title: Using intracellular markers to identify a novel set of surface markers for live cell purification from a heterogeneous hIPSC culture

city: Cambridge

first: Alison

last: O'Neil

state: MA

address: 7 Divinity Ave

department: Stem Cell and Regnerative Biology

institute: Harvard University

summary:
We differentiated human iPSC to day 14 using our dopaminergic neuron protocol. At day 14, the cells were fixed, stained and FACS sorted in to the FOXA2/LMX1 double positive (wanted neural progenitor population) and double negative pools. We compared the RNA of the pools via microarray to identify surface markers in the double positive pool to be able to live purify the neural progenitors from the rest of the cells.
Human embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs) can provide sources for midbrain dopaminergic (mDA) neural progenitors (NPCs) for cell therapy to treat Parkinson’s disease (PD) patients. However, the well-known line-to-cell line variability in the differentiation capacity of individual cell lines needs to be improved for the success of this therapy. To address this issue, we sought to identify mDA NPC specific cell surface markers for fluorescence activated cell sorting (FACS). Through RNA isolation after sorting for NPCs based on staining for cell-specific transcription factors followed by microarray, we identified two positive cell surface markers (CORIN and CD166) and one negative cell surface marker (CXCR4) for mDA NPC sorting. These three markers can enrich dopaminergic NPCs to 90% purity, and the sorted NPCs more efficiently differentiate to mature dopaminergic neurons compared to unsorted or CORIN+ alone mDA NPCs. This surface marker identification strategy can be used broadly to facilitate isolation of cell subtypes of interest from heterogeneous cultures.
Complete processed data are not available

overall_design: The cell line 18a was produced in biological triplicate for the experiment.  The FACS sorted double positive was compared to the double negative pool of cells to identify markers upregulated in the double positive pool (neural progenitors)

first: Elizabeth

last: Paik

first: Shi-Yan

last: Ng

first: Chicheng

last: Sun

first: Lee

last: Rubin


title: Life Span Analysis of Brain Development, Gene Expression and Behavioral Phenotypes in the Ts1Cje, Ts65Dn and Dp16 Mouse Models of Down Syndrome

status: Public on May 23 2017

city: Bethesda

first: Faycal

last: Guedj

state: Maryland

address: 35A Convent DR

department: NHGRI

country: USA

institute: National Institute of Health

summary:
Down syndrome (DS), a genetic condition leading to intellectual disability, is characterized by triplication of human chromosome 21. Neuropathological hallmarks of DS include abnormal central nervous system development that manifests during gestation and extends throughout life. As a result, newborns and adults with DS exhibit cognitive and motor deficits and fail to meet typical developmental and lack independent life skills. A critical outstanding question is how DS-specific prenatal and postnatal phenotypes are recapitulated in different mouse models. To begin answering this question, we developed a life span approach to directly compare differences in embryonic brain development, cellularity, gene expression, neonatal and adult behavior behavior in three cytogenetically distinct mouse models of DS—Ts1Cje, Ts65Dn and Dp16/1Yey (Dp16).
In the last two decades multiple therapeutic trials have been attempted to improve cognition in humans with DS but the results of these interventions lacked efficacy despide their succes in the Ts65Dn mouse model of DS. To better understand how phenotypic changes in humans in DS are recapitulated in different mouse models, we copared embryonic brain development and gene expression, perinatal behavior and brain excitatoty/inhibitory cell distribution, and adult behavior and gene expression in the Dp16, Ts65Dn and Ts1Cje mouse models of DS. The objectives of this study were to determine the best model(s) for prenatal and postnatal therapeutic trials and to identify treatment endpoints that can be used to evaluate the fficacy of these therapies prior to human clinical trials. Our data showed that, at embryonic day 15.5, Ts65Dn mice are the most profoundly and consistently affected with respect to somatic growth, brain morphogenesis, and neurogenesis compared to Ts1Cje and Dp16 embryos. However, gene expression results show that both Ts65Dn and Ts1Cje embryonic forebrains have a relatively high number of differentially expressed genes compared to Dp16, with little overlap in gene identities and genomic distribution observed among these models. Additionally, postnatal histological analyses show varying degrees of cell population and brain histogenesis abnormalities among the three strains. Behavioral testing also highlights differences among the models in their ability to meet various developmental milestones. At adulthood, Ts65Dn and Ts1Cje showed hyperactive behavior in the open field test but not Dp16 mice. In the fear conditioning test, all three strains showed lower freezing versus eupploid mice; Dp16 were the most severely affected. In the Morris water maze, Ts65Dn showed significant delays in the hidden platform, probe and reversal trials. Dp16 mice showed milder deficits in the hidden platform trial but severe deficits in reversal. Ts1Cje mice had no spatial memory deficits. In the rotarod test, Dp16 performed poorly in fixed and accelerating speed trials, while Ts1Cje was only abnormal at high speeds. Ts65Dn rotarod performance was unaffected. Compared to euploid, Ts65Dn had a higher number of differentially expressed (DEX) genes in cortex and cerebellum, while Ts1Cje had more DEX genes in hippocampus and cerebellum. Dp16 had the lowest number of DEX genes in all regions analyzed. Pathway analyses highlighted commonly dysregulated pathways, including G-protein signaling, oxidative stress, interferon signaling, glycosylation and disulfide bonds.

overall_design: At embryonic day 15.5 (E15.5), we analyzed forebrain gene expression in Dp16 (n=6) and euploid littermates (n=6), Ts65Dn (n=5) and euploid littermates (n=6), and Ts1Cje (n=5) and euploid littermates (n=5) using Affymetrix mouse gene 1.0 ST array. At adulthood, we investigated gene expression and pathway abnormalities in the cerebral cortex, hippocampus and cerebellum obtained from 6-7 month old Dp16 (n=5) and euploid littermates (n=5), Ts65Dn (n=5) and euploid littermates (n=5), and Ts1Cje (n=5) and euploid littermates (n=5) using the same Affymetrix arrays. Data were normalized and analyzed to identify and accurately map genes that are significantly differentially expressed. Functional analyses were performed using DAVID and Ingenuity Pathway Analysis (IPA) to better characterize pathway similarities and differences in these mouse models. In separate experiments, we used histology, neonatal and adult behavioral approaches to link gene exression differences to potential cellular and behavioral deficits in each mouse model.

first: Nadine

last: Aziz

first: Luis

middle: J

last: Olmos-Serrano

first: Jeroen

middle: L

last: Pennings

first: Ashley

middle: E

last: Siegel

first: Diana

middle: W

last: Bianchi

first: Tarik

middle: F

last: Haydar


title: Expression data from the RWPE-1 prostate epithelial cell line overexpressing the miR-183 family cluster

city: Chicago

first: Larisa

last: Nonn

state: IL

address: 840 S. Wood St, MC847

department: Pathology

institute: University of Illinois at Chicago

summary:
The full genomic miR-183 cluster (4.8kb) was cloned into lentiviral vector CD511B-1 with polycistronic GFP. RWPE-1 were transduced with a lentivirus from this vector (RWPE-1 183FC), or a CD511B-1 scrambled control with polycistronic GFP (RWPE-1 control). RWPE-1 were FACS sorted by GFP expression and expanded in culture.
In RWPE-1 183FC, the miR-183 family members, miR-182, miR-96, and miR-183  were confirmed to be over-expressed at physioloically relevent levels, similar to the increased expression observed in prostate cancer epithelium.

overall_design: Six samples were analyzed, two sets of three replicates

first: LaTanya

middle: V

last: Williams


title: Expression data from colorectal cancer cell line HCT-116

city: GUANGZHOU

first: LIANG

middle: JIAN

last: KAI

state: GUANGDONG

address: NO.74 ZHONGSHAN NO.2 ROAD YUEXIU DISTRICT

department: PHARMACOLOGY

country: China

institute: SUN YAT-SEN UNIVERSITY

summary: We used microarrays to detail the global gene expression in cell line with or without M1 virus infection.

overall_design: Cell line with or without M1 virus infection were for RNA extraction and hybridization on Affymetrix microarrays.

first: Jiankai

last: Liang


title: Role of caveolin-1 in hepatocellular carcinoma arising from non-alcoholic fatty liver disease

city: Hamamatsu

first: Takanori

last: Sakaguchi

address: 1-20-1 Handayama Higashi-ku

department: Second Department of Surgery

country: Japan

institute: Hamamatsu University School of Medicine

summary: The molecular features of hepatocellular carcinoma arising from non-alcoholic fatty liver disease (NAFLD-HCC) are not well known. In this study, we investigated the mechanism by which NAFLD-HCC survives in a fat-rich environment. We found that caveolin (CAV)-1 was overexpressed in clinical specimens from NAFLD-HCC patients. HepG2, HLE, and HuH-7 HCC cell lines showed decreased proliferation in the presence of the saturated fatty acids palmitic acid and stearic acid, although only HLE cells expressed high levels of CAV-1. HLE cells treated with oleic acid (OA) showed robust proliferation, whereas CAV-null HepG2 cells showed reduced proliferation and increased apoptosis. CAV-1 knockdown in HLE cells attenuated the OA-induced increase in proliferation and enhanced apoptosis. Liquid chromatography-tandem mass spectrometry analysis revealed that the levels of OA-containing ceramide, a pro-apoptotic factor, were higher in HepG2 and CAV-1-deficient HLE cells than in HLE cells, suggesting that CAV-1 inhibits apoptosis by decreasing the level of OA-containing ceramide. These results indicate that CAV-1 is important for NAFLD-HCC survival in fatty acid-rich environments and is a potential therapeutic target.

overall_design: The aim of this study is to identify an important factor in HCC developing from NAFLD (NAFLD-HCC) and to elucidate its function. Human HCC tissues and the adjacent non-HCC tissues were separately excised from the resected specimens from 3 NAFLD-HCC patients and 3 patients with HCC arising from hepatitis C (HCV-HCC). Samples were snap-frozen with RNA later (Applied Biosystems, Grand Island, NY) in liquid nitrogen and stored at -80℃. Total RNA was extracted from the frozen resected sample using an RNeasy Mini Kit (Quiagen, Valencia, CA, USA). The intensity and quantity of total RNA was assessed with a Nanodrop ND-1000 spectrometer (Nanodrop Technologies, Wilmington, DE, USA). The gene expression profile of HCV-HCC and NAFLD-HCC was determined by Affymetrix Gene Chip Human Gene 2.0 ST array.

first: Makoto

last: Takeda

last: Hiraide

first: Yasushi

last: Shibasak

first: Yoshifumi

last: Morita

first: Hirotoshi

last: Kikuchi

first: Kouji

last: Ikegami

first: Mitsutoshi

last: Setou

first: Hiroyuki

last: Konno

first: Hiroya

last: Takeuchi


title: ChAT+ NK cells and ChAT- NK cells expression profile

city: Tianjin

first: Junwei

last: Hao

address: 154 Anshan Road, Heping District

institute: Tianjin Medical University General Hospital

summary: More insights into the character differences between ChAT+ and ChAT- NK cells were obtained based on the gene-expression patterns. A clear delineation between ChAT+ NK cells and ChAT- NK cells was observed, with a total of 300 genes over-expressed and 941 genes under-expressed significantly in the ChAT+ subset. It will provide evidences for further investigation into their functional characters

overall_design: NK cells from murine spleens were isolated by MACS sorting, and further purified into ChAT+ and ChAT- subsets based on ChAT-eGFP expression. The isolated ChAT+ or ChAT- NK cells from 2-4 mice were pooled into one sample to gain mRNA for microarray analysis. 4 samples from each group were acquired for expression profile analysis of the genes.


