title: Identification of symmetric methylation of histone H4 arginine 3 on KSHV genome (H4R3me2s ChIP-Seq)

city: Reno

first: Subhash

last: Verma

state: NV

address: 1664 N Virginia Street, MS 320

institute: University of Nevada, Reno

summary: The objective of this study was to identify the symmetric methylation sites on KSHV genome during latency and lytic reactivation

overall_design: KSHV infected, TRExBCBL1-RTA cells were induced with doxycycline for 12h to trigger the lytic reactivation, cells were crosslinked and subjected for chromatin isolation and sonication. ChIP assay was performed using anti-H4R3sym antibody, Control IgG antibody, or Histone H4 antibody.


title: ZEB1-regulated inflammatory phenotype in breast cancer cells

status: Public on Jun 16 2017

city: Tokyo

first: Daizo

last: Koinuma

address: Hongo 7-3-1, Bunkyo-ku

department: Pathology

country: Japan

institute: University of Tokyo

type: Genome binding/occupancy profiling by high throughput sequencing

type: Expression profiling by high throughput sequencing

summary:
This SuperSeries is composed of the SubSeries listed below.
Zinc finger E-box binding protein 1 (ZEB1) and ZEB2 induce epithelial-mesenchymal transition (EMT) and cancer progression. However, little is known about global picture of transcriptional regulation by ZEB1 and ZEB2. Here we identified an inflammatory phenotype regulated by ZEB1 using chromatin immunoprecipitation-sequencing (ChIP-seq) and RNA-sequencing (RNA-seq) in basal type breast cancer cells, followed by gene set enrichment analysis (GSEA) of ZEB1-bound genes.

overall_design: Refer to individual Series


title: Loss-of-function mutations TDRD7 lead to a rare novel syndrome combining congenital cataract and non-obstructive azoospermia in humans

status: Public on Jun 15 2017

city: changsha

first: xiong

last: bo

address: xiangya road

country: China

institute: xiangya

summary: Purpose: Comorbid familial non-obstructive azoospermia (NOA) and congenital cataract (CC) has not been reported previously, and no single human gene has been associated with both diseases in humans. Our purpose is to uncover novel human mutations and genes causing familial NOA and CC.  Methods: We performed whole-exome sequencing for two brothers with both NOA and CC from a consanguineous family.The proband was also carried out SNP array analysis. Mutation screening of TDRD7 was performed in another similar consanguineous family and 176 patients with azoospermia or CC alone and 520 healthy controls. Histological analysis was performed for the biopsied testicle sample in one patient, and knockout mice were constructed to verify the phenotype of the mutation in TDRD7.   Results: Two novel loss-of-function mutations (c.324_325insA (T110Nfs*30) and (c.688-689insA (p.Y230X), respectively) of TDRD7 were found in the affected patients from the two unrelated consanguineous families. Histological analysis demonstrated a lack of mature sperm in the male patient’s seminiferous tubules. The mutations were not detected in patients with CC or NOA alone. Mice with Tdrd7 gene disrupted at a similar position precisely replicated the human syndrome.   Conclusions: We identified TDRD7 causing CC as a new pathogenic gene for male azoospermia in human, with an autosomal recessive mode of inheritance.

overall_design: Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from peripheral blood samples.

first: Yue-Qiu

last: Tan

first: Chaofeng

last: Tu

first: Lanlan

last: Meng

first: Shiming

last: Yuan

first: Calvin

last: Sjaarda

first: Aixiang

last: Luo

first: Juan

last: Du

first: Wen

last: Li

first: Fei

last: Gong

first: Changgao

last: Zhong

first: Han-Xiang

last: Deng

first: Guangxiu

last: Lu

first: Ping

last: Liang

first: Ge

last: Lin


title: CLIP-seq analysis of NC-RNA interactions in wild-type and eccentric particles

city: Saint Louis

first: Sebla

middle: Bulent

last: Kutluay

state: Missouri

address: Washington University School of Medicine

country: USA

summary: Nucleocapsid (NC) CLIP-seq experiments were conducted on wild-type and eccentric HIV-1 virions generated in the presence of allosteric integrase inhibitor, BI-B2.

overall_design: NC CLIP-seq experiments were conducted by immunoprecipitation of NC-RNA complexes from fully formed mature and eccentric virus particles. Libraries of RNA molecules bound by NC were generated and sequenced by Illumina Hi-Seq2500 platform.

middle: B


title: The biological age linked with oxidative estress modifies breast cancer aggressiveness

status: Public on Jun 14 2017

city: Salamanca

first: Jesús

last: Pérez Losada

address: Campus Miguel de Unamuno

department: Centro de inv. del Cáncer (CIC).

country: Spain

institute: Inst. de Inv. Biomédica de Salamanca (IBSAL). H. U. de Salamanca. Inst. de Biología Molecular y Celular del Cáncer (IBMCC).

summary: The incidence of breast cancer increases with age until menopause, and breast cancer is more aggressive in younger women. The existence of epidemiological links between breast cancer and aging indicates that both processes possibly share some common mechanisms of development. Oxidative stress is associated with both cancer susceptibility and aging. Here we observed that ERBB2-positive breast cancer, developed from genetically different ERBB2-positive transgenic mice generated by a backcross, is more aggressive in younger than in older mice, similar to what occurs in humans. In this cohort, we estimated the oxidative biological age using a mathematical model that integrated several subphenotypes directly or indirectly related to oxidative stress. This model included the serum levels of HDL-cholesterol and magnesium that were determined at a disease-free stage, and total AKT1 and glutathione concentrations in the liver at the time of necropsy. Later we defined the grade of aging due to oxidative stress as the increment of aging, which was the difference between the predicted biological age and the chronological age. This comparison permitted the identification of the biologically younger mice with less oxidative stress and older mice with more oxidative stress than would be expected according to their chronological age. Interestingly, biologically older mice developed more aggressive breast cancer than the biologically younger mice. We identified genomic regions on chromosomes 2 and 15 that were linked to the grade of oxidative aging. The levels of expression of Zbp1 located on chromosome 2, a gene related to necroptosis and inflammation, positively correlated with the grade of oxidative aging and tumour aggressiveness. This study shows part of the complex interactions between breast cancer and aging.

overall_design: We have studied differential gene expression from livers in mice with different susceptibility with breast cancer. We evaluated 50 livers from mice with extreme values of grade of aging determined by a multivariate model.

first: María

middle: d

last: Sáez-Freire

first: Adrián

last: Blanco-Gómez

first: Andrés

last: Castellanos-Martín

first: Lars

last: Kaderali

last: Pérez-Losada


title: Expression data from wild type (No-0) and fbs1-1 insertion line whole Arabidopsis seedlings in cold

status: Public on Jun 13 2017

city: Tacoma

first: Bryan

last: Thines

state: Washington

address: 1500 North Warner Street

department: Biology

institute: University of Puget Sound

summary:
The ubiquitin 26S proteasome system (UPS) selectively degrades cellular proteins, which results in physiological changes to eukaryotic cells.  F-box proteins are substrate adaptors acting within the UPS and are responsible for the diversity of potential protein targets.  Plant genomes are enriched in F-box genes, but the vast majority of these have unknown roles.  This work investigated the Arabidopsis F-box gene F-BOX STRESS INDUCED 1 (FBS1) by identifying differentially expressed genes between wild type (No-0) and an fbs1 insertion line.
We used microarrays to identify candidate genes that are dependent upon the F-BOX STRESS INDUCED1 (FBS1) gene for normal expression

overall_design: Three independent sets of Arabidopsis wild type (No-0) and fbs1 knockout seedlings were grown in normal conditions for five days and then transferred to cold for seven additional days.  RNA was extracted from seedlings, processed according to standard Affymetrix protocols, and hybridized to Affymetrix ATH1 arrays.


title: Expression profile of (inducible) homozygous Apc loss in the mouse intestinal epithelium

city: Amsterdam

first: Jarom

last: Heijmans

address: Meibergdreef 69-71

department: Gastroenterology & Hepatology

country: Netherlands

institute: Academic Medical Center

summary: To asses the effect of Apc loss on the intestinal epithelium we induced homozygous VillinCreERT2 Apc flox/flox mice with tamoxifen on 3 consecutive days (day 0, 1 and 2), and harvested small intestinal epithelium on day 3.

overall_design: For CreERT2 mediated recombination, mice were given 5 injections with 50mg/kg tamoxifen (Sigma-Aldrich, St Louis, MO 10mg/ml in corn oil) intraperitoneally, during 3 consecutive days, and were sacrificed 24 hours thereafter. Control mice only carried the CreERT2 allele (not the Apc fl/fl alleles) and were treated under the same regimen.

first: Jooske

middle: F

last: van Lidth de Jeude

first: Gijs

middle: R

last: van den Brink


title: ERa DNA Binding Profiles of IGF1 and ICI182,780 treated mouse uterus from manuscript: Role of ERα in Mediating Female Uterine Transcriptional Responses to IGF1

city: Research Triangle Park

first: Sylvia

middle: C

last: Hewitt

state: NC

address: 111 Alexander Dr

department: RDBL

institute: NIEHS

summary: Estrogen (E2) signaling through its nuclear receptor, estrogen receptor α (ERα) increases insulin-like growth factor 1 (IGF1) in the rodent uterus, which then initiates further signals via the IGF1 receptor (IGF1R). Directly administering IGF1 results in similar biological and transcriptional uterine responses. Our studies using global ERα-null mice demonstrated a loss of uterine biological responses of the uterus to E2 or IGF1 treatment, while maintaining transcriptional responses to IGF1. To address this discrepancy in the need for uterine ERα in mediating the IGF1 transcriptional vs. growth responses, we assessed the IGF1 transcriptional responses in PgrCre+Esr1f/f (called ERαUtcKO) mice, which selectively lack ERα in progesterone receptor (PGR) expressing cells, including all uterine cells, while maintaining ERα expression in other tissues and cells that do not express Pgr. Additionally, we profiled IGF1-induced ERα binding sites in uterine chromatin using ChIP-seq. Herein, we explore the transcriptional and molecular signaling that underlies our findings to refine our understanding of uterine IGF1 signaling and identify ERα-mediated and ERα-independent uterine transcriptional responses. Defining these mechanisms in vivo in whole tissue and animal contexts provides details of nuclear receptor mediated mechanisms that impact biological systems and have potential applicability to reproductive processes of humans, livestock and wildlife.

overall_design: ERa Chip seq of IGF1 or ICI182,780 treated mouse usterine tissue, pools of 5 uteri/sample

first: Yukitomo

last: Arao

first: Katherine

middle: J

last: Hamilton

first: Sara

middle: A

last: Grimm

first: Kenneth

middle: S

last: Korach


title: Hippocampal transcriptomic responses to enzyme‐mediated cellular dissociation

city: Davis

first: Rayna

middle: Michelle

last: Harris

state: CA

address: 1 Shields Ave

institute: University of California Davis

summary: Single-neuron gene expression studies may be especially important for understanding nervous system structure and function because of the neuron-specific functionality and plasticity that defines functional neural circuits. Cellular dissociation is a prerequisite technical manipulation for single-cell and single cell-population studies, but the extent to which the cellular dissociation process affects neural gene expression has not been determined. This information is necessary for interpreting the results of experimental manipulations that affect neural function such as learning and memory. The goal of this research was to determine the impact of chemical cell dissociation on brain transcriptomes. We compared gene expression of microdissected samples from the dentate gyrus (DG), CA3, and CA1 subfields of the mouse hippocampus either prepared by a standard tissue homogenization protocol or subjected to a chemical cellular dissociation procedure. We report that compared to homogenization, chemical cellular dissociation alters about 350 genes or 2% of the hippocampal transcriptome. While only a few genes canonically implicated in long-term potentiation (LTP) and fear memory change expression levels in response to the dissociation procedure, these data indicate that sample preparation can affect gene expression profiles, which might confound interpretation of results depending on the research question. This study is important for the investigation of any complex tissues as research effort moves from subfield level analysis to single cell analysis of gene expression.

