involved with malignancy. At the exon-level, alternative splicing events were detected in ZNF195, DNMT3B and PMF1, and alternative promoters were detected for ASH2L and ETV5. These events were validated by RT-PCR-based methods in EC and ES lines, and further explored within a series of 25 primary tumours, where the alternative splicing event in the de novo DNA methyltransferase DNMT3B may have functional consequences. In conclusion, we have identified malignancy-specific gene expression differences within a rigorous pluripotent stem cell context. These findings are of particular interest for both germ cell tumour and ES cell biology, and in general to the concept of cancer stem cells.

overall_design: 5 EC and 6 ES cell lines gown on plastic and feeders respectively were sorted for the pluripotency marker SSEA3, then profiled on the Affymetrix Human Exon 1.0 ST platform. 3 additional EC lines grown on feeders and ES medium were also profiled in the same way. Data was analyzed using Qlucore (PCA), XRAY and limma (gene- and exon-level expression differences) and SAM (two-class pair-wise Significance of Microarrays).

first: Neil

last: Harrison

first: Anne

last: Bakken

first: Andreas

last: Hoff

first: Mark

last: Jones

first: Anita

last: Sveen

first: Harry

last: Moore

first: Peter

middle: W

last: Andrews

first: Ragnhild

last: Lothe

first: Rolf

middle: I

last: Skotheim


title: Genomewide analysis of PTEN deletion in mouse lung epithelial cells

city: Tampa

first: Ravi

last: Pathak

address: 12901 Bruce B Downs

institute: University Of South Florida

summary: Triple transgenic mice harboring a conditional Pten allele were developed  and Pten was conditionally deleted in vivo from the lung epithelial cells using the doxycycline dependent Cre/LoxP approach. Microarray analysis of lung RNA isolated from Pten-deleted lung epithelial cells (PtenΔ/Δ) and control mice was performed to identify potential PTEN responsive genes.

overall_design: Compound-transgenic mice harboring Pten gene with loxP-flanked exon-V (Ptenflox/flox), SP-C–rtTAtg/−; and TetO-Cretg/- were generated. Mice harboring SPC-rtTA/Ptenflox/flox, TetO-Cretg/-/Ptenflox/flox, SPC-rtTA, or TetO-Cretg/- as controls. Likewise, Dox treatment (E6.5 to E14.5) induced tumors in CCSP-rtTA/TetO-Cretg/-/LSL-KrasG12D/PtenΔ/Δ mice between 10-12 weeks of age.  Mice expressing rtTA, or bearing TetO-Cretg/- alone, were normal controls

first: Vrushank

last: Davé

middle: R


title: Phospholipase Cγ1 is crucially required for EpoR/JAK2 controlled erythropoietic differentiation.

first: Lars

last: Bullinger

summary: Erythropoiesis is a multi-step process in which the development of red blood cells occurs through expansion and differentiation of hematopoietic stem cells (HSCs) into more committed progenitors. In vivo and in vitro studies have pointed out the major role of proximal  erythropoietin receptor (EpoR) signaling  through JAK2 tyrosine-kinase as a central regulator of erythropoiesis 1,2. However, little is known on more distant signalling pathways driving EPO/JAK2-induced differentiation of erythroid progenitors. Here, we demonstrate that phospholipase Cγ 1 (PLCγ1) is activated downstream of EpoR/JAK2 and is crucially required for differentiation of erythroid progenitor cells. In the absence of PLCγ1, erythroid progenitors exhibited dramatically impaired differentiation and colony-forming potential. To identify PLCγ1 effector molecules involved in regulation of erythroid differentiation we performed global gene expression and methylome analysis. In PLCγ1-deficient erythroid progenitors, profound changes in the landscape of DNA methylation and gene expression were observed. Taken together, our findings identify PLCγ1 as a central regulator in erythroid development and highlight its physiological relevance in development and maintenance of normal hematopoiesis.

overall_design: RNA was isolated from 5x10^5 I/11 cells transfected with either scrambled or PLCg1 shRNA using TRIzol (Life Technologies). RNA was amplified using the Ovation Pico WTA system (Nugen) and labeled using the encore Biotin Module (Nugen). 5 ug of amplified and labeled DNA was hybridized to Affymetrix GeneChip Mouse Genome 430plus 2.0 microarrays according to the manufacturer’s recommendations (Affymetrix).

