title: Gene expression profiling of E13.5 Eda null embryonic mammary buds

city: Helsinki

first: Maria

last: Voutilainen

address: Viikinkaari 9

department: Institute of Biotechnology

country: Finland

institute: University of Helsinki

summary: TNF ligand ectodysplasin-A1 contributes to embryonic mammary gland development. We searched for target genes of the Eda pathway using profiling of genes differentially expressed in Eda-null mammary buds after a short exposure to recombinant Fc-Eda-A1 protein.

overall_design: Microdissected E13.5 Eda-/- epithelial mammary buds from 5-6 embryos were pooled together. Other half of an embryo was used as a control and the other half as a treated sample.  Littermates from 3 litters of B6CBA background were used for the analysis. Array and data analysis were performed in the Biomedicum Functional Genomics Unit (University of Helsinki, Finland).

first: Päivi

last: Lindfors

first: Marja

last: Mikkola


title: Chronic cardiac contractile dysfunction without hypertrophy does not provoke a compensatory transcriptional response

status: Public on Oct 12 2015

city: Indianapolis

first: Scot

middle: J

last: Matkovich

state: IN

address: Lilly Corporate Center

country: USA

institute: Eli Lilly and Company

type: Expression profiling by high throughput sequencing

summary: mRNA-sequencing from ribosomal RNA-depleted cardiac total RNA was performed 9 weeks after injection of rAAV6-PLCb1a, rAAV6-PLCb1b or rAAV6-blank viri into the tail vein of C57BL/6 male mice (7-8 weeks of age at time of injection).

overall_design: 6 biological replicates each of rAAV6-PLCb1a, rAAV6-PLCb1b or rAAV6-blank-treated mice.

first: Elizabeth

middle: A

last: Woodcock

first: David

middle: R

last: Grubb


title: Genomic Analysis Reveals Disruption of Striatal Neuronal Development and Therapeutic Targets in a Human Neural Stem Cell Model of Huntington’s Disease

status: Public on Oct 20 2015

city: Los Angeles

first: Giovanni

last: Coppola

state: CA

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

summary: We have utilized induced pluripotent stem cells (iPSCs) derived from Huntington’s disease patients (HD iPSCs) as a human model of HD and determined that the disease phenotypes only manifest in the differentiated neural stem cell (NSC) stage, not in iPSCs. To understand the molecular basis for the CAG repeat expansion dependent disease phenotypes in NSCs, we performed transcriptomic analysis of HD iPSCs and HD NSCs compared to isogenic controls using RNA-Seq. Differential gene expression and pathway analysis pointed to TGF-b and netrin-1 as the top dysregulated pathways. Using data driven gene coexpression network analysis, we identified seven distinct coexpression modules, and focused on two that were correlated with changes in gene expression in NSC due to the CAG expansion. Strikingly, our HD NSC model revealed the dysregulation of genes involved in neuronal development and the formation of the dorsal striatum in HD. Further, the striatal specific and neuronal networks disrupted could be modulated to correct HD phenotypes and provide novel therapeutic targets for HD

overall_design: Transcriptomic analysis of HD iPSCs and HD NSCs compared to isogenic controls using RNA-Seq.

first: Karen

last: Ring

first: Mahru

middle: C

last: An

first: Ningzhe

last: Zhang

first: Robert

middle: N

last: O’Brien

first: Eliana

middle: M

last: Ramos

first: Fuying

last: Gao

last: Atwood

first: Barbara

last: Bailus

first: Simon

last: Melov

first: Sean

last: Mooney

first: Lisa

last: Ellerby


title: MBNL1-mediated Regulation of Differentiation RNAs Promotes Myofibroblast Transformation and the Fibrotic Response

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

summary: The differentiation of fibroblasts into myofibroblasts mediates tissue wound healing and fibrotic remodeling. To better understand this process we performed a genome-wide screen in fibroblasts, which identified the RNA-binding protein muscleblind-like 1 (MBNL1) as a potent regulator of myofibroblast differentiation. MBNL1 promoted transformation of fibroblasts into myofibroblasts, while loss of Mbnl1 abrogated myofibroblast differentiation and impaired the fibrotic phase of wound healing in mouse models of myocardial infarction and dermal injury. Conditional fibroblast-specific MBNL1 transgenic mice showed a fibrotic phenotype in the absence of injury. Mechanistically, MBNL1 directly bound to and regulated the alternative splicing and stability of a network of myofibroblast differentiation specific genes, such as the nodal transcriptional regulator serum response factor (SRF). CRISPR-Cas9 mediated gene editing of the MBNL1 binding site in Srf impaired myofibroblast differentiation. These data establish a new RNA-dependent paradigm through MBNL1 that underlies global myofibroblast differentiation, the fibrotic response, and tissue wound healing.

overall_design: To elucidate the potential mechanism whereby MBNL1 programs myofibroblast differentiation, we analyzed the expression of polyadenylated transcripts by RNA sequencing (RNAseq) from Mbnl1+/+ and Mbnl1-/- MEFs that were infected with AdMBNL1, Adβgal (negative control), or treated with TGFβ (positive control for myofibroblast differentiation). To more rigorously identify RNAs that are directly regulated by MBNL1, RNA immunoprecipitation (RIP) assays were performed on rat cardiac fibroblasts infected with Adβgal (control) or a Flag epitope tagged AdMBNL1 construct (AdMBNL1-Flag). Flag antibody resin was used to immunoprecipitate all RNAs that bound to MBNL1, followed by RNAseq analysis.

first: Jennifer

last: Davis

first: Natasha

last: Ghearing

first: Suh-Chin

last: Lin

middle: Q

last: Kwong

first: Michelle

last: Sargent

first: Apoorva

last: Mohan

first: Maurice

middle: S

last: Swanson

first: Jeff

last: Molkentin


title: Puberty-specific promotion of mammary tumorigenesis by a high animal fat diet in P53 -/- mice

status: Public on Oct 24 2015

city: Chapel Hill

first: Melissa

last: Troester

state: NC

address: 2104H McGavran-Greenberg 135 Dauer Drive Campus Box 7435 27599-7435

department: Center for Environmental Health Sciences Integrated Sciences Facility Corencer Center

institute: University of North Carolina at Chapel Hill

summary: Gene expression for genes differentially expressed between early vs. late tumor onset and high fat diet (HFD) vs. low fat diet (LFD) in P53 -/- mice.

overall_design: 4 HFD early tumor onset, 7 HFD late tumor onset, 4 HFD to LFD switch with early tumor onset, 6 HFD to LFD switch with late tumor onset, 4 LFD early tumor onset, 7 LFD late tumor onset, 5 LFD to HFD switch with early tumor onset, 4 LFD to HFD switch with late tumor onset

first: Rich

last: Schwartz

first: Sandy

last: Haslam


title: Cacao interactions with pathogenic fungus Colletotrichum theobromicola and pathogenic oomycete Phytophthora palmivora

status: Public on Nov 16 2015

city: University Park

first: Mark

last: Guiltinan

state: Pennsylvania

address: 422 Life Sciences Bldg.

department: Plant Molecular Biology

institute: Penn State University

summary: Seedlings grown from seeds from open-pollinated mother trees of genotype UF12 were grown and at two months of age used to analyze response to treatment with the fungal pathogen Colletotrichum theobromicola and the oomycete pathogen Phytophthora palmivora.

overall_design: Same microarray design as described in Maximova, S. N., Florez, S., Shen, X., Niemenak, N., Zhang, Y., Curtis, W., & Guiltinan, M. J. (2014). Genome-wide analysis reveals divergent patterns of gene expression during zygotic and somatic embryo maturation of Theobroma cacao L., the chocolate tree. BMC plant biology, 14(1), 185.

first: Luis

last: Mejia

first: E

last: Herre

first: Andrew

last: Fister

first: Siela

last: Maximova


title: Gene expression and Gli1-ChIP in IhhN protein induced cells

status: Public on Oct 15 2015

city: Shanghai

first: Lu

last: Shen

address: RM 218 Little White House 1954 Huashan RD

department: Bio-X Institutes

country: China

institute: Shanghai Jiao Tong University

type: Genome binding/occupancy profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Gene Expression Profiling in Non-Human Primate Jejunum after Total-Body Irradiation

status: Public on Oct 17 2015

city: Houston

first: David

last: Loose

state: TX

address: 6431 Fannin St, MSB 4.130

department: Integrative Biology & Pharm

institute: University of Texas

summary:
This is an experiment to study the effects of total body irradiation on intestinal gene expression.
There are 24 male animals in the study; 4 controls, 10 animals received 6.7 Gy, 10 received 7.4 Gy. Animals were killed 4, 7 or 12 days after irradiation

overall_design: RNA was extracted from the Jejunum and hybridized to an Agilent 4x44 Rhesus v2 (Agilent-026806) chip

first: Junying

last: Zheng

first: Junru

last: Wang

first: Mylene

last: Pouliot

first: Simon

last: Authier

first: Daohong

last: Zhou

first: Martin

last: Hauer-Jensen


title: Genome-wide identification of vegetative phase transition-associated microRNAs and target predictions using degradome sequencing in Malus hupehensis

status: Public on Oct 10 2015

city: Yangling

first: zai

last: biechu

state: Shaanxi, P.R.China

address: 3 Taicheng Road

department: College of Horticulture

institute: Northwest A & F University

type: Non-coding RNA profiling by high throughput sequencing

summary:
Background: A long juvenile period between germination and flowering is a common characteristic among fruit trees, including Malus hupehensis (Pamp.) Rehd., which is an apple rootstock widely used in China. microRNAs (miRNAs) play an important role in the regulation of phase transition and reproductive growth processes.
Results: M. hupehensis RNA libraries, one adult and one juvenile phase, were constructed using tree leaves and underwent high-throughput sequencing. We identified 42 known miRNA families and 172 novel miRNAs. We also identified 127 targets for 25 known miRNA families and 168 targets for 35 unique novel miRNAs using degradome sequencing. The identified miRNA targets were categorized into 58 biological processes, and the 123 targets of known miRNAs were associated with phase transition processes. The KEGG analysis revealed that these targets were involved in starch and sucrose metabolism, and plant hormone signal transduction. Expression profiling of miRNAs and their targets indicated multiple regulatory functions in the phase transition. The higher expression level of mdm-miR156 and lower expression level of mdm-miR172 in the juvenile phase leaves implied that these two small miRNAs regulated the phase transition. mdm-miR160 and miRNA393, which regulate genes involved in auxin signal transduction, could also be involved in controlling this process. The identification of known and novel miRNAs and their targets provides new information on this regulatory process in M. hupehensis, which will contribute to the understanding of miRNA functions during growth, phase transition and reproduction in woody fruit trees.
Conclusions: A comprehensive study on M. hupehensis miRNAs related to the juvenile to adult phase transition was performed. The combination of sRNA and degradome sequencing can be used to better illustrate the profiling of hormone-regulated miRNAs and miRNA targets involving complex regulatory networks, which will contribute to the understanding of miRNA functions during growth, phase transition and reproductive growth in perennial woody fruit trees.

overall_design: In June, ‘Adult phase’ (A) leaves were collected as mixed samples from the tops of 18 6-year-old M. hupehensis (Pamp.) Rehd. trees and ‘Juvenile phase’ (J) leaves were collected from the base.And were used for small RNA and degradome sequencing for identification of vegetative phase transition-associated microRNAs and target predictions using degradome sequencing in Malus hupehensis.