overall_design: We compared gene expression of hippocampal tissue samples (CA1, CA3, DG) that were prepared by an enzymatic dissociation or homogenization protocol.

middle: M

first: Hsin-Yi

last: Kao

first: Juan Marcos

last: Alarcon

first: Hans

last: Hofmann

first: Andre

last: Fenton


title: Expression data of growing and senescent human fibroblasts (BJ cells) after p21 knockdown

city: Rehovot

first: Valery

last: Krizhanovsky

address: Herzel 234

department: Molecular Cell Biology

country: Israel

institute: Weizmann Institute of Science

summary:
Cellular senescence is a permanent state of cell cycle arrest that protects the organism from tumorigenesis and regulates tissue integrity upon damage and during tissue remodeling. However, accumulation of senescent cells in tissues during aging contributes to age-related pathologies.
A deeper understanding of the mechanisms regulating the viability of senescent cells is therefore required. Here we show that the CDK inhibitor p21 (CDKN1A) maintains the viability of DNA damage-induced senescent cells.

overall_design:
To identify the molecular mechanism controlling senescence cell viability, we studied the expression patterns of damage induced senescent (DIS) and control cells with and without p21 knockdown.
Growing and DIS BJ cells were transfected with siRNAs against p21 or control siRNAs. After 3 days, total RNA was extracted and gene expression was determined using Affymetrix microarrays.

first: Reut

last: Yosef


title: Microarray for whole mouse genome (Exon Array) for FFSS

city: Kansas City

first: Tarak

last: Srivastava

state: MO

address: 2401 Gillham Road

department: Pediatric Nephrology

institute: Children's Mercy Hospital

summary:
To study the gene expression changes following application of Fluid Flow Shear Stress (FFSS) stimulus at end, post-2hr and post-24hr on mouse podocytes.
We and others have started rethinking the concept of hyperfiltration as relative to changes in local biomechanical forces within the glomerulus. We believe that investigating the interplay of biomechanical forces on podocytes within the glomerulus may provide a better understanding of hyperfiltration-mediated kidney injury. The flow of glomerular ultrafiltrate creates shear stress on the surface of the podocyte. FFSS is largely exerted over the exposed outer aspect of major processes and the soma of podocytes. Our previous work suggests that COX2-PGE2-EP2 axis plays an important role in hyperfiltration-mediated injury, and targeting the EP2 receptor may have therapeutic significance. Thus to date we have identified COX-2-PGE2-EP2 axis in ‘mechanoperception’.  The next logical step in this pursuit will be to address ‘mechanotransduction’, i.e. how podocyte converts the mechanical stimulus into biochemical signals that elicit specific cellular responses. To address this we took the approach of big data analysis using whole exon array analysis following application of FFSS to podocytes, and then selecting and validating pathways identified by bioinformatics tools that held biological relevance in FFSS in other epithelial cells and in EP2-mediated signaling.

overall_design: 12 samples were analyzed. The samples were performed in triplicated for Control sample, for end of FFSS (end), at 2 hours following completion of FFSS (post-2hr) and 24 hours following completion of FFSS (post-24hr)


title: Direct and tissue-specific assessment of the damaging potential of regulatory SNPs

city: oxford

first: Jim

last: Hughes

address: Weatherall Institute Of Molecular Me

department: MHU

country: United Kingdom

institute: University of Oxford

summary: In the era of GWAS and personalized medicine systematically deciphering the impact of non-coding sequence variation on the regulatory genome is a critical bottleneck. Here we present Sasquatch a novel computational approach to estimate and visualize the effects of noncoding-variants on transcription factor (TF) binding using DNase I footprint data. Developed to provide an unbiased approach to prioritise non-coding variants for functional analysis, Sasquatch performs exhaustive, k-mer based analysis of average footprints to determine any k-mers potential for TF binding and quantifies how this is changed by sequence variants.  Importantly the approach only requires one DNase-seq dataset per cell-type, from any genotype and is resilient across differing experimental procedures and sequence depths. We have made Sasquatch available as a versatile, high-throughput, webtool incorporating pre-processed human data from the Encode project and we demonstrate its effectiveness using validated causal GWAS SNPs and known polymorphic TF binding sites in erythroid tissues.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: 2 biological replicates using 2 growth protocols and 2 background controls of DNaseq-seq and 1 replicate and 1 background of ATAC-seq.

first: Maria

last: Suciu

first: Ron

last: Schwessinger


title: Expression data of colorectal cancer HT-29 cells

first: Hiroyuki

last: Seimiya

address: 3-8-31 Ariake, Koto-ku

department: Cancer Chemotherapy Center

institute: Japanese Foundation for Cancer Research

summary: Colorectal cancer HT-29 cell line is a comonly-used human cancer cell line. We have used this cell line for examining the effect of various anticancer compounds on gene expression and we obtained gene expression data of untreated HT-29 cells as a control data for the analysis.

overall_design: We extracted RNA from HT-29 cells and obtained gene expression data.

first: Akihiro

last: Tomida


title: Kmt2a and Kmt2b Control Memory Function via Different Transcriptional Programs

status: Public on Jun 12 2017

city: Göttingen

first: Gaurav

last: Jain

state: Lower Saxony

address: Von-Siebold-Str. 3a, Office no: 2.212

country: Germany

institute: The German Center for Neurodegenerative Diseases (German: Deutsches Zentrum für Neurodegenerative Erkrankungen DZNE)

summary: We have analyzed changes in histone 3 lysine 4 methylation (H3K4me) and gene expression resulting either from Kmt2a or Kmt2b knockdown in adult hippocampal CA neurons in mice. We implemented Cre/loxP-mediated conditional knockout strategy in order to knockdown either of these histone methyltransferases in excitatory forebrain neurons in adult mice.

overall_design: Examination of H3K4me3 and H3K4me1 levels, and gene expression in hippocampal CA neurons of of adult Kmt2a cKO and Kmt2b cKO mice.

first: Cemil

last: Kerimoglu

last: Fischer


title: Single cell RNA-seq identifies a unique microglia type associated with Alzheimer’s disease [ChIP]

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

summary: Alzheimer's disease (AD) is a detrimental neurodegenerative disease with no effective treatments. Due to cellular heterogeneity, the roles of immune cell subsets in AD onset and progression are poorly understood. By transcriptional single cell sorting, we comprehensively map all immune populations in wild type and AD–transgenic (Tg-AD) mouse brains. We describe a novel microglia type associated with neurodegenerative diseases (DAM) and identify the markers, spatial-location, and pathways associated with these cells. Immunohistochemical staining of mice and human brain slices showed DAM with intracellular/phagocytic Aβ particles. Single cell analysis of DAM in Tg-AD and Trem2-/- Tg-AD revealed that the DAM program is activated in a two-step process. Activation is initiated in a Trem2 independent manner which involves down-regulation of microglia checkpoints, followed by activation of a Trem2-dependent program. These data identify a unique microglia-type, which may have important implications for future treatment of AD and other neurodegenerative diseases.

overall_design: Transcriptional profiling of single cells from immune populations of mouse models of neurodegenerative diseases with matched controls, generated from deep sequencing of tens of thousands of cells, sequenced in several batches on illumina Nextseq500

first: Hadas

last: Keren-Shaul

first: Amit

last: Spinrad

first: Assaf

last: Weiner

first: Orit

last: Matcovitch-Natan

first: David

last: Lara-Astiaso


title: Single cell RNA-seq identifies a unique microglia type associated with Alzheimer’s disease

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


title: Site-specific lambda-integrase-mediated seamless vector transgenesis in human LINE-1 elements for therapeutic protein expression

status: Public on Jun 10 2017

city: Singapore

first: Shawn

last: Hoon

address: 61 Biopolis Street

country: Singapore

institute: Agency for Science Technology and Research

summary: The advancement in translational research, such as gene therapy, stem cell engineering and molecular medicine, can be realized on the pretext of genetic engineering at cellular level. However, the challenge of inserting large transgene cassettes into the human genome could be an impediment to this advancement, which makes the cell engineering process a critical parameter. Current practices, including random integration transgenesis tools (viral and transposon-based) or specific genome manipulation tools (endonuclease-based) are suboptimal in delivering large transgenes and also pose safety concerns. To address this void, we had developed and reported a novel transgenesis tool derived from phage λ integrase that precisely recombines large plasmid DNA into an endogenous sequence found in about 1000 human Long INterspersed Elements-1 (LINE-1) in various human cell lines. As an improved extension to mitigate the biosafety concerns to the minimal and enhance the uptake and efficiency of transgene expression, we report here a technologically advanced λ-Int platform, wherein we show efficient derivation of seamless negatively supercoiled transgene vectors from the conventional plasmid DNA using in vitro intermolecular recombination followed by its integration into human LINE-1 elements via prototypical λ-Int system. Additionally, we have identified specific LINE-1 as preferred seamless vector insertion sites for λ-Int mediated transgenesis. Characteristically, this new platform achieves sustainable, high-level transgene expression as exemplified by a CD19 chimeric antigen receptor expression from targeted LINE-1 in hESCs cells. Therefore, we demonstrate that our novel seamless vector platform has the potential to be broadly applied across different applications in biotechnology and molecular medicine.

overall_design: 1 sample consisting of insertion mapped DNA of bulk HT1080 cultures was used to prepare the sequencing library.

first: Harshyaa

last: Makhija

first: Roy

last: Suki

first: Farid

last: Ghadessy

first: Desmond

last: Wong

first: Dario

last: Campana

first: Peter

last: Dröge


title: Bptf maintains chromatin accessibility and the self-renewal capacity of mammary gland stem cells [ATAC-Seq]

city: Cold Spring Harbor

first: Wesley

middle: D.

last: Frey

state: New York

address: One Bungtown Road

institute: Cold Spring Harbor Laboratory

summary: Chromatin remodeling is a key requirement for transcriptional control of cellular differentiation. However, the factors that alter chromatin architecture in mammary stem cells (MaSCs) are poorly understood. Here we show that Bptf, the largest subunit of the NURF chromatin remodeling complex, is essential for MaSC self-renewal and differentiation of epithelial cells in the mammary gland. Bptf depletion arrests cells at a previously undefined stage of epithelial differentiation that is associated with an incapacity to achieve the luminal cell fate. Moreover, genome-wide analysis of DNA accessibility following genetic and chemical inhibition of Bptf, suggests a role for this factor in maintaining the open chromatin landscape of cis-regulatory elements in mammary epithelial cells (MECs). Collectively, our study implicates Bptf in maintaining the unique epigenetic state of MaSCs.

overall_design: FACS-sorted mammary epithelial cells from Bptf WT and Bptf KO mice, and mammary epithelial cell line Eph4 were utilized for nuclei isolation and preparation of ATAC-seq libraries.

