title: hMTR4 plays a central role in creating balanced nuclear RNA pools for degradation and export III

city: Shanghai

first: Hong

last: Cheng

address: 320 YueYang Road

institute: Shanghai Institutes for Biological Sciences

summary: To eliminate the possibility that for a particular gene the increased RNA level is an effect of enhanced transcription. We carried out ChIP-seq for RNAPII to compare transcription of mRNAs and lncRNAs in control, hRRP40 and hMTR4 knockdown cells.  Among 15000 RNAPII binding peaks identified in these samples, only less than 50 peaks was significantly increased in hRRP40 or hMTR4 knockdown cells.

overall_design: DNAs isolated from input and IP sample in control, hRRP40 or hMTR4 knockdown HeLa cells were generated by deep sequencing, using Illumina HiSeq 2000.

first: Xudong

last: Wu

first: Mingshuang

last: Li


title: Integrated analysis of motif activity and gene expression changes of transcription factors

status: Public on Dec 04 2017

city: Odense M

first: Susanne

last: Mandrup

state: Fyn

address: Campusvej 55

department: Department of Biochemistry and Molecular Biologi

country: Denmark

institute: University of Southern Denmark

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The ability to predict transcription factors based on sequence information in regulatory elements is a key step in systems-level investigation of transcriptional regulation. Here, we have developed a novel tool, IMAGE, for precise prediction of transcription factors based on transcriptome profiling and genome-wide maps of enhancer activity. High precision is obtained by combining a near-complete database of position weight matrices (PWMs), generated by compiling public databases and systematic prediction of PWMs for uncharacterized transcription factors, with a state-of-the-art method for PWM scoring and a novel machine learning strategy, based on both enhancers and promoters, to predict the contribution of motifs to transcriptional activity. We applied IMAGE to published data obtained during 3T3-L1 adipocyte differentiation and showed that IMAGE predicts causal transcriptional regulators of this process with higher confidence than other methods. Furthermore, we generated genome-wide maps of enhancer activity and transcripts during human mesenchymal stem cell commitment and adipocyte differentiation and used IMAGE to identify positive and negative transcriptional regulators of this process. Collectively, our results demonstrate that IMAGE is a powerful and precise method for prediction of regulators of gene expression.

overall_design: Genome-wide characterization of the adipocyte differentiation of hMSC-TERT4 cells using MED1 ChIP-seq and RNA-seq

first: Jesper

middle: G

last: Madsen

first: Alexander

last: Rauch

first: Elvira

middle: L

last: Van Hauwaert

first: Søren

middle: F

last: Schmidt

first: Marc

last: Winnefeld


title: Antibodies That Convert Bone Marrow Into Trafficking Microglia-Like Cells Reduce Brain Amyloid

city: La Jolla

first: Padma

last: Natarajan

state: CA

address: 10550 N.Torrey Pines Road

department: CCBB

country: USA

institute: The Scripps Research Institute

summary: One goal of regenerative medicine is to repair damaged tissue. This requires not only generating new cells of the proper phenotype, but also selecting for those that properly integrate into sites of injury. In our laboratory we are using a cell migration based in vivo selection system to generate antibodies that induce cells to both differentiate and selectively localize to different tissues. Here we describe an antibody that induces bone marrow stem cells to differentiate into microglia-like cells that traffic to the brain where they organize into typical networks.   Interestingly, in the APP/PS1 Alzheimer's disease mouse model these induced microglia-like cells are found at sites of plaque formation and significantly reduce their number. These results raise the intriguing question as to whether one can use such antibody-induced differentiation of stem cells to essentially recapitulate embryogenesis in adults to discover cells that can regenerate damaged organ systems.

overall_design: Total RNAs were isolated in replicates of three from untreated human CD34+ cells, human CD34+ cells treated with B1 Ab, and human CD34+ cells treated with M-CSF.

first: KYUNG

middle: H

last: HAN

first: RICHARD

middle: A

last: LERNER


title: Characterizing 5-hydroxymethylcytosine in human prefrontal cortex at single base resolution.