first: Libo

last: Xing

first: Dong

last: Zhang

first: Youmei

last: Li

first: Caiping

last: Zhao

first: Songwen

first: Yawen

first: Mingyu

last: Han


title: Gene Expression Profiling in Non-Human Primate Colon after Total-Body Irradiation

overall_design: RNA was extracted from the Colon and hybridized to an Agilent 4x44 Rhesus v2 chip


title: Gene Expression Profiling in Non-Human Primate Ileum after Total-Body Irradiation

overall_design: RNA was extracted from the Ileum and hybridized to an Agilent 4x44 Rhesus v2 chip


title: Splenic bridging channel dendritic cells survey red blood cells for missing self-CD47

status: Public on Oct 01 2015

city: San Francisco

first: Jason

last: Cyster

address: 513 Parnassus Avenue, HSE-1001A

department: Microbiology and Immunology

institute: University of California, San Francisco

summary: In vivo exposure of  mouse CD4+ splenic DCs to sheep red blood cells causes prompt induction of multiple genes associated with DC activation.

overall_design: mRNA profiles from CD4 dendritic cells (sorted from mice immunized with either sheep red blood cells or PBS) were generated using an Illumia HiSeq 2500. Sequence reads passing a quality filter were aligned to mouse genome (mm10) using Tophat.

first: Tangsheng

last: Yi


title: Expression profiling reveals transcriptional regulation by Fbxw7/mTOR pathway in radiation-induced mouse thymic lymphomas

status: Public on Oct 31 2015

city: Berkeley

first: Antoine

last: Snijders

address: 1 Cyclotron Road

institute: Lawrence Berkeley National Laboratory

summary: We used gene transcript profiling to gain a deeper understanding of the role of FBXW7 in tumor development and to determine the influence of mTOR inhibition by rapamycin on tumor transcriptome and biological functions. In comparison to tumors from p53 single heterozygous (p53+/-) mice, we find that tumors from Fbxw7/p53 double heterozygous (Fbxw7+/-p53+/-) mice show significant deregulation of cholesterol metabolic processes independent of rapamycin treatment, while cell cycle related genes were upregulated in tumors from placebo treated Fbxw7+/-p53+/- mice, but not in tumors from rapamycin treated Fbxw7+/-p53+/- mice. On the other hand, tumors from rapamycin treated Fbxw7+/-p53+/- mice were enriched for genes involved in the integrated stress response, an adaptive mechanism to survive in stressful environments.

overall_design: p53+/− and p53+/−Fbxw7+/− mice were generated by crossing p53-/- mice with Fbxw7+/- mice.  At 5 weeks of age, mice were exposed whole-body to a single dose of 4 Gy X-ray irradiation.  Mice were divided randomly into two groups and treated with rapamycin or placebo.  RNA was isolated from thymic lymphomas.

first: Jian-Hua

last: Mao


title: The regional mouse microglial transcriptome during aging

city: Edinburgh

first: Barry

middle: W

last: McColl

address: 49 Little France Crescent

department: Centre for Discovery Brain Sciences

country: United Kingdom

institute: University of Edinburgh

summary: Microglia are the specialised macrophages of the central nervous system parenchyma. Diversity in macrophages is increasingly apparent in tissues outside the brain however understanding is negligible for microglia. In the present study, we present the first genome-wide analysis of microglia from discrete brain regions that reveals their multiple region-dependent transcriptional identities. Differences in bioenergetic and immunoregulatory pathways are the major sources of transcriptional heterogeneity. Region-specific differences in immunophenotype suggest cerebellar and hippocampal microglia exist in a more immune vigilant state, but distinct from the conventional M1/M2 paradigm of activation. Functional responses correlate with regional transcriptional immunophenotypes. We also show that region-dependent differences in microglial immunophenotype are superimposed upon a core profile distinguishing all microglia from systemic macrophages. We suggest microglial diversity may enable microglia to accomplish their wide-ranging homeostatic functions but could also underlie region-specific sensitivity to neuroinflammatory-mediated degeneration. During ageing key findings were made regarding the reinforcement of a specific cerebellar immunophenotype and a contrasting loss in the distinction of the phenotype of the hippocampus. The present dataset provide an extensive underpinning resource for future studies to further define how microglial diversity influences the healthy, ageing and diseased brain.

overall_design: In this study 4, 12 and 22 month old mice were transcardially perfused with 0.9% saline. Brains were collected and dissected into 4 regions: cerebellum, cortex, hippocampus, striatum. For the extraction of microglia tissue from 8 mice was pooled for each regional replicate and the experiment was performed in quadruplicates for each region. Microglia were extracted from each region using a magnetic bead based approach. Brain regions (2 animals per region) of 4 month old animals for total RNA extraction of homogenates were snap frozen and stored at (-80C). Total RNA was immediately isolated for purified microglia and stored (-80C) until performing microarray analysis of purified microglia and regional brain homogenates (n=56).

first: Kathleen

last: Grabert

first: Tom

last: Michoel

first: Michail

middle: H

last: Karavalos

first: Sara

last: Clohisey

first: J

middle: K

last: Baillie

first: Mark

middle: P

last: Stevens

last: Freeman

first: Kim

last: Summers


title: Accumulation of epigenetic alterations at the promoters of transcriptional regulator genes in the placentas of pregnancy cases with inadequate maternal gestational weight gain

status: Public on Sep 30 2015

city: Setagaya

first: Kazuhiko

last: Nakabayashi

state: Tokyo

department: Department of Maternal-Fetal Biology

country: Japan

institute: National Research Institute for Child Health and Development

type: Methylation profiling by genome tiling array

summary: The concept that fetal environment correlates with health later on has been defined as developmental origins of health and disease (DOHaD), in which epigenetic modifications are considered to serve as a memory of exposure to in utero environments. Although many animal studies have demonstrated direct associations of maternal nutritional conditions during pregnancy with epigenetic alterations in the offspring, such evidence from human studies has been very limited.   To gain more insight into the effects of in utero environments on the human placental epigenome, we obtained genome-wide methylation profiles for 34 postpartum placentas from pregnancies of normal and fetal growth restriction cases with various extents of maternal gestational weight gain (GWG).   Whereas we initially failed to identify specific loci whose methylation is commonly altered across all subjects in each of subgroups categorized by the extent of GWG and baby’s birth weight, the application of Smirnov-Grubbs' outlier test to the same dataset revealed the accumulation of epigenetic alterations in the placentas under the adverse in utero environments. This methodology is potentially applicable to various epigenome studies for human populations. Further annotations of the genomic and functional features of loci with altered DNA methylation demonstrated that environmentally induced hyper-methylation is significantly frequently occurred at the promoter region of transcriptional regulator genes including polycomb-targets and zinc-finger genes. Aberrant epigenetic modifications at such developmental regulator loci, if occurred in fetuses in a similar manner as observed in the placentas examined in this study, would elevate the risk of developing various diseases including metabolic and mental disorders in the later life.

overall_design: We subjected placentas from 14 fetal growth restriction (FGR) births and 19 births within the normal range of birth weight to genome-wide DNA methylation analysis using Infinium HumanMethylation450 BeadChip.

first: Tomoko

last: Kawai

first: Kenichiro

last: Hata


title: Late chick lung development

status: Public on Nov 01 2015

city: Boston

first: Maria

last: Loscertales

state: Ma

address: 185 Cambridge St

department: Pediatric Surgery

institute: Massachusetts General Hospital

summary: Type IV collagen is the main component of the basement membrane which gives strength to the blood-gas barrier. In avians the formation of the blood-gas barrier happens rapidly and before hatching. We have performed a microarray expression analysis in late chick lung development and found that COL4A1 and COL4A2 were among the most significantly upregulated genes during the formation of the avian blood-gas barrier. Our study showed that type IV collagen and therefore the basement membrane play fundamental roles in coordinating alveolar morphogenesis.

overall_design: Four developmental stages of chick lung maturation (E14, E15, E16, E18). Three biological replicates per time point.

first: Faouzi

middle: I

last: Maalouf


title: Genome-wide changes in transcript levels in tongues after 4-NQO and ethanol treatment

status: Public on Oct 06 2015

city: New York

first: Alison

last: Urvalek

state: NY

address: 1300 York Ave

institute: Weill Cornell Medical College

summary: Tobacco use and alcohol consumption are two major contributing factors for head and neck squamous cell carcinoma (HNSCC) carcinogenesis. We combined the 4-nitroquinoline-1-oxide (4-NQO) oral carcinogenesis mouse model and the Meadows-Cook alcohol mouse models and performed next generation genome-wide RNA-sequencing of tongues. We determined changes in transcript levels in four groups: 4-NQO followed by ethanol treatment (4-NQO/EtOH), 4-NQO followed by normal drinking water (4-NQO/Untr.), vehicle control followed by ethanol treatment (V.C./EtOH), and vehicle control followed by normal drinking water (V.C./Untr.). We found that the 494 gene transcripts were significantly changed (at least a 2-fold change where p<0.05) in the V.C./EtOH group compared to the V.C./Untr. group. The 4-NQO/Untr. group had 1,808 transcripts significantly changed compared to the V.C./Untr group, while the 4-NQO/EtOH group had 3,606 significantly changed transcripts as compared to the V.C/Untr. group. This study is the first to show that 4-NQO followed by ethanol cause the largest number of changes in transcript levels in the tongue.

overall_design: High-throughput Illumina HiSeq2000 Deep Sequencing results were compared to the mm9 mouse reference genome. Enrichment levels were determined using the Cufflinks software using the unit of fragments per kilobase per million reads (FPKM) model. n=3 for each treatment group.

first: Xiao-Han

last: Tang

first: Kwame

last: Osei-Sarfo

first: Lorraine

last: Gudas


title: Mouse embryonic fibroblasts (MEFs): Senescent cells vs Young cells

status: Public on Oct 29 2015

city: Dongguan

first: Yu-ning

last: Chen

address: Xin Cheng Avenue 1#, Songshan Lake

institute: Guangdong Medical University

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

summary: LncRNAs and mRNAs expression profile of  MEFs comparing senescent cells with young cells. The microarray with coverage of 41597 mouse lncRNAs and 35291 mouse mRNAs.

overall_design: In the study presented here, six samples were analyzed. Biological replicates: three Senescent MEFs, three Young MEFs,  independently grown and harvested.

first: Mei

last: Meng

first: Shun

last: Xu

first: Xingcong

last: Ren

first: Jay

last: Yang

first: Yu-qi

last: Dong

first: Xinguang

last: Liu

first: Jin-Ming

first: Xing-dong

last: Xiong


title: Genome wide expression analysis of BMP and LIF induce astrocyte differentiaion of mouse neural stem cells

city: Chicago

first: Chian-Yu

last: Peng

state: IL

address: 303 E. Chicago, Ave.

department: Neurology

institute: Northwestern University

summary: Astrocytes perform a wide array of physiological functions. Despite the well-known functional and morphological diversity of astrocytes, molecular markers that label sub populations of astrocytes are limited. BMP and LIF are known to generated astrocytes with different morphology and physiological properties. The goal of this study to identify genes that are differentially expressed in BMP and LIF generated astrocytes.

overall_design: We cultured neural stem cells (NSCs) derived from postnatal day 1 mouse brain, during the period of active cortical gliogenesis.  NSCs were first transduced with a retrovirus containing green fluorescent protein (GFP) under the control of the mouse GFAP promoter, and then differentiated in the presence of BMP or LIF with noggin, a BMP signaling inhibitor. After 7 days in culture total mRNA from GFP-expressing cells was collected and used for gene expression profiling.

