title: Imiquimod has strain-dependent effects in mice and does not uniquely model human psoriasis

city: Ann Arbor

first: William

middle: R

last: Swindell

state: MI

address: 1500 E. Medical Center Drive

department: Dermatology

institute: University of Michigan

summary: Background: Imiquimod (IMQ) produces a cutaneous phenotype in mice frequently studied as an acute model of human psoriasis. Whether this phenotype depends on strain or sex has never been systematically investigated on a large scale. Such effects, however, could lead to conflicts among studies, while further impacting study outcomes and efforts to translate research findings.  Methods: RNA-seq was used to evaluate the psoriasiform phenotype elicited by IMQ in both sexes of 7 mouse strains (C57BL/6J, BALB/cJ, CD1, DBA/1J, FVB/NJ, 129X1/SvJ and MOLF/EiJ).   Results: In most strains, IMQ altered gene expression in a manner consistent with human psoriasis, partly due to innate immune activation and decreased homeostatic gene expression. The IMQ response of MOLF males was aberrant, however, with decreased expression of differentiation-associated genes (elevated in other strains). Key aspects of the IMQ response differed between the two most commonly studied strains (BALB/c and C57BL/6). Compared with BALB/c, the C57BL/6 phenotype showed increased expression of genes associated with DNA replication, IL-17A activation and CD8+ T cells, but decreased expression of genes associated with interferon signaling and CD4+ T cells. Surprisingly, although IMQ-induced expression shifts mirrored psoriasis, correspondence was similar or better for other human skin diseases (e.g., eschars, acne, atopic dermatitis). For BALB/c, MOLF, and 129X1 strains, genes altered by IMQ corresponded better to those altered in human skin infections or wounds compared with those altered in psoriasis lesions.  Conclusions: These findings demonstrate strain-dependent aspects of IMQ dermatitis that warrant consideration in planning and interpreting experimental studies. We have further shown that IMQ does not uniquely model psoriasis but in fact triggers a core set of pathways active in diverse skin diseases. These observations challenge the view of IMQ dermatitis as a mouse phenotype uniquely appropriate for studying psoriasis as opposed to other human skin conditions.

overall_design: RNA-seq was used to investigate the psoriasiform phenotype that develops following topical IMQ treatment in male and female mice of 7 laboratory mouse strains (C57BL/6J, BALB/cJ, CD1, DBA/1J, FVB/NJ, 129X1/SvJ and MOLF/EiJ). Mouse back skin was treated with 62.5 mg AldaraTM (5% IMQ) or a non-toxic lanolin-derived occlusion cream (CTL) once per day for 5 consecutive days. Mice were sacrificed on day 6 and skin biopsies were collected. Overall, RNA-seq was used to profile transcriptomes of 56 CTL- and IMQ-treated skin samples (7 strains × 2 sexes × 2 treatments; n = 2 samples per strain/sex/treatment combination).

first: Johann

last: Gudjonsson

first: Nicole

last: Ward


title: Systematic Functional Perturbations Uncover a Prognostic Genetic Network Driving Human Breast Cancer

status: Public on Mar 23 2017

city: Boston

first: Kenneth

middle: N

last: Ross

state: MA

address: 450 Brookline Ave., Rm M640

department: Pediatric Oncology

country: USA

institute: Dana-Farber Cancer Institute

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.

overall_design: Refer to individual Series


title: The function of c-Fos in hepatocarcinogenesis

city: Vienna

first: Rainer

last: Hamacher

address: Waehringer Gürtel 18-20

department: Dept. for Internal Medicine I / Oncology

country: Austria

institute: Medical University Vienna - AKH

summary: c-Fos, a member of the stress-activated Activator Protein 1 (AP-1) transcription factor family, is expressed in human hepatocellular cancer (HCC). Using genetically engineered mouse models (GEMMs) we show that hepatocyte-specific expression of c-Fos leads to a proliferative, de-differentiated phenotype, whereas hepatocyte-specific deletion of c-Fos protects against diethylnitrosamine (DEN)-induced liver cancer. Furthermore, c-Fos-expressing livers resemble human HCCs based on expression profiles. In the present RNA seq, we intend to analyze the transcriptomic profile of livers at 2 and 4 mo hepatocyte-specific c-Fos expression compared to the corresponding age-matched control mice. Moreover, we analyzed livers of mice with hepatocyte-specific deletion c-Fos at 48h after DEN treatment compared to identically treated control mice.

overall_design: The general idea was to analyze the transcriptomic profile of hepatocyte-specific c-Fos over-expressing livers at 2 and 4 mo expression. Hereby, a hepatocyte-specific doxycycline (Dox)-switchable mouse model was (LAP-tTA; col1a1:Tet-O-fosFlag) was generated and c-Fos expression was induced at the age of 3 weeks by removal of doxycycline. Each sample LaptTA-fos-MUT represents an individual hepatocyte-specific c-fos expressing mouse at the indicated time-point and the corresponding identically treated control mouse LaptTA-fos-CO. Moreover, the transcriptomic profile of livers with hepatocyte-specific deletion of c-Fos at 48h after diethylnitrosamine (DEN)-induced liver cancer initiation was analyzed.  For hepatocyte-specific knock-out of c-Fos, mice with conditional alleles of c-fos and the Alfp-Cre transgene were used. Control mice only carried the Alfp-Cre transgene. At the age of 8 weeks these mice were injected with 100mg/kg DEN.  Each sample AlfpCre-fos-MUT_DEN represents an individual hepatocyte-specific c-fos knock-out mouse 48h after DEN and the identically treated control mouse AlfpCre-fos-CO-Cre+_DEN.

first: Osvaldo

last: Graña

first: Erwin

middle: F

last: Wagner


title: Nascent RNA sequencing reveals a dynamic global transcriptional response at genes and enhancers to the natural medicinal compound celastrol

status: Public on Mar 22 2017

city: Cold Spring Harbor

first: Noah

middle: E

last: Dukler

state: NY

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

summary: Most studies of responses to transcriptional stimuli measure changes in cellular mRNA concentrations.  By sequencing nascent RNA instead, it is possible to detect changes in transcription in minutes rather than hours, and thereby distinguish primary from secondary responses to regulatory signals.  Here, we describe the use of PRO-seq to characterize the immediate transcriptional response in human cells to celastrol, a compound derived from traditional Chinese medicine that has potent anti-inflammatory, tumor-inhibitory and obesity-controlling effects.  Our analysis of PRO-seq data for K562 cells reveals dramatic transcriptional effects soon after celastrol treatment at a broad collection of both coding and noncoding transcription units.  This transcriptional response occurred in two major waves, one within 10 minutes, and a second 40-60 minutes after treatment.  Transcriptional activity was generally repressed by celastrol, but one distinct group of genes, enriched for roles in the heat shock response, displayed strong activation.  Using a regression approach, we identified key transcription factors that appear to drive these transcriptional responses, including members of the E2F and RFX families.  We also found sequence-based evidence that particular TFs drive the activation of enhancers.  We observed increased polymerase pausing at both genes and enhancers, suggesting that pause release may be widely inhibited during the celastrol response.   Our study demonstrates that a careful analysis of PRO-seq time course data can disentangle key aspects of a complex transcriptional response, and it provides new insights into the activity of a powerful pharmacological agent.

overall_design: Samples taken a 6 time points, 2 replicates each

first: Adam

last: Siepel

first: John

last: Lis


title: Long-range signaling at the neural-intestinal axis promotes organismal heme homeostasis

status: Public on Mar 24 2017

city: Bethesda

first: Michael

last: Krause

state: MD

address: Bld. 5, Rm B104, 5 Memorial Dr.

institute: NIH/NIDDK

summary:
Purpose:  The goal of this study is to understand how dbl-1, which is made primarily in neurons, and hrg-7, which is exclusively made in the intestine, contribute to systemic heme homeostasis.
Methods: mRNA profiles of late L4 dbl-1(nk3) and hrg-7(tm6801) mutant C. elegans fed OP50 E. coli or OP50 + 50µM heme were compared to mRNA profiles from wildtype (WT) broodmates.  Profiles were generated with single-end 50 base reads obtained using Illumina’s HiSeq 2500.  Bioinformatics quality control was performed followed by alignment of reads to the ce10 reference genome using Tophat2, version 2.1.0.  We found differentially expressed genes using Cufflinks 2, version 2.2.1 with a cutoff of 0.05 on False Discovery Rate (FDR).
Results: We found a substantial overlap of genes regulated by both dbl-1 and hrg-7, including 49 heme-responsive genes (hrgs) in low heme (OP50) and 11 hrgs in high heme (OP50 + 50µM).  Additionally, our data indicate crosstalk between dbl-1 and hrg-7 signaling.  dbl-1 directly regulates hrg-7 expression, while hrg-7 regulates three components of the dbl-1 signaling pathway.
Conclusions: Our study demonstrates that communication between the neuron and intestine is essential for heme homeostasis.  Specifically, we report that HRG-7 functions as a secreted signaling factor which communicates intestinal heme status with extraintestinal tissues by integrating a DBL-1/BMP -dependent response from the neurons to transcriptionally regulate genes involved in heme homeostasis.
Cellular requirements for heme are fulfilled by a cell’s internal capacity to synthesize its own heme in a cell-autonomous manner.  However, growing evidence in vertebrates predicts that cellular heme levels in animals are not only maintained by heme synthesis, but also by distally located proteins that could signal systemic heme requirements to an inter-organ heme trafficking network through cell-nonautonomous regulation.  Using C. elegans, a genetically and optically amenable animal model for visualizing heme-dependent signaling, we show that HRG-7, an aspartic protease homolog, mediates inter-organ signaling between the intestine and neuron.  Loss of hrg-7 results in robust expression of intestinal heme importers and, remarkably, this occurs even under heme replete conditions when such transporters are not normally expressed.  HRG-7 functions as a secreted signaling factor, independent of a functional enzymatic active site, and communicates intestinal heme status with extraintestinal tissues by integrating a DBL-1/BMP -dependent response from the neurons to transcriptionally regulate intestinal heme homeostasis.  Given the evidence indicating that mechanisms of heme transport are conserved across metazoa, it is conceivable that the cell-nonautonomous signaling framework that we uncovered in C. elegans may have functional relevance for inter-organ regulation of iron and heme metabolism in humans.

overall_design: Comparison of mRNA profiles from dbl-1(nk3) mutant C. elegans vs. wildtype (WT) broodmates and hrg-7(tm6801) mutants vs (WT) broomates fed OP50 E. coli or OP50 + 50µM heme.  Biological duplicates were analyzed for dbl-1(nk3) mutants and (WT) broodmates.  Biological triplicates were analyzed for hrg-7(tm6801) mutants and (WT) broodmates.

first: Iqbal

last: Hamza

middle: W


title: Identification of HDA15-PIF1 as a Key Repression Module Directing the Transcriptional Network of Seed Germination in the Dark

city: Guangzhou

first: Xuncheng

last: Liu

state: Guangdong

address: Xingke Road, Tianhe District

country: China

institute: South China Botanical Garden, Chinese Academy of Sciences

summary: our analysis uncovered the role of histone deacetylation in light-regulated seed germination process and identified that HDA15-PIF1 as a key repression module directing the transcription network of seed germination

overall_design: whole genomic transcriptome analysis of wild type(Col) and hda15 mutant in FR(Dark) conditions,in triplicate, using an mRNA Seq Kit (Illumina).