middle: D

first: Camila

middle: O

last: Dos Santos


title: Fatty Acid Synthase Reprograms the Epigenome in Uterine Leiomyosarcomas

city: Duarte

first: Xiwei

last: Wu

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

summary: SK-UT-1 uterine leiomyosarcomas (Ut-LMS) cells were transduced with a fatty acid synthase (FASN)-containing retroviral vector to recapitulate the “lipogenic phenotype of cancer.” Consistent with this model, forced expression of FASN enhanced SK-UT-1 proliferation, migration, and cellular motion. Further investigation showed FASN promotes trimethylation of H3K9 (H3K9me3) and acetylation of H3K27 (H3K27ac) in SK-UT-1 cells. In contrast, siRNA targeting of FASN in high endogenous FASN expressing SK-LMS-1 Ut-LMS cells inhibits trimethylation of H3K9 and acetylation of H3K27. Palmitate, the predominant fatty acid product of FASN, increased H3K9me3, H3K27ac and H3K27me3 detection in SK-UT-1 cells. FASN promoted histone 3 methylation and acetylation through alteration of histone 3-modifying enzymatic activities (HDAC, HDM, HMT and HAT).ChIP-seq in SK-UT-1-FASN cells with anti-H3K9me3 antibody identified regions of enriched binding compared to vector-only cells. One differentially-enriched gene, CRISP1, was investigated further by ChIP-PCR. The transcriptionally repressive function of H3K9me3 was confirmed in CRISP1. Our results provide mechanistic insight into the pathobiology of the “lipogenic phenotype of cancer.” Here, FASN reprograms the Ut-LMS epigenome through chromatin remodeling to promote the “malignant phenotype.”

overall_design: Chromatin immunoprecipitation (ChIP) were performed on SK-UT-1-FASN and SK-UT-1-EV cells using the Magna ChIP A/G kit from (Millipore, Temecula, CA) following the manufacturer’s protocol. Anti-H3K9me3 antibody was used to immunoprecipitate cross-linked and fragmented chromatin DNA. This was followed by elution of protein/DNA complexes, reversal of the cross-links, and DNA purification.

first: Min

last: Guan


title: Capase-1 cleaves PPARg for potentitating the pro-tumor action of TAMs

city: Nanjing

first: Pingping

last: Shen

state: Jiangsu

address: 163 Xianlin Road

institute: Nanjing University

summary: Tumor-associated macrophages (TAMs) are increasingly viewed as a target of great relevance in the tumor microenvironment, because of their important role in cancer progression and metastasis. However, the endogenous regulatory mechanisms underlying TAM differentiation remain largely unknown. Here, we report that caspase-1 promotes TAM differentiation by cleaving peroxisome proliferator-activated receptor gamma (PPARγ) at Asp64, thus generating a 41 kDa fragment. This truncated PPARγ translocates to mitochondria, where it directly interacts with medium-chain acyl-CoA dehydrogenase (MCAD). This binding event attenuates MCAD activity and inhibits fatty acid oxidation, thereby leading to the accumulation of lipid droplets and promoting TAM differentiation. Furthermore, the administration of caspase-1 inhibitors or the infusion of bone marrow-derived macrophages (BMDMs) genetically engineered to overexpress murine MCAD markedly suppresses tumor growth. Therefore, targeting the caspase-1/PPARγ/MCAD pathway might be a promising therapeutic approach to prevent tumor progression.

overall_design: To further evaluate the effect of the caspase-1 inhibitor YVAD on TAM differentiation, we used a microarray platform to comprehensively analyze gene expression in THP-1 macrophages cocultured with MCF-7 cells in the presence or absence of YVAD and in THP-1 macrophages alone. We specifically selected genes associated with caspase-1 cleavage, with a particular emphasis on genes whose expression patterns changed after treatment with caspase-1 inhibitors, for example, genes up-regulated in the coculture group (Coculture vs Ctrl) but down-regulated upon administration of YVAD (YVAD vs Coculture), or vice versa.

first: Zhiyuan

last: Niu

first: Qian

last: Shi

first: Wenlong

last: Zhang

first: Yuxin

last: Shu

first: Nanfei

last: Yang

first: Bing

last: Chen

first: Qingsong

last: Wang

first: Xuyang

last: Zhao

first: Jiajia

last: Cheng

first: Xiujing

last: Feng

first: Zichun

last: Hua

first: Jianguo

last: Ji


title: Expression data from mouse liver

city: Tsukuba

first: Yang

last: LIU

state: Ibaraki.

address: 3-1-1 Koyadai, Tsukuba, Ibaraki

institute: Riken

summary:
Assisted reproductive technologies, including in vitro fertilization (IVF), are now frequently used, and increasing evidence indicates that IVF causes gene expression changes in children and adolescents that increase the risk of metabolic diseases. Although such gene expression changes are thought to be due to IVF-induced epigenetic changes, the mechanism remains elusive.
We tested whether the transcription factor ATF7, which mediates stress-induced changes in histone H3K9 tri- and di-methylation, the typical epigenetic silencing marks, is involved in the IVF-induced gene expression changes. We investigated the liver transcriptome in 3-week-old mice generated by IVF and normal mating.

overall_design: This series contains four sets of exression array data. For all sample, we use three CEL files generated by three independent biological samples.

last: Liu

first: Toshio

last: Maekawa

first: Keisuke

last: Yoshida

first: Hideki

last: Kaneda

first: Bruno

last: Chatton

first: Shigeharu

last: Wakana

first: Shunsuke

last: Ishii


title: The effect of EDI3 inhibition in MCF7 breast cancer cells

city: Dortmund

first: Rosemarie

last: Marchan

address: Ardeystrasse 67

department: Systems Toxicology

institute: Ifado

summary: EDI3 was shown to be relevant in cell migration, adhesion and spreading. Gene expression analysis was performed to determine the effect of EDI3 silencing in MCF7 cells in order to gain insight into potential underlying mechanisms.

overall_design: MCF7 cells were transfected with either scrambled or EDI3 siRNA. Three biological replicates each with three technical replicates were performed.

first: R

first: J

middle: G

last: Hengstler

last: Stewart

first: L

last: Lesjak


title: Gene expression data from primary human hepatocytes treated with GGF2 for 6, 24, or 72 h or 24 h with a 48 h washout.

city: Chapel Hill

first: Merrie

last: Mosedale

state: North Carolina

address: 301 Pharmacy Lane, Kerr Hall CB#7569

department: Division of Pharmacotherapy and Experimental Therapeutics

institute: UNC Eshelman School of Pharmacy

summary:
GGF2 is a recombinant human neuregulin-1β in development for chronic heart failure. Phase 1 clinical trials of GGF2 were put on hold when transient elevations in serum aminotransferases and total bilirubin were observed in 2 of 43 subjects receiving GGF2. However, aminotransferase elevations were modest and not typical of liver injury sufficient to result in elevated serum bilirubin. Several translational approaches were used to understand the liver response associated with GGF2.
Gene expression profiling was performed in sandwich-cultured human hepatocytes treated with GGF2 (0-3760 pM) for up to 72 h. Prior cytochrome P450 induction studies had unexpectedly demonstrated suppression of cytochrome P450 3A4 (CYP3A4) mRNA in primary human hepatocytes exposed to GGF2 for 24 h. Although no direct cytotoxicity was observed in response to GGF2, the suppression of CYP3A4 transcript levels in primary hepatocyte cultures had a temporal profile consistent with the transient bilirubin elevations observed in vivo. While downregulation of CYP3A4 alone should not influence serum bilirubin levels, it was reasoned that concomitant alterations in the expression of other liver proteins, such as those involved in bilirubin transport, could help to explain the liver response.

overall_design: 92 samples were analyzed representing N=1 per donor, time point, and treatment except 2 samples (Donor 4: 6 h: 0.376 pM GGF2 and Donor 5: 24 h: 0.1% GGF2 Buffer) that failed QC and 6 samples (Donor 1: 6 h) that clustered together and were > 3 SD away from the mean on a PCA plot suggesting that these samples may also be aberrant and were therefore omitted from analysis.


title: MAPK-triggered chromatin reprogramming by histone deacetylase in plant innate immunity

city: Thuwal

first: Alaguraj

last: Veluchamy

address: Thuwal

department: BESE

country: Saudi Arabia

institute: King Abdullah University of Science and Technology

summary: Microbial-associated molecular patterns (MAMPs) activate several MAP Kinases (MAPKs), which are major regulators of the innate immune response in Arabidopsis that induce large-scale changes in gene expression. Here, we determined whether MAMP-triggered gene expression involves chromatin modifications at the chromosomal level. Our results show that histone acetylation and deacetylation are major regulators of MAMP-triggered gene expression and implicate the histone deacetylase HD2B in the reprogramming of defense gene expression and innate immunity. The MAPK MPK3 directly interacts with and phosphorylates HD2B, thereby regulating the intra-nuclear compartmentalization and function of the histone deacetylase. By studying a number of gene loci that undergo MAMP-dependent activation or repression, our data reveal a mechanistic model for how protein kinase signaling directly impacts chromatin reprogramming in plant defense.

overall_design: Genome-wide correlation of H3K9ac modification and HD2B binding profile  to transcription.

first: David

last: Latrasse

first: Teddy

last: Jégu

first: Huchen

last: Li

first: Axel

last: de Zelicourt

first: Cécile

last: Raynaud

first: Stéphanie

last: Legras

first: Andrea

last: Gust

first: Olga

last: Samajova

first: Naganand

last: Rayapuram

first: Juan

last: Ramirez-Prado

last: Kulikova

first: Jean

last: Colcombet

last: Bigeard

first: Baptiste

last: Genot

first: Ton

last: Bisseling

first: Moussa

last: Benhamed

first: Heribert

last: Hirt


title: Study of gene expression of peripheral blood T cells in 25 healthy male donors of different age from 25 to 97 years

city: Bologna

first: Daniel

last: Remondini

address: Viale Berti Pichat 6/2

department: Physics and Astronomy - DIFA

country: Italy

institute: Bologna University

summary:
In this study we analyse a gene expression dataset, obtained by microarray hybridization, consisting of T lymphocytes from 25 healthy male volunteers with ages ranging over whole adult lifespan (25 to 97 years).
Large groups of genes exhibiting non-monotonic expression patterns over time were observed, highlighting similarities in gene expression profiles of young and ‘‘successfully aged’’ individuals.

overall_design: Twenty-five male subjects were selected for study participation, equally divided into five age-classes: A (25–35 years old), B (40–50 years old), C (55–65 years old), D (70–80 years old) and E (>90 years old).

first: Stefano

last: Salvioli

first: Mirko

last: Francesconi

first: Michela

last: Pierini

first: Dawn

last: Mazzatti

first: Jonathan

last: Powell

first: Isabella

last: Zironi

first: Ferdinando

last: Bersani

first: Gastone

last: Castellani

first: Claudio

last: Franceschi


title: TIPE1 suppresses invasion and migration through down-regulating Wnt/β-catenin pathway in gastric cancer

city: JiNan

first: zhang

last: yan

state: shandong

address: Culture west road

department: Department of pharmacology

institute: Shandong University

summary: We have employed whole genome microarray expression profiling as a discovery platform to identify genes with the potential to distinguish between the gastric cancer and adjacent nontumor tissue. The human gastric cancer tissue belonging to low-differentiated adenocarcinoma and adjacent nontumor tissue were analysed. Expression of TIPE1 and Wnt family from this signature was quantified in the same kind of samples by real-time PCR, confirming the change pattern.

first: Fan

last: Yi

first: Yan

last: Zhang


title: Gene expression profiels from organoids.

city: Glasgow

first: Patrizia

last: Cammareri

address: Garscube Estate

institute: CRUK Beatson Institute

summary:
Recent studies have suggested increased plasticity of differentiated cells within the intestine to act both as intestinal stem cells and tumour initiating cells. However, little is known of the processes that regulate this plasticity. Our previous work has shown that activating mutations of Kras or the NF-kB pathway can drive dedifferentiation of intestinal cells lacking Apc.
To investigate this process further, we profiled organoids by gene expression analysis. Organoids were isolated from VillinCreER Apcfl/fl KrasG12D crypts  (here called CC) or Villi (here called SFV).

