title: Syncytiotrophoblast generation from human pluripotent stem cells

summary:
Purpose: Syncytiotrophoblast (STB) is a multi-nucleated, terminally differentiated syncytium that covers the surface of the villous placenta and forms the major interface with maternal blood. It releases placental hormones and plays a primary role in exchange of gases, nutrients and waste products. Alterations in STB development and turnover have been implicated in placental diseases, including preeclampsia (PE). In vitro cell models are badly needed to study STB development and physiology due to inaccessibility to placental tissues during gestation. To establish in vitro STB model system, we generate STB and its mononucleated precursors from human embryonic stem cells (hESC) and profile for RNA content by RNAseq.
Methods: H1 Human ESC (WA01) were treated with BMP4, the ALK4/5/7 inhibitor (A83-01), and the FGF2 signaling inhibitor (PD173074) (BAP) to direct them to the trophoblast lineage and provided both STB and extravillous trophoblast. Syncytial areas emerged at day 8 BAP treatment ranged in diameter from ~40 µm to > 100 µm. The intact syncytial areas were isolated by sieving successively through 70 μm and 40 μm mesh cell strainers. The captured cells are recovered by inverting the strainer and rinsing with culture medium to separate large (>70 μm) and middle size cell sheets (40-70 μm). The fraction that passes through both sieves represents cells of smallest diameter (< 40 μm), presumably cytotrophoblast. Total 12 RNA samples from triplicate three size-fractioned BAP treated and three untreated hESC cultured in a FGF2 supplemented medium in parallel were analyzed.
Results: The larger > 70 μm areas stained positively for STB markers while ultrastructural analysis clearly revealed multi-nuclear cells with an extensive cytoplasm containing many prominent secretion granules.  The larger STB areas also had a larger DNA content that > 70 μm fraction contained 37 times more nuclear content and 40-70 µm fraction did 16 times more. Compared to the < 40 μm cell fraction, these larger cells over-expressed a full repertoire of genes characteristic of STB, e.g. CGA, CGB, PGF, ERVW1, GCM1. The smallest cell fraction had a DNA content consistent with mononuclear diploid cells, contained few secretory granules, and were only weakly positive for STB markers.
Conclusion: The data are consistent with the > 70 μm cells being mature STB, while the intermediate fraction may represent a precursor population. Human ESC directed along the trophoblast lineage by BAP treatment offers a useful model for following STB formation in vitro and suggest that this protocol may have utility in studying the basis of certain placental diseases, especially preeclampsia, where placental tissue isolated at term or after pregnancy terminations can only offer limited information.

overall_design: Three size fraction mRNA profiles of syncytial areas emerged at day 8 BAP treatment of hESC were generated by deep sequencing along with untreated hESC, in triplicate, using Illumina HiSeq 2500.

first: Shinichiro

last: Yabe

first: Danny

last: Schust


title: Distinctive Histogenesis and Immunological Microenvironment Based on Transcriptional Profiles of Follicular Dendritic Cell Sarcomas

status: Public on Apr 07 2017

city: Bologna

first: Maria Antonella

last: Laginestra

address: Via di Barbiano 1/10

department: Experimental Oncology Laboratory

country: Italy

institute: IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy

summary: Follicular dendritic cell (FDC) sarcomas are rare mesenchymal tumours (MTs) with variable clinical, morphologic and phenotypic characteristics. We investigated the transcriptome of 29 FDC sarcomas and compared it with that of other MTs, microdissected Castleman FDCs, and normal fibroblasts.  On unsupervised analysis, FDC sarcoma clustered with microdissected FDCs, distinct from other MTs and fibroblasts. The specific endowment of FDC-related programs in FDC sarcomas emerged by applying a gene signature consisting of 1,289 genes differentially expressed between microdissected FDCs and fibroblasts.   Supervised analysis comparing FDC sarcomas with microdissected FDCs and other MTs identified 370 and 2,927 differentially expressed transcripts, respectively, which pathway enrichment analysis mainly ascribed to signal transduction, chromatin organization, and extracellular matrix organization programs.  Since the transcriptome of FDC sarcomas retained similarity with that of FDCs, we investigated the immune landscape of FDC sarcoma by applying the CIBERSORT analysis to FDC sarcomas and non-FDC MTs, and demonstrated that FDC sarcomas were enriched in TFH and TREG populations, as confirmed in situ by immunohistochemistry.   The enrichment in specific T-cell subsets prompted investigating the mRNA expression of the inhibitory immune receptor PD-1 and of its ligands PD-L1 and PD-L2, which were found to be significantly more expressed in FDC sarcomas as compared with other MTs, a finding also confirmed in situ.  We demonstrated for the first time the transcriptional relationship of FDC sarcomas with non-malignant FDCs and their distinction from other MTs. Furthermore, we provided evidence of a peculiar immunological microenvironment associated with FDC sarcomas.

overall_design: Total RNA was obtained from 29 FDC sarcoma tumours, 32 other mesenchymal tumours, 5 FDCs microdissected from Castleman disease and 3 fibroblast samples. All samples are Formalin-fixed and paraffin-embedded tissue (FFPE).

first: Maria

middle: A

first: Claudio

last: Tripodo

last: Agostinelli

first: Giovanna

last: Motta

first: Sylvia

last: Hartmann

first: Claudia

last: Dӧring

first: Maura

last: Rossi

first: Federica

last: Melle

middle: R

last: Sapienza

first: Valentina

last: Tabanelli

first: Alessandro

last: Pileri

first: Fabio

last: Fuligni

first: Anna

last: Gazzola

last: Mannu

first: Carlo

last: Sagramoso

first: Silvia

last: Lonardi

first: Luisa

last: Lorenzi

first: Francesco

last: Bacci

first: Elena

last: Sabattini

first: Anita

last: Borges

first: Ingrid

last: Simonitsch-Klupp

first: Jose

last: Cabecadas

first: Elias

last: Campo

first: Juan

last: Rosai

first: Martin

middle: L

last: Hansmann

last: Facchetti

first: Stefano


title: Gene Expression Signatures of Motor Neuron Populations Isolated from Sporadic ALS

status: Public on Feb 01 2016

city: La Jolla

first: Ranjan

last: Batra

state: California

address: 2880 Torrey Pines Scenic Drive

department: Cellular and Molecular Medicine

country: USA

institute: University of California San Diego

type: Expression profiling by high throughput sequencing

summary: We used total RNA-sequencing (RNA-seq) to analyze ALS MN-specific gene-expression signatures in laser capture microdissected motor neurons from post-mortem lumbar spinal cords.