first: Dachuan

last: Gu


title: Sirtuin 1-chromatin-binding dynamics point to a common mechanism regulating microglial inflammatory targets in SIV infection and in the aging brain

city: San Diego

first: Maria

middle: Cecilia

last: Marcondes

state: CA

address: 3525 John Hopkins Ct. #200

institute: San Diego Biomedical Research Institute

summary: Microglia are critical regulators in neurodegenerative disorders. Since HIV infection results in neurological perturbations that are similar to those in aging, we examined microglial changes that might resemble aging, using SIV infection in rhesus macaques to model neuroAIDS.  We found that Sirt-1, a molecule that impacts survival and health in many models, was decreased in infected macaques. The role of Sirt-1 in neuroAIDS is unknown. We hypothesized that Sirt-1 silencing functions are affected by SIV. Mapping of Sirt-1 binding patterns to chromatin revealed that the number of Sirt-1-bound genes was 29.6% increased in microglia from infected animals with mild neuropathology, but 51% was decreased in severe neuropathology, compared to controls. Sirt-1-bound genes in controls largely participate on neuroinflammation. Promoters of type I IFN pathway genes IRF7, IRF1, IFIT1, and AIF1, showed Sirt-1 binding in controls, which was consistently lost after infection, together with higher transcription. This was also found in brains from old uninfected animals, suggesting a common regulation. Sirt-1 blockage in vitro modulated IRF7, IRF1 and AIF1 levels. Our data suggests that Sirt-1-inflammatory gene silencing is disturbed by SIV, resembling aging in brains. These findings may impact neurological consequences of HIV infection, aggravated and overlapping with the aging process.

overall_design: We investigated the hypothesis that in SIV infection a Sirt-1-regulated gene network may be involved in producing phenotypic changes in innate immune cells of the CNS, which are associated to the development of an inflammatory environment, and that may resemble the phenotype found in the aging population. To understand that, we used Chromatin Immunoprecipitation (ChIP) and NextGen ChIP-sequence9 to investigate genome-wide Sirt-1 binding targets, in microglia from control and SIV-infected macaques, and the changes produced by infection were compared in animals that exhibited or not severe encephalitis. After the identification of relevant targets, we further investigated the protein expression and distribution of selected candidate molecules in the brain of uninfected but aging monkeys (>19 years old). A ChIP reaction was carried out with 30ug of microglia chromatin and anti-Sirt-1 antibody (Millipore) extracted from 6 older rhesus macaques and 6 younger rhesus macaques. The ChIP DNA was processed into an Illumina ChIP-Seq library and sequenced to generate >2 million reads, which were aligned to the M.mulatta genome annotation (MacaM/Oct 2014 assembly) and 6.2 million unique aligns (removed duplicates) were obtained.

middle: G

first: Nikki

last: Bortell


title: Gene expression profiling of human MSC-educated macrophages vs. classical macrophages from bone marrow and blood

city: Madison

first: Christian

last: Capitini

state: WI

address: 1111 Highland Ave, WIMR 4137

institute: University of Wisconsin

summary: In comparison to MØs, MEMs have increased expression of the inhibitory molecules PD-L1, PD-L2, in addition to markers of alternatively activated macrophages: CD206 and CD163. RNA-Seq analysis of MEMs, as compared to MØs, show a distinct gene expression profile that positively correlates with multiple pathways important in tissue repair. MEMs also show increased expression of IL-6, TGF-β, Arginase-1, CD73, and decreased expression of IL-12 and TNF-α. We show that IL-6 secretion is controlled in part by the COX-2, arginase and JAK1/STAT1 pathway. When tested in vivo, we show that human MEMs significantly enhance survival from lethal GVHD, and improve survival of mice from radiation injury.

overall_design: Human macrophages were isolated from PBMCs and then exposed to MSCs. RNA was isolated then subjected to RNA-Seq.

first: Andrea

middle: B

last: Moffitt

middle: M


title: Next Generation Sequencing analysis using splenic DCs freshly isolated from Wild Type and TBK1-DKO mice

city: Houston

first: Shao-cong

last: Sun

state: TX

address: 7455 Fannin St.

department: Immunology

institute: MD Anderson Cancer Center

summary: In this experiment, we analyzed the gene expression profile of WT and TBK1-deficient splenic DCs by RNA sequencing based on three independent samples. The results revealed significant alterations in the expression of a number of genes, most notably the enhanced expression of a large subset of IFN-responsive genes in the TBK1-deficient DCs.

overall_design: Fresh splenic DC mRNA profiles of 8-week old wild type (WT) and TBK1-DKO mice were generated by deep sequencing, in triplicate

first: Yichuan

last: Xiao

first: Qiang

last: Zou

first: Xiaoping

last: Xie

first: Ganiraju

last: Manyam

first: Li

last: Zhang

first: Shao-Cong


title: Differential miRNA expression profiling of A549 cells infected with influenza A virus

city: Beijing

first: Bing-hui

last: Xia

address: No.20 Dongda Street, Fengtai District

institute: Beijing Institute of Biotechnology

summary: To further understand the roles of miRNA during influenza A virus infection, we performed miRNA profiling in human alveolar adenocarcinoma cell lines, A549 cells, infected with influenza A virus A/Beijing/501/2009(H1N1) and A/goose/Jilin/hb/2003(H5N1).

overall_design: A549 cells were either mock-infected or infected with influenza virus H1N1 or H5N1 at a MOI of 5. Total RNAs were isolated at 8 and 24 h post-infection and analysed for miRNA expression profiles. Each group was run in triplicate.

first: Binghui

first: Xiaowei

last: Zhou

first: Peitang

last: Huang


title: Sex differences in the molecular signature of the developing mouse hippocampus

city: Tallahassee

first: Joseph

middle: Ligon

last: Bundy

state: FL

address: 1115 W Call St

department: Department of Biomedical Sciences

institute: Florida State University

summary: A variety of neurological disorders, including Alzheimer’s disease, Parkinson’s disease, major depressive disorder, dyslexia and autism, are differentially prevalent between females and males. To better understand the possible molecular basis for the sex-biased nature of neurological disorders, we measured both mRNA and protein in the hippocampus of female and male mice at 1, 2, and 4 months of age with RNA-sequencing and mass-spectrometry respectively. Differential expression analyses identify 2699 genes that are differentially expressed between animals of different ages. 198 transcripts are differentially expressed between females and males at one or more ages. The number of transcripts that are differentially expressed between females and males is greater in adult animals than in younger animals.  Additionally, we identify 69 transcripts that show complex and sex-specific patterns of temporal regulation across all ages, 8 of which are heat-shock proteins. We also find a modest correlation between levels of mRNA and protein in the mouse hippocampus (Rho = 0.53). This study adds to the substantial body of evidence for transcriptomic regulation in the hippocampus during postnatal development.  Additionally, this analysis reveals sex differences in the transcriptome of the developing mouse hippocampus, and further clarifies the need to include both female and male mice in longitudinal studies involving molecular changes in the hippocampus.

overall_design: Hippocampal mRNA from 1, 2, and 4 month old male and female B6 mice were analyzed by RNA sequencing of 5 biological replicates using an Illumina HiSeq 2500

middle: L

first: Cynthia

last: Vied

first: Richard

middle: S

last: Nowakowski


title: Cohesin-dependent compaction of mitotic chromosomes in budding yeast

city: Cambridge

first: Anton

last: Goloborodko

state: Massachusetts

address: 77 Massachusetts Ave., E25-524

department: Physics

institute: MIT

summary: The extreme length of chromosomal DNA requires organizing mechanisms to both promote functional genetic interactions and ensure faithful chromosome segregation when cells divide. Microscopy and genome wide contact frequency (Hi-C) analyses indicate that intra-chromosomal looping of DNA is a primary pathway of chromosomal organization during all stages of the cell cycle (Dekker, J. & Mirny, L. . Cell 164, 1110–1121 (2016). Although the enzymatic pathways required for DNA loop formation are yet to be fully characterized, the activity of the SMC family of proteins has been consistently associated with this process in interphase and mitosis. Here we use Hi-C to study the reorganization of budding yeast chromosome conformation in early mitosis and the role of SMCs in this process. Using polymer simulations, we find that the differences between interphase and mitotic Hi-C maps can be explained by the formation of intra-chromosomal (cis-) loops in mitotic chromosomes. We demonstrate that mitotic SMC cohesin activity is required for formation of cis-loops, independently of sister-chromatid cohesion. In contrast, SMC condensin is not required for loop formation in these early mitotic cells. Rather condensin activity promotes distinct higher order structures in the chromosomes at centromeres and in the rDNA proximal regions. Thus we demonstrate that cohesin-dependent cis-loops provide the primary higher order organization of budding yeast mitotic chromosomes, independently of condensin and sister chromatid cohesion.

overall_design: This submission contains the following Hi-C experiments: 2 biological replicates of WT S. cerevisiae cells arrested in G1 and metaphase; 2 replicates of cohesin and condensin temperature-sensitive mutants arrested in metaphase; 1 replicate of cdc45-degron cells arrested in early mitosis and 1 replicate of temperature-sensitive cohesin mutant cdc45-degron cells arrested in early mitosis.

first: Stephanie

middle: A

last: Schalbetter

first: Geoffrey

last: Fudenberg

first: Jon-Matthew

last: Belton

first: Catrina

last: Miles

first: Miao

last: Yu

first: Job

last: Dekker

first: Leonid

last: Mirny

first: Jonathan

last: Baxter


title: MS2-affinity purification coupled with RNA sequencing (MAPS) reveals S. aureus RsaA sRNA targetome

status: Public on Mar 21 2017

city: Strasbourg

first: Stefano

last: Marzi

address: 2 allée Konrad Roentgen

department: UPR9002 - IBMC

country: France

institute: CNRS

summary: The virulon of Staphyloccocus aureus is controlled by intricate connections between transcriptional and post-transcriptional regulators including proteins and small non coding RNAs (sRNAs). Most of the sRNAs regulate gene expression through base-pairings with mRNAs. Here, we have applied and adapted the MS2-affinity purification approach coupled to RNA sequencing (MAPS) to determine the targetome of RsaA sRNA of S. aureus, known to repress the synthesis of the transcriptional regulator MgrA. Several mRNAs were enriched with RsaA expanding its regulatory network. Besides mgrA, several of these mRNAs encode a family of SsaA-like enzymes involved in peptidoglycan metabolism and the secreted anti-inflammatory FLIPr protein. Thus RsaA behaves as an attenuator of acute infections and shows that MAPS can also be easily applied in Gram-positive bacteria for the identification of sRNA targetome.

overall_design: Affinity purification of in vivo regulatory complexes coupled with high throughput RNA sequencing methodology or MAPS standing for “MS2 affinity purification coupled to RNA sequencing”. Identification of RNAs co-purified with MS2-RsaA in a S. aureus ΔRsaA strain. MS2 alone was used as control.

first: Pascale

last: Romby

first: Isabelle

last: Caldelari


title: Examination of E. faecalis toxin-antitoxin (TA) toxin Fst function utilizing a pheromone-inducible expression vector with tight repression and large dynamic range

city: Vermillion

first: Keith

last: Weaver

state: SD

address: 414 E. Clark Street

department: Division of Basic Biomedical Sciences

institute: University of South Dakota Sanford School of Medicine

summary: Tools for regulated gene expression in E. faecalis are extremely limited. In this study we describe the construction of an expression vector for E. faecalis, designated pCIE, utilizing the PQ pheromone-responsive promoter of plasmid pCF10. We demonstrate that this promoter is tightly repressed, responds to nanogram quantities of the peptide pheromone, and has a large dynamic range. To demonstrate its utility, the promoter was used to control expression of the toxic peptides of two par family toxin-antitoxin loci present in E. faecalis, parpAD1 of the pAD1 plasmid and parEF0409 located on the E. faecalis chromosome. Results demonstrated differences in the modes of regulation of toxin expression and in the effects of toxins of these two related systems. We anticipate that this vector will be useful for further investigation of par TA system function as well as the regulated expression of other genes in E. faecalis.