title: Gene Expression and SNP genotype data from induced Pluripotent Stem cells from healthy control donors

status: Public on May 22 2017

city: Oxford

first: Sally

middle: A

last: Cowley

address: South Parks Road

department: Sir William Dunn School of Pathology

country: United Kingdom

institute: University of Oxford

type:
Expression profiling by array
SNP genotyping by SNP array

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

overall_design: Refer to individual Series


title: Transcriptional response of Mycobacterium tuberculosis ΔlucA::hyg and complemented strains vs. WT in resting murine bone marrow-derived macrophages

city: Ithaca

first: Evgeniya

last: Nazarova

state: NEW YORK

address: C5 103 VMC Cornell University

department: Microbiology & Immunology

institute: Cornell University

summary: Transcriptional response of Mycobacterium tuberculosis ΔlucA::hyg mutant and complemented strains vs. WT  in resting murine bone marrow-derived macrophages was analyzed in this study. This data demonstrates that deletion of lucA leads to perturbed expression of the genes linked to fatty acid and cholesterol metabolism of the pathogen during macrophage infection. It supports an overall conclusion of the publication that LucA serves an important role in function of fatty acid and choletserol transporters.

overall_design: Transcriptional responses of M. tuberculosis to macrophage infection (day 3) were studied for 3 strains: wild type (WT), ΔlucA::hyg mutant and complemented strain (Comp). Biological replicates: 3 control (WT) replicates, 3 ΔlucA::hyg mutant replicates and 3 complemented strain replicates.

first: Christine

middle: R

last: Montague

first: David

middle: G

last: Russell

first: Brian

middle: C

last: VanderVen


title: Strand-specific RNA sequencing profile of wild type and dbp2∆ strains [re-analysis]

status: Public on May 20 2017

city: West Lafayette

first: Elizabeth

last: Tran

state: IN

address: 175 S. University Street

department: Biochemistry

institute: Purdue University

type: Expression profiling by high throughput sequencing

summary: By comparing differentially expressed genes in dbp2∆ to those of 700 other deletion strains from other studies, we report that CYC8 and TUP1, which form a complex and inhibit transcription of numerous genes, co-repress a common set of genes with DBP2. Functional annotation clustering analysis reveals that these co-repressed genes are related to cellular metabolism. Furthermore, we find that co-repressed genes have a higher propensity to be overlapped with long non-coding RNAs at their promoter/5' regions.

overall_design:
Strand-specific RNA profiles of a dbp2Δ strain and a wild type (reference) strain were generated using two replicates of each strain.

Please note that this study represents the re-analysis of the published GSE58097 data, generating re-analyzed count matrix (.xls), edgeR results (.xls) and gene tracks (.bedgraph).

first: Pete

last: Pascuzzi

first: Siwen

last: Wang


title: Acute heat stress induces differential gene expressions in the small yellow follicles of a layer-type strain of Taiwan country chickens

city: Taichung

first: San

middle: Yuan

last: Huang

address: Kuo-Kuang Rd.

department: Animal science

country: Taiwan

institute: National Chung Hsing University

summary: To realize the gene expression in response to acute heat stress in chicken small yellow follicles, we have employed whole genome microarray expression profiling as we have employed whole genome microarray expression profiling as a tool to identify genes response to acute heat stress. Female B strain Taiwan country chickens were subjected to acute heat stress (38℃) for 2 h, and then exposed to 25℃, with small yellow follicles collected 0, 2, and 6 h after the cessation of heat stress, using non heat-stressed hens as a control group (n = 3 hens per group). Based on a chicken 44K oligo microarray, 69, 51, and 76 genes were upregulated and 58, 15, 56 genes were downregulated after heat treatment of H2R0, H2R2, and H2R6, respectively, using a cutoff value of two-fold or higher in the small yellow follicles of the heat-stressed chickens from those of the control chickens. Upregulation of heat shock protein 25, interleukin 6, metallopeptidase 1, and metalloproteinase 13, and downregulation of type II alpha 1 collagen, discoidin domain receptor tyrosine kinase 2, and Kruppel-like factor 2 were confirmed through quantitative real-time polymerase chain reaction (qRT-PCR).

overall_design: Acute heat stress induced small yellow follicles gene experssion in L2 strain Taiwan country chicken was measured at 0, 2, and 6 h of recovery after 4 h of 36 Celsius degree acute heat stress.

first: San-Yuan

first: Chuen-Yu

last: Cheng

first: Wei-Lin

last: Tu

first: Chao-Jung

last: Chen

first: Hong-Lin

last: Chan

first: Chi-Feng

first: Hsin-Hsin

first: Pin-Chi

last: Tang

first: Yen-Pai

last: Lee

first: Shuen-Ei


title: RNA-dependent chromatin association of transcription elongation factors and Pol II CTD kinases

city: Goettingen

first: Michael

last: Lidschreiber

address: Am Fassberg 11

country: Germany

institute: Max-Planck-Institute for Multidisciplinary Scienes

type: Genome binding/occupancy profiling by high throughput sequencing

summary: For transcription through chromatin, RNA polymerase (Pol) II associates with elongation factors (EFs). Here we show that many EFs crosslink to RNA emerging from transcribing Pol II in the yeast Saccharomyces cerevisiae. Most EFs crosslink preferentially to mRNAs, rather than unstable non-coding RNAs. RNA contributes to chromatin association of many EFs, including the Pol II serine 2 kinases Ctk1 and Bur1 and the histone H3 methyltransferases Set1 and Set2. The Ctk1 kinase complex binds RNA in vitro , consistent with direct EF-RNA interaction. Set1 recruitment to genes in vivo depends on its RNA recognition motifs (RRMs). These results strongly suggest that nascent RNA contributes to EF recruitment to transcribing Pol II. We propose that EF-RNA interactions facilitate assembly of the elongation complex on transcribed genes when RNA emerges from Pol II, and that loss of EF-RNA interactions upon RNA cleavage at the polyadenylation site triggers disassembly of the elongation complex.

overall_design: In this study, we used photoactivatable ribonucleoside-enhanced crosslinking and immuno-precipitation (PAR-CLIP) (Hafner et al., 2010), a method that detects and maps direct protein-RNA interactions in vivo. We applied our recently optimized PAR-CLIP protocol (Baejen et al., 2014) to 14 transcription elongation factors of the yeast Saccharomyces cerevisiae. These elongation factors included Spt5, Spt6, all five subunits of the Paf1 complex, namely Cdc73, Ctr9, Leo1, Rtf1, and Paf1, the kinases Bur1 and Ctk1, and their cyclin partners Bur2 and Ctk2, respectively, and the histone methyltransferases Set1, Set2, and Dot1. To estimate background RNA binding we collected PAR-CLIP data for the transcription initiation factor TFIIB, which is recruited to promoter DNA before RNA is made. We also measured gene occupancies of EFs using ChIP-Seq and compared them with our PAR-CLIP occupancies.

first: Sofia

last: Battaglia

first: Carlo

last: Baejen

first: Phillipp

last: Torkler

first: Seychelle

last: Vos

first: Patrick

last: Cramer


title: Identification of microRNAs that are differentially expressed in drought and As stressed rice

city: Suzhou

first: Jiajia

address: Kerui Road

institute: Suzhou University of Science and Technology

summary: We have characterized the changes in miRNA expression profiles in rice leaves under drought stress and As stress and compared these to unstressed leaves. 10 pairs of drought responsive and 8 pairs of As responsive miRNA-gene were identified and validated by qRT-PCR. This study identifies putative specific miRNA-mRNA regulatory modules with roles during drought and As stress. Putative microRNAs identified in this study are involved in hormone signaling, lipid and carbohydrate metabolism, and antioxidant defence. The results of this study will assist in elucidating the role of miRNAs in post-transcriptional regulation of target genes during abiotic stress and may contribute to the development of strategies to engineer drought and heavy metal resistance.

overall_design: Expression profiles in 4-week-old rice leaves dehydrated by 20% polyethylene glycol for 48 hours was compared with that in untreated control with three biological replicates.Expression profiles in 4-week-old rice leaves stressed by 10 mM As(III) solution (NaAsO2) and 50 mM As(V) solution (Na2HAsO4) for seven days was compared with that in untreated control with three biological replicates.


title: Arginine-specific effects on the transcriptome of Streptococcus mutans probed by RNA-seq

city: Gainesville

first: Robert

last: Burne

state: Florida

address: 1395 Center Drive

department: Oral BIology

institute: University of Florida

summary: Streptococcus mutans is a common constituent of oral biofilms and a primary etiologic agent of human dental caries. The bacteria associated with dental caries have a potent ability to produce organic acids from dietary carbohydrates and to grow and metabolize in acidic conditions. In this study, we observed supplementation with 1.5% arginine (final concentration) had inhibitory effects on the growth of S. mutans in complex and chemically defined media, particularly when cells were exposed to acid or oxidative stress. Deep-sequencing of RNA (RNA-Seq) comparing the transcriptomes of S. mutans growing in a chemically defined medium with and without 1.5% arginine in neutral and acidic pH conditions and under oxidative stress conditions revealed interesting results. The results provide new insights into the mechanisms of action by which arginine inhibits dental caries through direct adverse effects on multiple virulence-related properties of the most common human dental caries pathogen. The findings significantly enhance our understanding of the genetics and physiology of this cariogenic pathogen.

overall_design: mRNA profiling of S. mutans UA159 in FMC medium with and without 1.5% Arginine at pH 7.0, pH 5.5 and on oxidative stress with 0.5 mM hydrogen peroxide.

first: Brinta

last: Chakraborty


title: A blood-based gene signature characterizing Idiopathic Parkinson's disease

city: Tel Aviv

first: David

last: Amar

address: Haim Levanon

department: Computer Science

country: Israel

institute: Tel Aviv University

summary: Establishing reliable biomarkers for assessing and validating clinical diagnosis at early prodromal stages of Parkinson’s disease is crucial for developing therapies to slow or halt disease progression. Here, we present the largest study to date using whole blood gene expression profiling from over 500 individuals to identify an 87-gene blood-based signature. Our gene signature effectively differentiates between idiopathic PD patients and controls in both a validation cohort and an independent test cohort, and further highlights mitochondrial metabolism and ubiquitination/proteasomal degradation as potential pathways disrupted in Parkinson’s disease.

overall_design: This repository contains the gene expression profiles collected in the GENEPARK consortium. The main study sought a classifier for IPD. These data contain 233 healthy controls, 205 IPD patients, and 48 patients with other neurodegenerative diseases (NDD). Other samples are available in the data and can be used for additional analyses. The largest class of these additional samples are 22 samples from genetic unaffected controls and 41 genetic PD patients.

first: Ron

last: Shamir

first: Borut

last: Peterin

first: Christine

last: Klein

first: Dimitri

last: Krainc


title: Microarray analysis of NIH/3T3 cells infected with wild type Semliki Forest virus (SFV) and its corresponding RDR mutant virus

status: Public on May 19 2017

city: Liverpool

first: Bahram

last: Ebrahimi

address: Crown Street

institute: Liverpool University

summary: Cultured NIH/3T3 cels were infeced at MOI of 10 with wild type and RDR mutant of SFV virus.. Total RNA was extracted 8 hours post-infection for gene expression analysis.