overall_design: To obtain transcriptome-wide gene expression measurements in adult spinal motor neurons (MNs), we performed laser capture microdissection (LCM) of lumbar spinal cord sections from 13 sporadic ALS patients and 9 controls, extracted total RNA, made RNA-seq libraries and sequenced the libraries on Illumina GA II platform

first: Kasey

last: Hutt

first: Eugene

last: Yeo

first: John

last: Ravits


title: Transient activation of the WNT pathway after disruption/remodeling of colorectal cancer cell clusters promotes a malignant phenotype

status: Public on Dec 10 2015

city: Kyoto

first: Masahiro

last: Inoue

state: Kyoto

address: Med-Pharm Collaboration Bldg 503, Shimoadachi-cho 46, Sakyou-ku, Kyoto, 606-8304, Japan

department: Clinical Bio-resource Research and Development

country: Japan

institute: Kyoto Univ Graduate School of Medicine

summary: Cancer progression and wound healing share some characteristics. Most colorectal cancers are differentiated adenocarcinomas that maintain three-dimensional structures to some extent. Hence, disruption of the architecture can provoke remodeling similar to the remodeling of normal intestinal epithelium. We used our recently developed three-dimensional culture system to investigate the response of cancer cell spheroids to mechanical disruption. Specifically, we developed a protocol for homogenous disruption of the spheroids that maintained the cell-cell contacts. After disruption, 9 spheroids from 9 patient samples reformed within a few hours, and 2 showed accelerated spheroid growth. Stemness increased after spheroid disruption, as assessed by marker expression, spheroid forming capacity, radiation sensitivity, and tumorigenesis. The spheroid-forming capacity increased in 6 of 11 spheroids. The disruption signature, as determined by gene expression profiling, supported the incidence of remodeling and predicted the prognosis of the colorectal cancer patients. WNT and HER3 signaling was increased in the reformed spheroids, and suppression of these signaling pathways attenuated the increases in growth and stemness after disruption. Thus, disorganized architecture in patient tumors might reflect the processes of disruption and subsequent remodeling and represent a cause rather than simply a consequence of malignancy progression.

overall_design: Gene expression in cancer tissue-originated spheroids (CTOSs) was measured at pre, 6 hr, 24 hr, and 4 days after mechanical disruption. One experiment was performed at each time point.


title: FOXP3+ regulatory T cell development and function require histone/protein deacetylase 3

status: Public on May 19 2015

city: Philadelphia

first: Wayne

middle: W

last: Hancock

state: PA

address: 916B ARC, 3615 Civic Ctr Blvd

institute: CHOP/UPenn

summary: Treg dysfunction is associated with a variety of inflammatory diseases. Treg populations are defined by expression of the oligomeric transcription factor FOXP3 and inability to produce IL-2, a cytokine required for T cell maintenance and survival. FOXP3 activity is regulated post-translationally by histone/protein acetyltransferases and histone/protein deacetylases (HDACs). Here, we determined that HDAC3 mediates both the development and function of the two main Treg subsets, thymus-derived Tregs and induced Tregs (iTregs). We determined that HDAC3 and FOXP3 physically interact and that HDAC3 expression markedly reduces Il2 promoter activity. In murine models, conditional deletion of Hdac3 during thymic Treg development restored Treg production of IL-2 and blocked the suppressive function of Tregs. HDAC3-deficient mice died from autoimmunity by 4-6 weeks of age; however, injection of WT FOXP3+ Tregs prolonged survival. Adoptive transfer of Hdac3-deficient Tregs, unlike WT Tregs, did not control T cell proliferation in naive mice and did not prevent allograft rejection or colitis. HDAC3 also regulated the development of iTregs, as HDAC3-deficient conventional T cells were not converted into iTregs under polarizing conditions and produced large amounts of IL-2, IL-6, and IL-17. We conclude that HDAC3 is essential for the normal development and suppressive functions of thymic and peripheral FOXP3+ Tregs.

overall_design: RNA was isolated using RNeasy kits (QIAGEN), and RNA integrity and quantity were analyzed by NanoDrop ND-1000 and Nanochip 2100 Bioanalyzer (Agilent Technologies). Microarray experiments were performed using whole mouse genome oligoarrays (Mouse430a, Affymetrix) and array data analyzed using MAYDAY 2.12 software. Array data were subjected to robust multiarray average (RMA) normalization and analyzed using Student’s t test. Only data with a false discovery rate-adjusted P value of less than 0.05 and at least 2× differential expression were included in the analysis. Data underwent z-score transformation for display.

first: Liqing

last: Wang

first: Yujie

last: Liu

first: Rongxiang

last: Han

first: Ulf

middle: H

last: Beier

first: Tricia

last: Bhatti

first: Tatiana

last: Akimova

first: Mark

middle: I

last: Greene

first: Scott

last: Hiebert


title: Targeting Mmp3 inhibits viability and metastasis of high-metastatic cancer cells

status: Public on Mar 30 2017

city: Okayama

first: Yuka

last: Okusha

state: Okayama

address: shikata-chou

institute: Okayama University

summary: Cancer metastasis remains an important unsolved problem. Matrix metalloproteinases (MMPs) have been shown to promote cancer cell transformation, migration, invasion, and metastasis through alteration of the extracellular microenvironment, and alter intracellular signaling and genome status. In addition, recent studies have shown intracellular and intranuclear localization, as well as roles of MMPs. In the present study, we examined gene expression signatures of high- and low-metastatic mouse colon cancer cells, and found that Mmp3 was expressed at the highest level in the high-metastatic cells. Profound nuclear localization of Mmps was found in primary explant sites as well as in areas of metastasis in lungs. In addition to the native 50-kDa Mmp3, a short 25-kDa PEX domain and active Mmp3 dimer were found in metastatic cancer cells, indicating novel roles for these forms. Knockdown of Mmp3 attenuated cancer cell viability, migration, and invasion in vitro, along with metastasis in an in vivo transplantation model, as well as cancer cell migration and invasion. These findings suggest that MMPs including intracellular, short, and dimerized forms are involved with malignant progression of cancer, thus they may be suitable as biomarkers and therapeutic targets.

overall_design: We analyzed gene expression signature of the highly evolved LuM1 as compared to that in the non-metastatic NM11 and the parental colon26 cells.

first: Takanori

last: Eguchi

first: Chiharu

last: Sogawa

first: Tatsuo

last: Okui

first: Keisuke

last: Nakano

first: Yuri

last: Namba

first: Hikari

last: Nobunaga

first: Kuniaki

last: Okamoto

first: Ken-ichi

last: Kozaki


title: Disease-associated mutation in SRSF2 misregulates splicing by altering RNA binding affinities

status: Public on Aug 10 2015

city: New York

first: James

middle: L.