overall_design: Examination of cellular effects of toxin FstEF0409 at two different levels compared to unexposed cells and comparison of the effects of the two related toxins FstEF0409 and FstpAD1. Average of two biological replicates.

first: K

first: D

last: Manias


title: The transcription factor Foxo1 controls germinal center B cell proliferation in response to T cell help

city: Suita-shi

first: Takeshi

last: Inoue

state: Osaka

address: 3-1 Yamadaoka

country: Japan

institute: Osaka University

summary: Germinal center (GC) B cells cycle between two states, the light zone (LZ) and the dark zone (DZ), and in the latter they proliferate and hypermutate their immunoglobulin genes. How this functional transition takes place is still controversial. In this study, we demonstrate that ablation of Foxo1 after GC development led to the loss of the DZ GC B cells and disruption of the GC architecture. Mechanistically, even upon provision of adequate T cell help, Foxo1-deficient GC B cells showed less proliferative expansion than controls. Moreover, we found that the transcription factor BATF was transiently induced in LZ GC B cells in a Foxo1-dependent manner and that deletion of BATF similarly led to GC disruption. Thus, our results are consistent with a model where the switch from the LZ to the DZ is triggered after receipt of T cell help, and suggest that Foxo1-mediated BATF up-regulation is at least partly involved in this switch.

overall_design: mRNA profiles of wild-type DZ, LZ, and Foxo1-deficient GC B cells were generated by deep sequencing in triplicate, using Illumina HiSeq 1500.

first: Chie

last: Kawai

first: Osamu

last: Ohara

first: Tomohiro

last: Kurosaki


title: RNAseq analysis in peripheral blood leukocytes between control (normoxia) and hypoxic mice +/- bacterial infection.

city: Edinburgh

first: John

middle: Paterson

last: Thomson

address: Crewe Road

department: MRC Human Genetics Unit

country: United Kingdom

institute: University of Edinburgh

summary: RNAseq analysis between control (normoxia) and hypoxic mice +/- bacterial infection. Murine peripheral blood leukocytes (1x10^6/condition) were lysed and RNA extracted using Qiagen mini total RNA isolation protocols (Qiagen, Germany). Samples were treated with DNase (Ambion), and sample integrity verified on the Agilent Bioanalyser with the RNA Nano chip. Illumina Tru-seq paired end strand specific sequencing (Illumina, USA) was carried out by on a NextSeq-550 sequencer (Edinburgh Clinical Research Facility, Western General Hospital, Edinburgh, Scotland, UK). 500ng of Total RNA underwent ribosomal RNA depletion (rRNA) prior to purification, fragmentation, random hexamer cDNA generation and purification with AMPure XP beads (Beckman-Coulter, USA). Multiple indexing adapters were ligated to ds cDNA with subsequent hybridisation onto flow cells, and DNA fragment enrichment by 15 cycle PCR for sequencing. Completed libraries were quantified by qPCR using the KAPA Illumina Library Quantification Kit (Illumina, USA) before multiplexing in two equimolar pools and running on two flow cells on the Illumina NextSeq 550. The resulting FastQ files were mapped to the reference genome (mm9) using the Tophat alignment tool (V1) on Illumina Basespace software and reads per kilobase per million (RPKM) scores calculated.

overall_design: We carry out paired end, strand specific RNAseq prior to sequencing on NextSeq-550 sequencer to report on the transcriptional landscape in replicate Murine peripheral blood leukocytes isolated from the following mice : normoxia naive control (n=2), normoxia naive bacterial infected (n=2), hypoxia (10% O2) exposed controls (n=2) and hypoxia (10% O2) exposed bacterial infected (n=2).

middle: P

first: Sarah

last: Walmsley

first: Richard

last: Meehan


title: Transcriptome analysis of wild-type and Yap-deficient embryonic lungs by RNA-Seq

city: SAN FRANCISCO

first: Chuwen

last: Lin

state: California

address: 555 MISSION BAY BLVD S, RM 212A

institute: University of California San Francisco

summary: We extracted total RNA from wild-type and Yap-f/f;Shh-Cre/+ embryonic lung 12.5 dpc, and perform RNA-Seq.

overall_design: mRNA profiles of embrynic lungs from wild type and Yap mutant littermates at 12.5 dpc were generated by deep sequencing in triplicate.

first: Pao-Tien

last: Chuang


title: Prioritization of Contaminants of Emerging Concern in wastewater treatment plant discharges using transcriptional effects in caged fish

city: Vicksburg

first: Natalia

last: Vinas

state: MS

address: 3909 Halls Ferry Rd

institute: Mississippi State University

summary: We applied an effects-based approach to determine if the impact of specific chemicals in mixtures discharged by waste water treatment plants could be linked to well-defined gene expression changes in exposed fish. Fathead minnows were deployed in cages for 2, 4, or 8 days at three locations near two WWTP discharge sites in the Saint Louis Bay, Duluth, MN and one upstream control site. The impact of 51 chemicals detected in the surface water on gene expression in ovaries of caged fish was determined using exposure activity ratios, existing knowledge on chemical:gene relationships, and analysis of gene expression co-variance with surface water chemistry. Thirty-two chemicals could be linked to gene expression and 12 were confirmed by other sources such as the Comparative Toxicogenomics Database (CTD). Chemical:gene associations determined by co-variation were supported by exposure activity ratios sufficient to cause biological effects, known chemical:gene associations from CTD, and upstream regulator analysis of the Ingenuity knowledge base. The analyses provided multiple lines of evidence that bisphenol A and estrone are likely sources of estrogenic effects on gene expression found at the study sites.

overall_design:
Fish were deployed at four sites in the St Louis River near Duluth, MN, USA. One site upstream of the WWTPs (Fond du Lac, FDL; N 46° 39.517, W 92° 16.951) was chosen as ‘reference’ location. Two sites were located near the Western Lake Superior Sanitary District (WLSSD) discharge. One (WLSSD-1; N 46° 45.460, W 92° 7.227) was located 10 m from the discharge, while the second (WLSSD-2; N 46° 45.347, W 92° 7.213) was located further in the main channel, 100 m from the discharge.  A fourth site was located near the Superior Municipal Treatment Plant discharge (SMTP; N 46° 43.758, W 92° 4.125). A detailed description of the caging system can be found in Kahl et al.32. Briefly, three buoys anchored to the bottom sediment at each site. Three cages of fish, each containing 6 male and 6 female adult fathead minnows (5-6 month old) were attached to a buoy and its anchor, suspending cages at a depth of 1-2 m. After 2, 4, or 8 d of exposure, fish from two cages, each from a separate buoy, were transferred into separate buckets containing surface water collected at the appropriate site, and transported to the laboratory (transit time <60 min) for sampling. Animals were not fed during transit nor in the field. Fish were individually anesthetized and euthanized with MS-222 (Argent, Redmond, WA, USA), weighed, and evaluated for any external lesions. Blood and tissues (liver, gonad) were collected and stored at -80°C until extracted and analyzed.

The normalized data were not available at the time of submission and therefore not included in these records.

first: T

last: Habib

first: L

last: Escalon

first: E

last: Perkins

last: Thomas

first: J

last: Cavallin

first: M

last: Weberg

last: Hughes

last: Jensen

last: Kahl

last: Villeneuve

first: G

last: Ankley


title: Transcriptome Analysis of Arabidopsis thaliana and Changes of Glucosinolates Metabolism Pathway Induced by Flg22

city: Harbin

first: xinxin

last: yu

address: gongbin street

institute: northeast agricultural university

summary:
Purpose: The goals of this study are to analyze the transcriptome of Arabidopsis thaliana treated after flg22 and to find changes of glucosinolate metabolism genes after treatment.
Methods: Total mRNA of 10 day wild-type Arabidopsis seedlings that were treated with and without flg22( final concentrations 1μmol/L) in 1/2 MS medium for 4h, were extracted respectively. Each sample was harvested in three independent biological replicates with equal weight and mixed ,subsequently sequencing. The sequence reads that passed quality filters were mapped to the Arabidopsis_thaliana genome (TAIR10.18).Then the mapping genes were used for the abundance and functional analysis.
Results: We mapped about 45 million and 52 million sequence reads of control sample and treatment sample to the Arabidopsis_thaliana  genome (TAIR10.18) and identified total 23,413 genes with Botiw/TopHat workflow. Comparison of the two samples showed 1,200 differentially expressed genes (DEGs), including 290 down-regulated and 910 up-regulated genes. The DEGs were associated with energy metabolism, amino acid metabolism and biosynthesis of secondary metabolites. After flg22 treatment, genes involved in indolic glucosinolate biosynthesis pathway were up-regulated significantly，which is further demonstrated by Real Time RT-PCR, while aliphatic glucosinolate pathway almost had no change,  indicating the important role of indolic glucosinolates in plant defense responses.
Conclusion: Our study provides the overall genetic resource of Arabidopsis_thaliana after treated by flg22 to date. These data will pave the way for further studies about deeply understand pathogen induced defense and the contribution of indolic glucosinolates.

overall_design: Two samples mRNA profiles of Arabidopsis thaliana seedlings treated and not treated by flg22 to final concentrations 1μmol/L for 4h ,were generated by deep sequencing, three biological replicates pooling together for each sample, using Illumina Hiseq 2000 platform.

first: Xinxin

last: Yu

first: Jinjun

last: Gao

first: Yong

last: Li

first: Jing


title: Transcriptome mapping and Hfq RIP-seq of Neisseria meningitidis

city: Würzburg

first: Lars

last: Barquist

state: Bayern

address: Josef-Schneider-Straße 2 / Bau D15

country: Germany

institute: Helmholtz Institute for RNA-based Infection Research

summary: Neisseria meningitidis is a human commensal that occasionally causes life-threatening infections such as bacterial meningitis and septicemia. Despite experimental evidence that gene regulation as well as the expression of small non-coding RNAs (sRNAs) affect meningococcal virulence, the organization of its transcriptome, including in particular the biogenesis of sRNAs and their mode of action, is only poorly understood. Here, we addressed these issues using a combination of high-throughput technologies. We applied differential RNA-seq (dRNA-seq) to produce a single-nucleotide resolution map of the primary transcriptome of N. meningitidis strain 8103. Our dRNA-seq analysis predicted 1,625 transcriptional start sites (TSS) including 65 non-coding RNA transcripts, of which 20 were further validated by Northern analysis. This allowed for the discovery of a novel CRISPR-associated sRNA with a Cas9-independent biogenesis. Genome-wide mapping of σ 70-dependent and independent promoters revealed that classical Escherichia coli-like σ70 promoter are absent in most of the protein coding genes in meningococci. The majority of the 706 primary TSSs (pTSSs) were associated with coding sequences, including 382 pTSS obtained for single genes and 240 pTSSs obtained for genes located in operons. By Hfq RNA immunoprecipitation sequencing (RIP-seq) we identified a large Hfq-centered post-transcriptional regulatory network comprising 24 sRNAs and 407 potential mRNA targets, and rifampicin stability assays demonstrated that Hfq binding confers enhanced stability on sRNAs. We finally confirmed the interactions of two sRNAs and their cognate target mRNA in vivo. Both directly repress prpB encoding a methylisocitrate lyse which was previously shown to be involved in meningococcal colonization of the human nasopharynx.The combination of both high-throughput approaches thus creates a compendium that not only provides a valuable data resource, but also allows for a better understanding of meningococcal transcriptome organization and riboregulation with implications for colonization of the human nasopharynx.