first: John

last: Kessler


title: High-resolution genomic profiling of disseminated tumor cells in prostate cancer

status: Public on Oct 02 2015

city: Seattle

first: Min

last: Fang

state: WA

address: 825 Eastlake Ave E, G7-500

department: Clinical Research Division

institute: Fred Hutchinson Cancer Research Center

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

summary: Circulating (CTCs) and disseminated (DTCs) tumor cells are of great interest to the field of cancer research as they provide a minimally-invasive window for assessing aspects of cancer biology including tumor heterogeneity, a means to discover biomarkers of disease behavior, and a way to identify and prioritize therapeutic targets in the emerging era of precision oncology.  However, the rarity of CTC/DTC poses a significant challenge to the consistent success in analyzing the molecular features of these cells including genomic aberrations.  Herein, we demonstrate our optimized and robust methods to reproducibly detect genomic copy number alterations in samples of 2-40 cells after whole-genome amplification using a high resolution SNP-array platform and refined computational algorithms.  We have determined the limit of detection for heterogeneity within a sample as 50% and also demonstrated success in analyzing single cells.  We validated the genes in genomic regions that are frequently amplified or deleted by qPCR and nCounter copy number quantification.  We further applied these methods to DTCs isolated from individuals with advanced prostate cancer to confirm the highly aberrant nature of these cells.  We compared copy number alterations of DTCs to matched metastatic tumors isolated from the same individual to gain biological insight.  These developments provide high-resolution genomic profiling of single and rare cell populations, and should be applicable to a wide-range of sample sources.

overall_design: Disseminated tumor cells (DTCs) were isolated from bone marrow aspirates of patients with advanced stages of prostate cancer (Adv-DTC), including men with androgen-dependent metastases and others with metastatic castration resistant prostate cancer (CRPC). Genomic profiling on 8 representative Adv-DTCs from 8 different patients were performed using Ilumina Human CytoSNP-12 bead array.

first: Yu

last: Wu

first: Jamie

last: Schoenborn

first: Colm

last: Morrissey

first: Jing

last: Xia

first: Sandy

last: Larson

first: Lisha

middle: G

last: Brown

first: Xiaoyu

last: Qu

first: Paul

last: Lange

first: Peter

last: Nelson

first: Robert

middle: L

last: Vessella


title: Gene Expression Profiling in Non-Human Primate Jejunum, Ileum and Colon after Total-Body Irradiation

first: David

last: Loose


title: Expression data from anti-mycoplasma drugs treated gastric cancer cells

status: Public on Oct 08 2015

city: beijing

first: shi

middle: qin

last: yuan

state: beijing

address: fucheng road 52#

department: tumor cancer research

institute: peking university

summary:
Various anti-mycoplasma drugs have different effects on cells growth
We used microarrays to detail the global programme of gene expression underlying gastric cancer cells treated with anti-mycoplasma drugs and identified distinct classes of up-regulated genes during this process.

overall_design: Gastric cancer cells treated with anti-mycoplasma drugs were selected for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain a disparate impact of gastric cancer cells treated with anti-mycoplasma drugs. To that end, we selected two cell lines of gastric cancer cell, AGS and BGC823, which were treated with four anti-mycoplasma drugs (A2PP, CIP, MYCO1 and MYCO2) separately.

first: Shiqin

last: Yuan


title: Effect of locally applied enalapril maleate on the gene expression profile in dorsal skin after UVB irradiation

status: Public on Sep 24 2015

city: Aomori

first: Yuji

last: Nakai

state: Aomori

address: 2-1-1, Yanagawa

department: Institute of Regional Innovation

institute: Hirosaki University

summary:
Renin-angiotensin system regulates cell proliferation, differentiation, apoptosis and tissue remodeling in skin. Previouly, we reported that angiotensin-converting enzyme (ACE) expression and angiotensin II level were enhanced by repeated UVB-irradiation of hairless mice skin, and ACE inhibitor enalapril maleate accelerated recovery of UVB-induced wrinkle. In present study, we analyzed gene expression with DNA microarray and protein distribution with immunofluorecence method to clarify the process of wrinkle repairing with enalapril maleate in UVB-irradiated hairless mouse.  In microarray analysis, we detected up-regulation of various extracullular matrix (ECM) genes and ECM related genes. In immunofluorescence, we confirm that type 1 collagen, fibrillin1, elastin, and dystroglycan 1 were decreased by repeated UVB-irradiation and the distribution of these components were improved by enalapril maleate treatment. In addition, ADAMTS2 and MMP-14, these were perticipate in ECM structure formation and degradation, were increased in enalapril maleate-treated mouse skin. While the functions of these molecules in skin is not clear yet, it is suggested that these molecules participate in improvement of wrinkles induced by UVB-irradiation.
SUBMITTER_CITATION: Yuko Matsuura-Hachiya, Yuji Nakai, Keiko Abe, Toshio Nishiyama, Koji Y. Arai (2015) "Recovery of extracellular matrix components by enalapril maleate during the repair process of ultraviolet B-induced wrinkles in mouse skin", Biochemistry and Biophysics Reports 4, 180-186, doi:10.1016/j.bbrep.2015.09.012

overall_design: Male hairless mice of the SKH-1 strain were purchased from Charles River Laboratories Japan, Inc. (Tokyo, Japan). These animals were approximately 6 weeks old at the start of the experiment. They were fed a commercial diet (CRF-1, Oriental Yeast Co., Ltd, Tokyo, Japan) ad libitum and allowed free access to water. The dorsal region of the mouse was repeatedly irradiated with UVB for 10 weeks. Enalapril maleate treatment was started at 1 week after 10-week irradiation. One hundred microliters of 1% w/v enalapril maleate dissolved in 30 vol % ethanol solution or 30 vol % ethanol (control) was applied 5 times a week for 2 consecutive weeks to the whole dorsal skin of each of the mice. All experimental procedures using mice were approved by the Animal Experiment Committee of Tokyo University of Agriculture and Technology (approval number 24-82).   The dosal region of the mouse was repeatedly irradiated with UVB for 10 weeks. Enalapril maleate treatment was started at 1 week after 10-week irradiation. One hundred microliters of 1% w/v enalapril maleate dissolved in 30 vol % ethanol solution or 30 vol % ethanol (control) was applied 5 times a week for 2 or 6 consecutive weeks to the whole dorsal skin of each of the mice. Each of the experimental groups comprised 6 mice. After 2- or 6-week drug treatment, skin samples were collected for microarray analysis.

first: Yuko

last: Matsuura-Hachiya

first: Keiko

last: Abe

first: Toshio

last: Nishiyama

first: Koji

last: Arai


title: Effect of Cnot7 expression on 4T1 mammary tumor cell line transcriptome

status: Public on Sep 22 2015

city: Rockville

first: Ying

last: Hu

email: yhu@mail.nih.gov, hunterk@mail.nih.gov

state: MD

address: 9609 Medical Center Dr.

department: NCI/CCR

institute: NIH

summary: The goal of this study was to determine what the effect of modulating Cnot7 expression levels would have on the steady state transcription program of the 4T1 mammary tumor cell line.

overall_design:
Three biological replicates for over expression compared to vector control.
Three biological replicates for two different shRNAs versus shScramble control

first: Kent

last: Hunter


title: Bioenergetic cues shift FXR splicing towards FXRα2 to modulate hepatic lipolysis and fatty acid metabolism

status: Public on Sep 28 2015

city: Huddinge

first: Karin

last: Dahlman-Wright

address: Blickagången 16

department: Department of Biosciences and Nutrition

country: Sweden

institute: Karolinska Institutet

summary: Farnesoid X receptor (FXR) plays a prominent role in hepatic lipid metabolism. The FXR gene encodes four proteins with structural differences suggestive of discrete biological functions about which little is known. We show that FXR isoforms have specific effects on hepatic metabolism and uncover novel pathways under their control. Gene expression profiling of hepatocytes expressing each FXR variant revealed large differences in their target gene sets. Notably, FXRα2 (but not α1) activates a broad transcriptional program in hepatocytes conducive to lipolysis, fatty acid oxidation, and ketogenesis. Consequently, FXRα2 decreases cellular lipid accumulation and improves insulin sensitivity. FXRα2 expression in Fxr-/- mouse liver activates a similar gene program and robustly decreases hepatic triglyceride levels. On the other hand, FXRα1 reduces hepatic triglyceride content to a lesser extent and does so through regulation of lipogenic gene expression. Bioenergetic cues, such as fasting and exercise, dynamically regulate Fxr splicing in mouse liver to increase Fxrα2 expression. Our results show that the main FXR variants in human liver (α1 and α2) reduce hepatic lipid accumulation through distinct mechanisms and to different degrees. Thus, pharmacological or lifestyle interventions, such as exercise, aimed at modulating hepatic FXR splicing may improve the therapeutic efficacy of FXR agonists.

overall_design: Primary hepatocytes from male C57BL/6J mice were isolated, cultured and transduced as previously described (Estall et al. 2009). To evaluate the gene programs regulated by each FXR isoform, we generated recombinant adenoviruses expressing each human FXR variant (FXRα1, α2, α3, and α4). All adenoviruses also express GFP from an independent CMV promoter. An adenovirus expressing GFP alone was used as a control. Hepatocytes were transduced overnight with each adenovirus and processed for RNA extraction 36 h post-transduction.

first: Jorge

last: Correia

first: Julie

last: Massart

first: Jan

middle: F

last: de Boer

first: Margareta

last: Porsmyr-Palmertz

first: Vicente

last: Martínez-Redondo

first: Leandro

middle: Z

last: Agudelo

first: Indranil

last: Sinha

last: Meierhofer

first: Vera

last: Ribeiro

first: Marie

last: Björnholm

first: Sascha

last: Sauer

first: Juleen

last: Zierath

first: Albert

last: Groen

last: Ruas


title: RNA IP Seq analysis of Cnot7 in 4T1 mammary tumor cells

status: Public on Sep 23 2015

last: Hu

summary: Native RNA immunoprecipitation of Cnot7-bound transcripts. Abstract: Accumulating evidence supports the role of an aberrant transcriptome as a driver of tumor cell metastatic potential. Deadenylation is a general regulatory node for post-transcriptional control by microRNAs and other determinants of RNA stability. We show here that CCR4-NOT subunit CNOT7 is a deadenylase-dependent driver of tumor cell autonomous metastatic potential. Metastasis promotion by CNOT7 is dependent on contact with CNOT1 and TOB1. We further show TOB1 independently drives metastasis. RNA-immunoprecipitation and integrated transcriptome wide analyses reveal that CNOT7-regulated transcripts are enriched for a tripartite 3’UTR motif bound by RNA-binding proteins known to complex with CNOT7, TOB1, and CNOT1. Collectively, our data support a model of CNOT7, TOB1, CNOT1, and RNA-binding proteins collectively exerting post-transcriptional control on a metastasis suppressive transcriptional program to drive tumor cell metastasis.