last: Manley

state: New York

address: 1212 Amsterdam Ave

department: Dept. of Biological Sciences

institute: Columbia University

summary: SRSF2 is an RNA binding protein that plays important roles in splicing of mRNA precursors. Mutations in SRSF2 are frequently found in patients with myelodysplastic syndromes and certain leukemias, but how they affect SRSF2 function has only begun to be examined. Here we used CRISPR/Cas9 to introduce the P95H mutation to SRSF2 in K562 leukemia cells, generating an isogenic model so that splicing alterations can be attributed solely to mutant SRSF2. We found that SRSF2 (P95H) misregulates 548 splicing events (<1% of total). Of these, 374 involve the inclusion of cassette exons, and the inclusion was either increased (206) or decreased (168). We detected a specific motif (UCCA/UG) enriched in the more included exons and a distinct motif (UGGA/UG) in the more excluded exons. RNA gel shift assays showed that a mutant SRSF2 derivative bound more tightly than its wild-type counterpart to RNA sites containing UCCAG, but less tightly to UGGAG sites. The pattern of exon inclusion or exclusion thus correlated in most cases with stronger or weaker RNA binding, respectively. We further show that the P95H mutation does not affect other functions of SRSF2, i.e., protein-protein interactions with key splicing factors. Our results thus demonstrate that the P95H mutation positively or negatively alters the binding affinity of SRSF2 for cognate RNA sites in target transcripts, leading to misregulation of exon inclusion. Our findings not only shed light on the mechanism of the disease-associated SRSF2 mutation in splicing regulation, but also reveal a group of mis-spliced mRNA isoforms for potential therapeutic targeting.

overall_design: Examination of differentially spliced events in K562 CRISPR cell clones (with wild-type or mutant SRSF2) by RNA sequencing

first: Siddhartha

last: Mukherjee


title: Common inflammatory pathways between NEC and Crohn's disease

status: Public on Jan 25 2016

city: Sherbrooke

first: Jean-François

last: Beaulieu

state: Québec

address: 3001, 12ème avenue nord

department: Anatomie & biologie cellulaire

country: Canada

institute: Université de Sherbrooke

summary: Necrotizing enterocolitis (NEC) is the most frequent life-threatening gastrointestinal disease experienced by premature infant occuring in neonatal intensive care units. NEC is associated with severe intestinal inflammation, intestinal perforation leading to mortality. The challenge for neonatologists is to detect early clinical manifestations of NEC. Therefore, one of the strategies to prevent or treat NEC would be to develop an early diagnostic tool allowing identification of preterm infants either at risk of developing NEC or at the onset of the disease. Illumina’s deep sequencing technology (RNA-seq) was used to establish the gene expression profile between resected ileal healthy preterm (control, n=5) and NEC diagnosed preterm infant (NEC, n=9) and analyzed by IPA Core analysis system. IPA analysis indicated that the most significant functional pathways overrepresented in NEC neonates were associated with innate immune functions, such as altered T and B cell signaling, B cell development, and the role of pattern recognition receptors in recognition of bacteria and viruses. Among genes that were strongly modulated in NEC neonates, we observed a high degree of similarity with those linked to the development of IBD. By comparing gene expression patterns between NEC and Crohn’s disease, we identified several new potential protein targets for helping to predict and/or diagnose NEC in preterm infant. Gene expression profile revealed an uncontrolled innate immune response in the intestine of NEC neonates. Moreover, comparative analysis between NEC and Crohn’s disease evidenced high degree of similarity between these two inflammatory diseases and allowed us to identify several new potential NEC biomarkers.

first: Eric

last: Tremblay

first: Marie-Pier

last: Thibault

first: Emanuela

last: Ferretti

first: Corentin

last: Babakissa

first: Valérie

last: Bertelle

first: Marcos

last: Bettolli

first: Karolina

last: Burghardt

last: Colombani

first: David

last: Grynspan

first: Emile

last: Levy

first: Sandeep

last: Mayer

first: Daniel

last: Ménard

first: Olivier

last: Mouterde

first: Ingrid

middle: B

last: Renes

first: Ernest

middle: G

last: Seidman


title: Circular RNA Expression Profile of Pancreatic Ductal Adenocarcinoma Revealed by Microarray.

status: Public on Nov 20 2015

city: Xi'an

first: Shibin

last: Qu

state: Shaanxi

address: 127 West Changle Road

department: Department of Hepatobiliary Surgery

country: China

institute: Xijing Hospital

summary: To explore the potential involvement of circular RNAs (circRNAs) in pancreatic ductal adenocarcinoma (PDAC) oncogenesis, we conducted circRNA profiling in six pairs of human PDAC and adjacent normal tissue by microarray. Our results showed that clusters of circRNAs were aberrantly expressed in PDAC compared with normal samples, and provided potential targets for future treatment of PDAC and novel insights into PDAC biology.

overall_design: Analyze circular RNA expression in pancreatic ductal adenocarcinoma (PDAC) by microarray platform.

first: Haimin

last: Li

first: Kefeng

last: Dou


title: Genome wide analysis of gene expression in conjunctiva whole tissue and primary conjunctival fibroblasts from patients with ocular mucous membrane pemphigoid and control patients

status: Public on Jan 29 2016

city: LA

first: Sarah

last: Ahadome

state: CA

address: 100 Stein Plaza

department: Jules Stein

institute: UCLA

summary: Identification of differentially expressed genes in conjunctiva and conjuntival fibroblasts from pemphigoid patients compared to control patients. Results indicate these differentially expressed genes, which could be further investigated as potential anti-fibrosis targets

overall_design: Total RNA was obtained from whole conjunctival tissue samples and primary conjunctival fibroblasts from patients with ocular mucous membrane pemphigoid, and control patients

first: John

last: Dart


title: Leaps and lulls in the developmental transcriptome of Dictyostelium discoideum