overall_design: differential RNA-seq at two different growth phases; Hfq RIP-seq

first: Nadja

last: Heidrich


title: Gene expression profiles of activin-A-induced human Tr1-like regulatory T cells and T conventional cells.

city: Athens

first: Anastasia

last: Kotanidou

address: 45 Ipsilantou Str

department: 1st Department of Critical Care Medicine and Pulmonary Services

country: Greece

institute: Evangelismos Hospital, National and Kapodistrian University of Athens

summary: The aim of our studies was to investigate the molecular mechanisms underlying the differentiation of human Tr1-like regulatory T cells by the cytokine activin-A. We employed high-throughput sequencing of the whole T cell transcriptome and characterized the  transcriptional profile of activin-A-induced human Tr1-like regulatory T cells (act-A-iTr1 cells) and compared it to those of Tconventional cells (Tconv). Our studies identified novel  immunoregulatory molecules/pathways involved in the differentiation and effector function of human act-A-iTr1 cells.

overall_design: Total RNA was extracted from human CD4+ T conventional and act-A-iTr1 cells. Two biological replicates were used for each condition. RNA-sequencing libraries were generated using the Illumina’s TruSeq RNA Library Preparation Kit v2 and the sequencing was implemented with HiSeq 2000.

first: Sofia

last: Tousa

first: Maria

last: Semitekolou

first: Ioannis

last: Morianos

first: Aggelos

last: Banos

first: Aikaterini

last: Trochoutsou

first: Tess

last: Brodie

first: Nikolaos

last: Poulos

first: Konstantinos

last: Samitas

last: Kapasa

first: Dimitris

last: Konstantopoulos

first: Giannis

last: Paraskevopoulos

first: Mina

last: Gaga

first: Catherine

last: Hawrylowicz

first: Federica

last: Sallusto

first: Georgina

last: Xanthou


title: Transcriptomic screen to identify genes regulated by Store-operated calcium entry in Drosophila pupal nervous system

city: Bangalore

first: Gaiti

last: Hasan

address: GKVK Campus,

country: India

institute: NCBS, TIFR

summary: Transcriptional regulation by Store-operated Calcium Entry (SOCE) is well studied in non-excitable cells. However, the role of SOCE has been poorly documented in neuronal cells with more complicated calcium dynamics. Previous reports demonstrated a requirement of neuronal SOCE for Drosophila flight. We identified the early pupal stage to be critical and used RNA-sequencing to identify SOCE mediated gene expression changes in the developing Drosophila pupal nervous system. We down-regulated dStim, the endoplasmic reticular calcium sensor and a principal component of SOCE in the nervous system for a 24h period during pupal development, and compared wild type and knockdown transcriptional profiles, immediately after knockdown as well as after a 36h recovery period.  We found that dStim knockdown altered the expression of a number of genes. We also characterized one of the down-regulated genes, Ral for its role in flight. Thus, we identify neuronal SOCE as a mechanism that regulates expression of a number of genes during the development of the pupal nervous system. These genes can be further studied in the context of pupal nervous system development.

overall_design: mRNA sequencing from two biological replicates each of wild type and dStim knockdown pupal brains at two time points - 36h APF (post 24h knockdown) and at 72h APF (Post knockdown and recovery)

first: Shlesha

last: Richhariya


title: Small chromosomal regions position themselves autonomously according to their chromatin class

city: Rotterdam

first: Harmen

middle: Jan George

last: van de Werken

address: Wytemaweg 80

department: Urology

country: Netherlands

institute: Erasmus MC

summary: The spatial arrangement of chromatin is linked to the regulation of nuclear processes. One striking aspect of nuclear organization is the spatial segregation of heterochromatin and euchromatin domains. The mechanisms of this chromatin segregation are still poorly understood. In this work we investigated the link between the primary genomic sequence and chromatin domains. We analyzed the spatial intranuclear arrangement of a human artificial chromosome (HAC) in a xenospecific mouse background and compared it to an orthologous region in the context of its native mouse chromosome. The two orthologous regions include segments that can be assigned to three major chromatin classes according to their gene abundance and repeat repertoire: (i) gene-rich and SINE-rich euchromatin, (ii) gene-poor and LINE/LTR-rich heterochromatin and (iii) gene-depleted and satellite DNA-containing constitutive heterochromatin. We show using FISH and 4C-seq technologies that chromatin segments ranging from 0.6 to 3 Mb cluster with segments of the same chromatin class. As a consequence, the chromatin segments acquire corresponding positions in the nucleus irrespectively of their chromosomal context, thus rendering this a chromosome segment autonomous property. Interactions with the nuclear lamina are also partially retained in the HAC but demonstrate less autonomy. Taken together, our results show that genomic segments autonomously fold and position themselves relative to other genomic parts, suggesting that the three major classes of chromatin constitute a blueprint for the overall nuclear architecture.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: We applied 4C-seq on several viewpoints in circular and linear human artificial chromosome (HAC) and its homologous region in human and mouse

middle: J

first: Josien

middle: C

last: Haan

first: Yana

last: Feodorova

first: Dominika

last: Bijos

first: An

last: Weuts

first: Koen

last: Theunis

first: Sjoerd

last: Holwerda

first: Wouter

last: Meuleman

first: Ludo

last: Pagie

first: Katharina

last: Thanisch

first: Heinrich

last: Leonhardt

first: Peter

last: Marynen

first: Bas

last: van Steensel

first: Thierry

last: Voet

last: de Laat

first: Irina

last: Solovei

first: Boris

last: Joffe


title: Circulating microRNAs on Day 60 of pregnancy

city: Easter Bush

first: Jason

last: Ioannidis

state: Midlothian

address: Easter Bush Veterinary Campus

department: Developmental Biology

institute: The Roslin Institute

type: Non-coding RNA profiling by high throughput sequencing

summary: Poor reproductive performance remains a major issue in the dairy industry, with extremely low calving rates (34 %) affecting milk production, profitability and the economy in general. Early pregnancy detection can help identify non-pregnant animals within three weeks of insemination, minimizing delays and shortening calving intervals. However current pregnancy detection methods are not accurate enough to support such reproductive management programs. MiRNAs have been proposed as non-invasive biomarkers of pregnancy and several reproductive diseases in humans. We previously identified miR-26a as a potential early pregnancy biomarker in cattle. In the current study, using miRNA sequencing, we identified and validated differentially expressed miRNAs on Day 60 of pregnancy compared to Day 0 (non-pregnant), and we investigated the expression of these validated miRNAs in early pregnancy aiming to identify additional early pregnancy biomarker candidates. The expression levels of selected miRNAs which are differentially expressed during pregnancy will also be investigated as part of this study.

overall_design: In this experiment a total of 22 bovine plasma samples were analyzed using Illumina miRNA sequencing. These samples were collected at two time-points during pregnancy from each of 11 animals (Day 0, non-pregnant baseline and Day 60 of pregnancy) in a repeated-measures design. Therefore this study included 11 biological replicates for each of the two time-points analyzed.

first: Xavier

last: Donadeu


title: Etv target genes in mouse alveolar type II cells

city: South San Francisco

first: Sarah

middle: K

last: Kummerfeld

address: 1 DNA Way

institute: Genentech

summary:
RNA was purified from lung tissue and isolated Alveolar type II cells.
The "SAMPLE_ID" sample description is a sample identifier internal to Genentech.
The ID of this project in Genentech's ExpressionPlot database is PRJ0005064

overall_design: RNA from lung and Alveolar type II cells of the following mutant mice: (1) KRaswt/d12;RosaCreERT2 n=4 (2) KRaswt/d12; Etv5loxp/loxp;RosaCreERT2 n=4 (3) KRaswt/d12; Etv4KO/KO; Etv5loxp/loxp;RosaCreERT2 n=4

first: Zhen

last: Zhang


title: microRNA profiling in normal and hyperplastic human and murine parathyroid glands

city: Jerusalem

first: Iddo

middle: Z.

last: Ben-Dov

address: Ein Kerem

department: Nephrology and Hypertension

country: Israel

institute: Hadassah Medical Center

summary: Secondary hyperparathyroidism (SHP) is a common complication of chronic kidney disease (CKD) and correlates with morbidity and mortality. In this study we profiled microRNAs (miRNA) in parathyroids from different experimental SHP models and uremic patients and studied the function of specific miRNA using antagonizing oligonucleotides (anti-miRs). miRNA profiles established by small RNA deep sequencing showed that human, rat and mouse parathyroids share the same most abundant miRNAs. Principal component analyses clearly segregated parathyroids from SHP rats from normal rats, based on their miRNA expression profiles. Similar findings were observed in hyperplastic parathyroids from CKD patients compared to normal parathyroids from patients without kidney disease. We identifed specific parathyroid miRNAs that were dysregulated in all experimental SHP models studied. let-7i was decreased and miR-141 and miR-148a were increased in the parathyroids of rats with prolonged CKD induced by an 8 w adenine high phosphorus diet. Down-regulation of let-7 by anti-miRs increased PTH secretion in normal and in CKD rats, as well as in parathyroid organ cultures. Anti-miR-148 prevented the increase in serum PTH in CKD rats and decreased secreted PTH in parathyroid organ cultures. Our findings characterized parathyroid miRNA profiles and demonstrated conservation of the abundant miRNAs in different species. The evolutionary conservation of abundant miRNAs and their regulation in SHP suggest that miRNAs are important for parathyroid function and the development of SHP. Down-regulation of let-7 and miR-148 affects PTH secretion in vivo and in vitro, suggesting a role for these miRNAs in SHP. We propose that let-7 restrains while miR-148 promotes PTH secretion. In CKD, the decrease in parathyroid let-7 and the increase in miR-148 miRNAs may contribute to the development of SHP.

sample_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Between 2 and 6 biological replicates are studied in each parathyroid control and hyperplastic group in humans and several different murine models (normal rats, short-, intermediate- and long-term uremia in rats, hypocalcemia in rats and normal mice), and in additional several human thyroid specimens; altogether 55 samples.

first: Vitali

last: Shilo

first: Irit

last: Levi

first: Tally

last: Naveh-Many

middle: Z


title: Transcriptomic and Epigenomic analysis of Huntington's disease and control patient iPSC-derived neural cells

status: Public on Mar 20 2017

city: Irvine

first: Ryan

middle: Gar-Lok

last: Lim

address: 845 Health Sciences Rd.

department: MIND

institute: UC Irvine

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

overall_design: Refer to individual Series


title: CHANGES IN DNA ACCESSIBILITY OCCUR IN PUTATIVE ENHANCER REGIONS OF A SUBSET OF T CELL MEMORY RESPONSIVE GENES

city: Bruce

first: Kristine

last: Hardy

state: ACT

address: University of Canberra

country: Australia

institute: University of Canberra

summary: Naive T cells exist in a resting state until activated by the antigen they are specific for. Upon activation, T cells produce cytokines and other proteins necessary to fight infections and proliferate to produce more T cells specific for that antigen. Some of these descendants will be long-lived memory T cells, which will return to a resting state but are primed for a more rapid and robust immune response upon re-exposure to the same antigen. The molecular mechanisms responsible for this enhanced response are still unclear. Using a Jurkat cell culture model of transcriptional memory we have investigated the possibility that previously stimulated cells have differences in DNA accessibility compared to non-stimulated cells. We used Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) in conjunction with high throughput sequencing to identify changes in DNA accessibility in response to stimulation, resting and re-stimulation. We found that although many of the changes in accessibility that were induced upon stimulation, were reversed upon stimulus withdrawal and resting of the cells, a large proportion remain accessible and a subset of these are near genes that have enhanced induction upon re-stimulation. Interestingly the accessibility associated with these ‘memory-responsive’ genes was not always at the transcription start site but sometimes occurred in putative enhancers of these genes. The role of Protein Kinase C in mediating these changes in accessibility was also examined using the inhibitor rottlerin.