overall_design: NIH/3T3 cells were cultured at 80 confluency prior to infection with SFV wild type or SFV-RDR mutant viruses.  Mock infection included NIH/3T3 cells without virus infection.  All experiments were carried out in triplicate.

first: Ebrahimi

last: Bahram


title: Whole genome expression data from female adult Drosophila melanogaster midguts

city: Glasgow

first: Julia

last: Cordero

address: Garscube Estate. Switchback Road

institute: University of Glasgow

summary:
The highly conserved Wnt signaling pathway drives intestinal homeostasis across species. Apc is a negative regulator of Wnt signaling. Loss of function mutations in Apc are found in 80-90% of human colorectal cancers. Importantly, Apc loss is widely known as the key driving event in the disease.
We used microarray analysis of adult Drosophila midguts to study the molecular mechanisms regulated upon loss of Apc in the intestine.

overall_design: Whole midguts from 7 day olfd adult female animals where dissected for RNA isolation and Affymetrix microarray hybridization. Tissues from a wild type strain (w1118) and whole null mutant Apc1 (Apc1Q8, also refered to as Apc1-/-) animals were used in the study.

middle: B

first: Gabriella

last: Kalna

first: Owen

last: Sansom


title: Exon Level Expression Profiling of Epididymal Adipose Tissue: During Chronic Glucocorticoid Treatment While Consuming an N-6 Rich High Fat Diet

city: fort collins

first: Jessica

middle: Lynn

last: Hill

state: colorado

address: 502 west lake street

department: Food Science and Human Nutrition

institute: Colorado State University

summary:
Transcriptome analysis of total RNA from C57BL/6 epididymal adipose tissue samples
Exogenously administered glucocorticoids (GC) are used for the treatment of numerous pathologies, however their chronic usage is associated with alterations in lipid metabolism and adipose tissue function. The combination of chronic GC usage with consumption of a high fat diet poses an even greater risk for the development of adverse metabolic outcomes. We evaluated the effect of chronic GC usage in combination with a 45% high fat diet rich in n-6 polyunsaturated fatty acids (PUFA) on visceral adipose tissue gene expression in C57BL/6 male mice.

overall_design: We analyzed epididymal adipose tissue from 8 male C57BL/6 mice using the Affymetrix GeneChip Mouse Gene 2.0 ST Array. Array data was processed by Affymetrix GeneChip Command Console (AGCG) Software and Affymetrix Expression Console Software. No techinical replicates were performed.

first: Marie

last: van der Merwe

first: Thomas

last: Sutter


title: YY1 haploinsufficiency causes an intellectual disability syndrome featuring transcriptional and chromatin dysfunction [ChIP-seq]

city: Milano

first: Giuseppe

last: Testa

address: Via Adamello, 16

country: Italy

institute: European Institute of Oncology & University of Milano, Italy

summary: Yin and yang 1 (YY1) is a well-known zinc-finger transcription factor with crucial roles in normal development and malignancy. YY1 acts both as a repressor and an activator of gene expression. We have identified 23 individuals with de novo mutations or deletions of YY1 and phenotypic features that define a syndrome of cognitive impairment, behavioral alterations, intrauterine growth retardation, feeding problems, and various congenital malformations. Our combined clinical and molecular data define the ‘YY1 syndrome’ as a haploinsufficiency syndrome. Through immunoprecipitation of YY1-bound chromatin from person-derived cells, using antibodies recognizing both ends of the protein, we show that YY1 deletions and missense mutations lead to a global loss of YY1 binding, with a preferential retention at high-occupancy sites. Finally, we uncover a widespread loss of H3K27 acetylation in particular on the YY1-bound enhancers, underscoring a crucial role for YY1 in enhancer regulation. Collectively, these results define a clinical syndrome caused by haploinsufficiency of YY1 through dysregulation of key transcriptional regulators.

overall_design: Individuals with mutations or deletion in YY1 were identified among patients with idiopathic intellectual disability. LCLs were established from 4 of these patients (1 deletion, 2 missense mutations, and 1 non-sense mutation undergoing non-sense-mediated decay) and from unrelated controls. These lines were profiled for genome-wide YY1 occupancy using two antibodies respectively binding each end of the protein, as well as for H3K27ac and H3K27me3.

first: Michele

last: Gabriele

first: Anneke

middle: T

last: Silfhout

first: Pierre-Luc

last: Germain

first: Alessandro

last: Vitriolo

first: Raman

last: Kumar

first: Jozef

last: Gecz

last: Koolen

first: Bert

last: de Vries


title: Transcriptomic analysis of a Saccharomyces cerevisiae mutant with extended chronological life span

city: Istanbul

first: Zeynep

middle: Petek

last: Cakar

state: Istanbul

address: ITU MOBGAM, SARIYER

department: Molecular Biology, Genetics and Biotechnology

country: Turkey

institute: Istanbul Technical University

summary: A Saccharomyces cerevisiae mutant with extended chronological life span was obtained by using an evolutionary engineering strategy, based on successive batch cultivation under gradually enhanced caloric restriction. The mutant strain SRM11 was selected which had about 50% longer life span than the reference strain. Whole-genome transcriptomic analysis of SRM11 with respect to the reference strain was performed to identify differences in gene expression levels between the two strains.

overall_design: To perform the comparative whole-genome transcriptomic analysis of the selected mutant SRM11 with respect to the reference strain, Agilent Yeast One-Color DNA microarray systems were used. Prior to gene expression analysis, three replicates of each culture were grown in yeast minimal medium (YMM) at 30°C and 150 rpm. Total RNA isolation was carried out by using RNeasy Mini Kit (Qiagen) at logarithmic phase of growth (OD600 ~1.0).

first: Mevlut

last: Arslan

first: H

middle: I

last: Kisakesen

first: Alican

last: Topaloglu

first: Z

middle: P


title: rAAVr3.45-IL10 infected human neural stem cells(hNSCs) gene expression analysis

status: Public on May 18 2017

city: Seoul

first: Mira

last: Cho

address: Yonsei-ro 50, GS Caltex Research hall 206

department: Chemical and Biomolecular Engineering

country: South Korea

institute: Yonsei Univeristy

summary: The safety and efficacy(IL10 expression level) of a recombinant adeno-associated virus derivative (rAAVr3.45) were examined to evaluate its potential as a gene carrier for preparing interleukin-10 (IL10)-secreting human neural stem cells (HFT13) that can treat ischemic injuries or neurodegenerative diseases.

overall_design: Two samples were prepared; One for control group (normal human neural stem cells) and the other for experimental group (human neural stem cells infected by AAV r3.45 IL10)

first: Jae-Hyung

last: Jang


title: YY1 haploinsufficiency causes an intellectual disability syndrome featuring transcriptional and chromatin dysfunction.

overall_design: Individuals with mutations or deletion in YY1 were identified among patients with idiopathic intellectual disability. LCLs were established from 4 of these patients (1 deletion, 2 missense mutations, and 1 non-sense mutation undergoing non-sense-mediated decay) as well as from unrelated controls, and their transcriptome and epigenome were compared.


title: Expression data of thymospheres

city: Rehovot

first: Jakub

last: Abramson

address: Herzl 234

department: Immunology

institute: Weizmann Institute

summary: Evidence suggests that a stem cell-driven differentiation hierarchy maintains the dynamic thymic epithelial cell (TEC) network that governs T lymphocyte development. The identification of TEC stem/progenitor cells has been a major focus in the field and several candidates with contrasting phenotypes have been described. a Foxn1neg EpCAMneg cell population was shown to generate so-called thymospheres. We used Affymetrix mouse 1ST arrays to analyze their gene expression profile.

overall_design: CD45- MACS depleted thymic stromal cells were cultured at previously described (Ucar et al. Immunity 2014). These were then analyzed by gene expression profiling. Specifically, total RNA was extracted using Trizol. Purified total RNA was then amplified using the MessageAmp RNA kit (Ambion). Biotinylated cRNA was then hybridized to Affymetrix Mouse Gene 1-ST arrays by the genomics core at the Weizmann Institute


title: AAV(Adeno-associated virus) infected human neural stem cells(hNSCs) gene expression analysis

summary: The safety and efficacy of a recombinant adeno-associated virus derivative (rAAVr3.45) were examined to evaluate its potential as a gene carrier for preparing interleukin-10 (IL10)-secreting human neural stem cells (HFT13) that can treat ischemic injuries or neurodegenerative diseases.

overall_design: Two samples were prepared; One for control group (normal human neural stem cells) and the other for experimental group (human neural stem cells infected by AAV r3.45 with no transgene)


title: The difference of placental fibroblast between normal pregnancy and preeclampsia

city: Fukuoka

first: Takako

last: Ohmaru

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

department: Department of Gynecology and Obstetrics

institute: Graduate School of Medical Sciences, Kyushu University

summary:
Fibrosis are known as one of the characteristic pathological findings of placenta in preeclampsia (PE). The mechanism underlying tissue injury when placental stroma is exposed to hypoxia and inflammatory stimulation is unclear. We focused on the relationship between pathogenesis of PE and placental fibrosis, and investigated the changes of fibrosis related factors (FRFs) in placental stroma.
The mRNA levels of fibrosis related factors in PE were higher than those in normal pregnancy (NP). Those under hypoxia and by TGF-β stimulation were more prominent in PE compared with NP. The contraction rate of PE had significantly higher than that of NP. The significant elevation of plasma level of TGF-β in PE was indicated compared with those in NP.

overall_design: The placental fibroblasts of PE are more sensitive to hypoxia and TGF-β stimulation than those of NP, and are prone to produce fibrosis. This study showed the possibility the placental fibrosis in PE pregnancy is induced by hypoxia and TGFβ stimulation.

first: Kazuo

last: Asanoma


title: Gene Expression data from induced Pluripotent Stem cells from healthy control donors

first: Sally

last: Cowley

summary:
We have generated human induced Pluripotent Stem cells (hiPSc) using Retroviral or Sendai virus-mediated delivery of reprogramming factors. hiPSc lines have been screened using SNP array to assess chromosomal stability (alongside the fibroblast lines from which they derived), and validation of the pluripotency of the hiPSc lines is provided by Pluritest assessment of transcriptome datasets, prior to differentiation and downstream assays.
MAPT genetic variation and neuronal maturity alter isoform expression affecting axonal transport in iPSC-derived dopamine neurons. Joel E Beevers, Mang-Ching Lai, Heather A Booth, Federico Zambon, Laura Parkkinen, Jane Vowles, Sally A Cowley, Richard Wade-Martins, Tara M Caffrey. Stem Cell Reports 2017

overall_design: human iPSc lines were derived from human dermal fibroblasts from 3 control donors (newly-derived lines are reported here; for lines that have been previously described and for fibroblasts from which lines have been derived, refer to current manuscript for relevant references). SNP and gene expression datasets were generated.

first: Joel

last: Beevers

first: Mang-Ching

last: Lai

first: Heather

last: Booth

first: Federico

last: Zambon

first: Laura

last: Parkkinen

first: Jane

last: Vowles

first: Richard

last: Wade-Martins

first: Tara

middle: M

last: Caffrey


title: Single Cell RNA-Sequencing using smart-seq2 of young and old murine hematopoietic stem cells

city: Cambridge

first: Anthony

last: Green

state: Cambridgeshire

address: Hills Road

department: Department of heamatology

institute: University of Cambridge

summary: Ageing of the hematopoietic stem cell (HSC) compartment is characterized by skewing towards the myeloid lineage and reduced stem cell function, the molecular basis of which is largely unknown. Using single cell approaches we identify features contributing to HSC exhaustion with age. A distinct subpopulation of old HSCs carried a signature indicative of impaired stem cell function, activating p53 targets involved in senescence. In the same HSCs, we identified pro-proliferative JAK/STAT and MAPK signalling. We hypothesized that prolonged proliferation of HSCs leads to cell cycle arrest with age and therefore challenged HSCs with a constant proliferative stimulus mediated by a constitutively active form of Jak2, Jak2V617F. Indeed we observed expansion of the p53 positive population and functional impairment of the challenged HSCs. Our results reveal unexpected heterogeneity in the rate of HSC ageing and strongly implicate a role for proliferation in the p53 mediated functional decline of old HSCs.