status: Public on Apr 21 2015

city: Houston

first: Gad

last: Shaulsky

state: TX

address: One Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

summary: Development of the soil amoeba Dictyostelium discoideum is triggered by starvation. When placed on a solid substrate, the starving solitary amoebae cease growth, communicate via extracellular cAMP, aggregate by tens of thousands and develop into fully integrated multicellular organisms. Early phases of the developmental program are often studied in cells starved in suspension while cAMP is provided exogenously. Previous studies revealed massive shifts in the transcriptome under these developmental conditions and a close relationship between gene expression and morphogenesis, but were limited by the sampling frequency and the resolution of the methods. Here, we combine the superior depth and specificity of RNA-seq with high frequency sampling during filter development and cAMP pulsing in suspension. We found that the developmental transcriptome exhibits mostly gradual changes interspersed by a few instances of large changes. Considering the whole transcriptome as a single phenotype, we treated each time point as an independent entity and were able to characterize development as groups of similar time points separated by gaps. The grouped time points represent gradual changes in mRNA abundance and the gaps represent times during which many genes are differentially expressed rapidly. Comparing development on solid substrate to development in suspension revealed that gene expression in filter developed cells lagged behind cells treated with exogenous cAMP in suspension. The high sampling frequency revealed many genes whose regulation is reproducibly more complex than indicated by previous studies. Gene Ontology enrichment analysis showed that the transition to multicellularity at the mound stage coincided with rapid accumulation of transcripts associated with mitosis and DNA replicative processes. Later development included the up-regulation of organic signaling molecules and co-factor biosynthesis. We observed multiple instances of enrichment of oxidation-reduction and reactive oxygen related terms. Our analysis also demonstrated a high level of synchrony between the developing structures throughout development. Our data describe D. discoideum development as a series of coordinated cellular and multicellular activities. Coordination occurred within fields of aggregating cells and between multicellular bodies, such as mounds or migratory slugs that experience both cell-cell contact and various soluble signaling regimes. These time courses, sampled at the highest temporal resolution to date in this system, provide a comprehensive resource for future studies of developmental gene expression.

overall_design: Dictyosteloium discoideum gene expression (mRNA) profiles from two experimental time courses: development on filters and cAMP signaling in suspension. Filter development consists of 2 replicates of 19 time point samples, while cAMP in suspension contains 3 replicates of 10, 10 and 9 samples each.

first: Rafael

middle: D

last: Rosengarten

first: Balaji

last: Santhanam

first: Danny

last: Fuller

first: Mariko

last: Katoh-Kurasawa

first: William

middle: F

last: Loomis

first: Blaz

last: Zupan


title: Agilent 4x44K expression array for squamous cell carcinoma of the lung

status: Public on Mar 11 2015

city: Nashville

first: Pierre

last: Massion

state: TN

address: 2220 Pierce Ave

department: Vanderbilt Ingram Cancer Center

institute: Vanderbilt University

summary: Total RNA of 24 SCC tumors were isolated and profiled for mRNA expression measurement with  Agilent 4x44K Array

overall_design: Tumor samples were assayed on Agilent Human gene expression 4x44K Microarray with manufacturer's recommended procedures for microarray-based one-color.

first: Jun

last: Qian

first: Yong

last: Zou


title: Agilent 244A aCGH array for squamous cell carcinoma of the lung

type: Genome variation profiling by genome tiling array

summary: 24 SCC tumors were profiled for copy-number alterations with the high-resolution Agilent 244A aCGH Array

overall_design: Tumor samples were assayed on Agilent Human Genome CGH 244A Microarrays for surveying genomic alterations in squamous carcinoma of the lung.  Human male or female blood genomic DNA (Promega) was used as reference. Individual log2 ratios of background subtracted signal intensities were obtained from the Agilent Feature Extraction software version 9.5.The normalized data were further analyzed using Agilent DNA Analytics Software (version 4.0) with ADM-2 algorithm, which is an aberration detection algorithm that identifies all aberrant intervals in a given sample with consistently high or low log ratios based on the statistical score.


title: Squamous cell carcinoma of the lung

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

overall_design: Refer to individual Series


title: Genes Differentially Expressed in Slow Wilting Phenotypes under a High Vapor Pressure Deficit

status: Public on Jul 15 2014

city: Raleigh

first: Elizabeth

last: Scholl

state: NC

address: 1 Lampe Drive, CB 7566, Ricks Hall

department: BRC

institute: NC State University

summary:
The purpose of this study is to compare transcriptome profiles of one fast wilting and two slow wilting genotypes under low- and high- vapor pressure deficit
Experiments: Five differential expression analyses were performed. 1. Differences within the Hutchesen line for slow and fast wilting; 2. Differences within the PI471938 line for slow and fast wilting; 3. Differences within the PI416937 line for slow and fast wilting; Differences between Hutchesen, PI471938 and PI416937 (regardless of pheotype); 5. Comparison between all lines and all pheotypes
Methods: RNASeq data was generated using the Illumina HiSeq. Data passing quality control was processed as follows: Alignment to reference genome Gmax_109 using Tophat2 followed by the Tuxedo pipeline (cufflinks, cuffmerge, cuffdiff).

overall_design: Three cultivars, (wild-type Hutchesen and two parentla lines - PI471938 and PI416937; two conditions (normal and slow-wilting); two reps each for a total of 12 samples

first: Earl

last: Taliercio


title: Expression data from glioma cells exposed to interferon (IFN)-beta

status: Public on Mar 31 2014

city: Duesseldorf

first: Karl

last: Koehrer

address: Universitaetsstr. 1

department: BMFZ

country: Germany

institute: University of Duesseldorf

summary:
Glioma cells are sensitized to the alkylator temozolomide after exposure to IFN-beta. In glioma-initiating cells (GIC), IFN-beta alone reduces clonogenicity. We investigated differentially expressed genes with or without IFN exposure in either longterm glioma cells or GIC.
We used microarrays to investigate differential gene regulation in glioma cells after exposure to either ddH20 or IFN-beta 300 IU/ml at 6 h or 24 h.

overall_design: We used either the longterm cell line LNT-229 or the GIC cell lines GS-2 and GS-9 and exposed them to either IFN-beta 300 IU/ml or ddH20 for 6 h or 24 h.

first: C

last: Happold

first: M

last: Silginer

first: A

middle: M

last: Florea

first: R

last: Deenen


title: Identification of transcript dysregulation in patients with Autism Spectrum Disorders

status: Public on Nov 22 2014

city: MARSEILLE CEDEX 09

first: Aurelie

last: Bergon

address: parc scientifique de Luminy, case 928

country: France

institute: TAGC INSERM U1090

summary: In order to unveil the molecular mechanisms at play during the development of autistic brains, we studied cells that are representative of the very early stages of ontogenesis, namely stem cells. We used nasal olfactory stem cells that are readily accessible and can be biopsied safely. We recruited a relatively homogeneous cohort of nine adults with severe autism and low to very low developmental disabilities, and included two more adults with either Asperger syndrome or high-functioning autism, to enlarge the spectrum. The cohort was then paired with 11 age- and gender-matched control individuals. Stem cells were purified, banked and used for a transcriptomic study.

overall_design: Two-colors experiment. The cohort was then paired with 11 age- and gender-matched control individuals. Stem cells were purified, banked and used for a transcriptomic study. Validation by reverse transcription design.