status: Public on Dec 05 2017

city: Montreal

first: Alain

last: Pacis

state: QC

address: 740 Dr Penfield Ave

country: Canada

institute: Canadian Centre for Computational Genomics (C3G)

type: Methylation profiling by high throughput sequencing

summary: The recent discovery that methylated cytosines are converted to 5-hydroxymethylated cytosines (5hmC) by the family of ten-eleven translocation enzymes has sparked significant interest on the genomic location, the abundance in different tissues, the putative functions, and the stability of this epigenetic mark. 5hmC plays a key role in the brain, where it is particularly abundant and dynamic during development. Here, we comprehensively characterize 5hmC in the prefrontal cortices of 24 subjects. We show that, although there is inter-individual variability in 5hmC content among unrelated individuals, approximately 8 % of all CpGs on autosomal chromosomes contain 5hmC, while sex chromosomes contain far less. Our data also provide evidence suggesting that 5hmC has transcriptional regulatory properties, as the density of 5hmC was highest in enhancer regions and within exons. Furthermore, we link increased 5hmC density to histone modification binding sites, to the gene bodies of actively transcribed genes, and to exon-intron boundaries. Finally, we provide several genomic regions of interest that contain gender-specific 5hmC. Collectively, these results present an important reference for the growing number of studies that are interested in the investigation of the role of 5hmC in brain and mental disorders.

overall_design: Characterization of 5-hydroxymethylcytosine (5hmC) in the prefrontal cortices of 24 subjects.

first: Jeffrey

last: Gross

first: Gary

last: Chen

first: Luis

middle: B

last: Barreiro

first: Carl

last: Ernst

first: Gustavo

last: Turecki


title: hMTR4 plays a central role in creating balanced nuclear RNA pools for degradation and export I

status: Public on Dec 06 2017

first: Hong

last: Cheng

department: Shanghai Institute of Biochemistry and Cell Biology

country: China

summary: To define the in vivo targets of the human nuclear exosome, we performed stranded RNA-seq using rRNA-depleted RNAs isolated from nuclei of HeLa cells. To compare the RNA levels in each sample in an unbiased fashion, we added spike-in controls to equal amount of total nuclear RNAs.

overall_design: rRNA-depleted RNAs isolated from nuclei of control, hRRP40 or hMTR4 siRNA treated HeLa cells were generated by deep sequencing, using Illumina HiSeq 2000.

first: Xudong

last: Wu


title: RNA-Sequencing of EC and PVC from aged APOE mice

city: New York

first: Karen

last: Duff

state: NY

address: 630 West 168th Street, P & S 12-440

department: Pathology and Cell Biology

institute: Columbia University Medical Center

summary: RNA-Sequencing of entorhinal cortex and primary visual cortex from 14-15 month old APOE3/4 vs. APOE3/3 targeted replacement mice.

overall_design: Entorhinal cortex and primary visual cortex tissue from 14-15 month old APOE mice (10 male APOE3/3s and 19 male APOE3/4s) were collected, and RNA was extracted using Trizol. Starting with 2 μg of total RNA per sample, Poly(A)+ mRNA was purified, fragmented and then converted into cDNA using the TruSeq RNA Sample Prep Kit v2. For RNA-Sequencing of the cDNA, we hybridized 5 pM of each library to a flow cell, with a single lane for each sample, and we used an Illumina cluster station for cluster generation. We then generated 149bp single end sequences using an Illumina Hi-Seq sequencer.

first: Tal

last: Nuriel

first: Allissa

last: Dillman

first: Mark

middle: R

last: Cookson

middle: E


title: Switch of mitochondrial superoxide dismutase into a prooxidant peroxidase in manganese-deficient cells

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary: Superoxide radical anion and other Reactive Oxygen Species are constantly produced during respiration. In mitochondria, the dismutation of the superoxide radical anion is accelerated by the mitochondrial superoxide dismutase 2 (SOD2), an enzyme that has been traditionally associated with antioxidant protection. However, increases in SOD2 expression promote oxidative stress, indicating that there may be a prooxidant role for SOD2. We show that SOD2, which normally binds manganese, can incorporate iron and generate an alternative isoform with peroxidase activity. The switch from manganese to iron allows FeSOD2 to utilize H2O2 to promote oxidative stress. We found that FeSOD2 is formed in cultured cells. FeSOD2 causes mitochondrial dysfunction and higher levels of oxidative stress in cultured cells. We show that formation of FeSOD2 converts an antioxidant defense into a prooxidant peroxidase that leads to cellular changes seen in multiple human diseases.