overall_design: 192 single HSCs from 2 young WT or Jak2V617F and 2 old WT or Jak2V617F animals were used for comparison

first: Kristina

last: Kirschner


title: Global analysis of liver RNA from male and female Wildtype mice vs Ikbkb-deleted in hepatocyte mice fed high cholesterol and saturated fat diet (HCFD)

city: Los Angeles

first: Hidekazu

last: Tsukamoto

state: CA

address: 1333 San Pablo Street MMR414

institute: University of Southern California

summary:
Hepatocyte IKKβ deficiency worsens HCFD-induced NASH in male but not female mice.
To help understand this gender difference, we performed microarray analysis for liver RNA samples to determine genes which are differentially regulated by IKKβ deficiency in male but not female mice as compared to Wildtype mice.

overall_design: Male and female Wildtype mice vs Ikbkb-deleted in hepatocyte mice were fed either standard rodent chow or HCFD from 2.5 months of age for 20 weeks.

first: Noriko

last: Matsushita


title: DNA methylation of human colorectal cancer and HeLa sample

status: Public on May 17 2017

city: Philadelphia

first: Wanding

last: Zhou

state: PA

address: 3501 Civic Center Blvd

department: Pathology and Lab Medicine

institute: Children's Hospital of Philadelphia

type: Methylation profiling by genome tiling array

summary: Genome wide DNA methylation profiling of normal and tumor colorectal cancer samples, HCT116 DKO (DNMT1 (-/-) and DNMT3b (-/-)), M.sssI treated DKO cell lines, and human cervical cancer cell line HeLa. The Illumina Infinium Human DNA methylation EPIC Beadchip was used to obtain DNA methylation profiles across approximately 85,000 CpGs in the above samples.

overall_design: Bisulphite converted DNA from the 8 samples were hybridised to the Illumina Infinium MethylationEPIC BeadChips

first: Hui

last: Shen

first: Peter

last: Laird


title: Transcriptome analysis of collagen-adhered S. gallolyticus subsp. gallolyticus [UCN 34]

city: Bad Oeynhausen

first: Imke

last: Grimm

address: Georgstraße 11

department: Institut für Laboratoriums- und Transfusionsmedizin

institute: Herz- und Diabeteszentrum NRW; Universitätsklinikum der Ruhr-Universität Bochum

summary: Streptococcus gallolyticus subsp. gallolyticus is a commensal of the human gastrointestinal tract and a pathogen of infective endocarditis and other biofilm-associated infections with exposed collagen. Therefore, this study focuses on the characterization of the biofilm formation and collagen adhesion of S. gallolyticus subsp. gallolyticus under different conditions. It has been observed that lysozyme triggers biofilm formation divergently in the analyzed S. gallolyticus subsp. gallolyticus strains. The transcriptome analysis was performed for two strains which form more biofilm in the presence of lysozyme. Lysozyme leads to higher expression of genes of transcription and translation, of the dlt operon (cell wall modification), of hydrogen peroxide resistance proteins and of two immunity proteins which could be involved in biofilm formation. Furthermore, the adhesion ability of 73 different S. gallolyticus subsp. gallolyticus strains to collagen type I and IV was analyzed. High adhesion ability was observed for the strain UCN 34, whereas the strain DSM 16831 adhered only marginally to collagen. The full genome microarray analysis revealed strain-dependent gene expression due to adhesion. The expression of genes of a transposon and a phage region in strain DSM 16831 were increased, which corresponds to lateral gene transfer. Adherence to collagen leads to a change in the expression of genes of nutrients uptake in the strain UCN 34.

overall_design: Analysis of two S. gallolyticus subsp. gallolyticus strains (DSM 16831 and UCN 34) in BHI medium adhered to collagen type I compared to planktonic control (BHI medium without collagen) after 2 hours of incubation. For each strain and condition three biological replicates were taken and normalized on the planktonic control.

first: Tanja

last: Vollmer

first: Jens

last: Dreier


title: Expression data from pancreatic cancer cell line SW1990

city: GUANGZHOU

first: LIANG

last: KAI

address: NO.74 ZHONGSHAN NO.2 ROAD YUEXIU DISTRICT

institute: SUN YAT-SEN UNIVERSITY

summary: We used microarrays to detail the global gene expression in cell line with or without M1 virus infection.

overall_design: Cell line with or without M1 virus infection were for RNA extraction and hybridization on Affymetrix microarrays.

first: Jiankai

last: Liang


title: Transcriptome analysis of S. gallolyticus subsp. gallolyticus

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

sample_organism: Streptococcus gallolyticus subsp. gallolyticus ATCC BAA-2069

sample_organism: Streptococcus gallolyticus subsp. gallolyticus DSM 16831

overall_design: Refer to individual Series


title: Influence of CNTRENE C100LM Carbon Nanotube Material on the Growth and Regulation of Escherichia coli

city: Springfield

first: Paul

last: Schweiger

state: MO

address: 901 S. National Ave

department: Biology

institute: Missouri State University

summary: Influence of global gene expression of Escherichia coli when exposed to CNTRENE C100LM carbon nanotubes

overall_design: Total RNA was obtained from Escherichia coli grown in the presence of CNTRENE C100LM until cells reached mid-log phase and compared to unexposed cells

first: Schweiger

last: Paul

first: Twibell

last: Brittany


title: Gene knockout of Zmym3 in mice arrests spermatogenesis at meiotic metaphase with defects in spindle assembly checkpoint

city: Beijing

first: Chunsheng

last: Han

state: Beijing

address: 1-5 Beichen West Road, Chaoyang District

department: Institute of Zoology

institute: Chinese Academy of Sciences

summary: To elucidate the molecular bases for the infertile phenotype of Zmym3 KO mice at the mRNA expression level, we carried out RNA sequencing (RNA-seq) analysis on cultured spermatogonial stem cells (SSCs), c-KIT+ pre-meiotic cells induced from SSCs and spermatocytes directly isolated from adult mouse testes.

overall_design: The cells used for RNA-Seq analysis including SSCs from Zmym3 WT and KO mice (SSC:WT and SSC:KO), c-KIT+ pre-meiotic cells induced from SSCs (c-KIT+ WT and c-KIT+:KO) and spermatocytes from 5- and 7-month mice (5m-SC:WT, 5m-SC:KO, 7m-SC:WT and 7m-SC:KO).

first: Xiangjing

last: Hu

first: Xiwen

last: Lin


title: Riboflavin depletion regulates cell proliferation and cell cycle progression‑associated genes in HEK293T cells

status: Public on May 16 2017

city: Shantou

first: Lin

last: Long

state: Guangdong

address: No.22, Xinling Road

department: Department of Biochemistry and Molecular Biology

institute: Shantou University Medical College

summary:
Transcriptome analysis of RNA samples from riboflavin-depleted HEK293T cells.
Riboflavin is an essential component of the human diet and its derivative cofactors have an established role in oxidative metabolism. Riboflavin deficiency has been linked with various human diseases. In this study, we have modelled riboflavin deficiency in HEK293T cell line, shown remarkable increase of cell proliferation. The aim of the present study is to develop a cell culture model of riboflavin depletion and analyze its molecular mechanism of acceleration cell proliferation. So, we used Affymetrix Human Transcriptome Array 2.0 to identify genes that were differentially expressed upon riboflavin-depleted HEK293T cells.

overall_design: Human embryonic kidney SV40 transformed cell line, HEK293T, was grown in culture and treated to riboflavin depletion. Cells sub-cultured in Dulbecco’s Modified Eagle’s medium (DMEM) or riboflavin-deficient DMEM medium for 25 generations and isolated RNA subjected to microarray analysis. No technical replicates were performed.

first: En-Min

last: Li

first: Li-Yan

last: Xu


title: Genome-scale fluctuations in the cytotrophoblast epigenome over gestation and in placental pathologies

city: San Francisco

first: Joseph

last: Costello

department: NeuroSurgery

institute: UCSF

summary: Embryonic and extraembryonic development quickly diverges. Other than a globally hypomethylated genome, little is known about the epigenetic changes of placental cells throughout gestation. We profiled DNA methylation and activating/repressing histone modifications of cytotrophoblasts and four extraembryonic compartments in 2nd trimester and at term. Unexpectedly, in cytotrophoblasts, H3K9me3 occupancy precisely overlapped domains with more pronounced DNA hypomethylation and repressed transcription. At term, immunoblotting and -localization revealed extensive depletion of this and other histone modifications that paralleled increased genome-wide DNA methylation, which included hundreds of promoters. Candidate enhancers within embryonic stem cell differentially methylated regions (DMRs) revealed pluripotency factors, while those within cytotrophoblast DMRs revealed transcription factor binding motifs and genes that regulate placental development. DNA methylation, RNA, and miRNA profiling of the extraembryonic compartments identified regional specializations and gestational age regulation. Cytotrophoblast mRNAs that were down-regulated at term were enriched for genes up-regulated in severe preeclampsia. Correspondingly, immunoanalyses of cytotrophoblast histone modifications showed strong H3K27ac upregulation in severe preeclampsia. Thus, as gestation proceeded, certain cytotrophoblast histone modifications declined precipitously while, in pregnancy complications, these normal patterns were markedly perturbed. These data suggested an unusual genome-scale pattern of alterations in the abundance of histone modifications over the lifetime of the placenta. Marked alterations in this pattern were associated with pregnancy complications, indicating a possible causative role.

overall_design: DNA methylation profiling of amnion, basal plate, chorion, trophoblast, and villi in 2nd trimester and at term.

first: Bo

last: Zheng

first: Ginell

last: Elliot

first: Yan

last: Zhou

first: Guangfeng

last: Zhao

first: Daofeng

first: Rebecca

last: Lowdon

first: Matthew

last: Gormley

first: Mirhan

last: Kapidzic

first: Joshua

last: Robinso

first: Michael

last: McMaster

first: Chibo

last: Hong

first: Tali

last: Mazor

first: Emily

last: Hamilton

first: Renee

middle: L

last: Sears

first: Erica

last: Pehrsson

first: Marco

last: Marra

first: Stephen

last: Jones

first: Misha

last: Bilenky

first: Martin

last: Hirst

first: Ting

last: Wang

first: Susan

middle: J

last: Fisher


title: Transcriptome analysis of lysozyme treated S. gallolyticus subsp. gallolyticus [UCN34]

first: Imke

last: Grimm

platform_organism: Streptococcus gallolyticus subsp. gallolyticus

overall_design: Analysis of two S. gallolyticus subsp. gallolyticus strains (BAA-2069 and UCN 34) in BHI medium with 10 mg/ml lysozyme compared to control (BHI medium without lysozym) after 5 hours of incubation. For each strain and condition three biological replicates were taken and normalized on the control without lysozyme.