first: François

last: Féron

first: Delphine

last: Stephan

first: Bruce

last: Mesnage

first: Emmanuelle

last: Lacassagne

first: Arnaud

last: Devèze

first: Béatrice

last: Loriod

first: Sebastien

last: Rousseau

first: Carole

last: Tardif

first: Emmanuel

last: Nivet

first: Bruno

last: Gepner

first: Madeleine

last: Garcia


title: SUMOylation Regulates the Anti-Proliferative Gene Signature Programs of Glucocorticoid Receptor (U2Os cell line)

status: Public on Nov 05 2013

city: Kuopio

first: Ville

last: Paakinaho

address: Yliopistonranta 8

department: School of Medicine

country: Finland

institute: University of Eastern Finland

summary: In addition to the glucocorticoids, the glucocorticoid receptor (GR) is regulated by post-translational modifications, including SUMOylation. We have analyzed how SUMOylation influences the activity of endogenous GR target genes and the receptor chromatin binding by using isogenic HEK293 cells expressing wild-type GR (wtGR) or SUMOylation-defective GR (GR3KR). Gene expression profiling revealed that both dexamethasone up- and down-regulated genes are affected by the GR sumoylation and that the affected genes are significantly associated with pathways of cellular proliferation and survival. The GR3KR-expressing cells proliferated more rapidly and their anti-proliferative response to dexamethasone was less pronounced than in the wtGR-expressing cells. ChIP-seq analyses indicated that the SUMOylation modulates the chromatin occupancy of GR on several loci associated with cellular growth in a fashion which parallels with their differential dexamethasone-regulated expression between the two cell lines. Moreover, genome-wide SUMO-2/3 marks, which were generally associated with active chromatin, showed markedly higher overlap with the wtGR cistrome than with the GR3KR cistrome. In sum, our results indicate that the SUMOylation does not simply repress the GR activity, but regulates the activity of the receptor in a target locus selective fashion, playing an important role in controlling the GR activity on genes influencing cell growth.

overall_design: Total RNA isolated from U2Os cell lines stably expressing either wild-type GR (wtGR) or SUMOylation-defective GR (GR3KR) treated with either vehicle (EtOH) or 100 nM of dexamethasone (dex) for 6h.

first: Jorma

middle: J

last: Palvimo


title: Aza treated AML3 cells

status: Public on Jul 01 2014

city: Glasgow

first: Peter

last: Adams

address: Switchback Rd, Bearsden

country: United Kingdom

institute: University of Glasgow, Beatson Institute for Cancer Research

type: Methylation profiling by high throughput sequencing


title: Daytime soybean transcriptome fluctuations during water deficit stress

status: Public on Jul 07 2015

city: Londrina

first: Alexandre

middle: Lima

last: Nepomuceno

state: Paraná

address: Rodovia Carlos João Strass, s/n Acesso Orlando Amaral

country: Brazil

institute: Embrapa Soja

summary: By sequencing 36 cDNA libraries with Illumina technology, we identified genes differentially expressed in soybean plants in response to water deficit and genes that were either up- or down-regulated in different periods of the day. Of 54,175 predicted soybean genes (Glyma v1.1), 35.52% exhibited expression oscillations in a 24 h period. This number increased to 39.23% when plants were submitted to water deficit. Major differences in gene expression were observed in the control plants from late day (ZT16) until predawn (ZT20) periods, indicating that gene expression oscillates during the course of 24 h in normal development. Under water deficit, dissimilarity increased in all time-periods, indicating that the applied stress influenced gene expression. Results suggest that time of day, as well as light and temperature oscillations that occur considerably affect the regulation of water deficit stress response in soybean plants.

overall_design: Gene expression analysis of soybean leaves under water deficit in 6 periods of day by sequencing 36 libraries, in triplicate, in Illumina platform.

first: Fabiana

last: Rodrigues

first: Renata

last: Pagliarini

first: Juliana

last: Gomes

first: Thiago

last: Nakayama

first: Hugo

last: Molinari

first: Francisco

middle: P

last: Lobo

first: Frank

last: Harmon


title: Expression data from untreated and Aza treated AML3 cells

first: Xue

last: Lei

address: 10901 N Torrey Pines Rd

institute: SBP medical discovery institute

summary: AML3 cells were treated with Azacytidine and compared against untreated cells

overall_design: We used RNA-Seq to detail the global programme of gene expression in human untreated and Azacytidine treated AML3 cells

first: Kirstin

last: Lund

first: Tony

last: McBryan

first: John

last: Cole


title: Genomic and Transcriptomic Hallmarks of Poorly-Differentiated and Anaplastic Thyroid Cancers

status: Public on Feb 15 2016

city: Boston

first: Iñigo

last: Landa

state: Massachusetts

address: 77 Avenue Louis Pasteur, 4BF Building, Room 645A

department: Medicine/Endocrinology

institute: Brigham and Women's Hospital, Harvard Medical School

summary: BACKGROUND. Poorly-differentiated (PDTC) and anaplastic (ATC) thyroid cancers are rare and frequently lethal tumors, which so far have not been subjected to comprehensive genetic characterization.  METHODS. We performed next generation sequencing of 341 cancer genes in 117 PDTCs and ATCs, and a transcriptomic analysis of a representative subset of 37 tumors. Results were analyzed in the context of The Cancer Genome Atlas (TCGA) study of papillary thyroid cancers (PTC).  RESULTS. ATCs have a greater mutation burden than PDTCs, and higher mutation frequency of TP53, TERT promoter, PI3K/AKT/mTOR pathway effectors, SWI/SNF subunits and histone methyltransferases. BRAF and RAS are the predominant drivers, and dictate remarkably distinct tropism for nodal vs. distant metastases in PDTC. RAS and BRAF sharply distinguish between PDTCs defined by the Turin (PDTC-Turin) vs. MSKCC (PDTC-MSK) criteria, respectively. Mutations of EIF1AX, a component of the translational preinitiation complex, are markedly enriched in PDTCs and ATCs, and have a striking pattern of co-occurrence with RAS. TERT promoter mutations are rare and subclonal in PTCs, whereas they are clonal and highly prevalent in advanced cancers. Application of the TCGA-derived BRAF-RAS score (a measure of MAPK transcriptional output) shows a preserved relationship with BRAF/RAS mutation in PDTCs, whereas ATCs are BRAF-like irrespective of driver mutation.   CONCLUSIONS. These data support a model of tumorigenesis whereby PDTCs and ATCs arise from well-differentiated tumors through the accumulation of key additional genetic abnormalities, many of which have prognostic and possible therapeutic relevance. The widespread genomic disruptions in ATC compared to PDTC underscore their greater virulence and higher mortality.