overall_design: Two-condition experiments, CC and SFV organoids. Biological replicates: 3 CC and 3 SFV independently grown and harvested. One replicate per array. Each replicate represents a single mouse.

first: Owen

last: Sansom


title: Gene Expression profiles from allograft tumours

summary:
Recent studies have suggested increased plasticity of differentiated cells within the intestine to act both as intestinal stem cells and tumour initiating cells. However, little is known of the processes that regulate this plasticity. Our previous work has shown that activating mutations of Kras or the NF-kB pathway can drive dedifferentiation of intestinal cells lacking Apc.
To investigate this process further, we profiled tumours generated by subcutaneous injection of spheroids derived from villi (here called SFV) and from crypts (here called CC) purified from VillCreER Apcfl/fl KrasG12D mice.

overall_design: Allograft tumours were generated injecting VillCreER Apcfl/fl KrasG12D CC and SFV (purified from mouse small intestine) in female athymic CD-1 nude mice. Tumours were collected at end-point. Two-condition experiments, CC and SFV tumours. Biological replicates: 3 CC and 3 SFV independently grown and harvested. One replicate per array.


title: Affymetrix SNP6.0 array data for PAX5 amplified acute lymphoblastic leukemia

status: Public on Jun 09 2017

city: Newcastle upon Tyne

first: Claire

middle: Joanne

last: Schwab

state: Tyne and Wear

address: Level 5, Sir James Spence Institute, Queen Victoria Rd

department: Northern Institute for Cancer Research

institute: Newcastle University

summary: Intragenic PAX5 amplification in  <1%of B-cell precursor acute lymphoblastic leukaemia.  Affymetrix SNP 6.0 array analysis was undertaken in patients who showed amplication of PAX5 by MLPA testing using the P335-IKZF1 MLPA kit (www.mlpa.com, MRC Holland, The Netherlands)

overall_design: We performed Affymetrix SNP 6.0 array on genomic DNA extracted from bone marrow samples taken at diagnosis in 7 patients and at relapse in one patient.

first: Christine

last: Harrison


title: The linker histone H1.2 directs the genome-wide chromatin-association and facilitates the biological effects of the retinoblastoma tumour suppressor protein

city: Oxford

first: Edward

last: Hookway

state: Oxfordshire

address: Botnar Research Centre, Windmill Road

institute: NDORMS, University of Oxford

summary: ChIPseq of Retinoblastoma protein in MCF7 cells in which linker histone H1.2 has been knocked down.

overall_design: ChIPseq of pRb in one cell line with H1.2 knockdown and control.

first: Shonagh

last: Munro

first: E


title: Aedes aegypti response to bloodfeeding and bacterial ingestion in midgut tissues of females from two strains

city: Baltimore

first: George

last: Dimopoulos

state: MD

address: 615 N Wolfe St.

department: Molecular Microbiology and Immunology

institute: Johns Hopkins School of Public Health

summary: Rockefeller and Singapore strain Aedes aegypti female mosquitoes differ in the number of bacteria present in the midgut. Females from each strain were either maintained on 3% sucrose solution, fed a sterile blood meal, or fed a blood meal containing a cocktail of bacteria. Differential transcript abundance was compared between females from each strain/treatment combination and a common reference sample pool. The overall goal was to determine how gene expression in Rockefeller females differs from Singapore females in order to better understand why the gut microbiome differs between the strains.

overall_design: 15 midguts collected per sample, 3 replicate samples per treatment. Treatments: Rockefeller Sucrose fed vs. Reference, Rockefeller blood fed vs. Reference, Rockefeller blood + bacteria fed vs. Reference, Singapore Sucrose fed vs. Reference, Singapore blood fed vs. Reference, Singapore blood + bacteria fed vs. Reference.

first: Sarah

last: Short

first: Emmanuel

last: Mongodin

first: Hannah

last: MacLeod

first: Octavio

last: Talyuli


title: Bptf maintains chromatin accessibility and the self-renewal capacity of mammary gland stem cells

first: Wesley

last: Frey

overall_design: Refer to individual Series


title: Bptf maintains chromatin accessibility and the self-renewal capacity of mammary gland stem cells [ChIP-Seq]

overall_design: FACS-sorted mammary epithelial cells and/or mammary epithelial cell line Eph4 were utilized for chromatin isolation and pulldown utilizing antibodies that recognized histone H3K27ac and c-Myc. Pulldown chromatin was purified and DNA utilized for the preparation of ChIP-seq libraries.

first: Camila

last: Dos Santos


title: Single cell RNA-seq identifies a unique microglia type associated with Alzheimer’s disease [RNA]

city: Rehovot

first: Ido

last: Amit

institute: Weizmann Institute of Science

summary: Alzheimer's disease (AD) is a detrimental neurodegenerative disease with no effective treatments. Due to cellular heterogeneity, the roles of immune cell subsets in AD onset and progression are poorly understood. By transcriptional single cell sorting, we comprehensively map all immune populations in wild type and AD–transgenic (Tg-AD) mouse brains. We describe a novel microglia type associated with neurodegenerative diseases (DAM) and identify the markers, spatial-location, and pathways associated with these cells. Immunohistochemical staining of mice and human brain slices showed DAM with intracellular/phagocytic Aβ particles. Single cell analysis of DAM in Tg-AD and Trem2-/- Tg-AD revealed that the DAM program is activated in a two-step process. Activation is initiated in a Trem2 independent manner which involves down-regulation of microglia checkpoints, followed by activation of a Trem2-dependent program. These data identify a unique microglia-type, which may have important implications for future treatment of AD and other neurodegenerative diseases.

overall_design: Transcriptional profiling of single cells from immune populations of mouse models of neurodegenerative diseases with matched controls, generated from deep sequencing of tens of thousands of cells, sequenced in several batches on illumina Nextseq500

first: Hadas

last: Keren-Shaul

first: Amit

last: Spinrad

first: Assaf

last: Weiner

first: Orit

last: Matcovitch-Natan


title: Inflamatory response-related gene expression in the uteri of Dogs with Pyometra

city: Poznań

first: Marcin

last: Ruciński

state: Wielkopolska

address: Święcickiego 6

department: Histology and Embryology

country: Poland

institute: Poznań University of Medical Sciences

summary:
Pyometra, which is accompanied by bacterial contamination of the uterus, is defined as a complex disease associated with the activation of several systems, including the immune system.
The objective of the study was to evaluate the gene expression profile in dogs with pyometra compared with those that were clinically normal.

overall_design: The study included uteri from 43 mongrel bitches (23 with pyometra, 20 clinically healthy). RNA used for the microarray study was pooled to four separated vials for control and pyometra.

first: Bartosz

last: Kempisty

first: Dorota

last: Bukowska

first: Joanna

last: Budna

first: Piotr

last: Celichowski


title: Gene expression data from primary human hepatocytes treated with tolvaptan for 4, 24, or 72 h

first: Merrie

last: Mosedale

summary:
A micropatterned coculture model (HepatoPac®) was used to explore the possibility that changes in exosome content precede overt necrosis in response to tolvaptan, a drug known to cause idiosyncratic drug-induced liver injury.  Hepatocytes from 3 human donors were exposed to a range of tolvaptan concentrations bracketing plasma Cmax (0.01 - 50 µM) or DMSO control continuously for 4, 24, or 72 h.
While ALT release was not significantly affected, tolvaptan exposure resulted in increased release of exosomal microRNA-122 (miR-122) into the medium. Microarray analysis was used to idenfity the activation of molecular stress response pathways most associated with increases in exosomal miR-122.

overall_design: 54 samples were analyzed representing N=1 per donor, time point, treatment, and concentration


title: The effect of  GPAM silencing in MCF7 breast cancer cells

first: Rosemarie

last: Marchan

summary: GPAM is well characterized in triglyceride synthesis, but has never been implicated in cancer. Our study report a role for GPAM in cell migration. Gene expression changes after GPAM silencing was investigated to gain insight into possible mechanisms underlying GPAM's role in cell migration.

overall_design: GPAM was silenced in MCF7 cells using two independent siRNA oligos targeting two different exons. Non-transfected cells and cells transfected with a scrambled siRNA were used as controls. Four biological replicates were performed.

first: R

first: B

last: Buettner


title: RNA-seq on rRNA depleted libraries from exponentially growing Halobacterium salinarum NRC-1 strains Δura3 and Δhlx2

status: Public on Jun 07 2017

city: Durham

first: Cynthia

last: Darnell

address: 130 Science Drive

department: Biology

institute: Duke University

overall_design: Differential gene expression in Δhlx2 mutant compared to parent strain

middle: L

first: Amy

middle: K

last: Schmid


title: Expression data from WT liver DX5- NK cells and dnTGFbRII liver DX5- NK cells

city: Hefei

first: Zhe-Xiong

last: Lian

state: Anhui

address: Huangshan Road 443, Western Campus of USTC

department: School of Life Sciences and Institution of Immunology

institute: University of Science and Technology of China

summary:
Liver is a unique immunological organ containing large number of NK cells which play an important role in the maintenance of liver homeostasis, especially the specific liver resident DX5- NK cell subset.
We used microarrays to detail the differences of normal DX5- NK cells and the DX5- NK cells in inflammatory environment.

overall_design: WT and dnTGFbRII mice liver DX5- NK cells were sorted for RNA extraction and hybridization on Affymetrix microarrays. We wanted to analysis the changes of liver resident NK cells in inflammatory environment.

first: Zhi-Bin

last: Zhao

first: Hong-Di

last: Ma


title: Mycobacterium tuberculosis PtpA ChIP-chip on U937 cells using Monoclonal ANTI-FLAG(R) M2 antibody

city: Beijing

first: Cuihua

last: Liu

address: Beijing

institute: Institute of Microbiology, Chinese Academy of Sciences

summary: We found that Mtb PtpA also enters into the nucleus of host cells, we thus sought to investigate how nuclear PtpA regulates host gene expression.

overall_design: Two samples were designed


title: Progressive  motor  neuron  pathology  and  the  role  of  astrocytes  in  a  human  stem  cell model of VCP-related ALS [terminally differentiated iPSC-derived astrocytes]

city: Martigny

first: Raphaelle

last: Luisier

state: Valais

address: Rue Marconi 19, PO Box 592

country: Switzerland

institute: Idiap Research Institute

summary: Motor   neurons (MNs)   and   astrocytes   (ACs) are   implicated   in   the   pathogenesis   of amyotrophic  lateral  sclerosis  (ALS),  but  their  interaction  and  the  sequence  of  molecular events leading to MN death remain unresolved. Herewe optimized directed differentiation of induced pluripotent stem cells (iPSCs) into highly enriched (>85%) functional populations of  spinal  cord  MNs  and  ACs.  We  identifysignificantlyincreased  cytoplasmic  TDP-43  and  ER stress as  primary  pathogenic  events in patient-specific  valosin-containing  protein  (VCP)-mutant MNs, with  secondary  mitochondrial  dysfunction  and  oxidative  stress.  Cumulatively these  cellular  stresses  result  in  synaptic  pathology  and  cell death  in  VCP-mutant  MNs. We additionallyidentify  a  cell-autonomous VCP-mutant  AC  survival  phenotype, which   is   not attributable  to  the  same  molecular  pathology  occurring in VCP-mutant MNs. Finally, through iterative  co-culture  experiments,  we  uncover  non-cell-autonomous  effects  of  VCP-mutant ACs  on  both  control  and  mutant  MNs.  This  work  elucidates  molecular  events  and  cellular interplay thatcould guide future therapeutic strategies in ALS.