overall_design: 8 different biological samples were analysed. FAIRE samples and a Total Input sample were obtained.

first: Sudha

last: Rao

first: WenJuan

last: Tu


title: ChIP-seq analysis of the LuxR-type regulator VjbR reveals novel insights into the Brucella virulence gene expression network

city: Buenos Aires

first: Sieira

last: Rodrigo

address: Av. Patricias Argentinas 435

country: Argentina

institute: Fundacion Instituto Leloir

summary: We report ChIP-seq and RNA-seq analyses of the Brucella abortus LuxR-type transcription factor VjbR

overall_design: The analyses were performed with wild-type or vjbR mutant bacteria incubated under conditions mimicking the intracellular environment encountered by Brucella within the host cell.

first: Rodrigo

last: Sieira


title: mRNAseq of Huntington's disease and control patient iPSC-derived neural cells

summary:
Purpose: The goals of this study are to compare the transcriptomic profile (mRNA-seq) of HD  and control patient iPSC-derived neural cells to identify alterations in gene expression
Methods:  RNA were isolated from HD and control iPSC-derived neural cells. mRNAseq using Illumina Truseq mRNA PolyA+ v2 lib prep and Hiseq 2000. Statistical difference in mRNA levels were calculated with subsequent GO and pathway analysis
Results: mRNAseq and statistical analysis revealed 1869 differentially expressed genes between HD and control iPSC-derived neural cells.
Conclusions: Our study shows 1869 differentially expressed genes between HD and control iPSC-derived neural cells, and reveals gene networks that relevant to the mechanism of HD pathogenesis.

overall_design: mRNA profiles of HD and control iPSC-derived neural cells were generated by mRNAseq, in duplicate, using Illumina Truseq mRNA PolyA+ v2 and Illumina Hiseq 2000.

first: Leslie

last: Thompson


title: SMN deficiency in spinal muscular atrophy causes widespread intron retention and DNA damage

city: Cambridge

first: John

last: Carulli

address: 115 Broadway

department: Computational Biology and Genomics

institute: Biogen

summary: Spinal muscular atrophy is the leading genetic cause of infant mortality and is caused by homozygous loss of the SMN1 gene.  We investigated global transcriptome changes in the spinal cord of inducible SMA mice. SMN depletion caused widespread retention of introns with weak splice sites or belonging to the minor (U12) class.  We further demonstrated accumulation of DNA double strand breaks in the spinal cord of SMA mice and in human SMA cell culture models.  DNA damage was partially rescued by suppressing the formation of R-loops, which accumulated over retained introns.  We propose that instead of single gene effects, pervasive splicing defects caused by SMN deficiency trigger a global DNA damage and stress response, thus compromising motor neuron survival.

overall_design:
mRNA-seq: Total spinal cord from SMA and Control mice (rescue experiment) at d20 and d30; human SH-SY5Y cells expressing SMN or Control shRNA for 7d; human iPSC-derived motor neurons expressing SMN or Control shRNA for 5d; total spinal cord from SMA and Control mice (induction experiment) at d10, d20, and d30.
DRIP-seq:  SH-SY5Y cells expressing SMN or Control shRNA for 7d and immunoprecipitated with S9.6 antibody targeting RNA:DNA hybrids.

first: Mohini

last: Jangi


title: H3K27ac ChIP-seq BTIC vs. DGC

city: cleveland

first: xiuxing

last: wang

state: OH

address: 9500 euclid ave

institute: cleveland clinic

summary: Brain tumor initiating cells (BTICs), also known as cancer stem cells, hijack high-affinity glucose uptake normally active in brain to maintain energy demands in dynamic tumor microenvironments. Using unbiased metabolomics and genomic analyses, we discovered that de novo purine synthesis is functionally upregulated in BTICs, mediating glucose-sustained anabolic metabolism. Inhibiting purine synthesis abrogated BTIC growth, self-renewal, and in vivo tumor formation by depleting intracellular pools of purine nucleotides, supporting purine synthesis as potential therapeutic point of fragility. In contrast, differentiated brain tumor cells retained proliferative potential with targeting of purine biosynthetic enzymes, suggesting a selective dependence in BTICs. Upstream transcriptional activation of purine synthesis is mediated by MYC. Elevated expression of purine synthetic enzymes correlates with poor prognosis in glioblastoma patients. Collectively, our results suggest that a stem-like state in brain cancer is associated with metabolic reprogramming to fuel tumor hierarchy, revealing potential BTIC cancer dependencies amenable to targeted therapy.

overall_design: We report associated H3K27ac ChIP-seq data from matched BTICs and serum-differentiated glioma cell models.

first: Xiuxing

last: Wang

first: Stephen

last: Mack

first: Jeremy

middle: N

last: Rich


title: RNA-seq of Arabidopsis thaliana seedlings growing in the presence of a bacterial synthetic community under full and low phosphate conditions [PBI]

city: Piracicaba

first: Paulo

last: Teixeira

state: SP

address: Av. Pádua Dias, 11

department: Biology

country: Brazil

institute: University of São Paulo (ESALQ/USP)

summary: This study evaluates the transcriptome of Arabidopsis thaliana seedlings growing in the presence of a 35-member bacterial SynCom under different phosphate availability

overall_design: Arabidopsis seeds (wild-type Col-0 and the mutants phr1 and phr1 phl1) were germinated on Johnson medium containing 0.5 % sucrose with 1 mM Pi (in the form of KH2PO4) for 7 days in the vertical position. Plants were then transferred to 50 µM Pi (low) or 625 µM Pi (high) media (without sucrose) alone or with the Synthetic Community at 10E5 c.f.u / mL for another 12 days before harvesting. Plants were grown in a growth chamber in a 15-h dark/9-h light regime (21°C day /18°C night). The experiment includes a total of ten biological replicates for Col-0 and phr1 and six for phr1 phl1 from five independent experiments

first: Gabriel

last: Castrillo

first: Sur

last: Herrera Paredes

first: Jeff

last: Dangl


title: Direct transcriptional integration of phosphate starvation and disease resistance in response to a root microbiome


title: Epigenetics of Huntington's disease and control patient iPSC-derived neural cells

first: Ryan

last: Lim

summary: The goals of this study are to compare the epigenetic states of HD  and control patient iPSC-derived neural cells to identify differences in chromatin state. We performed ChIP-seq in these cell lines for H3K4me3, H3K27ac, and H3K36me3 in these cell lines and found significant epigenetic differences between HD and control-derived cells.

overall_design: ChIP-seq for H3K4me3, H3K27ac, and H3K36me3 was performed in 4 HD iPSC-derived neural cell lines (2 biological replicates each from 2 patients) and 3 control cell lines.

first: Amanda

last: Kedaigle

first: Ernest

last: Fraenkel


title: Sequencing analysis of m6A-methylated RNAs responding to UV

city: Chicago

first: zhike

last: lu

state: IL

address: 5801 South Ellis Avenue

department: department of chemistry

institute: University of Chicago

summary: m6A RNA immunoprecipitation experiments were conducted to identify RNAs that are directly m6A-methylated by the METTL3 methylatransferase specifically in response to UV.

overall_design: WT and METTL3 KO U2OS cells were subjected (plus UV condition) or not (minus UV condition) to a 50 J dose of UVC irradiation. Following irradiation, cells were lyzed and total RNAs were extracted. Poly A+ RNAs were isolated and subjected to m6A RNA precipitation.

first: Benoit

last: Laurent

first: Sigrid

last: Nachtergaele

first: Zhike

last: Lu


title: Omega-6 and omega-3 oxylipins are implicated in soybean oil-induced obesity

city: Elk Grove

first: joseph

last: dhahbi

state: ca

address: 9700 West Taron Drive

department: Medical Education

institute: California Northstate University College of Medicine

summary: Soybean oil consumption is increasing worldwide and parallels the obesity epidemic in the U.S. Rich in unsaturated fats, especially linoleic acid, soybean oil is assumed to be healthy, and yet it induces obesity, diabetes, insulin resistance and fatty liver in mice. The genetically modified soybean oil Plenish came on the U.S. market in 2014: it is low in linoleic acid and similar to olive oil in fatty acid composition. Here we show that Plenish induces less obesity than conventional soybean oil: metabolomics, proteomics and a transgenic mouse model implicate oxylipin metabolites of omega-6 and omega-3 fatty acids (linoleic and α-linolenic acid, respectively), which are generated by target genes of nuclear receptor HNF4α. While Plenish induces less insulin resistance than conventional soybean oil, it results in hepatomegaly and liver dysfunction as does olive oil. Altering the fatty acid profile of soybeans could help reduce obesity but may also cause liver complications.

overall_design: cDNA isolated from livers from WT or α7HMZ mice, were 100bp pair-ended sequenced using Illumina TruSeq RNA Sample Prep v2 Kit

first: J

last: Dhahbi

first: F

last: Sladek


title: RNA-seq of Arabidopsis thaliana seedlings growing in the presence of a bacterial synthetic community under full and low phosphate conditions [PBI_preTreat]

summary: This study evaluates whether different pre-treatments (+Pi, -Pi and +Phi) influences the phosphate starvation transcriptional response triggered by a bacterial synthetic community in Arabidopsis seedlings.

overall_design: Arabidopsis seeds (wild-type Col-0 and the mutants phf1 and phr1 phl1) were germinated on Johnson medium containing 0.5 % sucrose with 1 mM Pi (+Pi), 5 µM (-Pi) or 1 mM Phosphite (+Phi). After seven days, plants were transferred to 50 µM Pi (low Pi) or 625 µM Pi (high Pi) media (without sucrose) alone or with the Synthetic Community at 10E5 c.f.u / mL for another 12 days before harvesting. Plants were grown in a growth chamber in a 15-h dark/9-h light regime (21°C day /18°C night). The experiment includes a total of four biological replicates from two independent experiments


title: Expression analysis of  BCR/ABL expressing Kit+ cells derived from wild type and ROSACreERT2c-Fosfl/flDusp1-/- bone marrow cells by RNA seq

city: Cincinnati

first: Mohammad

last: Azam

address: 3333 Burnet Avenue

department: Division of Experimental Hematology

institute: Cincinnati Childrens Hospital and Medical Center

summary: We performed whole genome expression analysis using BCR/ABL expressing Kit+ cells derived from wild type and ROSACreERT2c-Fosfl/flDusp1-/- bone marrow cells. Wild type kit+ cells were treated with DFC+BCI and DFC+BC+Im to mimic the genetic loss of c-Fos and Dusp1.

overall_design: The experiment was designed to test whether chemical inhibition by FOS and Dusp1 Inhibitor mimics the genetic deletion of cFOS and Dusp1 in mouse primary cells transduced with BCR-ABL. This data is part of the super series Mechanism of Oncogene addiction GSE75058.