first: Tanja

last: Vollmer

first: Jens

last: Dreier


title: Transcriptome analysis of lysozyme treated S. gallolyticus subsp. gallolyticus [BAA-2069]


title: Influence of AE104(∆zur) mutant of Cupriavidus metallidurans on Zn stress

city: Halle/Saale

first: Cornelia

last: Große

department: Faculty of Biology/Microbiology

summary: Response of Cupriavidus metallidurans AE104 and delta zur mutant to Zn stress

overall_design: In this study Zn-treatment was performed to acquire expression profiles of the total genome of Cupriavidus metallidurans

last: Grosse

first: Dietrich

middle: H

last: Nies


title: Next-Generation Sequencing Facilitates Quantitative Analysis of Rumen Epithelium Transcriptomes

city: Nanjing

first: Hong

last: Shen

address: Weigang No.1

institute: Nanjing Agriculture University

summary: We compared the biological processes altered by an increase of dietary concentration from 10% to 35% (energy-rich status) with those altered by an increase of dietary concentration from 35% to 65% (energy-excess status).

overall_design: Examination of the goat rumen epithelium from 3 groups that were fed with 3 different types of concentrate diet.

first: Zhongyan

last: Lu


title: Global RNA-binding profile of the mRNA export adaptor ALYREF

city: Shanghai

last: Cheng

address: 320 YueYang Road

department: Shanghai Institute of Biochemistry and Cell Biology

institute: Shanghai Institutes for Biological Sciences

summary: The TREX complex (TREX) plays key roles in nuclear export of mRNAs.  However, little is known about its transcriptome-wide binding targets.  We used individual cross-linking and immunoprecipitation (iCLIP) to identify the binding sites of ALYREF, an mRNA export adaptor in TREX, in human cells.  As expected, iCLIP reads are mainly mapped to exons of mRNAs.  Globally, ALYREF binding shows two apparent enrichments on the mRNA, one is near the 5’ end and the other is very close to the 3’ end.  In addition, numerous middle exons harbor ALYREF binding sites.  CBP80 and PABPN1 mainly affect ALYREF binding at the 5’ and the 3’ region, respectively.  Interestingly, we found that the 3’ processing factor CstF64 directly interacts with ALYREF and is required for the overall binding of ALYREF on the mRNA.  Sequence analysis led to the identification of multiple

overall_design: ALYREF iCLiP

first: Min

last: Shi

first: Xudong

last: Wu

first: Guohui

last: Li


title: Blood transcriptional signatures for disease progression in a rat model of osteoarthritis

city: Krakow

first: Marcin

last: Piechota

address: Smetna 12

department: Molecular Neuropharmacology

country: Poland

institute: Institute of Pharmacology PAS

summary: Biomarkers of osteoarthritis (OA) that can accurately diagnose the disease at the earliest stage would significantly support efforts to develop treatments for prevention and early intervention. The different stages of disease progression are described by the complex pattern of transcriptional regulations. The dynamics in pattern alterations were monitored in each individual animal during the time-course of OA progression.

overall_design: Blood samples were collected from a tail vein of individual male Wistar rats with monosodium iodoacetate (MIA) induced OA (0, 2, 14, 21, 28 days after the treatment). MIA-treated animals were compared to intact controls. Six replicate samples were analyzed per each experimental group. We used whole-genome microarrays (Affymetrix Rat Gene 2.0 ST) to identify OA-related molecular signatures in the blood.

first: Katarzyna

last: Starowicz

first: Michal

last: Korostynski


title: Polycomb group gene E(z) is required for spermatogonial dedifferentiation in Drosophila adult testis

status: Public on May 15 2017

city: baltimore

first: Xin

last: Chen

state: MD

address: 3400 N Charles St

institute: The Joihns Hopkins University

summary: Dedifferentiation is an important process to replenish lost stem cells during aging or regeneration after injury to maintain tissue homeostasis. Here we report that Enhancer of Zeste [E(z)], a component of the Polycomb Repression Complex 2 (PRC2), is required for the partially differentiated germ cell to dedifferentiate, in order to maintain a stable pool of germline stem cells (GSCs) within the niche microenvironment. During aging, germ cells with reduced E(z) activity have defects in maintaining GSCs, which is not due to increased GSC death or premature differentiation. We found evidence that the decrease of GSCs upon inactivation of E(z) in the germline is likely attributed by defective dedifferentiation. In addition, E(z) mutant germ cells fail to replenish lost GSCs during recovery from genetically manipulated GSC depletion. Together, our data suggest that E(z) acts intrinsically in germ cells for the dedifferentiation process to replenish lost GSCs during both aging and tissue regeneration.

overall_design: Examination of H3K4me3 and RNA polymerase II between E(z) bam double mutant testes and bam mutant testes (submitted in GSE19325 (GSM480446, GSM480449)).

first: Suk

last: Eun

first: Lijuan

last: Feng

first: Luis

last: Cedeno-Rosario

first: Qiang

last: Gan

first: Gang

last: Wei

first: Kairong

last: Cui

first: Keji

last: Zhao


title: Reticulon-1 and reduced migration towards chemoattractants by macrophages differentiated from the bone marrow of UV-irradiated and UV-chimeric mice

status: Public on May 12 2017

city: Perth

first: Kim

middle: Warwick

last: Carter

state: Western Australia

address: 100 Roberts Road, Subiaco

country: Australia

institute: Telethon Kids Institute

summary: The ability of macrophages to respond to chemoattractants and inflammatory signals is important for their migration to sites of inflammation and immune activity and for host responses to infection. Macrophages differentiated from the bone marrow of UV-irradiated mice, even after activation with LPS, migrated inefficiently towards CSF-1 and CCL2. When bone marrow cells were harvested from UV-irradiated mice, and transplanted into naïve mice, the recipient mice (UV-chimeric) had reduced accumulation of elicited macrophages in the peritoneal cavity in response to inflammatory thioglycollate or alum. Macrophages differentiating from the bone marrow of UV-chimeric mice also had an inherent reduced ability to migrate towards chemoattractants in vitro, even after LPS activation. Microarray analysis identified reduced reticulon-1 mRNA in macrophages differentiated from the bone marrow of UV-chimeric mice. By using an anti-reticulon-1 antibody, a role for reticulon-1 in macrophage migration was confirmed. The proposal that reduced reticulon-1 is responsible for the poor inherent ability of macrophages to respond to chemokine gradients was supported by Western blotting. In summary, skin exposure to erythemal UV radiation can modulate macrophage progenitors in the bone marrow such that the properties of their differentiated progeny respond inefficiently to signals to accumulate at sites of inflammation and immunity.

overall_design: Donor BM cells were isolated from congenic B6.SJL-Ptprca (CD45.1 alloantigen) mice that had been administered 8 kJ/m2 UVR to their shaved backs three days previously. BM cells from tibias and femurs were disaggregated and passed through sterile cotton wool to remove bone debris. Red blood cells were lysed with ammonium chloride. The recipient mice were 8-week-old C57BL/6J mice (CD45.2 alloantigen) that were gamma-irradiated (2 x 550 rad) using a 137Cs source (Gammacell 3000 Elan, MDS Nordion, Ottawa, Canada) prior to injection of 2 x 10e6 donor BM cells. Control chimeric mice were gamma-irradiated and injected with 2 x 10e6 BM cells from naïve congenic B6.SJL-Ptprca mice (shaved but not UV-irradiated).

first: Terence

last: McGonigle

first: Amy

last: Dwyer

first: Eloise

last: Greenland

first: Naomi

last: Scott

first: Kevin

middle: N

last: Keane

first: Helen

middle: S

last: Goodridge

first: Philip

last: Newsholme

first: Fiona

last: Pixley

first: Prue

last: Hart


title: Expression data from Germ-Free (GF) and L.NK318.1-colonized (NK318.1) mice intestinal epithelial cells and Peyer's patches cells

city: Tianjin

first: Rongcun

last: Yang

address: Weijin Road 94

institute: Nankai university

summary:
Lactobacillus NK318.1 is a commensal microbe isolated from the mouse intestinal feces in our lab. To examined the potential role of L. NK318.1 in the gut immunity, we monocolonized GF mice with L.NK318.1. And, we conducted a microarray experiment to compare the transcriptomes of GF and NK318.1 mice intestines under the same experimental condition
We used microarrays to detail the global programme of gene expression in intestinal epithelial cells (IEC) and Peyer's patches cells (PP) of GF and NK318.1 mice.

overall_design: IEC and PP of GF and NK318.1 mice of the same physiological and maintaining condition were isolated and then total RNAs were extracted from them, which could reflect the respective transcription profile of  GF and NK318.1 mice. These RNAs were detected by microarray and the influence of L.NK318.1 on intestine could be revealed to some extent.


title: Gene Expression Differences in Pediatric Lymphatic Cystic Malformations:  Size Really Matters

status: Public on May 11 2017

city: Little Rock

first: Horacio

last: Gomez-Acevedo

state: Arkansas

address: 4301 W. Markham St

department: Biomedical Informatics

institute: University of Arkansas for Medical Sciences

summary:
Microcystic and macrocystic lymphatic malformations are similar but clinically distinct infantile malformations, with distinct clinical responses and prognoses.
In this study, we identify considerable differences in gene expression between the microcystic and macrocystic malformation subtypes with respect to healthy tissue.

overall_design: Tissue was collected from children with lymphatic cystic malformations. Patient's normal skin from demographically matched children were used as controls.

first: Annjanette

last: Stone

first: Weleetka

first: Gresham

last: Richter


title: Transcriptome analysis of collagen-adhered S. gallolyticus subsp. gallolyticus [DSM 16831]

first: Imke

last: Grimm

first: Tanja

last: Vollmer

first: Jens

last: Dreier


title: Genome wide Mms1-binding sites in S. cerevisiae

city: Groningen

first: Katrin

last: Paeschke

address: Antonius Deusinglaan 1

department: European Institute for the Biology of Ageing

country: Netherlands

institute: University Medical Center Groningen

summary: ChIP-seq analysis of endogenous tagged Mms1-Myc13

overall_design: Mms1 was endogenously tagged with Myc13. Chromatin immunoprecipitation of performed using anti-Myc antibody, we generated genome-wide Mms1 binding profile in S. cerevisiae. The goal of this study was to identify where Mms1 binds in the genome and correlate this to replication fork pausing sites. Our results show that Mms1 binds to  specific G-rich  motifs which cause replication pausing.

first: Katharina

last: Wanzek


title: Expression data from WT and atrap mutant Arabidopsis rosette leaves

city: Riverside

first: Huan

last: Wang

address: 900 University Ave

institute: UC Riverside

summary:
AtRAP, which is a bacterial-induced small RNA target gene, negatively regulate plant defense response.
To identity genes that are regulated by AtRAP, we performed microarray analysis on the (Wild Type) WT and atrap mutant.

overall_design: We profiled changes in gene expression in the atrap mutant by using Affymetrix microarrays. Three biological replicates were performed using 3-week old rosette leaves from WT and atrap mutant plants.

first: Hailing

last: Jin


title: Cardiomyocyte Specific Deletion of Sirt1 Gene Sensitizes Myocardium to Ischemia and Reperfusion Injury

city: jackson

first: lin

last: wang

state: Mississippi

address: 2501 River Oaks Blvd Apt 11 B

institute: UMMC

summary: A longevity gene, sirtuin 1 (SIRT1) and energy sensor AMP-activated protein kinase (AMPK) have common activators such as caloric restriction, oxidative stress and exercise.The objective is to characterize the role of cardiomyocyte SIRT1 in age-related impaired ischemic AMPK activation and increased susceptibility to ischemic insults.