overall_design: 37 tumor specimens, including 17 poorly-differentiated and 20 anaplastic thyroid cancers were expression-profiled with Affymetrix U133 plus 2.0 array

first: Tihana

last: Ibrahimpasic

first: Laura

last: Boucai

first: Rileen

last: Sinha

first: Jeffrey

last: Knauf

first: Snjezana

last: Dogan

first: Ronak

last: Shah

first: Julio

middle: C

last: Ricarte-Filho

first: Gnana

last: Krishnamoorthy

first: Bin

last: Xu

first: Nikolaus

last: Schultz

first: Michael

last: Berger

first: Chris

last: Sander

first: Barry

middle: S

last: Taylor

first: Ronald

last: Ghossein

first: Ian

last: Ganly

first: James

last: Fagin


title: SUMOylation Regulates the Anti-Proliferative Gene Signature Programs of Glucocorticoid Receptor (ChIP-seq)

first: Ville

last: Paakinaho

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: Examination of GR and SUMO-2/3 binding from isogenic HEK293 cell lines stably expressing either wtGR or GR3KR, in biological duplicates, using Illumina HiSeq 2000. GR binding from control HEK293 (FRT) cell line and input sample from FRT were used as controls for GR. Sequenced IgG sample from FRT cell line was used as control for SUMO-2/3

first: Jorma

last: Palvimo


title: SUMOylation Regulates the Anti-Proliferative Gene Signature Programs of Glucocorticoid Receptor


title: Affymetrix expression array data for melanoma progression to the brain

status: Public on Sep 19 2013

city: Santa Monica

first: Dave

last: Hoon

address: 2200 Santa Monica Boulevard

department: Translational Molecular Medicine

institute: Saint John's Cancer Institute

summary: Melanoma is one of the most aggressive and treatment-resistant cancers. It represents the most life-threatening neoplasm of the skin, and its incidence has been increasing for the last three decades. Melanoma evolves from the local transformation of melanocytes to primary tumors, which can metastasize to multiple organs. Brain metastases represent one of the most significant causes of death in cutaneous melanoma patients. Despite aggressive multi-modality threapy, patients with melanoma brain metastasis have a median survival of less than a year, with a majority of these patients dying as a result of their intracranial disease. To identify alterations in gene expression related to brain metastasis, we used Affymetrix expression arrays to assess differentially expressed genes in melanocytes, lymph node metastases, and brain metastases.

overall_design: Total RNA from twenty-two specimens representing normal melanocytes (n=3), melanoma lymph node metastasis (n=12), and melanoma brain metastasis (n=7) was extracted and analyzed by Affymetrix expression arrays. Melanocytes specimens were used as control samples. Melanocytes were acquired from Invitrogen (LifeTechnologies). Metastatic melanoma specimens were taken from different patients, established as cell lines in the John Wayne Cancer Institute. Early passages (less than 6) were used to perform expression analysis.

first: Sharon

last: Huang


title: Genome-wide DNA methylation, gene expression, and copy number integrative analysis of melanoma brain metastasis

type:
Expression profiling by array
Methylation profiling by array


title: Affymetrix SNP array data for metastatic melanoma specimens

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

summary: Comparison between the copy number of differentially methylated sites between lymph node metastasis from melanoma patients with good prognosis and melanoma brain metastasis. All samples are taken from different patients, and were established as cell lines in the John Wayne Cancer Institute.

overall_design: Sixteen metastatic melanomas were run on Affymetrix Genome-Wide Human SNP Array 6.0. Lymph node metastases and brain metastases genetic copy number variations were compared.


title: Stabilization competency signature

status: Public on Jan 01 2013

city: Toronto

first: Yu

last: Liu

state: ON

address: 600 University Ave

department: Molecular Genetics

institute: University of Toronto

summary: Comparison of gene expresion profile of 4 SC clones and 4 SI clones at different time points defined a stabilization competency signiture required for successful reprogramming

overall_design: mRNA profilling 4 SI clones at 5 time points, 4 SC clones at 6 time points, and 3 feeder samples.

first: Jeffrey

last: Wrana

first: Azadeh

last: Golipour

first: Laurent

last: David


title: Spaceflight Modulates Gene Expression in Astronauts

status: Public on Oct 15 2013

city: Tempe

first: Jennifer

last: Barrila

state: AZ

address: 1001 S McAllister Ave

department: Biodesign Center for Fundamental and Applied Microbiomics

institute: Arizona State University

summary: Astronauts are exposed to a unique combination of stressors during spaceflight, which leads to alterations in their physiology and potentially increases their susceptibility to infectious pathogens.  Here we report the first microarray evaluation of any astronaut tissue sample, specifically whole blood, before and after spaceflight using an array comprising 234 well-characterized stress response genes. Differentially regulated genes included those important for DNA repair, oxidative stress, and protein folding/degradation.

overall_design:
Microarrays comprising 234 well characterized stress-related genes were used to profile transcriptomic changes in six astronauts before and after short-duration spaceflight.  Blood samples were collected for analysis from each eastronaut 10 days prior and 2-3 hours after return from spaceflight.

Data submitted for platform GPL140 contain genes that have been pre-filtered by the analytical software to remove values of low certainty, resulting in missing values for some samples.  Unfortunately, these original data are no longer available due to physical damage at Tulane University during hurricane Katrina, but the processed values were retained in redundant locations and these are submitted for upload to GEO.

middle: A

first: C

last: Ott

first: Carly

last: LeBlanc

first: Satish

middle: K

last: Mehta

first: Aurélie

last: Crabbé

first: Phillip

last: Stafford

first: Duane

last: Pierson

first: Cheryl

last: Nickerson


title: A positive feedback loop links opposing functions of P-TEFb/Cdk9 and histone H2B mono-ubiquitylation to regulate transcript elongation in fission yeast

status: Public on Dec 01 2012

city: Montréal

first: François

last: Robert

address: 110, avenue des Pins Ouest

department: Chromatin and Genomic Expression

institute: Institut de recherches cliniques de Montréal (IRCM)

type: Genome binding/occupancy profiling by genome tiling array

summary: Transcript elongation by RNA polymerase II (RNAPII) is accompanied by conserved patterns of histone modification within transcribed regions, but it remains uncertain how these modifications influence, or are influenced by, properties of the elongation complex. Here we establish an intimate link between Cdk9, the kinase component of positive transcription elongation factor b (P-TEFb), and mono-ubiquitylation of histone H2B (H2Bub1), in the fission yeast Schizosaccharomyces pombe. Mutations that impair Cdk9 function reduce H2Bub1 levels in vivo. Conversely, mutations that prevent H2Bub1 decrease phosphorylation of elongation factor subunit Spt5, a sensitive and specific indicator of Cdk9 activity. Chromatin immunoprecipitation (ChIP) analysis suggests this is due to impaired Cdk9 recruitment to H2Bub1-deficient chromatin. P-TEFb and H2Bub1 pathways also interact genetically: mutation of the histone H2B ubiquitin-acceptor residue decreases the requirement for Cdk9 activity in vivo, and multiple cdk9 mutations suppress morphological defects of H2Bub1-deficient strains. Moreover, H2Bub1 loss causes redistribution of transcribing RNAPII on chromatin that is corrected by a hypomorphic cdk9 mutation. Therefore, whereas mutual dependence of Spt5 phosphorylation and H2Bub1 suggests positive feedback between P-TEFb and the ubiquitylation machinery, mutual suppression by cdk9 and H2Bub1-pathway mutations indicates an antagonistic relationship, whereby the activities must be balanced to properly regulate elongation.