title: Etv5 target genes in AT2 cells and mouse lung

first: Sarah

last: Kummerfeld

summary:
RNA was purified from lung tissue and isolated Alveolar type II cells.
The "SAMPLE_ID" sample description is a sample identifier internal to Genentech.
The ID of this project in Genentech's ExpressionPlot database is PRJ0007671

overall_design:
RNA from lung and Alveolar type II cells of the following mutant mice:
(1) SpcCreERT2;RosatdTomato n=5 ; (2) SpcCreERT2;RosatdTomato;Etv5ko/loxp  n= 5

first: Zhen

last: Zhang


title: Systemic human ILC precursors provide a substrate for tissue ILC differentiation

status: Public on Mar 19 2017

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

institute: Weizmann Institute of Science

summary: Innate lymphoid cells (ILC) represent innate versions of T helper and cytotoxic T cells that differentiate from committed ILC precursors (ILCP). Still, how ILCP relate to mature tissue-resident ILCs remains unclear. We observed that a population of CD117+ ILC from peripheral blood (PB) of healthy donors does not represent any conical ILC subset, but expressed marker (CD117) commonly expressed by hemato-lymphoid progenitors. We therefore hypothesized PB CD117+ ILC might include uncommitted lymphoid precursors. In order to further understand the identity of PB CD117+ ILC, we profiled the transcriptome of highly purified circulating CD117+ ILC compared to CD34+ HSC, the latter representing immature hematopoietic progenitors with multi-lineage potential. Clear differences in gene expression profiles emerged, with a large cluster of 1540 genes expressed at substantially higher levels in CD117+ ILC. In contrast, CD34+ HSC cells highly expressed genes involved in the broad development of diverse hematopoietic lineages. Compared to HSC, CD117+ ILC express high levels of TF that have been shown to be essential for murine ILC development and we did not detect transcripts characteristic of T and B cells development. Transcriptomic analysis suggested that CD117+ ILC represent lymphoid-biased progenitors carrying a TF expression profile resembling a multi-potent ILC precursor (ILCP).

overall_design: CD117+ ILC and CD34+ HSC were freshly isolated by FACS of peripheral blood of two healthy adult individuals. In total, 4 samples were analyzed and comparing between two cell populations.

first: James

last: Di Santo

first: Ai

middle: I

first: Franziska

last: Paul


first: Ralph

last: Stadhouders

address: Dr. Molewaterplein 50

department: Pulmonary Medicine

institute: Erasmus Medical Center

summary: Innate lymphoid cells (ILCs) represent innate versions of T helper and cytotoxic T cells that differentiate from committed ILC precursors (ILCP). Still, how ILCP relate to mature tissue-resident ILCs remains unclear. We identify ILCP that are present in the blood and all tested lymphoid and non-lymphoid human tissues. Human ILCP fail to express the signature transcription factors (TF) and cytokine outputs of mature NK cells and ILCs but are epigenetically poised to do so. Human ILCP robustly generate all ILC subsets in vitro and in vivo. While human ILCP express RAR related orphan receptor C (RORC), circulating ILCP can be found in RORC-deficient patients that retain potential for EOMES+ NK cells, T-BET+ ILC1, GATA-3+ ILC2 and for IL-22+ but not for IL-17A+ ILC3. We propose a model of tissue ILC differentiation (‘ILC-poiesis’) whereby diverse ILC subsets are generated in situ from ILCP in response to environmental stressors, inflammation and infection.

overall_design: 2-4 biological replicate ChIP-Seq experiments.

first: Ai-Ing

last: di Santo


title: Ectopic Drosophila AKH overexpression effect on gene expression in the 3rd instar larval fat body

status: Public on Mar 18 2017

city: Boston

first: Wei

last: Song

email: rocwsong@gmail.com, songw@whu.edu.cn

address: 77 Ave Louis Pasteur, NRB 336

department: Department of Genetics

institute: Harvard Medical School

summary: Analysis of the larval fat bodies overexpressing AKH, which activates AKH signaling in the fat body in an autocrine manner. As a homolog of human glucagon, AKH causes dysregulation of carbohydrate metabolism and hyperglycemia. Results provide insight into the AKH effects on metabolic gene expression.

overall_design: The fat bodies were dissected from late 3rd instar Drosophila larvae of control (R4-Gal4/+) and AKH-overexpressing (UAS-AKH/+; R4-Gal4/+) strains.RNAs were extracted for deep sequencing, in triplicate, using Illumina Hiseq 2000.

first: Daojun

last: Cheng

first: Norbert

last: Perrimon


title: Precocious Interleukin 21 expression in naïve mice defines a novel stage of T-follicular helper cell development

city: Bar Harbor

first: Xulong

last: Wang

address: 600 Main Street

institute: The Jackson Laboratory

summary: To define early forming IL21-expressing CD4+ T cells at the transcriptional level, we performed RNAseq on FACS-purified splenic CD4+ T cells from naïve 4 wk old IL21-VFP reporter mice based on the following criteria: naïve ICOSlo/- VFP- (N); activated ICOShi VFP- cells not expressing IL21 (ACT); and activated IL21-expressing cells ICOShi VFP+ cells (ACT IL21)

overall_design: mRNA profiles of FACS-purified VFP-ICOS-, VFP-ICOS+, and VFP+ICOS+ CD4+ cell pools from naïve 4 wk old IL21-VFP reporter mice were generated by deep sequencing, in duplicate, using Illumina MiSeq

first: Elisabeth

middle: B

last: Adkins

first: Thomas

last: Sproule

first: Giljun

last: Park

first: Gregory

last: Christianson

last: Lane-Reticker

middle: W

last: Carter

first: Herbert

last: Morse III

first: Derry

last: Roopenian


title: Genome-wide mapping of histone H3 lysine 9 dimethylation in normal myeloid cells and acute myeloid leukemia

first: Anna

last: Salzberg

state: MA

address: 399 Binney St UNIT 300

institute: Rubius Therapeutics

summary: Histone H3 lysine 9 (H3K9) is a target for posttranslational histone methylation associated with gene repression. Most of H3K9me2 modification in mammalian cells is mediated by histone methyltransferase G9a that is essential for mouse embryo development and plays an oncogenic role in acute myeloid leukemia (AML), a highly malignant blood cancer. In this study,  ChIP-sequencing was used to conduct a detailed whole-genomic characterization of the localization and expression of H3K9me2 and to identify epigenetic changes associated with normal myeloid differentiation and AML.  Genome-wide computational analysis using hidden Markov model was employed to map multiple associations of chromatin modification topographies with transcription in leukemia and define chromosomal domains undergoing epigenetic changes in AML

overall_design: ChIP-Seq with antibodies against H3K9me2 was used with normal human granulocytes (2 samples), CD34+ hematopoietic progenitors (2 samples), K562 cells (2 intact samples and 2 samples  treated with G9a inhibitor UNC0638), and primary myeloblasts from 8 different acute myeloid leukemia samples. Each H3K9me2 ChIP-seq was repeated twice. In addition, control experiments for antibody specificity were conducted with ChIP input DNA (16 samples), and ChIP-seq with antibodies against histone H3K9me3 (4 samples), histone H3K4me2 (1 sample), and nonmodified histone H3 C-tail (2 samples).

first: Sergei

last: Grigoryev


title: Transcriptional profile of  homozygous inactivation of Nf1 in mature oligodendrocytes

status: Public on Mar 17 2017

first: Kwangmin

last: Choi

state: Ohio

address: 333 Burnet Avenue

department: Experimental Hematology & Cancer Biology

institute: Cincinnati Children's Hospital Medical Center

summary:
White matter abnormalities have been observed in Neurofiromatosis type 1 (NF1) patients and in mouse models of the disease, and disturbed myelin has been proposed to cause of neurological issues in NF1 patients. Analysis of the transcriptional changes following inactivation of Nf1 in mature oligodendrocytes, the cell type producing myelin, can give information on the molecular pathways affected in NF1.
Homozygous inactivation of Nf1 was induced by Tamoxifen treatment of adult PlpCreER;Nf1flox/flox mice, 1 month later, RNA from the optic nerve was isolated and sequenced

overall_design: We isolated optic nerves from adult control and Nf1 mutant animals 1 month after tamoxifen treatment and performed whole-genome RNA sequencing. Total RNA was isolated from optic nerves using Trizol reagent (Invitrogen) followed by chloroform extraction and purification by RNeasy kit (Qiagen). Integrity of RNA was evaluated by Agilent Bioanalyzer 2100 (RIN>8.5) and cDNA was amplified by Ovation system v2 (NuGEN). RNA sequencing (35-40 million sequencing reads) was performed using paired-end BP flow cell. RNA-Seq data was mapped to the reference genome mm10, and fold change and variance were calculated using DESeq2 package in R.

first: Alejandro

last: López-Juárez

first: Haley

middle: E

last: Titus

first: Nancy

last: Ratner


title: Discovery of Novel Determinants of Endothelial Lineage: Insights from Chimeric Heterokaryons

city: Houston

first: Alin

last: Tomoiaga

address: 6670 Bertner Ave

institute: Houston Methodist Research Institute

summary: Our study provides a systematic and mechanistic approach for identifying key regulators in directed differentiation of pluripotent stem cells to a variety of somatic cell lineages.

overall_design: RNA-Seq data were generated for mouse ESC and human endothelial cells: separate, co-cultered and fused samples have been analyzed

first: Wing

middle: T

last: Wong

first: Xiaoyu

last: Tian


title: Genome-wide analysis of the toxic effect of hydroxyl-modified Graphene quantum dots (GQD) on normal human esophageal epithelial cells

city: Suzhou

first: Ming

last: Li

address: No. 199 Ren'ai Road

institute: Soochow University

summary: The objective was to investigate the toxic effect of hydroxyl-modified Graphene quantum dots (GQD) on normal human esophageal epithelial cells at gene expression level. Gene expression profilings between GQD and vehicle treated cells were compared.

overall_design: HET-1A cells were seeded in 6-cm dishes and treated with 50 μg/mL hydroxyl-modified Graphene quantum dots (GQD) and equivalent volume of vehicle in triplicate. After 24 hours of incubation, cells were harvested. Total RNA were extracted and subjected to gene expression profiling assays.

first: Zengfu

last: Shang


title: The pennycress (Thlaspi arvense) nectary transcriptome

city: Duluth

first: Marshall

last: Hampton

state: MN

address: 1117 University Drive

institute: University of Minnesota Duluth

summary: Nectaries are the glands responsible for nectar secretion. To understand the genetic programming underlying nectar production, nectaries were collected from Thlaspi arvense cultivar MN108 at two developmental time points, with RNA being isolated and subjected to Illumina RNA-seq analysis.

overall_design: Thlaspi arvense cultivar MN108 plants were grown on Sun Gro LC8 soil under a 16 hr day/8 hr night cycle, photosynthetic photon flux of 150 μmol m-2 s-1, and a temperature of 21°C. Two types of RNA samples were prepared from pennycress nectaries: mature nectaries (equivalent to Stage 14–15 flowers from Arabidopsis thaliana), and immature nectaries (equivalent to Stage 11–12 flowers from Arabidopsis thaliana). Mature nectaries secrete nectar, whereas immature nectaries are pre-secretory. All nectary tissues were separately dissected by hand from the flowers of primary inflorescences of ca. 40 day-old plants. Due to the small size of nectaries, dissections took place over several days from 4–8 hours after dawn (h.a.d.). Isolated nectaries were pooled in RNAlater™ solution (Ambion, Austin, TX) on ice, and stored at 4°C prior to RNA extraction. Up to four nectaries were collected per flower, with approximately 100 nectaries being processed as a single RNA sample. Each biological replicate was represented by nectaries pooled from different sets of plants. RNA was extracted from nectaries by mechanical disruption, with a microcentrifuge pestle, and using the RNAqueous®-Micro micro scale RNA isolation kit (Ambion, Austin, TX) with Plant RNA Isolation Aid (Ambion, Austin, TX). Agarose gel electrophoresis and UV spectrophotometry were used to assess RNA quality for all samples prior to submission to the University of Minnesota Genomics Center for barcoded library creation and Illumina HiSeq 2500 sequencing. Six TruSeq RNA v2 libraries were created (triplicate samples for immature and mature nectaries) and sequenced via 50 bp, paired-end runs on the HiSeq 2500 using Rapid chemistry. All libraries were pooled and sequenced across two lanes to achieve the equivalent of 1 lane output. This generated ≥120 M reads for each lane and the average quality scores were above Q30.