overall_design: 48 total samples, 4-5 biological replicates, two forms of control: input samples and vector controls

first: Farhoud

last: Faraji

first: G

last: Winkler

first: Markus

last: Hafner


title: Efficacy of retinoids in IKZF1-mutated BCR-ABL1 acute lymphoblastic leukemia

status: Public on Sep 04 2015

city: Memphis

first: Chunxu

last: Qu

state: TN

address: 262 Danny Thomas Pl

department: Pathology

institute: St Jude Children's Research Institute

summary:
Alterations of IKZF1, encoding the lymphoid transcription factor IKAROS, are a hallmark of high risk acute lymphoblastic leukemia (ALL), however the role of IKZF1 alterations in ALL pathogenesis is poorly understood. Here we show that in mouse models of BCR-ABL1 leukemia, Ikzf1 and Arf alterations synergistically promote the development of an aggressive lymphoid leukemia. Ikzf1 alterations were associated with acquisition of stem cell-like features, including self-renewal and increased bone marrow stromal adhesion. Rexinoid receptor agonists reversed this phenotype, in part by inducing expression of IKZF1, resulting in abrogation of adhesion and self-renewal, cell cycle arrest and attenuation of proliferation without direct cytotoxicity. Retinoids potentiated the activity of dasatinib in mouse and human BCR-ABL1 ALL, providing a new therapeutic option in IKZF1-mutated ALL.
Significance: The outcome of therapy for high-risk acute lymphoblastic leukemia remains suboptimal despite contemporary chemotherapy and the advent of targeted therapeutic approaches. Recent genomic studies have identified deletions or mutations of IKZF1 as a hallmark of high-risk ALL, but an understanding of how IKZF1 alteration contribute to leukemia development are lacking. Here we show that IKZF1 alterations drive lymphoid lineage, a stem cell-like phenotype, abnormal bone marrow adhesion, and poor responsiveness to tyrosine kinase inhibitor (TKI) therapy. Using a high-content screen, we show that retinoids reverse this phenotype in part by inducing expression of wild type IKZF1, and increase responsiveness to TKIs. These findings provide new insight into the pathogenesis of high-risk ALL and potential new therapeutic approaches.

overall_design: Pre-B mRNA profiles of p185 MIG and IK6 cells, DMSO or drug treated, in 3 or 4 replicates, using Illumina HiSeq 2500.

first: Michelle

last: Churchman

first: Charles

last: Mullighan


title: Integrated Transcriptome and Proteome Analyses Reveal Organ-Specific Proteome Deterioration in Old Rats

first: Michael

last: Harris

address: Barker Hall

department: MCB

institute: UC Berkeley

summary: Aging is associated with the decline of protein, cell, and organ function. Here, we use an integrated approach to characterize gene expression, bulk translation, and cell biology in the brains and livers of young and old rats. We identify 468 differences in protein abundance between young and old animals. The majority are a consequence of altered translation output, that is, the combined effect of changes in transcript abundance and translation efficiency. In addition, we identify 130 proteins whose overall abundance remains unchanged but whose sub-cellular localization, phosphorylation state, or splice-form varies. While some protein-level differences appear to be a generic property of the rats’ chronological age, the majority are specific to one organ. These may be a consequence of the organ’s physiology or the chronological age of the cells within the tissue. Taken together, our study provides an initial view of the proteome at the molecular, sub-cellular, and organ level in young and old rats.

overall_design: RNA-Seq and ribosome profiling from matched young and old rat liver and brain

first: Alessandro

last: Ori

first: Brandon

last: Toyama

first: Thomas

last: Bock

first: Murat

last: Iskar

first: Peer

last: Bork

first: Nicholas

middle: T

last: Ingolia

first: Martin

last: Hetzer

last: Beck


title: Profiling status epilepticus-induced changes in hippocampal RNA expression using high-throughput RNA sequencing

status: Public on Aug 27 2015

city: Columbus

first: Katelin

middle: Libby

last: Hansen

address: 333 W. 10th Ave

department: Neuroscience

institute: The Ohio State University

summary: Status epilepticus (SE) is a life-threatening condition that can give rise to a number of neurological disorders, including learning deficits, depression, and epilepsy. Many of the effects of SE appear to be mediated by alterations in gene expression. To gain deeper insight into how SE affects the transcriptome, we employed the pilocarpine SE model in mice and Illumina-based high-throughput sequencing to characterize alterations in gene expression from the induction of SE, to the development of spontaneous seizure activity. While some genes were upregulated over the entire course of the pathological progression, each of the three sequenced time points (12-hour, 10-days and 6-weeks post-SE) had a largely unique transcriptional profile. Hence, genes that regulate synaptic physiology and transcription were most prominently altered at 12-hours post-SE; at 10-days post-SE, marked changes in metabolic and homeostatic gene expression were detected; at 6-weeks, substantial changes in the expression of cell excitability and morphogenesis genes were detected.  At the level of cell signaling, KEGG analysis revealed dynamic changes within the MAPK pathways, as well as in CREB-associated gene expression. Notably, the inducible expression of several noncoding transcripts was also detected. These findings offer potential new insights into the cellular events that shape SE-evoked pathology.

overall_design: cDNA from two animals was pooled into two independent biological replicates for each timepoint  (ie. two sets  of two animals per experimental group: control, 12 hours, 10 days, 6 weeks). Samples were sequenced using a Genome Analyzer II (GAII) at a concentration of 10pM in each lane. Base-calling was conducted with the standard Illumina Analysis Pipeline 1.0 (Firescrest-Bustard). Eight FASTQ sequence files (sequencing reads plus quality information) were generated and mapped to the mouse genome (UCSC mm9) using the Bowtie algorithm with default settings. A C++ program was used to count the number of uniquely mapped reads within exons of Ref-Seq genes (UCSC Genome Browser mm9 annotation).

first: Kensuke

last: Sakamoto

first: Carl

last: Pelz

first: Soren

last: Impey

first: Karl

last: Obrietan


title: Nucleosomal chromatin in the mature sperm of Drosophila melanogaster.

city: Burley-in-Wharfedale

first: David

middle: Edwin

last: Iles

state: West Yorkshire

address: 50 Hall Drive

institute: Omics Ltd.

summary: Nucleosomal chromatin persists in the mature sperm of Drosophila melanogaster. Paternal epigenetic marks of repression and active transcription are found within many genes essential for embryogenesis. These marks are delivered at fertilization and are subsequently maintained in the early embryo.

overall_design: The detection and localization of nucleosomal DNA in D. melanogaster spermatozoal chromatin.

first: Abdul

last: Elnfati

last: Miller


title: Comparison of miRNA expression profiles in pituitary–adrenal axis between Beagle and Chinese Field dogs after chronic stress exposure

status: Public on Aug 30 2015

city: Guangzhou

first: Zhenhui

last: Li

address: Tianhe District Wushan road

institute: South China Agricultural University

summary:
Purpose: The miRNA profiles were compared among groups of chronic stress exposure and control in two different breeds to identify the differentially expressed miRNAs related to response to chronic stress in the pituitary-adrenal axis.
Methods: 6 male adult CFD and 6 Beagles were chosen at random with the similarities in good health, weight and other aspects. Separately, 3 of these two breeds were freely selected for the stress exposure via intermittent electrical stimulation and restraint stress, while the other 3 of these two breeds were non-disposed for normal control.The details for the disposal of dogs were: every morning dogs were restrained and electrical stimulations were exerted with a stable current of 10 mA for 6 s and then with a 6 s interval, lasting for 20 min every day. The duration of disposal was ten days.ll 12 dogs were killed by air embolism in the 11th day. Subsequently, pituitary and adrenal cortex tissues were fast collected and isolated for further high-sequencing.
Results: 8 small miRNA libraries were constructed for miRNA-seq. A number of reads ranging from 15,926,611 to 81,028,035 was obtained in those 8 groups.a total of 29 (7 up, 22 down), 37 (16 up, 21 down), 30 (22 up, 8 down), 23 (16 up, 7 down), 21 (15 up, 6 down), 50 (11 up, 39 down), 28 (6 up, 22 down) and 40 (29 up, 11 down) DE-miRNAs (P-value < 0.001, log2(Fold_change) >1) were detected in the comparisons of BAC1_vs_BAC2, BAC1_vs_CFDAC1, BAC2_vs_CFDAC2, CFDAC1_vs_CFDAC2, BP1_vs_BP2, BP1_vs_CFDP1, BP2_vs_CFDP2 and CFDP1_vs_CFDP2, respectively
Conclusions: Our results shed light on the miRNA profiles with and within chronic stress exposure in adrenal cortex and pituitary.

overall_design: Adrenal cortex and pituitary miRNA profiles of adult Chinese Field Dog and Beagle under chronic stress exposure and normal control, including BAC1 (Beagle adrenal cortex with disposal), BAC2 (Beagle adrenal cortex with non-disposal), BP1 (Beagle pituitary with disposal), BP2 (Beagle pituitary with non-disposal), CFDAC1 (Chinese Field Dog adrenal cortex with disposal), CFDAC2 (Chinese Field Dog adrenal cortex with non-disposal), CFDP1 (Chinese Field Dog pituitary with disposal), CFDP2 (Chinese Field Dog pituitary with non-disposal), were generated by deep sequencing, using Illumina Hiseq 2000.

first: Wei

last: Luo

first: Qinghua

last: Nie


title: High hydrostatic pressure adaptive strategies in an obligate piezophile Pyrococcus yayanosii and piezosensible Pyrococcus furiosus

status: Public on Sep 09 2015

city: Thuwal

first: Gregoire

last: Michoud

address: KAUST

country: Saudi Arabia

institute: KAUST

summary:
Pyrococcus yayanosii CH1 is the first and only obligate piezophilic hyperthermophilic microorganism discovered so far, that extends the physical and chemical limits of life on Earth and strengthens the idea of the existence of a hyperthermophilic biosphere in the depth of our planet. It was isolated from the Ashadze hydrothermal vent at 4,100 m depth.
Multi-omics analyses where performed in order to study the mechanisms implemented by the cell to face high hydrostatic pressure variations. In silico analyses showed that P. yayanosii genome is highly adapted to its harsh environment with precisely a loss of aromatic amino acid biosynthesis and the high constitutive expression of the energy metabolism compared to others non obligate piezophilic Pyrococus. Differential proteomics and transcriptomics analyses identified key hydrostatic pressure responsive genes involved in translation, chemotaxis, energy metabolism (hydrogenases and formate metabolism) and CRISPR-cas.

sample_organism:
Pyrococcus furiosus
Pyrococcus yayanosii

overall_design: Cells were grown at different hydrostatic pressures (20, 52 and 80 Mpa for P. yayanosii and 0.1 and 45 Mpa for P. furiosus) until they reached the middle of the exponential phase. Each culture was done 3 times independantly.

first: Grégoire

first: Mohamed

last: Jebbar


title: Genome-wide analysis of p53 transcriptional programs in B cells upon exposure to genotoxic stress in vivo [DNAse-Seq]

status: Public on Aug 24 2015

city: Milan

first: Marco

middle: J.

last: Morelli

address: via Adamello 16

department: Center for Genomic Science of IIT@SEMM

country: Italy

institute: Istituto Italiano di Tecnologia

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The tumor suppressor p53 is a transcription factor that coordinates the cellular response to DNA damage. Here we provide an integrated analysis of p53 genomic occupancy and p53-dependent gene regulation in the splenic B and non-B cell compartments of mice exposed to whole-body ionizing radiation, providing insight into general principles of p53 activity in vivo. In unstressed conditions, p53 bound few genomic targets; induction of p53 by ionizing radiation increased the number of p53 bound sites, leading to highly overlapping profiles in the different cell types. Comparison of these profiles with chromatin features in unstressed B cells revealed that, upon activation, p53 localized at active promoters, distal enhancers, and a smaller set of unmarked distal regions. At promoters, recognition of the canonical p53 motif as well as binding strength were associated with p53-dependent transcriptional activation, but not repression, indicating that the latter was most likely indirect. p53-activated targets constituted the core of a cell type-independent response, superimposed onto a cell type-specific program. Core response genes included most of the known p53-regulated genes, as well as many new ones. Our data represent a unique characterization of the p53-regulated response to ionizing radiation in vivo.

overall_design: Mapping accessible chromatin regions in splenic B cells

middle: J


title: Gene expression during primary osteoblast differentiation

city: Hamburg

first: Thomas

last: Streichert

address: Martinistr. 52, Campus Forschung N27, 2. OG

department: Institute For Clinical Chemistry / Central Laboratories

country: Germany

institute: University Medical Center Hamburg-Eppendorf

summary: In order to identify genes with differential expression in primary murine osteoblasts we compared the transcriptomes of these cells at day 5 and day 12 of differentiation

overall_design: CD11b-negative cells derived from calvariae of newborn mice were differentiated into osteoblasts by addition of ascorbic acid and ß-glycerophosphate for 5 or 12 days.