overall_design: In order to study the genome-wide localization of H2Bub1 in Schizosaccharomyces pombe, H2Bub1, H2B-Flag as well as RNAPII (along with associated DNA sequences) were immunoprecipitated using repectively anti-H2Bub1, anti-Flag and anti-8WG16 antibodies. The ChIPs were performed in duplicate from WT cells as well as in the H2B-K119R mutant. The extracted DNA was hybridized to a DNA microarray containing an average of 4 probes per kilobase across the whole yeast genome. The combined datasets are available in the supplemental files of the related publication.

first: Laia

last: Viladevall

first: Karen

last: Lee

first: Pierre-Étienne

last: Jacques

first: Viviane

last: Page

first: Susanne

last: Schneider

first: Chao

last: Zhang

first: Beate

last: Schwer

first: Francois

first: Robert

last: Fisher

first: Jason

last: Tanny


title: Somatic copy-number mosaicism in human skin revealed by induced pluripotent stem cells (sequencing)

status: Public on Oct 31 2012

city: New Haven

first: Flora

last: Vaccarino

state: CT

address: 230 South Frontage Road

department: Child Study Center

institute: Yale University

summary: Reprogramming human somatic cells into induced pluripotent stem cells (iPSC) has been suspected of causing de novo copy number variations (CNVs). To explore this issue, we performed a whole-genome and transcriptome analysis of 20 human iPSC lines derived from primary skin fibroblasts of 7 individuals using next-generation sequencing. We find that, on average, an iPSC line manifests two CNVs not apparent in the fibroblasts from which the iPSC was derived. Using qPCR, PCR, and digital droplet PCR (ddPCR) to amplify across the CNVs' breakpoints, we show that at least 50% of those CNVs are present as low frequency somatic genomic variants in parental fibroblasts and are manifested in iPSC colonies due to their clonal origin. Hence, reprogramming does not necessarily lead to de novo CNVs in iPSC, since most of line-manifested CNVs reflect somatic mosaicism in the human skin. Moreover, our findings demonstrate that clonal expansion, and iPSC lines in particular, can be used as a discovery tool to reliably detect low frequency CNVs in the tissue of origin. Overall, we estimate that approximately 30% of the fibroblast cells have somatic CNVs, suggesting widespread somatic mosaicism in the human body. Our study paves the way to understanding the fundamental question of the extent to which cells of the human body normally acquire structural alterations in their DNA post-zygotically.

overall_design: We have generated and characterized hiPSC lines derived from skin fibroblasts collected from seven members of two families, which were competent to be differentiated into neuronal progenitors and neurons

first: Alexej

last: Abyzov

first: Jessica

last: Mariani

first: Dean

last: Palejev

first: Ying

first: Michael

last: Haney

first: Livia

last: Tomasini

first: Anthony

last: Ferrandino

first: Lior

middle: R

last: Belmaker

first: Anna

last: Szekely

last: Wilson

first: Arif

last: Kocabas

first: Nathaniel

middle: E

last: Calixto

first: Elena

middle: L

last: Grigorenko

first: Anita

last: Huttner

first: Katarzyna

last: Chawarska

first: Sherman

last: Weissman

first: Alexander

last: Urban

first: Mark

last: Gerstein


title: Genome-wide analysis of 4-day old (P4) Tdrd7 null mouse lens

status: Public on Feb 21 2012

first: Anton

last: Aboukhalil

state: MA

address: 77 Avenue Louis Pasteur, 464

institute: Massachusetts Institute of Technology

summary:
Analysis of Tdrd7 deficiency in mouse lens epithelial-derived cell line at gene expression level. The hypothesis tested was that Tdrd7 is involved in post-transcriptional control of gene expression in the lens. Results provide evidence for differential regulation of genes involved in lens homeostasis and cataract formation in the absence of Tdrd7.
In eukaryotic cells, cytoplasmic RNA granules (RGs) function in the post-transcriptional control of gene expression.  However, the involvement of RGs and their component proteins in vertebrate organogenesis is unknown.  We report two independent cases of pediatric cataract with loss-of-function mutations in TDRD7, which encodes a Tudor domain RNA binding protein.  TDRD7 deficiency in chick lens produces cataracts, and Tdrd7 null mouse mutants develop cataracts, as well as features of glaucoma and male sterility due to azoospermia.  In lens fiber cells, TDRD7 is necessary for the RG-mediated post-transcriptional control of critical lens mRNAs, while in the testis it functions as a component of a specialized RG, the chromatoid body.  These findings define a new role for RGs in vertebrate organogenesis, and a novel mechanism for cataractogenesis.

overall_design: Total RNA obtained from P4 Lens from Tdrd7 null mice compared to that of Tdrd7 heterozygous mice.

first: Salil

last: Lachke

first: Richard

last: Maas


title: RNA-Seq of human neurons derived from iPS cells Reveals candidate long non-coding RNAs Involved in neurogenesis and neuropsychiatric disorders.

status: Public on Oct 06 2011

city: bronx

first: Mingyan

last: Lin

state: ny

address: 1300 Morris Park Avenue

institute: Albert Einstein college of medicine

summary: As a preliminary step towards applying next generation sequencing using neurons derived from patient-specific iPSCs, we have carried out an RNA-Seq analysis on control human neurons. Dramatic changes in the expression of coding genes, long non-coding RNAs (lncRNAs), pseudogenes, and splice isoforms were seen during the transition from pluripotent stem cells to early differentiating neurons. A number of genes that undergo radical changes in expression during this transition include candidates for schizophrenia (SZ), bipolar disorder (BD) and autism spectrum disorders (ASD) that function as transcription factors and chromatin modifiers, such as POU3F2 and ZNF804A, and genes coding for cell adhesion proteins implicated in these conditions including NRXN1 and NLGN1. In addition, a number of novel lncRNAs were found to undergo dramatic changes in expression, one of which is HOTAIRM1, a regulator of several HOXA genes during myelopoiesis. The increase we observed in differentiating neurons suggests a role in neurogenesis as well. Finally, several lncRNAs that map near SNPs associated with SZ in genome wide association studies also increase during neuronal differentiation, suggesting that these novel transcripts may be abnormally regulated in a subgroup of patients.