first: Tina

last: Schnöder

first: Florian

last: Heidel

first: Thomas

last: Fischer


title: Early effects of Serum Response Factor (SRF) gene deletion on the vascular gene expression

city: Paris

first: Guillaume

last: Galmiche

address: 7 quai Saint-Bernard

department: Aging, stress and inflammation

summary:
The objective of this study is to assess the early effects of the Serum Response Factor deletion on the vascular gene expression program.
To generate smooth muscle specific SRF knockout, 4 month-old [SRF-flex2neo -SM22CreERT2ki/+] mice (SRFSMKO mice) were injected i.p. with 1mg of tamoxifen for 3 days. All control (SRF-flex2neo littermates) and SRFSMKO mice were systematically injected with tamoxifen to normalize for any effects due to tamoxifen.

overall_design: Mice were sacrificed 8 days after tamoxyfen injection for RNA extraction and hybridization on Affymetrix microarrays.

first: Zhenlin

last: Li

first: Sylvain

last: Baulande

first: Pascal

last: Soularue


title: Growth factor independence 1b (Gfi1b) is required for erythroid cell maturation and regulates embryonic globin expression [Mouse430_2]

city: Essen

first: Cyrus

last: Khandanpour

state: NRW

address: Hufelandstr. 55

department: Department of Hematology

institute: University Hospital Of Essen

summary:
Growth factor independence 1b (Gfi1b) is a DNA binding repressor of transcription with vital functions in hematopoiesis. Gfi1b-null embryos die at midgestation very likely due to defects in erythro- and megakaryopoiesis. To analyze the full functionality of Gfi1b in erythropoiesis, we used conditionally deficient mice that harbor floxed Gfi1b alleles and the Mx-Cre transgene inducible by pIpC treatment.
We used bone marow cells from 12 weeks old wild type C57BL/6 mice or conditional Gfi1b knock-out mice, both carrying the Mx-cre transgene induced by five treatments with pIpC (500µg each) every other day and sacrificed 42 days after the first injection. Ter119 positive erythroid cells were isolated by flow cytometry and RNA from these cells was isolated using the Trizol procedure according to the manufacturers instructions for gene expression analysis on Affymetrix MOE_430 2.0 expression arrays (GPL 1261)

overall_design: We used microarray-based gene expression profiling to analyze the effect of loss of Gfi1b expression in Ter119 positive erythroid cells from mouse bone marrow.

first: L

last: Vassen

first: H

last: Beauchemin

first: W

last: Lemsaddek

first: J

last: Krongold

first: M

last: Trudel

first: T

last: Möröy


title: Quantitative Dynamics of Chromatin-state Reprogramming for the Mouse Germ-Cell Specification Pathway In Vitro

status: Public on Mar 20 2015

city: Nara

first: Kazuki

last: Kurimoto

address: 840 Shijo-Cho, Kashihara

department: School of medicine

institute: Nara Medical University

summary:
We re-analyzed gene expression in the primordial germ cell (PGC) specification pathway in vitro, by using previously deposited microarray data.
The germ cell lineage produces either spermatozoa or oocytes and, by their fusion, creates zygotes with full developmental potential, thereby perpetuating and diversifying organisms' genetic as well as epigenetic information across generations.  In mice, PGCs are specified in the most posterior part of epiblast (monolayer epitherium-like cells, from which the whole embryonic part of conceptus will be derived) around embryonic day (E) 6.25 by a cytokine BMP4.  To recaptulate this pathway, an in vitor system was established by Hayashi et al. (2011, 2012): epiblast-like cells (EpiLCs) are induced from embryonic stem cells (ESCs) by cytokine Activin and bFGF, and then PGC-like cells (PGCLCs) are induced from EpiLC by cytokines including BMP4.  Similar to the in vivo PGCs, PGCLCs exhibit mesoderm-like profile 2 days after induction (d2 PGCLCs), and then 6 days after induction (d6 PGCLCs), they acquire profiles like PGCs at E9.5 in vivo.

overall_design: We down-loaded data from GEO database (GSM744093, GSM744094, GSM744095, GSM744096, GSM1070847, GSM1070848, GSM744101, GSM744102), and analyzed byu using dChip

first: Yukihiro

last: Yabuta

first: Katsuhiko

last: Hayashi

first: Hiroshi

last: Ohta

last: Kiyonari

first: Yoshinobu

last: Moritoki

first: Kenjiro

last: Kohri

last: Kimura

first: Yuki

last: Kato

last: Shirahige

first: Mitinori

last: Saitou