overall_design: Previously characterized MCF-7 derived cells, neo, and SOD2-overexpressing cells, Mn11, were grown in medium with and without manganese supplementation. We grew those cells for 21 days before cells were collected. We then compared the gene expression of Mn11 cells supplemented or not with manganese versus neo cells supplemented or not with manganese to show the specific effects of manganese incorporation into SOD2, excluding the possible background effects associated with manganese supplementation to the parental cell line.

first: Douglas

last: Ganini

first: Janine

last: Santos

first: Marcelo

last: Bonini

first: Ronald

middle: P

last: Mason


title: Sequential gene activation and extensive gene imprinting during early embryo development in maize

city: Stockholm

first: Cheng

last: Zhao

state: Stockholm

address: H9 Klinisk vetenskap,171 77 Stockholm

department: Clinical Science

country: Sweden

institute: Karolinska institute

summary: The embryo is responsible for transmitting genetic information to the next generation. However, the underlying gene expression and gene imprinting during early embryo development remain largely elusive in maize. Using high-throughput RNA sequencing, we analyzed the allelic gene expression patterns of maize embryos from reciprocal crosses between inbred lines B73 and Mo17 at six time points (3 to 13 days after pollination). A total of 9532 genes were found to be differentially expressed in developmental stage, 3512 of 9532 genes were affected by cross direction. Co-expression analysis uncovered the sequential gene activations during maize embryo development. Further, we found 64 embryo strongly imprinted genes, including 57 maternally expressed imprinted genes (MEG) and 7 paternally expressed imprinted genes (PEG) in the maize embryo. Among them, 20 genes were continuously imprinted and 36 imprinted genes were newly identified. By applying In situ hybridization, we verified that six of the differentially expressed genes showed enriched transcription in the embryo. In addition, mutant analyses indicated that three of the imprinted genes displayed reduced embryo size. Therefore, our data shed new light on our understanding of the gene expression and gene imprinting in early maize embryo development, and suggested that imprinted genes are important for proper embryo development.

overall_design: Embryos of 5DAP,7DAP,9DAP,11DAP,13DAP by manual, 3DAP and 5DAP by laser microdissection, and  5DAP endosperm of B73 X Mo17 and Mo17 X B73  were collected for RNA-seq analysis.  Three biological replicates were performed for each  sample.

first: Dexuan

last: Meng

first: Jianyu

first: Haishan

last: Luo

first: Mujiao

last: Xie

first: Renyi

last: Liu

first: Jinsheng

last: Lai

first: Xiaolan

last: Zhang

first: Weiwei

last: Jin


title: RNA-DamID reveals cell-type-specific binding of roX RNAs at chromatin entry sites

city: Cambridge

first: Andrea

last: Brand

address: Tennis Court Rd

country: United Kingdom

institute: The Gurdon Institute

summary: Thousands of long noncoding RNAs (lncRNAs) have been identified in eukaryotic genomes, many of which are expressed in spatially and temporally restricted patterns. Nonetheless, the roles of the majority of these transcripts are still unknown. One of the mechanisms by which lncRNAs function is through the modulation of chromatin state. To assess the functions of lncRNAs we developed RNA-DamID, a novel approach that detects lncRNA-genome interactions in a cell-type specific manner in vivo with high sensitivity and accuracy. Identifying the cell-type-specific genome occupancy of lncRNAs is key to understanding their mechanisms of action in development and disease. We used RNA-DamID to investigate targeting of the lncRNAs in the Drosophila dosage compensation complex (DCC) and show that initial targeting is cell-type-specific.

overall_design: RNA-DamID of roX1 and roX2 in male and female larval tissues

first: Seth

middle: W

last: Cheetham


title: Single cell RNA-seq of mouse brain astrocyte transcriptomes

city: Uppsala

first: L.

last: He

address: Dag Hammarskjölds Väg 20

institute: Uppsala University

summary: By analyzing 250 astrocyte single cell transcriptomes from adult brain, we provide gene expresssion profile of brain astrocyte

overall_design: We chose adult mice about 3 months old and analysed single cells in the brain. We chose a methodology based on fluorescence-activated cell sorting (FACS) into 384-well plates followed by the SmartSeq2 methodology.