overall_design:
we want to compared wt and sirt1 ko mice heart, both basal and ischemia /reperfusion condition
List is : 1. WT BASAL; 2. WT ISCHEMIA/REPERFUSION; 3. wt cardiomyocytes; 4. SIRT1 KO cardiomyocytes; 5. SIRT1 KO BASAL; 6. SIRT1 KO ISCHEMIA/REPERFUSION

first: Ji

last: Li

first: Lin

first: Yina

last: Ma

first: Yanqing


title: In Vitro Characterization of SK-ES1 Preclinical Radiation-Adapted Model for Ewing Sarcoma

status: Public on May 10 2017

city: Houston

first: Mary

last: Shapiro

state: Texas

address: 1102 Bates St.

department: Pediatric Hematology and Oncology

institute: Baylor College of Medicine

summary: Analysis of differentially expressed genes in wild type SK-ES1 Ewing Sarcoma cells when compared to SK-ES1 Ewing Sarcoma cells that received six 4 Gy fractions (cumulative dose of 24 Gy) of ionizing radiation (radiation-adapted cell line). The hypothesis tested being that repeated ionizing radiation exposure of modifies radiation therapy response in Ewing Sarcoma.

overall_design: Total RNA obtained from wild type SK-ES1 cells and radiation-adapted SK-ES1 cells.

first: Jason

last: Yustein


title: In Vitro Characterization of MHH-ES-1 Preclinical Radiation-Adapted Model for Ewing Sarcoma

summary: Analysis of differentially expressed genes in wild type MHH-ES-1 Ewing Sarcoma cells when compared to MHH-ES-1 Ewing Sarcoma cells that received six 4 Gy fractions (cumulative dose of 24 Gy) of ionizing radiation (radiation-adapted cell line). The hypothesis tested being that repeated ionizing radiation exposure of modifies radiation therapy response in Ewing Sarcoma.

overall_design: Total RNA obtained from wild type MHH-ES-1 cells and radiation-adapted MHH-ES-1 cells.


title: In Vitro Characterization of A4573 Preclinical Radiation-Adapted Model for Ewing Sarcoma

summary: Analysis of differentially expressed genes in wild type A4573 Ewing Sarcoma cells when compared to A4573 Ewing Sarcoma cells that received six 4 Gy fractions (cumulative dose of 24 Gy) of ionizing radiation (radiation-adapted cell line). The hypothesis tested being that repeated ionizing radiation exposure of modifies radiation therapy response in Ewing Sarcoma.

overall_design: Total RNA obtained from wild type A4573 cells and radiation-adapted A4573 cells.


title: Monocyte subsets exhibit transcriptional plasticity and a shared response to interferon in SIV-infected rhesus macaques

city: Chestnut Hill

first: Kenneth

last: Williams

state: MA

address: 140 Commonwealth Ave

institute: Boston College

summary: The progression to AIDS is influenced by changes in the biology of heterogeneous monocyte subsets. Classical (CD14++CD16-), intermediate (CD14++CD16+), and nonclassical (CD14+CD16++) monocytes may represent progressive stages of monocyte maturation or disparate myeloid lineages with different turnover rates and function. To investigate the relationship between monocyte subsets and the response to SIV infection, we performed microarray analysis of monocyte subsets in rhesus macaques at three timepoints: prior to SIV infection, 26 days post-infection, and necropsy with AIDS. Genes with a 2-fold change between monocyte subsets (2023 genes) or infection timepoints (424 genes) were selected. We identify 172 genes differentially expressed among monocyte subsets in both uninfected and SIV-infected animals. Classical monocytes express genes associated with inflammatory responses and cell proliferation. Nonclassical monocytes express genes associated with activation, immune effector functions, and cell cycle inhibition. The classical and intermediate subsets are most similar at all timepoints, and transcriptional similarity between intermediate and nonclassical monocytes increases with AIDS. Cytosolic sensors of nucleic acids, restriction factors, and interferon-stimulated genes are induced in all three subsets with AIDS. We conclude that SIV infection alters the transcriptional relationship between monocyte subsets and that the innate immune response to SIV infection is conserved across monocyte subsets.

overall_design: 30 total samples representing sorted CD14++CD16-, CD14++CD16+, and CD14+CD16++ peripheral blood monocytes from 4 rhesus macaques at three different stages of SIV infection (pre-infection, day 26 post-infection, and at necropsy with AIDS) are included.

first: Brian

last: Nowlin


title: Gene expression profiling of acute type A aortic dissection combined with in vitro assessment

city: Saitama

first: Naoyuki

last: Kimura

state: Saitama

address: 1-847, Amanuma, Omiya-ku

department: Cardovascular Surgery

institute: Saitama Medical Center, Jichi Medical University

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

summary: Chronic inflammation characterized by MMP-TIMP dysregulation, increased VEGFA expression, and TGF-β signaling in the development of aortic dissection.

overall_design: Total RNA, including microRNA (miRNA), was isolated from the intima-media layer of dissected ascending aorta obtained intraoperatively from acute type A aortic dissection (ATAAD) patients without familial thoracic aortic disease (n = 6) and that of non-dissected ascending aorta obtained from transplant donors (n = 5). Gene expression profiling was performed with mRNA and miRNA microarrays, and results were confirmed by quantitative polymerase chain reaction (qPCR). Target genes and miRNA were identified by gene ontology analysis (GOA) and a literature search.

first: Kyoko

last: Futamura

first: Akio

last: Matsuda


title: In Vitro and In Vivo Characterization of a Preclinical Radiation-Adapted Model for Ewing Sarcoma

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

overall_design: Refer to individual Series


title: CD161 defines a distinct subset of pro-inflammatory NK cells that are present in the inflamed gut

city: Oxford

first: Timothy

last: Hinks

state: United Kingdom

address: John Radcliffe Hospital, Headley Way, Oxford

department: NDM Experimental Medicine - New College

institute: University of  Oxford

summary: CD161 is a C-type lectin like receptor expressed on the majority of Natural Killer (NK) cells, however, the significance of CD161 expression on NK cells has not been comprehensively investigated. We used microarrays to compare gene expression between healthy human CD161+ and CD161- NK cells.

overall_design: Gene expression of sort purified, resting human CD161+ and CD161- NK cells from peripheral blood was measured in 4 healthy donors.

first: Ayako

last: Kurioka

first: Emanuele

last: Marchi

first: Paul

last: Klenerman


title: Different expression pattern between HepG2 parental and HepG2 with suppression of LRH-1 expression

city: Shenzhen

first: Xiao

last: Lijia

address: Xinhu road 1333

institute: Shenzhen Hospital of Southern Medical University

summary: In the study presented here,gene expression microarray was performed between HepG2 and HepG2LRH-1/- cells, in which LRH-1 expression is suppressed by TALENs.

first: Lijia

last: Xiao


title: Gene expression analysis in whole blood samples obtained from donors diagnosed with MDD compared to healthy controls

city: Cambridge

first: Gwenael

last: Leday

address: Forvie Site, Robinson Way

department: School of Clinical Medicine

institute: University of Cambridge

summary: This study investigated gene expression changes in whole blood samples obtained from donors diagnosed with major depressive disorder (MDD) compared to healthy controls. Micro-array data were available from whole blood on patients with MDD (N=128, 64 with generalised anxiety disorder, diagnosed by the MINI questionnaire, and 64 without anxiety disorder) and healthy controls (N=64). RNA was isolated from all samples using the standard PAXgene protocol on the Qiagen Biorobot 8000. All samples gave good quality RNA, as assessed by Agilent Bioanalyser. The yield range was 0.86-15.05ug with an average of 6.25ug. Samples were then randomised into batches, with each batch containing a representative number of controls, depression with anxiety and depression without anxiety, and the same ratio of females to males (3:1). 50ng of RNA from each sample was converted to a biotin labeled cDNA probe using NuGEN SPIA amplification. The probes were then hybridized to Affymetrix U133_Plus2.0 Genechips.

overall_design:
Measurements from whole blood samples for 128 patients with MDD (among which 64 have been diagnosed with generalised anxiety disorder) and 64 healthy controls
contributor: MRC ImmunoPsychiatry Consortium/GlaxoSmithKline

first: Fiona

last: Kelly

first: Gwenaël

first: Petra

middle: E

last: Vértes

first: Sylvia

last: Richardson

first: Johnathan

middle: R

last: Greene

first: Tim

last: Regan

first: Shahid

last: Khan

first: Robbie

last: Henderson

first: Tom

last: Freeman

first: Carmine

last: Pariante

first: Neil

middle: A

last: Harrison

first: Hugh

middle: V

last: Perry

first: Wayne

last: Devrets

first: Gayle

last: Wittenberg

first: Edward

last: Bullmore


title: Gene expression kinetics in Raw264.7 Cells following treatment with potential probiotics strains Lactobacillus acidophilus MTCC-10307 and Bacillus clausii MTCC-8326 : NT (Time matched untreated cells) vs. Probiotics treated cells

city: Bhubaneswar

first: Biswaranjan

last: Pradhan

state: ODISHA

address: Jatni

department: Biological Sciences

country: India

institute: National Institute of Science Education and Research Bhubaneswar

summary: Gene expression kinetics in RAW 264.7 cells on treatment with Lactobacillus acidophilus MTCC-10307 and Bacillus clausii MTCC-8326.

overall_design: Eight conditions of the expriment, Untreated RAW 264.7 cells (NT) vs. treatment with Lactobacillus acidophilus MTCC-10307 and Bacillus clausii MTCC-8326 separately at MOI of 100 with 4 time points. Biological replicates: 3 in each case (Equal amount of total RNA from each replicate pulled together for microarray).

first: Pradhan

last: Biswaranjan

first: Aich

last: Palok


title: mRNA/miRNA expression profiles of human primary adipocytes exposed to low doses of bisphenols A, F and S

status: Public on May 09 2017

city: Lille

first: Odile

last: Poulain-Godefroy

address: 1, rue du Pr Calmette

department: Center for Infection and Immunity of Lille (CIIL)

country: France

institute: Université Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille


title: mRNA/miRNA expression profiles of human primary adipocytes exposed to low doses of bisphenols A, F and S [mRNA]

summary: Bisphenols F (BPF) and S (BPS) are BPA structural analogs used in many marketed products as a replacement for BPA. Since sparse toxicological data are available yet for these bisphenol substitutes, our objective was to comprehensively characterize bisphenols gene targets in a human primary adipocyte model, using chronic exposure at two concentrations: a “low-dose” similar to the dose usually encountered in human biological fluids and a higher dose.

overall_design: Bisphenols A, F and S have been added at 10 nM or 10 µM during the differentiation of human primary adipocytes from subcutaneous fat of three non-diabetic Caucasian female patients. Gene expression (mRNA/lncRNA) arrays and microRNA arrays, have been used to assess coding and non-coding RNA changes. All RNAs are measured in the same samples, with multiple replicates for each patient, four per pre-adipocyte and differentiated adipocyte and two per adipocyte differentiated with each BP.