overall_design: Bulk RNA-seq at different timepoints throughout a 35-day differentiation protocol that converted iPSC cells to highly enriched motor neurons and a further dataset from terminally differentiated iPSC-derived astrocytes

first: Claire

last: Hall

first: Zhi

last: Yao

first: Minee

last: Choi

first: Giulia

last: Tyzack

first: Andrea

last: Serio

first: Jasmine

last: Harley

first: Elisavet

last: Preza

first: Charlie

last: Arber

first: Sarah

last: Crisp

first: P

last: Watson

first: Dimitri

last: Kullmann

first: Andrey

last: Abramov

first: Selina

last: Wray

first: Russell

last: Burley

first: Sam

middle: H

last: Loh

first: Miguel

last: Martins

first: Molly

last: Stevens

first: Nicholas

last: Luscombe

first: Christopher

last: Sibley

first: Andras

last: Lakatos

first: Jernej

last: Ule

first: Sonia

last: Gandhi

first: Rickie

last: Patani


title: ChIP-Sequencing of p705 Stat3 in oligodendrocyte progenitor cells.

city: Rochester

first: John

last: Mariani

state: NY

address: 601 Elmwood Avenue

department: Neurology

institute: University of Rochester

summary: We examine the role of Stat3 in oligodendrocyte progenitor cells and determine that direct binding of Stat3 to the Etv6 promoter, and subsequent upregulation, in part, promotes differentiation.

overall_design: Examination of Stat3 DNA binding in oligodendrocyte progenitor cells.

middle: N

first: Gareth

last: John


title: Viable RNaseH1 knockout mice show RNaseH1 is essential for R loop processing, mitochondrial and liver function

status: Public on Jun 06 2017

city: Carlsbad

first: Sagar

last: Damle

address: 2855 Gazelle Ct

institute: Ionis Pharmaceuticals

summary: Using RNAseq we describe transcriptional changes downstream of liver-specific knockout of RNaseH1, including effects on mitochondrial function, fibrosis and cell cycle

overall_design: We perform RNAseq on mouse livers under conditions of constitutive or inducible knockout of RNaseH1

first: Walt

last: Lima


title: Genome-scale Activation Screen Identifies a LncRNA Locus Regulating a Gene Neighborhood [ChIP-Seq]

city: Cambridge

first: Julia

last: Joung

state: MA

address: 75 Ames St

institute: Broad Institute

summary: The mammalian genome contains thousands of loci that transcribe long noncoding RNAs (lncRNAs), some of which are known to play critical roles in diverse cellular processes through a variety of mechanisms. While some lncRNA loci encode RNAs that act non-locally (in trans), emerging evidence indicates that many lncRNA loci act locally (in cis) to regulate expression of nearby genes—for example, through functions of the lncRNA promoter, transcription, or transcript itself. Despite their potentially important roles, it remains challenging to identify functional lncRNA loci and distinguish among these and other mechanisms. To address these challenges, we developed a genome-scale CRISPR-Cas9 activation screen targeting more than 10,000 lncRNA transcriptional start sites (TSSs) to identify noncoding loci that influence a phenotype of interest. We found 11 novel lncRNA loci that, upon recruitment of an activator, each mediate BRAF inhibitor resistance in melanoma. Most candidate loci appear to regulate nearby genes. Detailed analysis of one candidate, termed EMICERI, revealed that its transcriptional activation results in dosage-dependent activation of four neighboring protein-coding genes, one of which confers the resistance phenotype. Our screening and characterization approach provides a CRISPR toolkit to systematically discover functions of noncoding loci and elucidate their diverse roles in gene regulation and cellular function.

overall_design: ChIP-seq for histone modifications in A375 cells

first: Feng

last: Zhang


title: The expression profile of human peripheral blood mononuclear cells miRNA is altered by dengue virus serotype-3 and antibody-dependent enhancement infection

city: Kunming

first: Qiangming

last: Sun

state: Yunnan

address: 935 Jiaoling Road

institute: Chinese Academy of Medicine Science and Peking Union Medical College

type: Non-coding RNA profiling by high throughput sequencing

summary: To compare miRNA expression progiles in human PBMCs with DENV-3 and DENV-3 ADE infections using high-throughput sequencing

overall_design: We defined the following experimental groups: DENV-3-none-0h, DENV-3-8h, DENV-3-24h, DENV-3 of ADE-8h, DENV-3 of ADE-24h,

first: Liming

last: Jiang


title: ChIP-Seq and RNA-seq in oligodendrocyte progenitor cells

status: Public on Jun 08 2017

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


title: Activation of Lineage-Regulators and Transposable Elements Across a Pluripotent Spectrum

first: Charles

last: Bradshaw

address: Tennis Court Road

department: Gurdon Institute

institute: University of Cambridge

type: Methylation profiling by high throughput sequencing

summary: Embryonic stem cells (ESC) are characterised by the pluripotent capacity to generate all embryonic lineages. Here we show ESC can occupy a spectrum of distinct transcriptional and epigenetic states in response to varied extrinsic conditions. This spectrum broadly corresponds to a developmental continuum of pluripotency and is coupled with a gradient of increasing global DNA methylation. Each pluripotent state is linked with activation of distinct classes of transposable elements (TE), which in turn influence ESC through generating chimeric transcripts. Moreover, varied ESC culture parameters differentially license activation of master lineage-regulators, including Sox1, Gata4 or Blimp1, and influence differentiation. The activation of Blimp1 is prevalent in 2i (without-LIF) conditions, and marks a dynamic primordial germ cell (PGC)-like sub-state, that is directly repressed by Klf4 downstream of LIF/STAT3 signalling. Thus, extrinsic cues establish a spectrum of pluripotent states, in part by modulating sub-populations, as well as directing the transcriptome, epigenome, and TE.

overall_design: Replicate RNA-seq and Methyl-seq datasets from mESC (129 or B6 background), maintained in multiple pluripotent culture parameters.

first: Jamie

last: Hackett


title: SNP array data for adult T-cell leukemia (ATL)

city: Kiyotake

first: Shingo

last: Nakahata

state: Miyazaki

address: 5200 Kihara

institute: University of Miyazaki

summary:
To identify chromosomal alterations in ATL, SNP array analyses were performed in 19 leukemia cell samples from ATL patients and 9 ATL-related cell lines. ATL displayed complex chromosomal abnormalities, but it contained recurrent chromosomal amplification and deletion, including 14q11 and 14q32, which may be associated with the development of ATL.
Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from cryopreserved peripheral blood samples and from cell line samples.

overall_design: Copy number analysis of Affymetrix GeneChip Human Mapping 250K Nsp or 250K Sty arrays were performed for leukemic cell samples from 9 acute-type and 10 chronic-type ATL patients and 9 ATL-related cell lines.

first: Kazuhiro

last: Morishita


title: SHP2 Is Required for BCR-ABL1-Induced Hematologic Neoplasms

city: Toronto

first: Pamela

last: Ohashi

state: Ontario

address: 610 University Ave

country: Canada

institute: Princess Margaret Cancer Centre

summary: BCR-ABL1-targeting tyrosine kinase inhibitors (TKIs) have revolutionized treatment of Philadelphia chromosome-positive (Ph+) hematologic neoplasms. Nevertheless, acquired TKI resistance remains a major problem in chronic myeloid leukemia (CML), and TKIs are less effective against Ph+ B-cell acute lymphoblastic leukemia (B-ALL). GAB2, a scaffolding adaptor that binds and activates SHP2, is essential for leukemogenesis by BCR-ABL1, and a GAB2 mutant lacking SHP2 binding cannot mediate leukemogenesis. Using a genetic loss-of-function approach and bone marrow transplantation (BMT) models for CML and BCR-ABL1+ B-ALL, we show that SHP2 is required for BCR-ABL1-evoked myeloid and lymphoid neoplasia. Ptpn11 deletion impairs initiation and maintenance of CML-like myeloproliferative neoplasm, and compromises induction of BCR-ABL1+ B-ALL. SHP2, and specifically, its SH2 domains, PTP activity and C-terminal tyrosines, is essential for BCR-ABL1+, but not WT, pre-B cell proliferation. The MEK/ERK pathway is regulated by SHP2 in WT and BCR-ABL1+ pre-B cells, but is only required for the proliferation of BCR-ABL1+ cells. SHP2 is required for SRC family kinase (SFK) activation only in BCR-ABL1+ pre-B cells. RNAseq reveals distinct SHP2-dependent transcriptional programs in BCR-ABL1+ and WT pre-B cells. Our results suggest that SHP2, via SFKs and ERK, represses MXD3/4 to facilitate a MYC-dependent proliferation program in BCR-ABL1-transformed pre-B cells.

overall_design:
RNA-Seq expression profiling of 16 mouse pre-B cell samples:
4 BCR-ABL/SHP2+/+
4 BCR-ABL/SHP2-/+
4 BCR-ABL/SHP2+/-
4 BCR-ABL/SHP2-/-

first: Shengqing

last: Gu

first: Azin

last: Sayad


title: Loss of Function Mutations in ETS2 Repressor Factor (ERF) Reveal a Balance Between Positive and Negative ETS Factors Controlling Prostate Oncogenesis [VCaP ChIP-Seq]

city: New York

first: Rohit

last: Bose

address: 1275 York Ave

institute: Memorial Sloan Kettering Cancer Center

summary: Half of prostate cancers are caused by a gene-fusion that enables androgens to drive expression of the normally silent ETS transcription factor ERG in luminal prostate cells1-4.  Recent prostate cancer genomic landscape studies5-10 have reported rare but recurrent point mutations in the ETS repressor ERF11.  Here we show these ERF mutations cause decreased protein stability and ERF mutant tumours are mostly exclusive from those with ERG fusions.  ERF loss recapitulates the morphologic and phenotypic features of ERG gain in primary mouse prostate tissue, including expansion of the androgen receptor (AR) transcriptional repertoire, and ERF has tumour suppressor activity in the same genetic background of PTEN loss that yields oncogenic activity by ERG.  Furthermore, in a human prostate cancer model of ERG gain and wild-type ERF, ChIP-seq studies indicate that ERG inhibits the ability of ERF to bind DNA at consensus ETS sites.  Consistent with a competition model, ERF loss rescues ERG-positive prostate cancer cells from ERG dependency. Collectively, these data provide evidence that the oncogenicity of ERG is mediated, in part, by displacement of ERF and raise the larger question of whether other gain-of-function oncogenic transcription factors might also inactivate endogenous tumour suppressors.

overall_design: VCaP cells were infected with Tet-inducible shERG lentivirus and selected with antibiotics.  Subsequently, cells were treated with 100ng/mL doxycycline vs vehicle.  Samples were then sonicated and genomic DNA extracted for ChIP-seq.

first: Ping

last: Wang

first: Anna

last: Patruno

first: Yilin

last: Zhao

first: Deyou

last: Zheng

last: Sawyers


title: Loss of Function Mutations in ETS2 Repressor Factor (ERF) Reveal a Balance Between Positive and Negative ETS Factors Controlling Prostate Oncogenesis [Organoids ChIP-Seq]

overall_design: Normal murine prostate-derived organoids were infected with Tet-inducible FLAG-ERG lentivirus and selected with antibiotics.  Subsequently, cells were treated with 100ng/mL doxycycline vs vehicle.  Samples were then sonicated and genomic DNA extracted for ChIP-seq.