first: Francesca

last: Del Gaudio

first: Urban

last: Lendahl


title: Cell Type-Specific Chromatin Signatures Underline Regulatory DNA Elements in Human Induced Pluripotent Stem Cells and Somatic Cells

city: Stanford

first: Joseph

last: Wu

state: Carlifornia

address: Stanford University School of Medicine

institute: Stanford University School of Medicine

summary: Regulatory DNA elements in the human genome play important roles in determining the transcriptional abundance and spatiotemporal gene expression. It is a mystery how chromatin marks in regulatory elements are modulated to establish cell type-specific gene expression. Here we profiled a variety of epigenetic marks in the regulatory elements using massive ChIP-seq (n=84). We uncovered two classes of regulatory elements: Class I was identified with ubiquitous enhancer (H3K4me1) and promoter (H3K4me3) marks in all cell types, whereas Class II was enriched with H3K4me1 and H3K4me3 in a cell type-specific manner. For common genes regulated by both promoters and enhancers, Class I promoters displayed dominant regulatory effects on transcriptional abundance. Moreover, human iPSCs and somatic cells selected their preferential regulatory elements to maintain cell type-specific gene expression. Our study provides valuable resources for deciphering the epigenetic modulation of regulatory elements that fine-tune spatiotemporal gene expression in human development and diseases.

overall_design: Large scale RNA-seq (n=6) and ChIP-seq (n=84) of 12 human cell lines, including fibroblast cells (FBs), endothelial cells (ECs), cardiac progenitor cells (CPCs), and induced pluripotent stem cells (iPSCs).

first: Ming-Tao

first: Ning-Yi

last: Shao

first: Michael

last: Snyder


title: Gene Expression Profiling of one melanoma cell line after shRNA-mediated knockdown of JMJD2C or LSD1

city: Berlin

first: Maja

last: Milanovic

address: Augustenburgerplatz 1

department: Hematology and Oncology

country: Germany

institute: Charite University Medicine, Berlin

summary: We hypothesize that knockdown of the H3K9 demethylases JMJD2C or LSD1 results in decreased proliferation and tumorigenic potential

overall_design: Examination of gene expression in one melanoma cell line following knockdown of JMJD2C or LSD1

first: Yong

last: Yu

first: Kolja

last: Schleich

first: Clemens

last: Schmitt

first: Soyoung

last: Lee


title: hMTR4 plays a central role in creating balanced nuclear RNA pools for degradation and export II

first: Hong

last: Cheng

summary: To define the in vivo targets of the human nuclear exosome, we performed stranded RNA-seq using polyA RNAs isolated from nuclei of HeLa cells. To compare the RNA levels in each sample in an unbiased fashion, we added spike-in controls to equal amount of total nuclear RNAs.

overall_design: PolyA RNAs isolated from nuclei of control, hRRP40 or hMTR4 siRNA treated HeLa cells were generated by deep sequencing, in triplicate, using Illumina HiSeq 2000.

first: Xudong

first: Mingshuang

last: Li


title: An Integrated miRNA Expression Atlas of Arabidopsis thaliana

city: Beiing

first: Yijun

last: Qi

address: NO.1 Qinghuayuan

department: School of Life Sciences

institute: Tsinghua University

type: Non-coding RNA profiling by high throughput sequencing

summary: MicroRNAs (miRNAs) are 21-24 nucleotide (nt) small non-coding RNAs that regulate a wide variety of biological processes at the posttranscriptional level. MiRNA expression often exhibits spatial and temporal specificity. However, genome-wide miRNA expression patterns in different Arabidopsis organs during plant development have not yet been fully investigated. In this study, we sequenced 59 small RNA libraries generated from different tissue types at different developmental stages of Arabidopsis. We then re-annotated Arabidopsis miRNAs based on the most recent criteria. Global analysis of miRNA expression patterns showed that most miRNAs are ubiquitously expressed in different organs or tissues. But a small set of miRNAs, either previously annotated or newly identified, show highly specific expression patterns. In addition, the expression of some miRNA members belonging to the same family is strictly regulated spatially and temporally. Unexpectedly, we found that quite a few miRNAs are produced from different arms of their hairpin precursors at different developmental stages, suggesting that arm switching could be a general and important mechanism in developmental regulation.