first: Marie

last: Verbanck

first: Mickaël

last: Canouil

first: Audrey

last: Leloire

first: Véronique

last: Dhennin

first: Xavier

last: Coumoul

first: Loïc

last: Yengo

first: Philippe

last: Froguel


title: mRNA/miRNA expression profiles of human primary adipocytes exposed to low doses of bisphenols A, F and S  [miRNA]


title: Expression data from Trp53- or Atm-deficient Eµ-TCL1 murine CLL cells

city: Cologne

first: H. Christian

last: Reinhardt

address: Weyertal 115B

department: Department I of Internal Medicine

institute: University Hospital of Cologne

summary:
To analyze expression differences between Trp53 pro-and deficient as well as Atm pro- and deficient murine CLL tumors developing in the Eµ-TCL1 mouse model, we analyzed splenocytes isolated from heavily infiltrated spleens of sick mice.
To investigate differences in the response to cyclophosphamide, we also analyzed splenocytes from leukemic animals that were isolated twelve hours after intraperitoneal injection of cyclophosphamide.

overall_design: Eµ:TCL1;Cd19:Cre;Atmfl/fl (TCA), Eµ:TCL1;Cd19:Cre;Trp53fl/fl (TCP) and Eµ:TCL1;Cd19:Cre (TC) mice were monitored for disease progression by MRI and were sacrificed when strongly infiltrated spleens were detectable, either with or without acute stimulation by injection of cyclophosphamide ('CTX', 200mg/kg, i.p.) 12 hours prior to splenocyte isolation.

first: H

middle: C

first: G

last: Knittel


title: RNA-Seq Reveals Age- and Species Differences of CAR-targeted Drug-Processing Genes in Liver

city: Seattle

first: lihua

last: cheng

state: WA

address: 4225 Roosevelt

department: DEOHS

institute: universtiy of washington

summary:
Purpose: Next-generation sequencing (NGS) has been utilized for systems-based analysis of all liver samples. The goals of this study are to use NGS-derived mouse CAR and human CAR initiated transcriptome profiling (RNA-seq) and find out similarity and difference drug processing gene (DPG) pattern after CAR activation in different genotype include WT (C57BL/6 and human CAR transgenic mice with C57BL/6 background)
Methods: Liver mRNA profiles of  wild-type (WT) and human CAR knockin (hCAR-TG) mice at the age of day 5 and day 60 treated with mouse CAR activator (TCPOBOP) and human CAR activator (CITCO) respectively were generated by deep sequencing, in triplicate, using HiSeq 2000 sequencer. The sequence reads that passed quality filters were analyzed at the transcript level with followed method: HISAT followed by Cufflinks.
Results: Using an optimized data analysis workflow,RNA-Seq generated approximately 47 to 68 million reads per sample, among which approximately 40 to 60 million reads were uniquely mapped to the mouse reference genome (NCBI GRCm/38/mm10). And we identified 393 drug processing genes in the livers of WT and hCAR-TG with  with HISAT workflow. RNA-seq data confirmed that among all the 393 DPGs with known important functions in xenobiotic biotransformation, 90 DPGs were not expressed in livers of any groups (threshold: average FPKM < 1 in all treatment groups); whereas a total of 303 genes were expressed in livers of at least one groups, among which 258 DPGs were differentially regulated by mCAR or hCAR activation in either Day 5 or Day 60 (FDR-BH<0.05), and 45 genes were stably expressed among all treatment groups.
Conclusions: Our study represents the first detailed analysis of drug processing genes, with 3 biologic replicates, generated by RNA-seq technology. The optimized data analysis reported here should provide a framework for comparative investigations of expression profiles by mouse CAR activation and human CAR activation. Our results show that NGS offers a comprehensive and  accurate quantitative and qualitative evaluation of mRNA content within tissues.

overall_design: Liver mRNA profiles of wild type (WT) and human CAR knockin (hCAR-TG) mice at the age of day 5 and day 60 treated with TCPOBOP and CITCO respectively were generated by deep sequencing, in triplicate, using HiSeq 2000 sequencer.

first: Sunny

last: Cheng

first: Chris

last: Frazar


title: Cdk10KO mouse tissues

city: Singapore

first: Hyungwon

last: Choi

address: 14 Medical Drive, MD6 #08-01

country: Singapore

institute: National University of Singapore

summary: To study the function of Cdk10 in the developing mouse embryo, we isolated eight tissues [heart, brain, liver, stomach, thymus, lung, spleen, kidney, intestine] on the day the pups were born [P0]. Each tissue was immediately processed for mRNA isolation.

overall_design: Tissues from P0 mouse tissues were analyzed for changes in gene expression

first: Philipp

last: Kaldis

first: Shuhui

last: Lim


title: DNA methylation signatures of chronic alcohol dependence in purified CD3+ T-cells of patients undergoing alcohol treatment

status: Public on May 13 2017

city: Vancouver

first: Michael

middle: S.

last: Kobor

state: BC

address: 950 West 28th Avenue

department: Medical Genetics

country: Canada

institute: Centre for Molecular Medicine and Therapeutics / University of British Columbia

summary: Several studies have shown an association of alcohol dependence with DNA methylation, suggesting that environmentally-induced changes on epigenomic variation may play an important role in alcohol dependence. In the present study, we analyzed genome-wide DNA methylation profiles of purified CD3+ T-cells from pre- and post-treatment alcohol dependent patients, as well as closely matched healthy controls. We identified 59 differentially methylated CpG sites comparing patients prior to treatment with healthy controls and were able to confirm 8 of those sites in additional analyses for differentially methylated regions. Comparing patients before and after a 3-week alcohol treatment program we revealed another unique set of 48 differentially methylated CpG sites. Additionally, we found that the mean global DNA methylation was significantly lower in patients prior to treatment compared to controls, but reverted back to levels similar to controls after treatment. We validated top-ranked hits derived from the epigenome-wide analysis by pyrosequencing and further replicated two of them in an independent cohort and confirmed differential DNA methylation of HECW2 and SRPK3 in whole blood. This study is the first to show widespread DNAm variation in a disease-relevant blood cell type and implicates HECW2 and SRPK3 DNAm as promising candidates to follow up in future studies.

overall_design: The Illumina Infinium HumanMethylation450 Beadchip was used to obtain genome-wide DNA methylation from purified CD3+ T-cells of a well-characterized cohort of long-term chronic alcohol dependent (AD) patients participating in a clinical 3-week alcohol treatment program, along with the profiles of closely matched healthy controls. These measures were used to identify AD-associated DNA methylation signatures in T-lymphocytes, assess intevention-related changes in  DNA methylation, and test for replication of AD-associated differential DNA methylation in an independent cohort.

first: Christof

last: Brückmann

first: Sumaiya

last: Islam

first: Julia

last: MacIsaac

first: Alexander

last: Morin

first: Kathrin

last: Karle

first: Adriana

last: Di Santo

first: Richard

last: Wüst

first: Immanuel

last: Lang

first: Anil

last: Batra

first: Vanessa

last: Nieratschker


title: A genome-wide CRISPR screen identifies genes critical for resistance to FLT3 inhibitor AC220

status: Public on May 06 2017

city: Philadelphia

first: Jian

last: Huang

address: 3500 N Broad St

department: 9Department of Pathology and Laboratory Medicine

country: USA

institute: Temple University

summary: To understand the mechanisms of drug resistance to AC220, we undertook an unbiased approach with a novel CRISPR pooled library to screen new genes whose loss of function confers resistance to AC220. In our screen, we identified SPRY3, an intracellular inhibitor of FGF signaling, and GSK3, a canonical Wnt signaling antagonist, and demonstrated that re-activation of downstream FGF/Ras/ERK and Wnt signaling as major mechanisms of resistance to the FLT3 inhibitor. We also confirmed our findings in primary AML patient samples. We demonstrated that the expression level of SPRY3 and GSK3A is dramatically reduced in AC220 resistant AML samples and SPRY3 deleted primary AML cells are resistant to AC220. Intriguingly, we found that expression of SPRY3 is greatly reduced in GSK3 knockout AML cells, which positioned SPRY3 downstream of GSK3 in the resistance pathway. Taken together, our study identified novel genes whose loss of function confers resistance to a selective FLT3 inhibitor and revealed the underlying mechanism, thereby providing new insight into signaling pathways that contribute to the acquired resistance in AML.

overall_design: We performed a genome-wide CRISPR genetic screen in MV4-11, a human AML line harboring a FLT3-ITD mutation, to identify genes whose loss of function confers drug resistance to the FLT3 inhibitor AC220.


title: Epigenomic Atlas of Early Human Craniofacial Development

city: Farmington

first: Justin

last: Cotney

state: CT

address: 400 Farmington Avenue

department: Genetics and Genome Sciences

institute: UConn Health

summary: Interactions between putative enhancer region and locations on the same chromosome in mouse E11.5 craniofacial tissue

overall_design: Circularized Chromosome Confirmation Capture with Sequecing (4C-seq) determination of long-distance interactions originating from putative enhancer region distal to the HoxA cluster and locations near and within the anterior HoxA cluster using two independent samples of mouse craniofacial tissue

first: Andrea

last: Wilderman


title: Tumor-derived exosomal lnc-Sox2ot promotes EMT and stemness by acting as a ceRNA in pancreatic carcinoma

city: Chongqing

first: Li

last: Zhonghu

address: No. 30 Gaotanyan Street, Shapingba District,

country: China

institute: Hepatobiliary Surgery Institute

summary: Exosomes have recently been shown to play vital roles in cancer biology, but the roles and mechanisms of exosomal lncRNA in pancreatic ductal adenocarcinoma (PDAC) remain unknown. Here, we identified a lncRNA Sox2ot from exosomes of highly invasive PDAC cells and found Sox2ot was associated with poor prognosis. Sox2ot competitively binds the miR-200 family to upregulate Sox2, thus inducing EMT and stem features. We further confirmed the transmission of the exosomes from producer cells to recipient PDAC cells and liver cells in vitro and in vivo, and found that circulatory exosomes were mostly aggregated in liver to change the ahhesion to cancer cells. Therefore, the exosomal Sox2ot plays important roles and may be a useful maker for PDAC prognosis.

overall_design: tumor exosomes of Hs766t and Hs766t-l2 were analyzed for lncRNA microarray study.

first: Zhonghu

last: Li

first: Xiaowu


title: Identification of p53-regulated genes in breast epithelial cells using MCF10A with wild-type p53 or p53-null

city: Tokyo

first: Koichi

last: Matsuda

address: Shirokanedai

country: Japan

institute: The University of Tokyo

summary: Microarray-based gene expression analysis of MCF10A p53+/+ and MCF10A p53−/− treated with doxorubicin to activate p53 in time-dependent manner.

overall_design: MCF10A p53+/+ and MCF10A p53−/− cells were treated with 0.5 μg/ml of doxorubicin for 2 hours. Total RNA was isolated at 12, 24, and 48 hours after the treatment; including non-treated cells (0 hour) as controls.

first: Varalee

last: Yodsurang

first: Chizu

last: Tanikawa

first: Takafumi

last: Miyamoto

first: Paulisally

last: Yi Lo

first: Makoto

last: Hirata


title: SET1A/COMPASS and shadow enhancers in the regulation of homeotic gene expression

city: Chicago

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

summary: The homeotic (Hox) genes are highly conserved in metazoans, where they are required for various processes in development and misregulation of their expression is associated with human cancer. In the developing embryo, Hox genes are sequentially activated in time and space according to their genomic position within Hox gene clusters. Accumulating evidence implicates both enhancer elements and non-coding RNAs in controlling this spatiotemporal expression of Hox genes, but disentangling their relative contributions is challenging.  Here, we identify two cis-regulatory elements (E1 and E2) functioning as shadow enhancers to regulate the early expression of the HoxA genes. Simultaneous deletion of these shadow enhancers in embryonic stem cells leads to impaired activation of HoxA genes upon differentiation, while knockdown of a long non-coding RNA overlapping E1 has no detectable effect on their expression. Although MLL/COMPASS family of histone methyltransferases are known to activate transcription of Hox genes in other contexts, we find that individual inactivation of the MLL1-4/COMPASS family members has little effect on early Hox gene activation. Instead, we demonstrate that SET1A/COMPASS is required for full transcriptional activation of multiple Hox genes, but functions independently of the E1 and E2 cis-regulatory elements. Our results reveal multiple regulatory layers for Hox genes to fine-tune transcriptional programs essential for development.