title: Structural basis for 5’-ETS recognition by Utp4 at the early stages of ribosome biogenesis

city: Heidelberg

first: Ed

last: Hurt

address: Im Neuenheimer Feld 328

department: BZH

institute: Biochemie Zentrum Heidelberg

summary:
Eukaryotic ribosome biogenesis begins with the co-transcriptional assembly of the 90S pre-ribosome.
The ‘U three protein’ (UTP) complexes and snoRNA particles arrange around the nascent pre-ribosomal RNA chaperoning its folding and further maturation.
The earliest event in this hierarchical process is the binding of the UTP-A complex to the 5’-end of the pre-ribosomal RNA (5’-ETS).
This oligomeric complex predominantly consists of β-propeller and α-solenoidal proteins.
Here we present the structure of the Utp4 subunit from the thermophilic fungus Chaetomium thermophilum at 2.15 Å resolution and analyze its function by UV RNA-crosslinking (CRAC) and in context of a recent cryo-EM structure of the 90S pre-ribosome.
Utp4 consists of two orthogonal and highly basic β-propellers that perfectly fit the EM-data.
The Utp4 structure highlights an unusual Velcro-closure of its C-terminal β-propeller as relevant for protein integrity and Utp8 recognition in the context of the pre-ribosome.
We provide a first model of the 5’-ETS RNA from an internally hidden 5’-end up to the region that hybridizes to the 3’-hinge sequence of U3 snoRNA and validate a specific Utp4/5’-ETS interaction by CRAC analysis.
Altogether Utp4 is central to the UTP-A complex and organizes the 5’-ETS for further maturation.

sample_organism:
Saccharomyces cerevisiae
Thermochaetoides thermophila

overall_design: In vitro-UV CRAC analysis

first: Fabiola

last: Calviño

first: Markus

last: Kornprobst

first: Géza

last: Schermann

first: Fabienne

last: Birkle

first: Klemens

last: Wild

first: Tamás

last: Fischer

first: Yasar

last: Ahmed

first: Irmgard

last: Sinning


title: Genome-scale Activation Screen Identifies a LncRNA Locus Regulating a Gene Neighborhood

first: Julia

last: Joung

overall_design: Refer to individual Series


title: PSIP1/p75 promotes tumorigenicity in breast cancer cells by promoting the transcription of cell cycle genes

city: Bethesda

first: Yuelin

middle: Jack

last: Zhu

address: 9000 Rockville Pike

department: Genetics Branch, Center for Cancer Research

institute: NCI

summary: Breast cancer (BC) is a highly heterogeneous disease, both at the pathological and molecular level, and several chromatin-associated proteins play crucial roles in breast cancer initiation and progression. Here, we demonstrate the role of PSIP1 (PC4 and SF2 interacting protein)/p75 (LEDGF) in breast cancer progression. PSIP1/p75, previously identified as a chromatin-adaptor protein, is found to be upregulated in basal-like/triple negative breast cancer (TNBC) patient samples and cell lines. Immunohistochemistry in tissue arrays showed elevated levels of PSIP1 in metastatic invasive ductal carcinoma. Survival data analyses indicated that the levels of PSIP1 showed a negative association with TNBC patient survival. Depletion of PSIP1/p75 significantly reduced the tumorigenicity and metastatic properties of TNBC cell lines while its over-expression promoted tumorigenicity. Further, gene expression studies revealed that PSIP1 regulates the expression of genes controlling cell-cycle progression, cell migration, and invasion. Finally, by interacting with RNA polymerase II, PSIP1/p75 facilitates the association of RNA pol II to the promoter of cell cycle genes and thereby regulates their transcription. Our findings demonstrate an important role of PSIP1/p75 in TNBC tumorigenicity by promoting the expression of genes that control the cell cycle and tumor metastasis.

overall_design: RNA samples were collected in biological triplicates from M4 control and PSIP1sh2 knockdown M4 cells.

first: Deepak

last: Singh

first: Xiao

last: Li

first: Ashish

last: Lal

first: Kannanganattu

middle: V

last: Prasanth


title: Transcriptional alterations of virulence-associated genes in extended spectrum beta-lactamase (ESBL)-producing uropathogenic Escherichia coli during morphologic transitions induced by ineffective antibiotics

city: Örebro

first: Robert

last: Kruse

address: S grevrosengatan

department: Medical Sciences

country: Sweden

institute: Örebro University

summary:
The present study examines changes in global gene expression patterns and in virulence factor-associated genes in an extended spectrum beta-lactamase (ESBL)-producing UPEC (ESBL019) during the morphologic transitions induced by an ineffective antibiotic and in the presence of human primary bladder epithelial cells.
The morphological shifts induced by ineffective antibiotics are associated with significant transcriptional virulence alterations in ESBL-producing UPEC, which may affect survival and persistence in the urinary tract.

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

overall_design: Changes in global gene expression patterns and in virulence factor-associated genes in an extended spectrum beta-lactamase (ESBL)-producing UPEC (ESBL019) during the morphologic transitions induced by an ineffective antibiotic (ceftibuten) in the presence of human primary bladder epithelial cells was evaluated by microarray after 4 hours. Four different morphologies were studied; Coliform, Transition (from Coli into Filamented), Filamented and Reverted (reverted back from a Filamented shape into a coli shape). Four independent experiments were included in each group.

first: Isak

last: Demirel

first: Katarina

last: Persson


title: Expression data from RA-FLSs with PMPs

city: Yangzhou

first: Wenwen

last: Wang

address: 11 Huaihai Road

institute: Clinical Medical College and 2School of Medicine, Yangzhou University, Yangzhou, P.R. China

summary:
Platelet microparticles (PMPs) are closely related to the activity of rheumatoid arthritis, and promote the migration and invasion of rheumatoid arthritis fibroblast-like synoviocytes (RA-FLSs).
In order to identify the possible mechanisms of the promotion effect on migration and invasion of RA-FLS by PMP, we used microarray analysis to detect the gene expressions of RA-FLSs after treatment with PMPs.

overall_design: RA-FLSs after treated with or without PMPs were selected for RNA extraction and detection on Affymetrix

first: Jiahuan

last: Liu

first: Binzhou

last: Yang

first: Zhongshuang

last: Ma

first: Guiping

first: Weigan

last: Shen

first: Yu

last: Zhang


title: Aplysia Pleural Ganglia 7 Days After Long-Term Sensitization Training

city: River Forest

last: Calin-Jageman

state: IL

address: 7900 West Division

department: Psychology

institute: Dominican University

summary: We used a custom-designed microarray and qPCR to characterize the transcriptional response that persists 7 days after long-term sensitization training in the marine mollusk Aplysia californica, a time-point at which recall has decayed but savings memory is still possible to induce.  Aplysia were exposed to a 1-day unilateral LTS training protocol (4 rounds of noxious shock at 30 min intervals, each shock 10s of 1/2s off 1/2on 90mA 60-hz biphasic square-wave shock).  Training produced robust sensitization in all animals (measured as an increase in T-SWR response from baseline to 24h after training).  One week (7 days) after training, animals were again post-tested, and showed little-to-no evidence of recall (average change from baseline = -4% on the trained side, -4% on the untrained side).  Pleural ganglia were then harvested.  Samples from a left-trained and right-trained animal were combined to smooth out lateralized gene expression.  The pleural ganglia contains the VC nociceptors, which are thought to play a primary role in expressing LTS memory.

overall_design: Within-subjects comparison.  Each array is a two-color approach hybridized to a matched trained and untrained set of samples (with each sample containing tissue from a left- and right-trained animal).  Conducted with 8 biological replicates, meaning 8 arrays, each comparing paired trained and untrained samples.

first: Irina

middle: E


title: MYD88 L265P differential expression analysis

first: James

middle: Q

department: National Cancer Institute, Center for Cancer Research

institute: National Institutes of Health

summary:
The wider transcriptional effects of MYD88L265P were explored by analysing the microarray datasets using the limma package. We focussed on evidence for differential expression between Myd88L265P and Card11L232LI transduced B cells because both cell populations were actively proliferating at the time of RNA isolation.
When the transcriptome of MYD88L265P expressing B cells was compared with empty vector-expressing B cells using limma, 111 genes had strong evidence for differential expression with 88 increased in MYD88L265P cells. Compared to CARD11L232LI expressing B cells, 84 genes had strong evidence for differential expression in MYD88L265P B cells with 30 increased, including the plasma cell induced genes Prdm1 and Igj.

overall_design: Duplicates of transduced B cells, including empty vector controls were cultured without anti-CD40 for 24hr and EGFP+ cells sorted using FACSAria cell sorter. For microarray analysis, sorted cells were resuspended in TRIzol and RNA extracted. mRNA expression was analyzed on Affymetrix mouse ST 1.0 arrays as per the manufacturer’s instructions. Microarray data were subjected to quality control, normalization and differential expression analysis in limma.

first: Yogesh

last: Jeelall

first: Peter

last: Humburg

first: Emma

last: Batchelor

first: Sarp

last: Kaya

first: Hee-Min

last: Yoo

first: Keisuke

last: Horikawa

first: Christopher

middle: C

last: Goodnow


title: Loss of Function Mutations in ETS2 Repressor Factor (ERF) Reveal a Balance Between Positive and Negative ETS Factors Controlling Prostate Oncogenesis

first: Rohit

last: Bose


title: Gene expression profile of Dclk1+ murine normal intestinal and tumor cells

status: Public on Jun 05 2017

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary: Accumulating evidence has shown the existence of tumor stem cells, and many researchers and clinicians are focusing on the therapeutic potential of targeting tumor stem cells. Previously, we reported that doublecortin like kinase 1 (Dclk1) marks tumor stem cells but not normal stem cells in ApcMin/+ mouse intestine, and that selective ablation of Dclk1+ cells results in collapse of the intestinal tumors without any apparent damages in the normal mucosa. Here, we sought to clarify gene expresion profile of Dclk1+ cells by microarray analyses in mouse normal intestinal epithelium and ApcMin/+ mouse intestinal tumors. Microarray analyses demonstrated that genes related to microtubules and actin cytoskeleton (e.g., Rac2) were highly expressed in Dclk1+ normal intestinal and tumor cells. We found the expression of Src family kinases (i.e., Hck, Lyn, Csk, and Ptpn6) in Dclk1+ normal intestinal and tumor cells.

overall_design: Dclk1- Tumor was extracted from intestinal tumors of a Dclk1CreERT2/+; ApcMin/+ mouse at the age of 17 weeks. Dclk1+ Tumor was extracted from intestinal tumors of seven Dclk1CreERT2/+; ApcMin/+ mice at the age of more than 16 weeks. Dclk1- Normal was extracted from normal small intestine of a Dclk1CreERT2/+ mouse at the age of 26 weeks. Dclk1+ Normal was extracted from normal small intestines of two Dclk1CreERT2/+ mice at the age of 26 weeks.