first: Clay

first: Jason

last: Thomas


title: Mechanism of Oncogene Addiction

first: Mohammad

last: Azam

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

overall_design: Refer to individual Series


title: On the Relationships in Rhesus Macaques between Chronic Ethanol Consumption and the Brain Transcriptome (Cortical Area 32 - A32)

city: Portland

first: Priscila

last: Darakjian

state: OR

address: 3181 SW Sam Jackson Park Road, L470

department: Behavioral Neuroscience

institute: Oregon Health and Science University

summary: This is the first description of the relationship between chronic ethanol self-administration and the brain transcriptome in a non-human primate (rhesus macaque). Twenty nine male animals self-administered ethanol on a daily basis for over 12 months. Gene transcription was quantified with RNA-Seq in the cortical Area 32. We constructed coexpression and cosplicing networks, and we identified areas of preservation and areas of differentiation between regions and network types. Correlations between intake and transcription included largely distinct gene sets and annotation categories across brain regions and between expression and splicing; positive and negative correlationswere also associated with distinct annotation groups. Our cosplicing analysis further identified the genes affected only at the exon inclusion level. In the Area 32 coexpression network, we identified a distinct hub set that included Ppp3r1 and Myeov2. Overall, the data illustrate that excessive ethanol self-administration is associated with broad expression and splicing mechanisms that involve membrane and synapse genes.

overall_design: Thirty one samples of Rhesus Macaques that were experimentally naïve at the onset of alcohol induction (Macaca mulatta, n = 31, 4-11 years, 6-8 kg), were first induced to drink 4% (w/v) ethanol and then allowed to self-administer ethanol for over 12 months under open access conditions (22h/d, 7d/wk) with concurrent meals and continuous access to water. We then removed one outlier resulting in 30 samples presented here.

first: Ovidiu

middle: D

last: Iancu

first: Alexander

last: Colville

first: Nicole

last: Walter

first: Denesa

last: Oberbeck

first: James

last: Daunais

first: Christina

middle: L

last: Zheng

first: Robert

last: Searles

first: Shannon

last: McWeeney

first: Kathleen

last: Grant

last: Hitzemann


title: RNA-seq of Arabidopsis thaliana seedlings treated with MeJA or flg22 under full and low phosphate conditions

first: Paulo

last: Teixeira

summary: This study evaluates the transcriptome of Arabidopsis thaliana seedlings chronically exposed to the hormone Methyl Jasmonate (MeJA) or to the bacterial elicitor flg22 (a 22-amino acid peptide from flagellin). Treatments were performed under high and low phosphate availability using wild-type Col-0 plants and the phr1 phl1 mutant.

overall_design: Arabidopsis seeds (wild-type Col-0 and the phr1 phl1 mutant) were germinated on Johnson medium (1 % sucrose) containing 1 mM Pi (in the form of KH2PO4) for 7 days in the vertical position and then transferred to 1 mM Pi and 5 µM Pi media containing 1 % sucrose either alone or supplemented with 10 µM MeJA or 1 µM flg22. Whole seedlings were harvested 12 days after the transferring. Plants were grown in a growth chamber in a 15-h dark/9-h light regime (21°C day /18°C night). The experiment includes a total of six biological replicates from two independent experiments per condition.

first: Gabriel

last: Castrillo

first: Sur

last: Herrera Paredes

first: Jeff

last: Dangl


title: Analysis of nonsense-mediated mRNA decay in daf-2 mutants

city: Daejeon

first: Seung-Jae

middle: V

last: Lee

address: 291 Daehak-ro

department: Biological Sciences

country: South Korea

institute: KAIST

summary: To exmine the role of nonsense-mediated mRNA decay process in the longevity regulation of daf-2 mutants, we sequenced transcriptomes from day 1 adult Caenorhabditis elegans: Bristol N2 (wild-type), and smg-2(qd101), daf-2(e1370) and smg-2(qd101); daf-2(e1370) mutants.

overall_design: Determination of transcript levels in N2 (wild-type), smg-2(qd101), daf-2(e1370), and smg-2(qd101); daf-2(e1370) animals by using deep sequencing, in duplicate

first: Heehwa

middle: G

last: Son

first: Hong-Gil

last: Nam

first: Seokjin

last: Ham

first: Tae-Young

last: Roh


title: Motivated cocaine seeking lead to transgenerational epigenetic inheritance of vulnerability to cocaine addiction

city: Shanghai

first: Qiumin

last: Le

address: 130 Dong'an Road

institute: Fudan University

type: Methylation profiling by high throughput sequencing

summary: Familial transmission and high heritability of liability for drug abuse has been demonstrated by large scale epidemiological and twin studies, but the role of pre-existing susceptibility to addiction is still not clear. Our data show that F1 and F2 offspring sired by rats with high motivation for drug reinforcement and drug intake during cocaine self-administration maintained their ancestor’s addict-like behavior. This paternal transmission of drug addiction is an acquired trait that is dependent on cocaine induced high motivation in F0. Reduced representation bisulfite sequencing of F0 and F1 sperm DNA reveal a few persistent epigenetic changes in genes that critically regulate early development and morphogenesis. These epigenetic traits may underlie alterations in the neurological basis that lead to the transmission of cocaine motivation. Our results reveal the epigenetic transgenerational inheritance of drug craving and provide a potential etiology in cocaine abuse vulnerability.

overall_design: In order to investigate the transgenerational inheritance of acquired cocaine motivation traits by DNA methylation, we performed reduced-representation bisulfite sequencing (RRBS) to assess the DNA methylation-enriched sites in sperms of Saline-F0, Addict-like F0, Non-Addict-like F0, Addict-like F1, Non-Addict-like F1 rats. Sequencing was performed with sperms from three to four individual rats of each group at 20M-read scale, respectively.

first: Biao

last: Yan

first: Yanqing

last: Li

first: Xiangchen

last: Yu

first: Haikun

last: Song

first: Dingailu

last: Ma

first: Feizhen

last: Wu

first: Lan


title: On the Relationships in Rhesus Macaques between Chronic Ethanol Consumption and the Brain Transcriptome

first: Priscila

last: Darakjian


title: Gene Expression Profiling of Patient-Derived Pancreatic Cancer Xenografts predicts sensitivity to the BET bromodomain inhibitor JQ1: Implications to individualized medicine efforts

city: Quebec

first: Ezequiel

last: Calvo

state: Quebec

address: 2705 Boul. Laurier

department: Molecular Endocrinilogy

country: Canada

institute: CRCHUL

summary: c-Myc controls more than 15% of genes responsible for proliferation, differentiation, and cellular metabolism in pancreatic as well as other cancers making this transcription factor a prime target for treating patients. The transcriptome of 55 patient derived xenografts show that 30% of them share an exacerbated expression profile of MYC transcriptional targets (MYC-high). This cohort is characterized by a high level of Ki67 staining, a lower differentiation state and a shorter survival time compared to the MYC-low subgroup. To define classifier expression signature, we selected a group of 10 MYC targets transcripts which expression is increased in the MYC-high group and 6 transcripts increased in the MYC-low group. We validated the ability of these markers panel to identify MYC-high patient-derived xenografts from both: discovery and validation cohorts as well as primary cells cultures from the same patients. We then showed that cells from MYC-high patients are more sensitive to JQ1 treatment compared to MYC-low cells, in both monolayer and 3D cultured spheroids, due to cell cycle arrest followed by apoptosis. Therefore, these results provide new markers and potentially novel therapeutic modalities for distinct subgroups of pancreatic tumors and may find application to the future management of these patients within the setting of individualized medicine clinics.

overall_design: 30 primary Pancreatic ductal adenocarcinoma (PDAC) tumors obtained from surgery and 25 biopsy samples taken by endoscopic ultrasound-guided fine-needle aspiration (EUS-FNA) were implanted subcutaneously into mice and preserved as Patient Derived Xenografts (PDX). Growth rates to reach a tumor volume of 1 cm3 ranged from 2 to 6 months in most of the PDX. Total RNA was obtained from the 55 PDX, and the gene expression profiling was performed using Affymetrix platform.

first: Benjamin

last: Bian

first: Martin

last: Bigonnet

first: Odile

last: Gayet

first: Celine

last: Loncle

first: Aurélie

last: Maignan

first: Marine

last: Gilabert

first: Vincent

last: Moutardier

first: Stephane

last: Garcia

first: Olivier

last: Turrini

first: Jean-Robert

last: Delpero

first: Marc

last: Giovannini

first: Philippe

last: Grandval

first: Mohamed

last: Gasmi

first: Mehdi

last: Ouaissi

first: Veronique

last: Secq

first: Flora

last: Poizat

first: Marion

last: Rubis

first: Jean-Luc

last: Raoul

first: Gwen

last: Lomberk

first: Raul

last: Urrutia

first: Andres

last: Saul

first: Nelson

last: Dusetti

first: Juan

last: Iovanna


title: Downregulation of autolysin-encoding genes by phage-derived lytic proteins inhibits biofilm formation in Staphylococcus aureus

status: Public on Mar 16 2017

city: Oviedo

first: Lucia

last: Fernandez

address: C/ Francisco Pintado Fe 26

country: Spain

institute: Instituto de Productos Lacteos de Asturias (IPLA-CSIC)

summary: Phage-derived lytic proteins are a promising alternative to conventional antimicrobials. One of their most interesting properties is that they do not readily select for resistant strains, which is likely due to the fact that their targets are essential for the viability of the bacterial cell. Moreover, genetic engineering allows the design of new "tailor-made" proteins that may exhibit improved antibacterial properties. One example of this is the chimeric protein CHAPSH3b, which consists of a catalytic domain from the virion-associated peptidoglycan (PG) hydrolase of phage vB_SauS-phiIPLA88 (HydH5) and the cell wall binding domain of lysostaphin. CHAPSH3b had previously shown the ability to kill S. aureus cells. Here, we demonstrate that this lytic protein also has potential for the control of biofilm-embedded S. aureus cells. Additionally, subinhibitory doses of CHAPSH3b can decrease biofilm formation by some S. aureus strains. Transcriptional analysis revealed that exposure of S. aureus cells to this enzyme leads to the downregulation of several genes coding for bacterial autolysins. One of these proteins, namely the major autolysin AtlA, is known to participate in staphylococcal biofilm development. Interestingly, an atl mutant strain did not display inhibition of biofilm development when grown at subinhibitory concentrations of CHAPSH3b, contrary to the observations made for the parental and complemented strains. Also, deletion of atl led to low-level resistance to CHAPSH3b and endolysin LysH5. Overall, our results reveal new aspects that should be considered when designing new phage-derived lytic proteins aimed for antimicrobial applications.

overall_design: 6 samples were analyzed, corresponding to 3 biological replicates of two different conditions (biofilm sample treated with endolysin LysH5 and control biofilm).