overall_design: Exploring the roles of Hox gene enhancers and COMPASS family of methyltransferases in Hox gene activation by examining histone modifications, gene expression, and chromatin conformation at Hox clusters.

first: Kaixiang

last: Cao

first: Clayton

middle: K

last: Collings


title: Global gene expression studies for coronary artery disease and its severity in North Indian population

city: Lucknow

first: Sudeep

last: Kumar

state: Uttar Pradesh

address: Raebareli Road

department: Cardiology

institute: Sanjay Gandhi Post Graduate Institute of Medical Sciences

summary: Genes expression profiling for coronary artery disease (CAD) and its severity were performed in North Indian Population. For CAD a total of 394 differentially expressed genes, of which 331 genes were found to be up-regulated and 63 genes were found to be down-regulated (? 2.0 fold changes, p-value <0.05). The expression analysis for severity of CAD identified 424 genes up-regulated and 97 down-regulated differentially expressed genes in SVD compared to controls, while 239 genes up-regulated and 125 genes down-regulated genes in TVD compared to controls. The microarray data was validated in different cohort with same inclusion criteria using Real-Time PCR. The mean fold mRNA expression levels for genes were calculated. APOA1, CFTR, SRC, ICAM1, ESR1, SHANK2, ITGA1, IFT22, ZGPAT and THBD were selected for this validation which showed similar patterns as found on microarray experiment.

overall_design: A total of 12 non-diabetic male patients with stable CAD from North Indian population were selected for this study. We included 6 patients of single vessels disease (SVD) and 6 patients of triple vessels disease (TVD) defined by coronary angiogram. The weight of lesion was scored with modified Gensini Scoring. The Subjects with atypical angina having normal coronary angiogram were recruited in controls group.

first: Shiridhar

last: Kashyap

first: Vikas

last: Agrawal

first: Shubha

last: Phadke


title: Gene expression analysis of ex-Foxp3 Th2 cells during Heligmosomoides polygyrus infection

status: Public on May 04 2017

city: Manchester

first: Victoria

last: Pelly

state: Manchester

address: Wilmslow road

country: United Kingdom

institute: Cancer Research UK, Manchester Cancer Research Centre

summary:
Gene expression of Treg cells that have lost Foxp3 expression and acquired Il4 expression following adoptive transfer into T-cell deficient mice (HpTR-IL-4gfp+), cmpared to conventional Treg cells isolated from H. polygyrus-infected wild-type mice (HpTR) and Th2 cells generated from naïve T cells following adoptive transfer into H. polygyrus-infected T-cell deficient mice (nT-IL-4gfp+).

Immunity to intestinal helminth infections requires the rapid activation of T helper 2 (Th2) cells. However, simultaneous expansion of regulatory CD4+Foxp3+ T (Treg) cells impedes protective responses, resulting in chronic infections. The ratio between regulatory and effector T cells can therefore determine the outcome of infection. The re-differentiation of Treg into T helper (Th) cells has been identified in hyper-inflammatory diseases. In this study, we asked whether ex-Treg Th2 cells develop and contribute to type 2 immunity. Using multi-gene reporter and fate-reporter systems we demonstrate that a significant proportion of Th2 cells derive from Foxp3+ cells following Heligmosomoides polygyrus infection and airway allergy. Ex-Foxp3 Th2 cells exhibit characteristic Th2 effector functions and provide immunity to H. polygyrus. Through selective deletion of Il4ra on Foxp3+ cells, we further demonstrate IL-4 is required for the development of ex-Foxp3 Th2 cells. Collectively, our findings indicate that converting Treg cells into Th2 cells could concomitantly enhance Th2 cells and limit Treg-mediated suppression.

overall_design: Naïve T cells were FACS-sorted from naive wild-type mice. HpTR cells were FACS-sorted from H. polygyrus-infected mice. HpTR cells and nT cells were transferred to T-cell deficient mice infected with H. polygyrus. IL-4gfp-expressing cells were FACS-sorted from HpTR (HpTR-IL-4gfp+) or nT (nT-IL-4gfp+) recipients. 3 biological samples were obtained from 3 independent experiments for each sample group.

first: Mark

last: Wilson


title: Mll3 and Mll4 facilitate enhancer RNA synthesis and transcriptional elongation from promoters independently of H3K4 monomethylation

status: Public on May 05 2017

city: Stanford

first: Kristel

last: Dorighi

state: CA

address: 1291 Welch Rd.

institute: Stanford University

summary: Monomethylation of histone H3 at lysine 4 (H3K4me1) and acetylation of histone H3 at lysine 27 (H3K27ac) are correlated with transcriptionally engaged enhancer elements, but the functional impact of these modifications on enhancer activity is not well understood. Here we used CRISPR/Cas9 genome editing to separate catalytic activity-dependent and independent functions of Mll3 (Kmt2c) and Mll4 (Kmt2d, Mll2), the major enhancer H3K4 monomethyltransferases. Loss of Mll3/4 catalytic activity and H3K4me1 from enhancers causes partial depletion of H3K27ac, but surprisingly minor effects on enhancer Pol II binding, enhancer RNA (eRNA) transcription and gene expression. In contrast, loss of Mll3/4 proteins results in dramatic reduction of eRNA production, concomitant with impaired transcriptional elongation at adjacent promoters. Altogether our results suggest the major coactivator function of Mll3/4 is largely independent of H3K4me1 and instead linked to enhancer Pol II occupancy, eRNA transcription and long-range influence on elongation at target promoters.

overall_design: ChIP-seq (Mll3/4, H3K4me1, H3K27ac and Pol II), RNA-seq, Start-seq and ATAC-seq, data from WT, knockout and catalytically-deficient Mll3/4 cell lines.


title: Glucose upregulates a limited number of genes in human beta cells.

city: Paris

first: Latif

last: Rachdi

address: 123 bvd Port-Royal

institute: Institut Cochin - Bat. Cassini

summary:
Although a large set of data is available concerning organogenesis in animal models, information remains scarce on human organogenesis. In this work, we performed temporal mapping of human fetal pancreatic organogenesis using cell surface markers. We demonstrate that in the human fetal pancreas at 7 weeks of development, the glycoprotein 2 (GP2) marks a multipotent cell population that will differentiate either into the acinar, ductal and endocrine lineages. Development towards the acinar lineage is paralleled by a substantial increase in GP2 expression. Conversely, a subset of the multipotent GP2+ population undergoes endocrine differentiation by down-regulating GP2 and CD142 and turning on NEUROG3, an early marker of endocrine differentiation. Endocrine maturation will progress by up-regulating SUSD2 and lowering ECAD levels. Finally, we show that in vitro differentiation of pancreatic endocrine cells derived from human pluripotent stem cells mimics key in vivo events. Our work constitutes a powerful approach to more precisely define intermediate cell population during conversion of multipotent progenitors into the 3 main human pancreatic cell types (acinar, ductal and endocrine) in vivo. As such, the data pave the way to extend our understanding of the origin of mature human pancreatic cell types and how such lineage decisions are regulated.
While the mechanisms by which glucose regulates insulin secretion from pancreatic beta cells are now well described, the way glucose modulates gene expression in such cells needs more understanding. Here, we demonstrate that MondoA, but not its paralogue ChREBP, is the predominant glucose-responsive transcription factor in human pancreatic beta EndoC-βH1 cells and in human islets. In high glucose conditions, MondoA shuttles to the nucleus where it is required for the induction of the glucose-responsive genes ARRDC4 and TXNIP, the latter being a protein strongly linked to beta-cell dysfunction and diabetes. Importantly, increasing cAMP signaling in human beta cells, using forskolin or the GLP-1 mimetic Exendin-4, inhibits the shuttling of MondoA and potently inhibits TXNIP and ARRDC4 expression. Furthermore, we demonstrate that modulating MondoA expression functionally affects glucose uptake. These results highlight MondoA as a novel target in beta cells that coordinates transcriptional response to elevated glucose levels.

overall_design: EndoC-βH1 treated glucose and Forskolin

first: Paul

last: Richards

first: Piero

last: Marchetti

first: Mathieu

last: Armanet

first: Masaya

last: Oshima

first: Catherine

last: Postic

first: Sandra

last: Guilmeau

first: Raphael

last: Scharfmann


title: Expression data of dorsolateral prostates from wild type, prostate-specific Pten knockout, and prostate-specific Pten and Pml double knockout mice

city: Boston

first: Ming

last: Chen

address: 330 Brookline Ave

department: Medicine and Pathology

institute: Beth Isreal Deaconess Medical Center/Harvard Medical School

summary: We used microarrays to analyze the global gene expression and to identify the differentially expressed genes among wild type, prostate-specific Pten knockout, and prostate-specific Pten and Pml double knockout prostates at 12 weeks of age.

overall_design: Prostate-specific Pten inactivation leads to indolent, non-lethal invasive prostate cancer after long latency, while compound loss of Pten and Pml drives lethal and metastatic disease. To gain insight into the molecular determinants by which loss of Pml promotes Pten-loss-driven prostate tumorigenesis, we conducted transcriptome comparison using microarray among 12-week-old wild type, Pb-Cre4;PtenLoxP/LoxP, and Pb-Cre4;PtenLoxP/LoxP;PmlLoxP/LoxP prostates.

first: M

first: P

last: Pandolfi


title: Expression data from young and aged Drosophila heads

city: Obu

first: Koichi

last: Iijima

state: Aichi

address: 7-430 Morioka-cho

department: Alzheimer's Disease Research

institute: National Center for Geriatrics and Gerontology

summary: We used microarrays to detail the global gene expression changes during aging in fly heads and identified genes related to the unfolded protein response are up-regulated upon aging.

overall_design: Drosophila heads were collected at young (2 days old) or aged (25 days old) stage for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain homogeneous populations of flies at each stage in order to increase the temporal resolution of expression profiles. To that end, we carefully raised, collected and aged flies under well-controlled conditions.


title: Gene expression profile of human antigen presenting cells with a tolerogenic phenotype

status: Public on May 03 2017

city: Heidelberg

first: Mariel

last: Eberle

address: Im Neuenheimer Feld 324

department: Department of Hygiene and Microbiology

institute: University Hospital Heidelberg

summary: Immature dendritic cells (DCs) that are incubated with TLR-ligands during in vitro differentiation develop a tolerogenic phenotype. Especially an early encounter of isolated monocytes with the Toll-like receptor 7/8 ligand R848 mediates a switch of pro-inflammatory to immunosupressive properties. We were strongly interested in the identification of factors that are involved in the differentiation of these tolerogenic cells, thus we performed gene expression analysis.

overall_design: Total RNA obtained from antigen presenting cells (APCs) treated with different TLR-ligands, namely LPS, R848 and PIC, during differentiation. Immature dendritic cells were adducted as comparison.

first: Dagmar

last: Hildebrand

first: Sabinde

last: Woelfle