first: Benjamin

last: Otto

first: Thorsten

last: Schinke


title: Identification of miRNAs and its targets using high-throughput sequencing and degradome analysis in male and female Asparagus officinalis.

status: Public on Sep 02 2015

city: Hangzhou

first: Li

last: Qin

state: Zhejiang

address: No. 866, Yuhangtang Road

department: Horticulture

institute: Zhejiang University

summary: Two independent small RNA (sRNA) libraries from male and female asparagus plants were sequenced, generating 4.13 and 5.88 million final cleaned reads, respectively. A total of 154 conserved miRNA belonging to 26 families, and 40 novel miRNA candidates that seemed to be specific to asparagus were identified, among them, 63 miRNAs exhibited significant differential expression between male and female plants, and 36 target mRNAs representing 44 conserved and fournovel miRNA in asparagus by high-throughput degradome sequencing analysis.

overall_design: Examination of small RNA in male and female asparagus using high-throughput sequencing

first: Jingli

last: Chen


title: Genes induced by partial down-regulation of ARID1A in breast cancer cell

status: Public on Sep 03 2015

city: Gifu

first: Tamotsu

last: Takeuchi

address: Yanagido

department: Pathology and Translational Research

institute: Gifu University School of Medcine

summary: Development of gene expression signatures for partial downreualtion of ARID1A protein.

overall_design:
ARID1A was down-regulated by si-RNA in a breast cancer cell, MDA-MB-157. Subsequently, RNAs was extracted from control siRNA treated cells or partially ARID1A-down regulated cells. cDNAs were synthesized and cRNAs were labeled using low input quick Amp labeling kit (Agilent). Aftere washing and dry, scanned by Agilent Technologies Micorarrray Scanner and calculated using Agilent Feature 10.7.3.1.
control siRNA treated MDA-MB-157 breast cancer cells (MOK) and siRNA-midiated ARID1A-downregulated MDA-MB157 breast cancer cells.

first: Takeuchi

last: Tamotsu


title: Development of gene expression signatures for SOX2 overexpressing human dental pulp stem cells

status: Public on Sep 30 2015

first: Pengfei

last: Liu

address: 190 Kai Yuan Avenue, Science Park

institute: Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences

summary: As a key factor for cell pluripotent and self-renewing phenotypes, SOX2 has attracted scientists’ attention gradually in recent years. However, its exact effects in dental pulp stem cells (DPSCs) are still unclear. In this study, we mainly investigated whether SOX2 could affect some biological functions of DPSCs.

overall_design: DPSCs were isolated from the dental pulp of human impacted third molar. SOX2 overexpressing DPSCs (DPSCs-SOX2) were established through retroviral infection. Whole genome expression of DPSCs-SOX2 was analyzed with RNA microarray.


title: Genome-wide analysis of p53 transcriptional programs in B cells upon exposure to genotoxic stress in vivo [RNA-Seq]

overall_design: Total RNA profiling of gene expression in the splenic B and non-B cell compartments of wild-type and Trp53-/-mice exposed to whole-body ionizing radiation by Illumina sequencing


title: CD-1mice: db/db vs db/+

status: Public on Sep 01 2015

city: Higashi-Hiroshima

first: Yanaka

last: Noriyuki

address: Kagamiyama 1-4-4

department: Graduate School of Biosphere Science

institute: Hiroshima University

summary: Transcriptional profiling of mouse white adipose tissues. The objective of this study is to explore gene expression profiles of obese adipose tissue by DNA microarray data analysis.

overall_design: Male db/db (BKS.Cg-m+/+ Lepr db/J, 6 weeks old) and db/+ (BKS.Cg-Dock7m +/+ Lepr db/J, 6 weeks old) mice were used in this experiment.

first: Noriyuki

last: Yanaka

first: Haruna

last: Suehiro

first: Yohei

last: Sanada


title: Comprehensive transcriptome profiles distinguish the CSP and XIP signaling pathways in Streptococcus mutans UA159

city: Cambridge

first: Tsute

state: MA

address: 245 First Street

department: Microbiology

institute: The Forsyth Institute

type: Expression profiling by genome tiling array

summary: In Streptococcus mutans, an oral colonizer associated with dental caries, competence for natural transformation can be triggered by both CSP and XIP pheromones. Competence induced by CSP is a late response that requires induction of the XIP encoding gene comS, but the mechanism(s) linking the two systems remains unknown. To learn how the CSP and XIP pheromone regulatory pathways are temporally linked, we mapped the global changes in gene expression at early and late phases of the CSP response and investigated the effect of deletion of comS on the S. mutans transcriptional profile. The early phase of the CSP response was characterized by an increase in gene expression at five loci associated with bacteriocin production and immunity. In the late phase, the up-regulated regions expanded to include a total of 27 loci, including comS and genes required for DNA uptake and recombination. In the absence of comS, no increase in expression of the genes up-regulated as a late response was observed in response to CSP, whereas expression of those regulated as an early response was maintained.  These results indicate that the entire late response to CSP depends on the expression of comS and that the immediate transcriptional response to CSP, mediated by ComE, is restricted to just five bacteriocin-related loci

overall_design: To distinguish the immediate, and presumably direct, regulatory response to CSP from later, and presumably indirect, effects of exposure to this pheromone, we have assembled a comprehensive strand-specific microarray census of mRNA in strain UA159 at both early and late times in the CSP response as well as in a comS mutant.

first: R

last: Khan

first: H

middle: V

last: Rukke

last: Høvik

middle: A

last: Åmdal

first: T

first: D

last: Morrison

first: F

middle: C

last: Petersen


title: RNA sequencing of transcriptomes in human brain regions: protein-coding and non-coding RNAs, isoforms and alleles

first: Amy

last: Hite

state: OH - Ohio

address: 1800 Cannon Drive 250 Lincoln Tower

department: Biomedical Informatics

type: Genome variation profiling by high throughput sequencing

summary:
We used RNA sequencing to analyze transcript profiles of ten autopsy brain regions from ten subjects. RNA sequencing techniques were designed to detect both coding and non-coding RNA, splice isoform composition, and allelic expression. Brain regions were selected from five subjects with a documented history of smoking and five non-smokers. Paired-end RNA sequencing was performed on SOLiD instruments to a depth of >40 million reads, using linearly amplified, ribosomally depleted RNA.
12 thousand protein coding and 2 thousand lncRNA transcripts were detectable at a conservative threshold. Of the aligned reads, 52% were exonic, 34% intronic and 14% intergenic. A majority of protein coding genes (65%) was expressed in all regions, whereas ncRNAs displayed a more restricted distribution. Profiles of RNA isoforms varied across brain regions and subjects at multiple gene loci, with neurexin 3 (NRXN3) a prominent example. Allelic RNA ratios deviating from unity were identified in > 400 genes, detectable in both protein-coding and non-coding genes, indicating the presence of cis-acting regulatory variants.
RNA sequencing identifies distinct and consistent differences in gene expression between brain regions, with non-coding RNA displaying greater diversity between brain regions than mRNAs. Numerous RNAs exhibit robust allele selective expression, proving a means for discovery of cis-acting regulatory factors with potential clinical relevance.

overall_design: Sequenced whole transcriptomes of 10 brain regions from 10 individuals, 5 smokers and 5 nonsmokers

last: Webb

first: Audrey

last: Papp

first: Wolfgang

last: Sadee


title: Identification of Kctd15 target genes in Xenopus animal caps injected with wnt3a and chordin

status: Public on Aug 26 2015

city: Bethesda

first: Igor

last: Dawid

address: 6 Center Drive

institute: NICHD, NIH

summary: We aimed to identify  genes that are inhibited by Kctd15 overexpression during neural crest (NC) induction. Injection of RNAs encoding Wnt3a and chordin into the embryo followed by animal cap explant culture leads to the induction of  NC marker genes as well as additional genes expressed in the neural plate border. Our previous study indicated that co-injection of kctd15 inhibits the induction of these markers. We injected four sets of RNAs, lacZ as control (L), wnt3a+chd (WC), wnt3a+chd+kctd15 (WCK), and kctd15 (K). After evaluation of marker gene expression with RT-PCR, we prepared probes with same RNA extract for Affymetrix DNA microarray. The hybridization, washing and scanning were perfomed following the manual from Affymetrix. Partek Genomics Suite was employed for data analysis.

overall_design: Xenopus embryos were injected with mRNAs at two-cell stage. When developing to stage 9, the animal caps were dissected for RNA extraction and hybridization on Affymetrix microarrays. According to the mRNAs injected, the animal caps (AC) were divided into four groups, including (1) AC injected with lacZ; (2) AC injected with kctd15; (3) AC injected with chordin and wnt3a; (4) AC injected with chordin, wnt3a and kctd15. The injected animal caps were cultured till stage 15 and then collected for RT-PCR and microarray assay. Each group had three repeats.

first: Chengdong

last: Wang

first: Martha

last: Rebbert

first: Xiongfong

last: Chen

first: Thomas

last: Wong

first: Alison

last: Heffer

first: Valeria

last: Zarelli

first: Hui

last: Zhao


title: Whole genome expression analysis of Human Induced pluripotent stem cells using Illumina Human HT-12 BeadChip

status: Public on Aug 15 2015

city: Walkersville

first: Behnam

last: Baghbaderani

address: 8830 Biggs Ford Road

institute: Lonza

summary: Whole genome expression analysis was performed on iPSC lines generated during different steps of a cGMP compliant manufacturing process at Lonza.  Hierarchical clustering of all lines and overall correlation co-efficiency (R2 value) between each line exhibited that the gene expression profile of these lines was closey related to each other and also other well chracterized lines previously generated using similar or different reprogramming methodologies.

overall_design: Total RNA was isolated from iPSC lines generated at the end of manufacturing process using the RNeasy Mini kit according to the manufacturer’s instructions (Qiagen, CA) and hybridized to Illumina Human HT-12 BeadChip (Illumina, Inc., CA, performed by Microarray core facility at the Burnham Institute for Medical Research). All the data processing and analysis was performed using the algorithms included with the Illumina BeadStudio software. The background method was used for normalization. The maximum expression value of gene for probe set was used as the expression value of the gene. For the processed data, the dendrogram was represented by global array clustering of genes across all the experimental samples using the complete linkage method and measuring the Euclidian distance. Expression of sample correlations was a measure of Pearson's coefficient, implemented in R System.