first: Yuichi

last: Yamaga

first: Akihisa

last: Fukuda

first: Yuki

last: Nakanishi

first: Takahisa

last: Maruno

first: Tsutomu

last: Chiba

first: Hiroshi

last: Seno


title: The effect of titanium dioxide (TiO2) nano-objects, and their aggregates and agglomerates greater than 100 nm (NOAA) on yeast under UV irradiation

city: Gifu

first: Akihiro

last: Moriyama

address: 1-1, Yanagido

institute: Gifu University

summary: Today, nanoparticles are used in various commercial products. One of the most common nanoparticles is titanium dioxide (TiO2). It has a catalytic activity and UV absorption (λ<400 nm), and it generates reactive oxygen species (ROS). The catalytic activity of TiO2 nanoparticle is capable of killing a wide range of microorganisms. In the environment, nanoparticles form structures consisting of primary particles, and their aggregates and agglomerates. These compounds are defined NOAA (nano-objects, and their aggregates and agglomerates greater than 100 nm). The unique properties of TiO2 nanoparticles can be maintained in the environment, thus, the growing use of TiO2 nanoparticles is raising concerns about the environmental risks. The assessment of biological and ecological effects of TiO2-NOAA is necessary. In our previous study, we assessed the effect of TiO2-NOAA on microbes by using Saccharomyces cerevisiae and Escherichia coli. It was shown that TiO2-NOAA decomposed methylene blue under UV irradiation. It suggested that TiO2-NOAA generated ROS under UV irradiation. However, TiO2-NOAA did not show growth inhibition in minimal agar medium under UV irradiation. By adding TiO2-NOAA in medium, colony formation was observed with UV intensity that inactivates microbes. Moreover, TiO2-NOAA adsorbed microbes. These results suggested that the amount of ROS generated by TiO2-NOAA was not enough to inactivate microbes, and TiO2-NOAA might protect microbes from UV. In this study, we assessed the effect of TiO2-NOAA in more detail by using S. cerevisiae. We used DNA microarray analysis for qualitative assessment. Further, we carried out quantitative assessment by using Real Time RT-PCR method for characteristic genes in DNA microarray analysis. To compare yeast cells in various conditions, six kinds of treatment conditions were prepared (Condition 1. adsorbed fraction to TiO2-NOAA under UV, 2. non-adsorbed fraction to TiO2-NOAA under UV, 3. adsorbed fraction to TiO2-NOAA without UV, 4. non-adsorbed fraction to TiO2-NOAA without UV, 5. irradiated UV and 6. negative control). From the result of DNA microarray analysis, the most number of genes was altered in Condition 1, followed by Condition 3 and 5. The genes related to oxidative stress, and the genes related to synthesis of trehalose and glycogen were significantly up-regulated of yeast cells in Condition 1 and 5, and Condition 1 and 3, respectively. These results suggest that yeast cells suffer oxidative stress by TiO2-NOAA under UV, and they also suffer membrane damage by TiO2-NOAA itself, as a result, they reserve energy sources. From the result of Real Time RT-PCR, genes related to oxidative stress (GRE2, SOD2) were up-regulated in Condition 1 and 3, however, these expression levels in each condition were not significant. And genes related to synthesis of trehalose and glycogen (GSY1, TPS2) were up-regulated in Condition 1 and 3. These results suggest that oxidative stress is caused not by TiO2-NOAA but by UV. It is also suggested that yeast cells were damaged at their membranes by TiO2-NOAA, as a result, genes related to synthesis of trehalose and glycogen were up-regulated. Thus, we suggest that the effect of TiO2-NOAA on yeast cells under UV irradiation is greater due to TiO2-NOAA itself than due to ROS generated by TiO2-NOAA.

overall_design: Series contains four hybridization results from independent biological samples respectively in five conditions (Condition 1. adsorbed fraction to TiO2-NOAA under UV, 2. non-adsorbed fraction to TiO2-NOAA under UV, 3. adsorbed fraction to TiO2-NOAA without UV, 4. non-adsorbed fraction to TiO2-NOAA without UV, 5. irradiated UV and 6. negative control).

first: Ikuho

last: Yamada

first: Hitoshi

last: Iwahashi


title: Expression data from ileum of adult male wild type and Slc51a knockout mice, where the basolateral membrane bile acid transporter subunit encoded by Slc51a is inactivated.

status: Public on Jun 02 2017

city: Atlanta

first: Paul

last: Dawson

state: GA

address: 1760 Haygood Drive

department: Division of Pediatric GI/Hepatology

institute: Emory University

summary:
To identify the dysregulated pathways responsible for the intestinal adaptive response in the Slc51a knockout mice.
We used microarrays to detail the ileal gene expression of wt and Slc51a knockout mice and identified distinct classes of up- and down-regulated genes in Slc51a knockout mice.

overall_design: To isolate ileal tissue to isolate RNA for microarray analysis of gene expression.

first: Jianing

last: Li

middle: A


title: A ROLE FOR DYSTONIA-ASSOCIATED GENES IN SPINAL GABAERGIC INTERNEURON CIRCUITRY

status: Public on Jun 03 2017

first: Jarret

last: Weinrich

state: New York

address: 1233 York Ave 16G

institute: Weill Cornell Graduate School of Medical Sciences

summary: Spinal interneurons are critical modulators of locomotor circuit function. In the dorsal spinal cord, a set of interneurons called GABApre presynaptically inhibits proprioceptive sensory afferent terminals, thus negatively regulating sensory-motor signaling. While deficits in presynaptic inhibition have been inferred in human locomotor diseases, including dystonia, it remains unknown whether GABApre circuit components are altered in these conditions. In this study, we use developmental timing to show that GABApre neurons are a late Ptf1a-expressing subclass and localize to the intermediate spinal cord. Using a microarray screen to identify genes expressed in this intermediate population, we find the kelch-like family member Klhl14, implicated in dystonia through its direct binding with torsion-dystonia related protein Tor1a. Furthermore, in Tor1a mutant mice in which Klhl14 and Tor1a binding is disrupted (Dyt1ΔE), GABApre-sensory afferent synapse formation is impaired. Our findings suggest a potential contribution of GABApre neurons to the deficits in presynaptic inhibition observed in dystonia.

overall_design: 9 total samples were analyzed: three replicates (1, 2, and 3) with samples from 3 regions of the spinal cord (D, I, and V) each.

first: Julia

last: Kaltschmidt

first: Juliet

last: Zhang

first: Jeffrey

middle: B

last: Russ

first: John

last: Comer

first: Praveen

last: Bommareddy

first: Richard

last: DiCasoli

last: Wright

first: Yuqing

first: Peter

middle: J

last: van Roessel


title: The deacetylase activity of histone deacetylase 3 is required for productive VDJ recombination and B cell development

city: Nashville

first: Scott

last: Hiebert

state: TN

address: 2220 Pierce Ave

department: Biochemistry

institute: Vanderbilt University

sample_organism:
Drosophila melanogaster
Mus musculus

platform_organism:
Drosophila melanogaster
Mus musculus


title: The deacetylase activity of histone deacetylase 3 is required for productive VDJ recombination and B cell development [ATAC-seq]

summary: Histone deacetylase 3 (HDAC3) is the catalytic component of NCoR/SMRT corepressor complexes that mediate the actions of transcription factors implicated in the regulation of B cell development and function. We crossed Hdac3 conditional knockout mice with Mb1-Cre knockin animals to delete Hdac3 in early progenitor B cells. The spleens of Hdac3F/-Mb1-Cre+/- mice were virtually devoid of mature B cells, and B220+CD43+ B cell progenitors accumulated within the bone marrow. Quantitative deep sequencing of the immunoglobulin heavy chain locus from B220+CD43+ populations identified a defect in VHDJH recombination with a severe reduction in productive rearrangements, which directly corresponded to the loss of pre-B cells from Hdac3D/- bone marrow. For Hdac3D/- B cells that did show productive VDJ rearrangement, there was significant skewing toward the incorporation of proximal VH gene segments and a corresponding reduction in distal VH gene segment usage. While transcriptional effects within these loci were modest, Hdac3D/- progenitor cells displayed global changes in chromatin structure that likely hindered effective distal V-DJ recombination. Re-introduction of wild type Hdac3 restored normal B cell development, whereas an Hdac3 point mutant lacking deacetylase activity failed to complement this defect. Thus, the deacetylase activity of Hdac3 is required for the generation of mature B cells.

overall_design: Bone marrow was isolated from Hdac3+/+   controls or Hdac3 deleted  mice at 8 weeks of age.  B220+CD43+ B cells were isolated from marrow by FACS and cells.  5% drosophila S2 cells were spiked into 50,000 sorted cells prior to initiation of ATAC protocol.

middle: W

first: Kristy

middle: R

last: Stengel


title: In vivo hyperoxia versus normoxia neonatal rat lung MSCs

city: Rotterdam

first: Jennifer

last: Collins

address: Wytemaweg 80

department: Pediatric Surgery

institute: Erasmus University Medical Center

summary: Background:  Bronchopulmonary dysplasia (BPD), the most common complication of extreme preterm birth, can be caused by oxygen-related lung injury and is characterized by impaired alveolar and vascular development. Mesenchymal stromal cells (MSCs) have lung protective effects. Conversely, BPD is associated with increased MSCs in tracheal aspirates.  Objective: To determine whether endogenous lung (L-)MSCs are perturbed in a well-established oxygen-induced rat model mimicking BPD features.  Methods:  Rat pups were exposed to room air or 95% oxygen from birth to postnatal day 10. On day 12, CD146+ L-MSCs were isolated and characterized according to the International Society for Cellular Therapy criteria. Epithelial and vascular repair potential were tested by scratch assay and endothelial network formation respectively, immune function by mixed lymphocyte reaction assay. Microarray analysis was performed using the Affymetrix GeneChip and gene set enrichment analysis (GSEA) software.   Results: CD146+ L-MSCs isolated from rat pups exposed to hyperoxia had decreased CD73 expression and inhibited lung endothelial network formation. CD146+ L-MSCs indiscriminately promoted epithelial wound healing and limited T-cell proliferation. Expression of potent anti-angiogenic genes of the axonal guidance cue and CDC42 pathways was increased after in vivo hyperoxia, whereas genes of the anti-inflammatory JAK/STAT and lung/vascular growth promoting Fibroblast Growth Factor (FGF) pathways were decreased.   Conclusions:  In vivo hyperoxia exposure alters the pro-angiogenic effects and FGF expression of L-MSCs.  Additionally, decreased CD73 and JAK/STAT expression suggest decreased immune function. L-MSC function may be perturbed and contribute to BPD pathogenesis. These findings may lead to improvements in manufacturing exogenous MSCs with superior repair capabilities.

overall_design: For the microarray analysis, CD146+ L-MSCs (passage 2) were expanded in 5% O2 (physiological oxygen) culture conditions and collected for RNA isolation. The experiment consisted of two groups: L-MSCs isolated from P12 rat pups exposed to 95% O2 from P0 to P10 (n=3) and L-MSCs isolated from P12 room air control pups (n=3).

first: Marissa

last: Lithopoulos

first: Claudia

last: dos Santos

first: Nahla

last: Issa

first: Marius

last: Möbius

first: Caryn

last: Ito

first: Shumei

last: Zhong

first: Arul

last: Vadivel

first: Bernard

last: Thébaud


title: The Staphylococcus aureus α-Acetolactate Synthase ALS Confers Resistance to Nitrosative Stress

city: Groningen

first: Anne

middle: de

last: Jong

address: Nijenborgh 7

department: Molecular Genetics

institute: university of Groningen

summary: Staphylococcus aureus is a worldwide pathogen that colonizes the human nasal cavity and is a major cause of respiratory and cutaneous infections. In the nasal cavity, S. aureus thrives with high concentrations of nitric oxide (NO) produced by the innate immune effectors and has available for growth slow metabolizing free hexoses, such as galactose. Here, we have used deep sequencing transcriptomic analysis (RNA-Seq) and 1H-NMR to uncover how S. aureus grown on galactose, a major carbon source present in the nasopharynx, survives the deleterious action of nitric oxide. We observed that, like on glucose, S. aureus withstands high concentrations of NO when using galactose. However, most likely this is achieved through a distinct metabolism that relies on the increased production of amino acids, such as glutamate, threonine and branched-chain amino acids. Moreover, we found that under these conditions the α-acetolactate synthase (ALS) enzyme, which converts pyruvate into α-acetolactate, plays a role in the resistance of S. aureus to NO. However, the role of ALS is not restricted to galactose but also extends to cells growing on glucose. The results suggest that ALS prevents intracellular acidification, promoting the production of branched-chain amino acids and activation of the TCA cycle. We show that ALS contributes to the successful infection of murine macrophages. Furthermore, ALS is also shown to contribute to the resistance of S. aureus to beta-lactam antibiotics such as methicillin and oxacillin.