first: Silvia

last: Gonzalez

first: Ana

last: Campelo

first: Beatriz

last: Martinez

last: Rodriguez

first: Pilar


title: Transcriptional landscape of the human cell cycle

city: Toronto

first: Housheng

middle: Hansen

last: He

state: Ontario

address: 101 College Street

institute: University of Toronto

summary: Steady-state  gene  expression  across  the  cell  cycle  has  been  studied  extensively.  However, 2 transcriptional gene regulation and histone modification dynamics at different cell cycle stages is3 largely  unknown.  By  applying  a  combination  of  GRO-seq,  RNA-seq and  histone  modification 4 ChIP-seq, we depicted a comprehensive transcriptional landscape at G0/G1, G1/S and M phases 5 of  breast  cancer  MCF-7  cells.  Importantly,  GRO-seq  and  RNA-seq  analysis  identified  different 6 cell  cycle  regulated  genes,  suggesting  a  lag  between  transcription  and  steady-state  expression 7 during the cell cycle. Interestingly, we identified genes actively transcribed at early M phase that 8 are longer in length and have low expression, which is accompanied by global increase of active 9 histone  modifications  of  H3K4me2  and  H3K27ac.  In  addition,  we identified  2,440  cell  cycle 10regulated   enhancer   RNAs   (eRNAs)   that   are   strongly   associated   with   differential   active 11transcription  but  not  stable  expression  levels  across  the  cell  cycle. Motif  analysis  on  dynamic 12eRNAs  predicted  KLF4  as  a  key  regulator  of  G1/S  transition, which  was  experimentally 13validated.  Altogether,  our   combined  analysis   characterized  the  transcriptional   and histone 14modification  profile of  the  human  cell  cycle  and  identified  novel  dynamic  transcriptional 15signatures across the cell cycle.

overall_design: MCF7 cells are synchronized to three different cell cycle stages: G0/G1, S and M phase. Global nuclear run-on followed by RNA sequencing (GRO-seq), ChIP-seq for H3K27ac and H3K4me2 modification were carried out in the synchronized cells. Dnase-seq were performed in asynchronized MCF7 cells.

first: Liu

last: Yin

first: Sujun

last: Chen

middle: H


title: Neuronal activity-induced late-onset alternative splicing and H3K9me3 modification

city: Beijing

first: Jisong

last: Guan

address: Tsinghua University, Haidian district, Beijing

department: School of life science

institute: Tsinghua University

summary: Activity-induced alternative splicing has emerged as an important mechanism for the dynamic modification of neuronal function. To examine whether activity could cause transcriptional programs alteration in alternative splicing and associative H3K9me3 in the specific genomic loci, we performed whole genome RNA-sequencing (RNA-seq) in cultured cortical neurons at 24 hours after membrane depolarization by exposure to high extracellular KCl (50mM, 10min). A transient neuronal activation could induce alternation of splice isoform choice in many genes at 24hrs after stimuli. To detect the correlation of activity-induced H3K9me3 accumulation with the splicing events, we performed ChIP-seq in hippocmapus of mice, which were subjected to enriched environment for 24 hours and kept in homecage for 1 week.

overall_design: Total RNA from primary cortical neurons at 24 hr after KCl (50mM, 10min) stimulation was used for RNA-seq to detect activity induced alternative splicing events. To detect neural activation-induced long-term alternations on H3K9me3 in neurons, H3K9me3 ChIP-seq was performed in mice hippocampal extracts at 1 week after enriched enrironment training.

first: Sanxiong

last: Liu

first: Xinlu

last: Ding


title: RNA-seq analysis of mutations inducing the loser status in Drosophila wing discs

city: Cambridge

first: Charles

last: Bradshaw

address: Tennis Court Road

department: Gurdon Institute

institute: University of Cambridge

summary: In order to investigate the mechanisms of cell competition, we analyzed the molecular differences between the prospective winner and loser cells in Drosophila wing discs. For this purpose we analyzed RNA-seq profiles generated for wild-type cells (prospective winners) and cells mutant for RpS3 and mahj, genes seemingly functionally unrelated, yet both causing the loser phenotype. As an interesting reference, we also generated data from cells with mutations in RpS15, which, like RpS3, is a ribosomal gene but itself does not trigger cell competition. Through in depth analysis we homed in on the subset of genes misregulated in both prospective loser cells mutants, which defines  "the molecular signature of prospective loser cells". Additionally, we provide RNA-seq data for RpS3 mutant discs upon inhibition of the JNK signalling pathway (by overexpression of the pathway inhibitor puckered) and compare this to reference RpS3 mutant cells, hence identifying those genes in RpS3 mutants that are differentially expressed in a JNK-dependent manner.

overall_design: Analysis of RNA-seq profiles from wild type and mutant Drosophila wing discs (RpS3, RpS15, mahj), each condition in at least two repeats. Additionally, provided are samples in triplicate of RpS3 mutant wing discs overepressing the JNK inhibitor puckered.

first: Iwo

last: Kucinski

first: Eugenia

last: Piddini


title: ChIP-seq of Atrophin in Drosophila S2 cells

first: Helen

last: McNeill

address: 600 University Ave.

institute: Lunenfeld Tanenbaum Research Institute

summary: Drosophila Atro mutants have a large range of phenotypes, including neurodegeneration, segmentation, patterning and planar polarity defects. Although Atro mutants have diverse phenotypes, little is known about Atro’s binding partners and downstream targets. We present the first genomic analysis of Atro using ChIP-seq against endogenous Atro. These data sets will serve as a valuable resource for future studies on Atro.

overall_design: We performed three independent biological replicates of Atro ChIP-seq experiments in untreated S2 cells.  A corresponding non-specific IgG control ChIP was performed with each Atro ChIP-seq and was used as a control.

first: Kelvin

last: Yeung


title: Retinoic acid signaling is dispensable for somatic development and function of the developing ovary

city: Minneapolis

first: Micah

last: Gearhart

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

department: Genetics, Cell Biology and Development

country: USA

institute: University of Minnesota

summary: Retinoic acid (RA) is a potent inducer of cell differentiation and plays an essential role in sex-specific germ cell development in the mammalian gonad. RA is essential for male gametogenesis and hence fertility. However, RA can also disrupt sexual cell fate in somatic cells of the testis, promoting transdifferentiation of male Sertoli cells to female granulosa-like cells when the male sexual regulator Dmrt1 is absent.  The feminizing ability of RA in the somatic testis suggests that RA might normally play a role in somatic cell differentiation or cell fate maintenance in the ovary. To test for this possibility we disrupted RA signaling in somatic cells of the early fetal ovary using three genetic strategies and one pharmaceutical approach. We found that deleting all three RA receptors (RARs) in the XX somatic gonad at the time of sex determination did not significantly affect ovarian differentiation, follicle development, or female fertility. Transcriptome analysis of adult triple mutant ovaries revealed remarkably little effect on gene expression in the absence of somatic RAR function.  Likewise, deletion of three RA synthesis enzymes (Aldha1-3) at the time of sex determination did not masculinize the ovary. A dominant-negative RAR transgene altered granulosa cell proliferation, likely due to interference with a non-RA signaling pathway, but did not affect granulosa cell specification or fertility.  Finally, culture of fetal XX gonads with an RAR antagonist blocked germ cell meiotic initiation but did not disrupt sex-biased gene expression. We conclude that RA signaling, although crucial in the ovary for meiotic initiation, is not required for granulosa cell specification, differentiation, or reproductive function.

overall_design: Ovaries from six week old mice with five replicates in each of two genotypes were analyzed by RNA-Seq

first: Anna

last: Minkina

first: David

last: Zarkower


title: PCGF6-PRC1 suppresses premature differentiation of embryonic stem cells by silencing germ cell-related genes

city: Yokohama

first: Takaho

middle: A.

last: Endo

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

department: IMS

institute: RIKEN


title: PCGF6-PRC1 suppresses premature differentiation of embryonic stem cells by silencing germ cell-related genes [ChIP-Seq]

summary:
ChIP-seq data of embryonic stem cells to detect Ring1b and Pcgf6 binding sites
ChIP-seq of embryonic stem cell H3K9me2 with or without Pcgf6.

overall_design:
ChIP-seq data of embryonic stem cells to detect Ring1b and Pcgf6 binding sites
ChIP-seq of  H3K9me2 with or without Pcgf6 using conditional KO mouse embryonic stem cell.

first: Mitsuhiro

last: Endoh

first: Haruhiko

last: Koseki

first: Jafar

last: Sharif

middle: A


title: Genome-wide maps of chromatin state and abundance of transcription factors IRF1 and IRF4 in Th9 cells

city: Marburg

first: Magdalena

last: Huber

address: Hans-Meerwein-Str. 2

institute: Institute of Medical Microbiology

summary: The goal of this study was to to compare changes in chromatin status evoked by IFN-g signalling in Th9 cells. Furthermore, the binding of transcription factors IRF1 and IRF4 in Th9 cells were analysed to analyse whether IRF4 abundance is affected by IFN-g-induced IRF1 binding at regulatory regions in Th9 cells.

overall_design: H3K27Ac, IRF1 and IRF4 binding profiles were generated in Th9 cells in the presence or abesence of IFN-g.

first: Lucia

last: Campos Carrascosa

first: Shimon

last: Sakaguchi

first: Yohko

last: Kitagawa

first: Federico

last: Marini


title: PCGF6-PRC1 suppresses premature differentiation of embryonic stem cells by silencing germ cell-related genes [RNA-Seq]

summary:
Expression data of ES cells with or without Pcgf6, Ring1A/B, Max and Mga.
Expression data of ES cells with or without Cbx1/3.

overall_design:
Mouse embryonic stem cells deficient for Pcgf6 and associating genes were evaluated using RNA-seq.
Mouse embryonic stem cells deficient for Cbx1/3 and associating genes were evaluated using RNA-seq.


title: Dido as a switchboard that regulates self-renewal and differentiation in embryonic stem cells

city: Madrid

first: Carlos

last: Martinez

state: Madrid

address: C/Darwin 3

department: Inmunology and Oncology

institute: Centro Nacional de Biotecnologia


title: Genome wide RNAi screen for regulators of mRNAs silenced in African trypanosome slender forms and expressed in stumpy forms

city: Edinburgh

first: Alasdair

last: Ivens

address: Kings Buildings

institute: Centre for Immunity, Infection and Evolution

summary: Bloodstream forms of T brucei s427 2T1 T7  p’5neo5’-ESAG9 3’UTR (long form) bloodstream forms were grown in vitro. They contained the NeoR gene under the control of the ESAG9 gene 3'UTR. Selection was based on increased resistance to G418 through the silencing of an ESAG9 repressor, leading to increased neoR expression

overall_design: RNA library insert amplicons were analysed by ion torrent sequence analysis of the selected populations

first: Keith

last: Matthews

first: Eva

last: Vidal


title: Genome-wide RNAi selection identifies a regulator of transmission stage-enriched gene families and cell-type differentiation in Trypanosoma brucei


title: RNA-seq Transcriptome analysis of REG9.1 (Tb927.11.14220) when overexpression is induced, or not using ectopic expression vector pLEW

summary: Bloodstream forms of T brucei AnTat1.1 were grown in vitro and REG9.1 was expressed by tetracycline induction of pLEW

overall_design: Two replicates of REG9.1 ectopic expression without induction (-tet) or with  induction (+tet) were analysed


title: RNA-seq Transcriptome analysis of REG9.1 (Tb927.11.14220) when RNAi is induced, or not

summary: Bloodstream forms of T brucei AnTat1.1 were grown in vitro and REG9.1 was silenced by tetracycline induction of RNAi

overall_design: Two replicates of REG9.1 without RNAi induction (-tet) or with RNAi induction (+tet) were analysed