first: Laura

last: Menendez

last: Fellner

first: Xianmin

last: Zeng


title: Transcriptional profiling to identify physical-chemical properties detrimental to nanomaterial-induced pulmonary response (part 1)

status: Public on Aug 20 2015

city: Ottawa

first: Andrew

last: Williams

state: ON

address: 50 Colombine Dr

country: Canada

institute: Health Canada

summary: We examined the use of toxicogenomics data to 1) elucidate the underlying mechanisms of pulmonary responses following exposures to titanium dioxide (TiO2) nanoparticles (NPs) of different size and surface charge, and 2) determine if such responses are influenced by embedding particles in complex paint matrix. Adult C57BL/6 mice were exposed via single intratracheal instillation to three doses of free forms of NRCWE-030 (10.5 nm), NRCWE-025 (38 nm), NRCWE-001 (10 nm, neutral charge) NRCWE-002 (10 nm, positive charge) or to sanding dusts of paint consisting of NRCWE-030+NRCWE-025 or NRCWE-025 alone. Controls were exposed to dispersion medium without NPs. TiO2NPs were characterized for size, surface area, and agglomeration status in the exposure medium. Hyperspectral microscopy was performed to detect TiO2NPs in lungs and to determine the in vivo status of matrix-embedded TiO2NPs. Pulmonary gene expression profiles were generated using DNA microarrays on lung tissues collected at 24 h and 28 d post exposure time points. Bioinformatics tools were used to characterize size and surface property-pertinent effects. The data from 360 individual arrays were collapsed into 567 differentially expressed genes (False discovery rate adjusted P ≤ 0.05 and fold change ≥ 1.5 in any one condition). Unsupervised hierarchical clustering of the 567 genes revealed that TiO2NPs clustered mainly based on the post-exposure time points and then by the particle types. A meta analysis using pathway tools showed that the combination of smaller size and positive surface charge contributes to the potency of TiO2NPs. Although embedding in matrix dampens the overall toxicity of TiO2NPs, the smaller size positively influences the toxicity. Paint matrix itself did not induce any response. Finally, the observed differences in response reflected the differences in severity of the response and not the underlying mechanisms.  Thus, transcriptional profiling is an effective tool to determine the important properties responsible for eliciting a response.

overall_design: Female C57BL/6 mice of 5-7 weeks old were obtained from Taconic (Ry, Denmark) and were allowed to acclimatise for 1-3 weeks before the exposure. All mice were given food (Altromin no.1324, Christian Petersen, Denmark) and water ad libitum. Mice were grouped in polypropylene cages with sawdust bedding at controlled temperature 21±1°C, humidity 50 ±10 % in a 12 h-light: dark cycle. The experiments were approved by the Danish “Animal Experiments Inspectorate” and carried out following their guidelines for ethical conduct and care when using animals in research. Animals were exposed to 18, 54, or 162 ug of Indoor-NanoTiO2 and Indoor-R dispersed in 10% bronchoalveolar lavage fluid (BAL), 0.9% NaCl. Each exposure group consisted of minimum of 5 animals. Controls were exposed to vehicle only. The data were compared to their respective controls within the group.


title: Transcriptional profiling to identify physical-chemical properties detrimental to nanomaterial-induced pulmonary response (part 4)

overall_design: Female C57BL/6 mice of 5-7 weeks old were obtained from Taconic (Ry, Denmark) and were allowed to acclimatise for 1-3 weeks before the exposure. All mice were given food (Altromin no.1324, Christian Petersen, Denmark) and water ad libitum. Mice were grouped in polypropylene cages with sawdust bedding at controlled temperature 21±1°C, humidity 50 ±10 % in a 12 h-light: dark cycle. The experiments were approved by the Danish “Animal Experiments Inspectorate” and carried out following their guidelines for ethical conduct and care when using animals in research. Animals were exposed to 54, 162 or 486 ug of NRCWE-032 and NRCWE-033 dispersed in in 10% bronchoalveolar lavage fluid (BAL), 0.9% NaCl. Each exposure group consisted of minimum of 5 animals. Controls were exposed to vehicle only. The data were compared to their respective controls within the group.


title: MVAC treated tumors

status: Public on Aug 18 2015

city: Houston

first: Woonyoung

last: Choi

address: 1515 Holcombe

institute: Md Anderson Cancer center

summary: validation of the survival outcomes from MVAC-Avastin treated tumors

overall_design: 22 NAC-MVAC and 27 adjuvant MVAC treated bladder cancer

first: I-ling

last: Lee

first: Arlene

last: Siefker-Radtke

first: David

last: McConkey


title: RelA/(p)ppGpp regulates the glucose-starvation induced stringent response in the zoonostic Streptococcus suis

status: Public on Aug 08 2015

city: Wuhan

first: Lu

last: Li

email: sakura.tree@163.com, xuzf@mail.hzau.edu.cn, xuzhuofei@sohu.com, kobe2071@tom.com

state: Hubei

address: Shizishan Street 1

institute: Huazhong Agricultural University

summary: Growth curves and (p)ppGpp accumulation assays showed that RelA inactivation could influence S. suis growth and led to incapacity of (p)ppGpp synthesis during glucose starvation. To identify the roles of RelA/(p)ppGpp in global gene regulation in S. suis, we compared the transcriptional profiles of SC-19 [a (p)ppGpp+ strain] and ΔrelA [a (p)ppGpp0 strain during glucose starvation] in both glucose-abundant and -deficient CDM in exponential phase by microarray analysis. A less stringent cut-off limit, 2-fold change, was used. qRT-PCR validation displayed the same trends observed in the microarrays

overall_design: relA mutant strain and its parents strain SC-19 were cultured in both glucose-abundant CDM (CDM containing 1% glucose) and glucose-deficient CDM (CDM containing 2% glucose) respectively. The bacteriain in exponential phase were collected for microarray analysis. Three independent experiments were performed.

first: Tengfei

last: Zhang

first: Rui

last: Zhou


title: Genome-wide analysis of p53 transcriptional programs in B cells upon exposure to genotoxic stress in vivo

first: Marco

last: Morelli

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

overall_design: Refer to individual Series


status: Public on Aug 19 2015

city: León

first: Alma

middle: María

last: Botas

state: León

address: Campus de Vegazana

country: Spain

institute: Área de Microbiología. Facultad de Ciencias Biológicas y Ambientales. Universidad de León

summary: S. coelicolor M145 and S. coelicolor ∆argR were grown in MG medium and samples from 3 biological replicates were taken at 32, 42, 49, 56 and 66 hours.

overall_design: Experiment with two strains and five culture-times: S coelicolor ∆argR vs S. coelicolor M145 at 32, 42, 49, 56 and 66 culture hours. 3 biological replicates.

first: Rosario

last: Pérez-Redondo

first: Antonio

last: Rodríguez-García

first: Paloma

last: Liras


title: Runx1- responsive genes in mdx muscles

status: Public on Aug 17 2015

city: Rehovot

first: kfir

middle: baruch

last: Umansky

state: Rehovot

address: POB 25

country: Israel

institute: Weizmann Institute

summary: RNA-seq was performed  to compare expression pattern of musles taken form two mice strains- mdx and mdx/Runx1f/f, which are double KO carrting a muscle specific ablation of Runx1  using a Myf5-Cre. This comparison revealed the Runx1- responsive gene set in mdx muscles. we could cross this data with prior retrived datd from privous experiments found in this GEO quary, to pinpiont Runx1 target genes in muscle rgeneration

overall_design: RNA  was extracted form  soleus muscles of 2 months old mice, n=3,4  for mdx and mdx/Runx1f/f, respectively . Differentially expressed genes were discovered using the DeSeq2 software

first: K

first: Y

last: Groner

first: E

last: Feldmesser


title: Transcriptional profiling to identify physical-chemical properties detrimental to nanomaterial-induced pulmonary response (part 2)

first: Andrew

overall_design: Female C57BL/6 mice of 5-7 weeks old were obtained from Taconic (Ry, Denmark) and were allowed to acclimatise for 1-3 weeks before the exposure. All mice were given food (Altromin no.1324, Christian Petersen, Denmark) and water ad libitum. Mice were grouped in polypropylene cages with sawdust bedding at controlled temperature 21±1°C, humidity 50 ±10 % in a 12 h-light: dark cycle. The experiments were approved by the Danish “Animal Experiments Inspectorate” and carried out following their guidelines for ethical conduct and care when using animals in research. Animals were exposed to 18, 54, or 162 ug of NRCWE-001 and NRCWE-002 dispersed in 2% serum in water. Each exposure group consisted of minimum of 5 animals. Controls were exposed to vehicle only. The data were compared to their respective controls within the group.


title: Enhanced Expression of FKBP51 in Endometrium of Women Using Long-Acting Progestin-Only Contraceptives: Implications for Functional Progesterone and Glucocorticoid Withdrawal

status: Public on Aug 14 2015

city: Columbus

first: S.

middle: Joseph

last: Huang

state: Ohio

department: Ob/Gyn

institute: The Ohio State University

summary: Use of long-acting progestin-only contraceptives (LAPCs) offers a discrete and highly effective family planning method. Abnormal uterine bleeding (AUB) is the major side effect of, and cause for, discontinuation of LAPCs. The endometria of LAPC-treated women display abnormally enlarged, fragile blood vessels, decreased endometrial blood flow and oxidative stress. To understand the mechanisms underlying AUB, we propose to identify LAPC-modulated unique gene cluster(s) in human endometrial stromal cells (HESCs). Protein and RNA isolated from cultured HESCs treated 7 days with estradiol (E2) or E2+medroxyprogesterone acetate (MPA) or E2+ etonogestrel (ETO) or E2+progesterone (P4) were analyzed by q-PCR and immunoblotting. HSCORES were determined for immunostained-paired endometria of pre-and 3 months post-Depo-Provera (Depo) treated women (n=6) and ovariectomized guinea pigs (GPs; n=12) treated with placebo or E2 or MPA or E2+MPA for 21 days. In HESCs, whole genome analysis identified a 67-gene group regulated by all three progestins, whereas a 235-gene group was regulated by E2+ETO and E2+MPA, but not E2+P4. Ingenuity pathway analysis identified glucocorticoid receptor (GR) activation as an upstream regulator of the 235 LAPCMPA and ETO-specific genes. Among these, microarray results demonstrated significant enhancement of FKBP51, a repressor of PR/GR transcriptional activity, by both LAPCsMPA and ETO. q-PCR and immunoblot analysis confirmed the microarray results. In endometria of post-Depo versus pre-Depo administered women, FKBP51 expression was significantly increased in endometrial stromal and glandular cells. In GPs, E2+MPA or MPA significantly increased FKBP51 immunoreactivity in endometrial stromal and glandular cells versus placebo- and E2-administered groups. LAPC MPA or ETO administration activates GR signaling and increases endometrial FKBP51 expression, which could be one of the mechanisms causing AUB by inhibiting feeds back to inhibit PR- and GR-mediated transcription. The resultant PR- and/or GR-mediated functional withdrawal may contribute to associated endometrial inflammation, aberrant angiogenesis, and bleeding.

overall_design: Total RNA (n=3) obtained from cultured HESCs treated with vehicle only (CON) or ETO or M or P for 6h.

first: Ozlem

last: Guzeloglu-Kayisli

first: Umit

last: Kayisli

first: Murat

last: Basar

first: Nihan

last: Semerci

first: Frederick

last: Schatz

first: Charles

last: Lockwood


title: Genome-wide analysis of p53 transcriptional programs in B cells upon exposure to genotoxic stress in vivo [ChIP-Seq]

first: Marco

summary: The tumor suppressor p53 is a transcription factor that coordinates the cellular response to DNA damage. Here we provide an integrated analysis of p53 genomic occupancy and p53-dependent gene regulation in the splenic B and non-B cell compartments of mice exposed to whole-body ionizing radiation, providing insight into general principles of p53 activity in vivo. In unstressed conditions, p53 bound few genomic targets; induction of p53 by ionizing radiation increased the number of p53 bound sites, leading to highly overlapping profiles in the different cell types. Comparison of these profiles with chromatin features in unstressed B cells revealed that, upon activation, p53 localized at active promoters, distal enhancers, and a smaller set of unmarked distal regions. At promoters, recognition of the canonical p53 motif as well as binding strength were associated with p53-dependent transcriptional activation, but not repression, indicating that the latter was most likely indirect. p53-activated targets constituted the core of a cell type-independent response, superimposed onto a cell type-specific program. Core response genes included most of the known p53-regulated genes, as well as many new ones. Our data represent a unique characterization of the p53-regulated response to ionizing radiation in vivo.