overall_design: Total RNAs were isolated from both iPS cells and differentiating neurons, and the sequenced material was pre-amplified using the NuGen Ovation amplification system.  RNA-Seq libraries were prepared and carried out on Illumina HiSeq200.

first: Erika

last: Pedrosa

first: Abhishek

last: Shah

first: Anastasia

last: Hrabovsky

first: Shahina

last: Maqbool

first: Deyou

last: Zheng

first: Herbert

last: Lachman


title: Control of oxidative stress by miRNA and impact on ovarian tumorigenesis

status: Public on Nov 01 2011

city: PARIS

first: Fatima

last: Mechta-Grigoriou

address: 26 rue d'Ulm

department: INSERM U830

institute: Institut Curie

summary: Transcriptome analysis of high-grade human ovarian adenocarcinomas. The hypothesis tested in the present study was that two reciprocal pathways, namely oxidative stress response and fibrosis, enable to build a hierarchical cluster of ovarian patients.

overall_design: Ovarian human tumor samples from Institut Curie were analysed on human genome U133 plus 2.0 array (Affymetrix). Microarray analysis was performed using Partek Genomic Suite software and transcriptomic data were normalized using GCRMA algorithm. Probes from oxidative stress response and fibrosis defined by Ingenuity software  were used to build a hierarchical cluster of ovarian patients.

first: Bogdan

last: Mateescu

first: Luciana

last: Batista

first: Odette

last: Mariani

first: Jean-Philippe

last: Meyniel

first: Paul

middle: H

last: Cottu

first: Xavier

last: Sastre-Garau


title: Mutations in the RNA Granule Component TDRD7 Cause Cataract and Glaucoma

first: Anton

last: Aboukhalil

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

overall_design: Refer to individual Series


title: Reprogramming of Human Fibroblasts into Hematopoietic Progenitors by Fusion With Human Fetal Liver CD34+ Cells

status: Public on Aug 04 2011

city: New York

first: Vladislav

last: Sandler

state: NY

address: 1300 York Ave.

department: Genetic Medicine

institute: Weill Cornell Medical College


title: Reprogramming of Human Fibroblasts into Hematopoietic Progenitors by Fusion With Human Fetal Liver CD34+ Cells (GenomeWideSNP_6)

summary: Reprogramming of the human fibroblast genome into the state of the hematopoietic progenitors

overall_design: Two samples analyzed.

first: Eric

last: Bouhassira

first: Nathalie

last: Lailler


title: SUMOylation Regulates the Anti-Proliferative Gene Signature Programs of Glucocorticoid Receptor (HEK293)

first: Ville

last: Paakinaho

overall_design: Total RNA isolated from isogenic HEK293 cell lines stably expressing either wild-type GR (wtGR) or SUMOylation-defective GR (GR3KR) treated with either vehicle (EtOH) or 100 nM of dexamethasone (dex) for 6h. All conditions are performed in triplicate

first: Jorma

last: Palvimo


title: Reprogramming of Human Fibroblasts into Hematopoietic Progenitors by Fusion With Human Fetal Liver CD34+ Cells (HuGene-1_0-st)

overall_design: Five samples analyzed.


title: Expression data from Caenorhabditis elegans exposed to ivermectin

status: Public on Apr 01 2011

first: Steven

middle: Thomas

last: Laing

address: 464 Bearsden Road

department: Veterinary Medicine

institute: University of Glasgow

summary:
We have investigated the transcriptomic response of the model nematode Caenorhabditis elegans to ivermectin (IVM); an important anthelmintic for human and animal parasite control.
The transcriptomic response of the mutant strain DA1316 avr-14(ad1302); avr-15(ad1250); glc-1(pk54), which is highly resistant to ivermectin due to null mutations in three glutamate-gated chloride channel subunits, was examined. Despite the resistant nature of this strain, pharyngeal pumping rate was decreased following 4 hrs exposure to 100ng/ml and 1μg/ml ivermectin resulting in significant change in the expression level of genes associated with a fasting response.

overall_design: Matched cultures of synchronised C. elegans were grown to L4 stage on standard NGM plates with an OP50 bacterial lawn. The nematodes were then transferred to NGM plates containing 100ng/ml ivermectin, 1μg/ml ivermectin, or DMSO excipient only (control) for 4 hours. RNA was extracted from five biological replicates including controls for both the 100ng/ml ivermectin and 1μg/ml ivermectin experiments and hybridised to Affymetrix arrays.

middle: T

first: Al

last: Ivens

first: John

last: Gilleard


title: Genome-wide analysis of short-term transcriptional responses in thrombin-stimulated vascular smooth muscle cells

status: Public on Apr 28 2009

city: Berlin

first: Solveig

last: Grossmann

address: Robert-Rössle-Str. 10

institute: FMP Berlin

summary:
The strength and duration of extracellular signal-regulated kinases 1/2 (ERK1/2) phosphorylation can define the phenotypic outcome of cells. Stimualtion of the proteinase-activated receptor (Par) triggers a Gi-dependent long-lasting transactivation of the epidermal growth factor receptor and subsequent ERK1/2 phosphorylation.
To understand the mechnaisms underlying this signaling cascade, microarray analysis was performed in vascular smooth muscle cells.

overall_design: Par receptors on neonatal rat aortic smooth muscle cells were stimulated with thrombin or TRAP in presence or abscence of Gi-uncoupling pertussis toxin.

first: Michael

last: Schaefer


title: Reprogramming of Human Fibroblasts into Hematopoietic Progenitors by Fusion With Human Fetal Liver CD34+ Cells (RNA-Seq)

overall_design: One sample analyzed.


title: Root tip: WT vs. rss3 and -NaCl vs. +NaCl

status: Public on Oct 15 2012

city: nagoya

first: yosuke

last: toda

state: aichi-ken

address: furo-cho chikusa-ku

institute: nagoya university

summary: Transcriptional profiling of WT and rss3 root tips, grown in the presense or absense of 100 mM NaCl for 3 days.

overall_design: WT (-NaCl), WT (+NaCl), rss3 (-NaCl), rss3 (+NaCl). Three biological replicates.

first: Yosuke

last: Toda

first: Shin

last: Takeda