sample_organism: Staphylococcus aureus subsp. aureus USA300_FPR3757

overall_design: mRNA profiles of S. aureus galactose-grown cells unexposed and exposed for 3h with NO were generated by deep sequencing, in duplicate, using an Ion Proton™ Sequencer.

first: Sandra

middle: M

last: Carvalho

last: de Jong

first: Tomas

last: Kloosterman

first: Oscar

middle: P

last: Kuipers

first: Lígia

last: Saraiva


title: Transcriptomic analysis of Arthrobacter sp. CGMCC 3584 responding to dissolved oxygen for cAMP production

city: Nanjing

first: Huanqing

last: Niu

state: Jiangsu

address: No.30, Puzhu South Road

institute: Nanjing Tech University

summary: Arthrobacter sp. CGMCC 3584 are able to produce high yields of extracellular cyclic adenosine monophosphate (cAMP), which plays a vital role in the field of treatment of disease and animal food, during aerobic fermentation. DNA array-based transcriptional analysis of Arthrobacter cells was conducted to elucidate the higher productivity of cAMP under high oxygen supply. Results showed that 14.1% and 19.3% of the whole genome genes were up-regulated and down-regulated notably, respectively. The largest group with altered transcriptional levels belonged to the group involved in carbohydrate transport and metabolism. Other large functional groups of differentially expressed genes changed significantly included amino acid transport and metabolism, inorganic ion transport and metabolism and transcription.

platform_organism:
Clostridium acetobutylicum
Arthrobacter sp.

overall_design: The agitations were set as 150 r/min and 350 r/min to construct low oxygen supply and high oxygen supply conditions, respectively, a 5-L fermenter. Samples (three biological replicates) were respectively collected at 12h, 24h, 36h and 48h under two different oxygen supply conditions for transcriptional analysis. Equal samples of each of the independent biological replicates were mixed together for DNA microarray analysis. Genes expression level ratios (high oxygen supply/low oxygen supply) ≥ 2 or ≤ 0.5 were considered to be significantly regulated.

first: Dong

last: Liu

first: Yong

last: Chen

first: Hanjie

last: Ying


title: Effects of RNase Y mutation on operon organization of Streptococcus pyogenes NZ131

city: Portland

first: Jens

last: Kreth

state: OR

address: 3181 SW Sam Jackson Park Rd., #L595

department: Restorative Dentistry

institute: Oregon Health and Science University

summary:
Purpose: RNase Y is a major enzyme responsible for mRNA degradation in Streptococcus pyogenes. The goals of this study are to understand whether RNase Y plays a role in operon transcription of S. pyogenes NZ131 by using RNA-seq analysis.

Methods: S. pyogenes mRNA profiles of wild type (WT) and RNase Y mutant (∆rny) were generated by deep sequencing, in duplicate, using Illumina Hiseq 2000. The sequence reads were aligned to the S. pyogenes genome using Bowtie2. The aligned files were sorted to BAM format and indexed using Samtools. The read depth of each base was derived from BAM files using BEDtools. Operon organization of S. pyogenes WT and ∆rny strains were predicted based on base reads.

Results: A total of 11 to 12 billion reads were obtained from each sample. More than 99% of these reads were mapped to the S. pyogenes genome. Predictions of operon organization using WT and  ∆rny samples showed little difference between the two strains.

Conclusions: Our result shows that the mutation of RNase Y does not affect the operon organization of S. pyogenes NZ131.

overall_design: Operon organization of S. pyogenes NZ131 wild type (WT) and RNase Y mutant (∆rny) are compared by using RNA-seq analysis

first: Chen

last: Zhiyun

first: Kreth

last: Jens


title: microRNA-143/145 loss induces Ras-signaling and cooperates with Pten-deficiency to promote basal-like breast cancer

first: Sharon

last: Wang

address: 67 College Street Room 456

institute: University of Toronto

type:
Expression profiling by array
Genome variation profiling by array

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


title: Pam3 generates immunosupressive macrophages using p38, MAPK and PTGS2 signaling

city: Frederick

first: Dennis

last: Klinman

state: Maryland

address: 1050 Boyles St

department: Cancer and Inflammation Program

summary: The gene expression pattern of PAM3 treated monocytes was compared to that of M-CSF, the conventional method of generating immunosuppressive macrophage.  Pathways regulated by NF-KB and Akt played a central role in the general process of monocyte to macrophage differentiation.  p38 MAPK and PTGS2 signaling biased this process towards the generation of immunosuppressive rather than pro-inflammatory macrophage whereas ERK and JNK were essential for Pam3 but not M-CSF driven maturation

overall_design: DR+ monocytes from six different donors were sorted from PBMC then cultured in the presence of Pam, mCSF 3 or left unstimulated for 4 hours. For microarray experiments total RNA was extracted, amplified into aRNA and coupled to Cy5.  Similarly amplified RNA from universal RNA was coupled to Cy3 and used as a reference for each array.

first: Defne

last: Bayik

first: Daniela

last: Verthelyi

first: Lydia

last: Haile

first: Debra

last: Tross


title: Genes directly regulated by NF-κB in human hepatocellular carcinoma HepG2

first: Wei

last: Dai

address: Sipailou 2#,Nanjing, Jiangsu Province, P. R. China

institute: Southeast University


title: microRNA-143/145 loss induces Ras-signaling and cooperates with Pten-deficiency to promote basal-like breast cancer [gene expression]

summary:
The tumor suppressor PTEN is frequently inactivated in breast and other cancers; yet, germ-line mutations in this gene induce non-malignant hamartomas, indicating dependency on additional cooperating events.  Here we show that most tumors derived from conditional deletion of mouse Pten in mammary epithelium are highly differentiated and lack transplantable tumor initiating cells (TICs) capable of seeding new tumors following orthotopic injection of FACS-sorted or tumorsphere cells. A rare group of poorly differentiated tumors did harbour transplantable TICs. These transplantable tumors exhibited distinct molecular classification, signaling pathways, chromosomal aberrations and mutational landscape, as well as reduced expression of microRNA-143/145. Stable knockdown of miR-143/145 conferred tumorigenic potential upon poorly transplantable Pten-deficient tumor cells through a mechanism involving induction of RAS signaling, leading to increased sensitivity to MEK inhibition. In humans, miR145-deficiency significantly correlated with elevated RAS pathway activity in basal-like breast cancer, and patients with combined PTEN/miR-145 loss or PTEN-loss/RAS pathway activation exhibited poor clinical outcome. These results underscore a selective pressure for combined PTEN loss together with miR-145 loss or high RAS-pathway activity in aggressive forms of breast cancer, and a need to identify and prioritize these tumors for aggressive therapy.
Expression data comparing 2 types of Pten-deficient tumors (spindle and poorly differentiated) with other models of mouse mammary tumors

overall_design: Wap-Cre:Ptenfl/fl tumors was compared with MMTV-Neu,and wild-type mammary glands

first: Jeff

first: Eldad

last: Zacksenhaus


title: LIN-41 and OMA ribonucleoprotein complexes mediate a translational repression-to-activation switch controlling oocyte meiotic maturation and the oocyte-to-embryo transition in Caenorhabditis elegans

city: Minneapolis

first: Micah

last: Gearhart

state: MN

address: 6-160 Jackson Hall, 321 Church St.

department: Genetics, Cell Biology and Development

institute: University of Minnesota

summary: An extended meiotic prophase is a hallmark of oogenesis. Hormonal signaling activates the CDK1/cyclin B kinase to promote oocyte meiotic maturation, which involves nuclear and cytoplasmic events. Nuclear maturation encompasses nuclear envelope breakdown, meiotic spindle assembly, and chromosome segregation. Cytoplasmic maturation involves major changes in oocyte protein translation and cytoplasmic organelles and is poorly understood. In the nematode Caenorhabditis elegans, sperm release the major sperm protein (MSP) hormone to promote oocyte growth and meiotic maturation. Large translational regulatory ribonucleoprotein (RNP) complexes containing the RNA-binding proteins OMA-1, OMA-2, and LIN-41 regulate meiotic maturation downstream of MSP signaling. To understand the control of translation during meiotic maturation, we purified LIN-41-containing RNPs and characterized their protein and RNA components. Protein constituents of LIN-41 RNPs include essential RNA-binding proteins, the GLD-2 cytoplasmic poly(A) polymerase, the CCR4-NOT deadenylase complex, and translation initiation factors. RNA sequencing defined mRNAs associated with both LIN-41 and OMA-1, as well as sets of mRNAs associated with either LIN-41 or OMA-1. Genetic and genomic evidence suggests that GLD-2, which is a component of LIN-41 RNPs, stimulates the efficient translation of many LIN-41-associated transcripts. We analyzed the translational regulation of two transcripts specifically associated with LIN-41 that encode the RNA regulators SPN-4 and MEG-1. We found that LIN-41 represses translation of spn-4 and meg-1, whereas OMA-1 and OMA-2 promote their expression. Upon their synthesis, SPN-4 and MEG-1 assemble into LIN-41 RNPs prior to their functions in the embryo. This study defines a translational repression-to-activation switch as a key element of cytoplasmic maturation.

overall_design: Transcripts present in cell lysates and immunoprecipitates from the OMA-1 and LIN-41 ribonuclear-protein complexes were profiles by RNA-seq in duplicate

first: Tatsuya

last: Tsukamoto

first: David

last: Greenstein


title: Genes directly regulated by NF-κB in human hepatocellular carcinoma HepG2 [RNA-seq]

summary: Over activation of NF-κB has close relationship with hepatitis and hepatocellular carcinoma (HCC). In this study, by manipulating NF-κB activity with its recognized activator TNFα and using ChIP-seq and RNA-seq techniques, we identified 699 NF-κB direct target genes (DTGs) in a widely used HCC cell line, HepG2, including 399 activated and 300 repressed genes. In these NF-κB DTGs, 216 genes (126 activated and 90 repressed genes) are among the current HCC gene signature. Functional annotation revealed that NF-κB DTGs in HepG2 cell are mainly related with many typical NF-κB-related biological processes, such as immune system process, response to stress, response to stimulus, defense response and signaling pathways of NF-kappa B. Some NF-κB DTGs are also involved in Hepatitis C and B pathways. The NF-κB DTGs were further confirmed by detecting the NF-κB binding and expression of 14 genes with ChIP-PCR and RT-PCR.

overall_design: RNA-seq was performed to determine the transcriptional effects of uninduced, TNFα-induced and siRNA and TNFα dually treated HepG2 cells with two biological replicates.

first: Jian

last: Wu

first: Shuyan

last: Zhang

first: Bingjie

last: Shi

first: Xinhui

last: Xu

first: Danyang

first: Jinke


title: Expression data from Nup210-depleted C2C12 myotubes

city: La Jolla

first: Andrew

middle: P.

last: Hodges

state: California

address: 10901 N Torrey Pines Rd

department: Bioinformatics Shared Resource

institute: SBP

summary: We used microarrays to identify the genome-wide changes in gene expression of post-mitotic muscle cells when Nup210 is depleted

overall_design: C2C12 cells were induced to differentiated and then infected with control or specific-shRNA carrying lentiviruses 36 hs later. Cells were allowed to differentiate for an additional 48hs and collected for microarray assays.

first: Maximiliano

last: D'Angelo