overall_design: Mapping p53 binding sites in the splenic B and non-B cell compartments of mice exposed to whole-body ionizing radiation


title: Transcriptional profile of Escherichia coli K12 strain DH10B harboring A1501 nitrogen fixation island (NFI) under nitrogen fixation conditions

status: Public on Aug 05 2015

city: Beijing

first: yongliang

last: yan

address: zhongguancun south 12th

institute: CAAS

summary: A1501 NFI is a genomic island derived from Pseudomonas stutzeri A1501. To study the molecular interactions of the P. stutzeri nif genes with the E. coli genome during nitrogen fixation, the NIF of A1501 was transferred into E. coli and comparative transcriptomics analyses were performed between nitrogen fixation conditions and nitrogen excess conditions.

sample_organism: Escherichia coli str. K-12 substr. DH10B

overall_design: RNA was extracted from E. coli K-12 DH10B cells with NFI cultured 20 h in NFDM medium under nitrogen fixation conditions (30℃, anaerobic, no ammonium) or nitrogen excess conditions (30℃, anaerobic, 20 mmol ammonium).

first: Min

last: Lin

first: Yunlei

last: Han

first: Yongliang

last: Yan

first: Yunhua

last: Zhan

first: Liang

last: Li


title: Molecular hydrogen stimulates the gene expression of a translational coactivator PGC-1alpha to enhance fatty acid metabolism

status: Public on Aug 06 2015

city: Kawasaki-city

first: Shigeo

last: Ohta

state: Kanagawa

address: 1-394, Kosugi-machi, Nakahara-ku

department: Department of Biochemistry and Cell Biology

institute: Institute of Development and Aging Sciences, Graduate School of Medicine, Nippon Medical School

summary: We previously reported that molecular hydrogen (H2) acts as a novel antioxidant to exhibits multiple-functions.  Moreover, long-term drinking of H2-water (water infused with H2) enhanced energy expenditure to improve obesity and diabetes in db/db mice, accompanied with the increased gene expression of an energy metabolism stimulatory hepatic hormone, fibroblast growth factor 21 (FGF21); however, the molecular mechanism is unknown particularly on whether this gene regulation is a primary cause or the secondary consequence. Pathway analyses based on comprehensive gene expression revealed the increased expression in various genes involved in fatty acid and steroid metabolisms.  As a transcription pathway, the PPARa signaling pathway was identified to up-regulate the genes by 14 day-ingestion of H2.  As an early event, the gene expression of PGC-1a was transiently increased at day 3, followed by increased expression of FGF21. In wild-type mice that fed with fatty-diet, H2-water improved the level of plasma triglyceride and extended their life span.

overall_design: H2 was ingested by ad libitum drinking H2-water for 14 days or by oral administration of an H2-producing material MgH2 for 1, 3 or 7 days. Comprehensive gene expression profile in liver of db/db mice was analyzed by DNA microarray.

first: Naomi

last: Kamimura

first: Harumi

last: Ichimiya


title: Transcriptomic analysis of a moderately growing subisolate Botryococcus braunii 779 (Chlorophyta) in response to nitrogen deprivation

status: Public on Aug 03 2015

city: Zhoushan

first: Jianhua

last: Liu

address: 10 Tiyu Road, Room 502

department: Ocean Research Centre of Zhoushan

summary: We report the transcriptomic response of a moderately growing subisolate from the culture of Botryococcus sp. CCALA-779 upon nitrogen deprivation (ND).

overall_design:
Examination of transcriptomes upon nitrogen deprivation (ND).

B.braunii_non_redundant_transcriptome_assembly_61220.fasta: non-redundant assembly (with 61220 in number) of B.braunii 779 transcriptome in this study
B.braunii_annotated_12292.fasta: investigated ESTs (with 12292 in number, which perfectly matches with our processed RNA expression profiling) in this study


title: Sox10 regulates stem/progenitor and mesenchymal cell states in mammary epithelial cells

status: Public on Aug 04 2015

city: La Jolla

first: Christopher

last: Dravis

state: CA

address: 10010 North Torrey Pines Road

department: GEL-W

institute: Salk Institute for Biological Studies


title: Transcriptional profiling to identify physical-chemical properties detrimental to nanomaterial-induced pulmonary response

first: Andrew

last: Williams


title: a phase 2 trial of DDMVAC and bevacizumab in urothelial cancer

first: Woonyoung

last: Choi

state: TX

summary: A prognostic gene expression signature in chemotherapy-naïve bladder cancer is predictive of clinical outcomes from neoadjuvant chemotherapy

overall_design: 61 FFPE bladder tumors were used to validate chemo-resistant subtype in bladder cancer

first: I-ling

last: Lee

first: Arlene

last: Siefker-Radtke

first: David

last: McConkey


title: Transcriptional profiling to identify physical-chemical properties detrimental to nanomaterial-induced pulmonary response (part 3)

overall_design: Female C57BL/6 mice of 5-7 weeks old were obtained from Taconic (Ry, Denmark) and were allowed to acclimatise for 1-3 weeks before the exposure. All mice were given food (Altromin no.1324, Christian Petersen, Denmark) and water ad libitum. Mice were grouped in polypropylene cages with sawdust bedding at controlled temperature 21±1°C, humidity 50 ±10 % in a 12 h-light: dark cycle. The experiments were approved by the Danish “Animal Experiments Inspectorate” and carried out following their guidelines for ethical conduct and care when using animals in research. Animals were exposed to 18, 54, or 162 ug of NRCWE-025 and NRCWE-030 dispersed in 2% serum in water. Each exposure group consisted of minimum of 5 animals. Controls were exposed to vehicle only. The data were compared to their respective controls within the group.


title: Expression profiling of fetal mammary cells that express ectopic levels of Sox10

summary: We use RNA-sequencing to generate gene expression profiles of fetal mammary cells that have been induced to overexpress Sox10.  These data highlight multiple  important molecular mechanisms that are altered in response to this perturbation, and offer a resource to probe the basis of the stem/progenitor and EMT-like functions that are mediated by Sox10 in mammary cells.

first: Benjamin

last: Spike


title: Mouse ESC-derived NSPCs NFIA OE (miRNA)

status: Public on Aug 01 2015

city: Shinjuku-ku

first: Jun

last: Tsuyama

address: 35 Shinanomachi

institute: Keio University School of Medicine

summary:
Since the NFI transcription factors have been shown to be key regulators of gliogenesis, we utilized this pathway to identify miRNAs involved in the regulation of the neurogenesis-to-gliogenesis switch by neural stem/progenitor cells (NSPCs).
We focused on miRNAs with expression levels that were differentially regulated downstream of NFIA, and established a mouse embryonic stem cell (ESC) line that expresses NFIA in a doxycycline (Dox)-dependent manner.

overall_design: NFIA-overexpressing (OE) and control NSPCs (neurospheres) derived from ESCs were purified from their mixed cultures (primary neursphsres (PNs) or secondary neurospheres (SNs) ) by fluorescence activated cell sorting and subjected to miRNAarray analysis.

first: Takuya

last: Shimazaki

first: Hideyuki

last: Okano


title: Mouse ESC-derived NSPCs NFIA OE (GE)

overall_design: NFIA-overexpressing (OE) and control NSPCs (neurospheres) derived from ESCs were purified from their mixed cultures (primary neursphsres (PNs) or secondary neurospheres (SNs) ) by fluorescence activated cell sorting and subjected to the gene expression microrray analysis.


title: Expression analysis of miR-302 knockout and wild-type embryos during neurulation

city: San Francisco

first: Ron

last: Parchem

address: 35 Medical Center Way

institute: UCSF

summary: Wild-type or miR-302 knockout tissue was isolated from embryos during neurulation in replicate

overall_design: Performed in biological triplicate except for E7.5 WT which was in duplicate and E9.5 timepoints which were in quadruplicate. Biological replicate samples represent independent embryos. Total RNA collected with Trizol. All processing conducted at the UCLA Neuroscience Genomics Core. MouseRef-8 v2.0 Expression BeadChips.

first: Parchem

last: Ron

first: Blelloch

last: Robert


title: Comparative transcriptome analysis in response to heat stress in Arabidopsis thaliana and Arabidopsis lyrata

city: Olomouc - Holice

first: Ales

last: Pecinka

address: Slechtitelu 31

department: Centre of Plant Structural and Functional Genomics

country: Czech Republic

institute: Institute of Experimental Botany

summary: Arabidopsis thaliana and Arabidopsis lyrata are two closely related Brassicaceae species, which are used as models for plant comparative biology. They differ by lifestyle, predominant mating strategy, ecological niches and genome organization. To identify heat stress induced genes, we performed RNA-sequencing of rosette leaves from mock-treated, heat-stressed and heat-stressed-recoved plants of both species.

sample_organism:
Arabidopsis thaliana
Arabidopsis lyrata subsp. lyrata

overall_design: Analysis of genetic element transcriptional changes in response to 6 hours of 37°C heat stress and 48 hours of recovery in Arabidopsis thaliana Col-0 and Arabidopsis lyrata MN47.

first: Björn

last: Pietzenuk

first: Vimal

last: Rawat

first: Korbininan

last: Schneeberger


title: Age-associated genomic methylation in the TOPS Family Study of Epigenetics Cohort

city: Milwaukee

first: Yi

last: Zhang

state: WI

address: 8701 W Watertown Plank Rd

department: Department of Medicine

institute: Medical College of Wisconsin

summary: Genome-wide age-associated methylation signatures of 485,000 CpG sites were profiled in 192 individuals, age 6-85, of Northern European ancestry were profiled using the Illumina HM450 array.

overall_design: Bisulphite converted DNA from the 192 samples were hybridized to the Illumina Infinium 450k Human Methylation Beadchip

first: Omar

last: Ali

first: Diana

middle: E

last: Cerjak

first: Jack

middle: W

last: Kent Jr

first: Roland

last: James

first: Melanie

last: Carless

first: John

last: Blangero


title: MicroRNA-153 regulates the acquisition of gliogenic competence by neural stem cells

first: Jun

last: Tsuyama

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


title: Expression data from primary multiple myeloma plasma cells from patients treated by  Total Therapy 2, 3 and Other protocols at baseline and relapse.

status: Public on Aug 13 2015

city: Little Rock

first: Joshua

last: Epstein

institute: University of Arkansas for Medical Sciances

summary: Global gene expression profile of primary multiple myeloma plasma cells from patients treated in Myeloma Institute for Research and Therapy was done using Affymetrix microarrays.

overall_design: MMPC were isolated from patients following Total Therapy 2, 3 and Other treatments at baseline and/or after relapse and GEP was done.

last: Shaughnessy


title: miR-153 overexpressing NSPCs derived from mouse ES cells

summary:
Mammalian neural stem/progenitor cells (NSPCs) sequentially generate neurons and glia during central nervous system (CNS) development. Several transcription factors and microRNAs (miRNAs) are involved in the temporal regulation of NSPC differentiation.
miRNA-153 (miR-153) as a modulator of NSPC specification. Overexpression (OE) of miR-153 delayed the onset of astrogliogenesis and maintained NSPCs in an undifferentiated state in vitro.

overall_design: miR-153-OE and control NSPCs (tertiary neurospheres (TNs) derived from mouse ES Cells via embryoid body formation) subjected to the gene expression microarray analysis.

first: Takuya

last: Shimazaki

first: Hideyuki

last: Okano


title: Complete hematologic response of early-T-cell progenitor acute lymphoblastic leukemia to the gamma-secretase inhibitor BMS-906024: genetic and epigenetic findings in an outlier case

status: Public on Jul 29 2015

city: Boston

first: Eric

last: Severson

address: 75 Francis Street

institute: Brigham and Women's Hospital

summary: Notch pathway antagonists such as gamma-secretase inhibitors (GSI) are being tested in diverse cancers, but exceptional responses have yet to be reported. We describe the case of a patient with relapsed/refractory early-T-cell progenitor acute lymphoblastic leukemia (ETP-ALL) who achieved a complete hematologic response following treatment with the GSI BMS-906024. Whole exome sequencing of leukemic blasts revealed heterozygous gain-of-function driver mutations in NOTCH1, CSF3R, and PTPN11, and a homozygous/hemizygous loss-of-function mutation in DNMT3A. The three gain-of-function mutations were absent from remission marrow cells, but the DNMT3A mutation persisted in heterozygous form in remission marrow, consistent with an origin for the patient’s ETP-ALL from clonal hematopoiesis. Ex vivo culture of ETP-ALL blasts confirmed high levels of activated NOTCH1 that were repressed by GSI treatment, and RNA-Seq documented that GSI downregulated multiple known Notch target genes. Surprisingly, one potential target gene that was unaffected by GSI was MYC, a key Notch target in GSI-sensitive T-ALL of cortical T cell type. H3K27ac superenhancer landscapes near MYC showed a pattern previously reported in acute myeloid leukemia (AML) that is sensitive to BRD4 inhibitors, and in line with this ETP-ALL blasts downregulated MYC in response to the BRD4 inhibitor JQ1. To our knowledge, this is the first example of complete response of a Notch-mutated ETP-ALL to a Notch antagonist and is also the first description of chromatin landscapes associated with ETP-ALL. Our experience suggests that additional attempts to target Notch in Notch-mutated ETP-ALL are merited.

overall_design: RNAseq and H3K27Ac ChIP seq of primary leukemic blasts treated in vitro with vehicle control or gamma-secretase inhibitor BMS-096024

first: Birgit

last: Knoechel

first: Ami

last: Bhatt

first: Li

last: Pan

first: Chandra

middle: S

last: Pedamallu

first: Alejandro

last: Gutierrez

first: David

middle: M

last: Dorfman

first: Frank

last: Kuo

first: Michael

last: Kluk

first: Andrew

last: Kung

first: Patrick

last: Zweidler-McKay

first: Matthew

last: Meyerson

first: Stephen

last: Blacklow

first: Daniel

last: DeAngelo

first: Jon

last: Aster


title: Seed transcriptome of xrn4-5 and vcs-8 mutants

city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

country: France

institute: IPS2_Institute of Plant Sciences Paris-Saclay

summary: au14-08_xrn_vcs - seed transcriptome of xrn4-5 and vcs-8 mutants. - Role of RNA degradation in seed dormancy. - Study of the seeds regulation by the RNA-decay. Comparison between Col0 total RNA and mutants xrn4-5 and vcs-8 RNA, affected in the dormancy and in RNA metabolism.

overall_design: 6 dye-swap - gene knock out

first: Juliette

last: Leymarie

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: Expression profiling of fetal mammary cells

first: Christopher

last: Dravis

summary: We use RNA-sequencing to generate gene expression profiles of fetal mammary cells with unique sorting strategies.  These analyses reveal that sorting fetal mammary cells with Sox10 and EpCAM sorting markers provides a stroma-free fMaSC-enriched cell population.  The gene expression profiling of these cells offers a resources to probe the molecular mechanisms that specify this unique cell state.

overall_design: Examination of 2 different sorting strategies for fetal mammary cells

first: Benjamin

last: Spike


title: Transcription factor Runx1 cooperates with MyoD and c-Jun to regulate the balance of myoblast proliferation/differentiation [ATAC-Seq]

status: Public on Jul 23 2015

first: kfir

last: Umansky

summary: Runx1 is expressed in regenrating muscle, specifically in the muscle adult stem cells- the satellite cells. Its exact role and target genes were yet to be identified. We report here the genome wide open chromatin paatern, as established by ATAC-seq

overall_design: Examination ofgenome wide pattern  naked and therefore trhansposase accecible genomic DNA in primary myoblasts (PM)

first: Kfir

middle: B

first: Ester

last: Felmesser

first: Yoram

last: Groner


title: Transcription factor Runx1 cooperates with MyoD and c-Jun to regulate the balance of myoblast proliferation/differentiation [ChIP-Seq Histone]

summary: Runx1 is expressed in regenrating muscle, specifically in the muscle adult stem cells- the satellite cells. Its exact role and target genes were yet to be identified. We report here the genome wide histone modification using an active enhancer pattern of H3K4 monomethylation (H3K4me1) and H3K27 acetylation (H3K27ac).

overall_design: Examination of genome wide chromatin binding of several TFs in primary myoblasts (PM)


title: Transcription factor Runx1 cooperates with MyoD and c-Jun to regulate the balance of myoblast proliferation/differentiation [Expression Study]

summary:
Runx1 is expressed in regenrating muscle, specifically in the muscle adult stem cells- the satellite cells. Its exact role and target genes were yet to be identified
This experiment aimed at determining the Runx1 regulated genes in muscle regeneration, specifically in Satellite cells

overall_design: To elucidate the Runx1-mediated transcriptional program involved in early stages of muscle regeneration, we compared gene expression profiles in WT and Runx1f/f primary myobalsts (PM). PM were purified from both genotypes , Total RNA was isolated, reverse-transcribed, fragmented, labeled and hybridized to Affymetrix MoGene 1.0 ST  DNA array.

first: KfirB

first: Yael

last: Gruenbaum-Choen

last: Feldmesser

first: Shirley

last: Horn-Saban

first: Dalia

last: Goldenberg


title: Cultured human adipose tissue pericytes and mesenchymal stromal cells display a very similar gene expression profile

status: Public on Jul 22 2015

city: Canoas

first: Lindolfo

last: da Silva Meirelles

state: RS

address: Av. Farroupilha 8001

department: PPGBioSaúde

country: Brazil

institute: Lutheran University of Brazil

summary: Mesenchymal stromal cells (MSCs) are cultured cells that can give rise to mature mesenchymal cells under appropriate conditions, and secrete a number of biologically relevant molecules that may play an important role in regenerative medicine. Evidence indicates that pericytes (PCs) correspond to mesenchymal stem cells in vivo and can give rise to MSCs when cultured, but a comparison between the gene expression profiles of cultured PCs (cPCs) and MSCs is lacking. We have devised a novel methodology to isolate PCs from human adipose tissue, and compared cPCs to MSCs obtained through traditional methods. Freshly isolated PCs expressed CD34, CD140b, and CD271 on their surface, but not CD146. Both MSCs and cPCs were able to differentiate along mesenchymal pathways in vitro, displayed an essentially identical surface immunophenotype, and exhibited the ability to suppress CD3+ lymphocyte proliferation in vitro. Microarray expression data of cPCs and MSCs formed a single cluster among other cell types. Further analyses showed that the gene expression profiles of cPCs and MSCs are extremely similar, although MSCs differentially expressed endothelial cell-specific transcripts. These results confirm, using the power of transcriptomic analysis, that PCs give rise to MSCs, and suggest that low levels of endothelial cells may persist in MSC cultures established using traditional protocols.

overall_design: Highly purified human adipose-tissue pericytes (AT3G5Cs) were isolated based on the expression of the antigen detected by the 3G5 antibody, lack of expression of CD31, and ability to adhere to tissue-cultured plastic whithin a short time. The in vitro properties of cultured AT3G5Cs were compared to those of adipose tissue mesenchymal stromal cells (ATMSCs) obtained through traditional methods. Gene expression profiles of cultured AT3G5Cs (n = 3 different biological samples) and ATMSCs (n = 3 different biological samples) were compared to each other by statistical analyses. Gene expression profiles of cultured AT3G5Cs and ATMSCs were compared to those of other cell types by clustering analyses.

first: Tathiane

last: Malta

first: Virgínia

last: Wagatsuma

first: Patrícia

last: Palma

first: Amélia

middle: G

last: Araújo

first: Kelen

last: Malmegrim

first: Fábio

last: Oliveira

first: Rodrigo

last: Panepucci

first: Wilson

last: Silva Jr.

first: Simone

middle: K

last: Haddad

first: Dimas

last: Covas


title: Transcription factor Runx1 cooperates with MyoD and c-Jun to regulate the balance of myoblast proliferation/differentiation [ChIP-seq]

first: kfir

last: Umansky

summary: Runx1 is expressed in regenerating muscle, specifically in the muscle adult stem cells- the satellite cells. Its exact role and target genes were yet to be identified. We report here Runx1 and potential TF counterparts bind important muscle differentiation related genes

overall_design: Examination of genome-wide chromatin binding of several TFs in primary myoblasts (PM)

first: Kfir

first: Ester

last: Felmesser


title: Expression data of LoVo cells treated by 10μM asymmetric dimethylarginine (ADMA) for 96h in serum starvation medium

status: Public on Jul 16 2015

city: Shanghai

first: houkai

last: li

state: Shanghai

address: 1200 Cailun Road, Building 1, Room 1531, Pudong New District

institute: Shanghai University of Traditional Chinese Medicine

summary: ADMA is an endogenous metabolite, which is elevated in cancer patients. Previously, we observed that ADMA treatment attenuated serum starvation-induced apoptosis in LoVo cells. However, the biological functions of ADMA in tumor cells are largely unknown. In current study, we used microarray and untargeted metabolic profiling to investigate the global impacts of ADMA on LoVo cells.

overall_design: Human derived LoVo cells were cultured in normal, serum free and serum free medium plus ADMA (10μM) for 96h, then cells were harvested for RNA extraction and hybridization on Affymetrix microarrays.The samples were grouped as CON, SF96,A96, respectively.

first: Houkai

last: Li


title: MicroRNA profiling in Atlantic killifish (Fundulus heteroclitus)

status: Public on Jul 20 2015

city: Woods Hole

first: Neelakanteswar

last: Aluru

address: 45 Water Street

department: Biology

institute: Woods Hole Oceanographic Institution

summary: The Atlantic killifish (Fundulus heteroclitus) is an ideal model species to study physiological and toxicological adaptations to stressors. Killifish inhabiting the PCB-contaminated Superfund site in New Bedford Harbor, MA (NBH) have evolved resistance to toxicity and activation of the aryl hydrocarbon receptor (AHR) signaling pathway after exposure to PCBs and other AHR agonists. Until recently, a lack of genomic information has limited efforts to understand the molecular mechanisms underlying environmental adaptation to stressors. The advent of high throughput sequencing has facilitated an unbiased assessment of coding as well as non-coding RNAs in any species of interest. Among non-coding RNAs, microRNAs (miRNAs) are important regulators of gene expression and play crucial roles in development and physiology. The objective of this study is to catalog the miRNAs in killifish and determine their expression patterns in the embryos from contaminated (NBH) and pristine (Scorton Creek, MA (SC)) sites. Embryos from NBH and SC were collected daily from 1 to 15 days post-fertilization and RNA from pooled samples from each site was sequenced using SOLiD sequencing. We obtained 7.5 and 11 million raw reads from pooled SC and NBH samples, respectively. Analysis of the sequencing data identified 216 conserved mature miRNA sequences that are expressed during development. Using the draft killifish genome, we retrieved the miRNA precursor sequences. Based on the capacity of these putative precursor sequences to form the characteristic hairpin loop (assessed using RNAfold), we identified 197 conserved miRNA sequences in the genome.

overall_design: MicroRNA expression profiles from two populations of Atlantic killfish were conducted.

first: Lily

last: Helfrich

first: Sibel

middle: I

last: Karchner

first: Mark

last: Hahn