overall_design: we constructed 59 small RNA libraries from root, shoot, leaf, flower, silique, seed and many other organs or cell types at different stages of Arabidopsis development

first: Le

last: Xu

first: Yugang

last: Hu

first: Jingrui

first: Yan


title: A novel addressable 9600-microwell array single cell RNA-seq method applied on fresh mouse cortical cells and frozen human cortical nuclei

first: Sten

last: Linnarsson

address: Scheeles väg 1

department: Medical Biochemistry and Biophysics

institute: Karolinska Institutet

summary: We adopted the STRT-seq [Islam et al., Nat Methods 11, 163-166 (2013)] RNA-seq technology to a 9600-well array and applied it to analyze single cells from mouse and human cortex single cells.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: 2192 single cells from mouse somatosensory cortex and 2028 single nuclei from human post-mortem middle temporal gyrus cortex.

first: Hannah

last: Hochgerner

first: Maithreyan

last: Srinivasan

first: Amit

last: Zeisel

first: Ed

last: Lein


title: Gene Expression Profiling of melanoma cell lines after shRNA-mediated knockdown of JMJD2C or LSD1

first: Maja

overall_design: Examination of gene expression in two melanoma cell lines following knockdown of JMJD2C or LSD1

first: Yong


title: RNA-seq transcriptonal profiling in mouse hearts under pressure overload

status: Public on Dec 03 2017

city: Memphis

first: Jian

state: Tennessee

address: 262 Danny Thomas Place, MS 345

department: Pathology

institute: St. Jude Children's Research Hospital

summary: Heart failure is a leading cause of death in US. Hypertension is one of the most important risk factor of heart failure. In the presence of high blood pressure, the heart manifests hypertrophic growth to ameliorate ventricular wall stress. This once adaptive response may progress into decompensation and heart failure. The precise mechanisms governing this transition remain elusive. Here, we take advantage of mouse surgical model transverce aortic constriction (TAC) to induce pressure overload in rodents. We harvest hearts at different time points post surgery and subject these samples for RNA-Seq analysis with an aim to identify early players in the process and elucidate the molecular mechanisms.

overall_design: Transcriptional profiling in mouse hearts after pressure overload by RNA-seq analysis.

first: Yuan

last: Wang

first: Yuannyu

last: Zhang

first: Zhao


title: Dynamic profiles of microRNAome in porcine liver

city: Wuhan

first: Yuhua

last: Fu

state: Hubei

address: No.1, Shizishan Street, 430070, Wuhan, China

department: College of Animal Science and Technology

institute: Huazhong Agricultural University

summary: To evaluate the roles of miRNA in porcine liver, dynamic profiles of microRNAome were investigated  in swine breeds with different traits of commercial interest, we sampled liver tissues from a Chinese well-known elite native breed of Enshi black pig, a Large White pig, and a Chinese wild boar living within the same environment at the same day-old(90d).

overall_design: Using high-throughput sequencing technology to reveal the characteristic of microRNAome during porcine liver development.

first: Changchun


title: Regulation of microRNAs in response to Deepwater Horizon oil in mahi-mahi (Coryphaena hippurus) embryos at 3 different stages.

city: Riverside

first: Daniel

last: Schlenk

address: 900 University Ave

institute: University of California, Riverside

summary:
Purpose:To help identify the role miRNAs in molecular mechanisms and pathways potentially involved in the developmental toxicity for fish exposed to Deepwater Horizon (DWH) oil,  miRNA-mRNA networks in mahi-mahi (Coryphaena hippurus) embryos exposed to different DWH oils (source and artificially weathered oil) were evaluated at different critical windows of development using High Throughput Sequencing (HTS).
Methods:miRNA profiles of 24, 48, 96 hpf mahi-mah larvae after slick and source oil exposure were generated by deep sequencing, in triplicate, using Illumina NextSeq v2. qRT–PCR validation was performed using SYBR Green assays.
Results: Exposure of embryos to slick oil resulted in more DE miRNAs than source oil at all developmental stages 24hpf, 48hpf, and 96hpf. There was also an increase in the number of DE miRNA as development progressed, with 96hpf having the highest number of DE miRNAs. The expression of miRNAs and their target mRNA was further compared using advanced bioinformatics with subsequent target organ predictions based on their interactions. Gene ontology (GO) analysis on the target mRNAs was consistent with pathway analysis of miRNAs, predicting disruption of cardiovascular system development after oil exposure and showed that specific miRNA–mRNA interactions may contribute to these effects.

overall_design: Total miRNA profiles of 24, 48, 96 hpf mahi-mah larvae after slick and source oil exposure were generated by deep sequencing, in triplicate, using Illumina Nextseq v2.

first: Graciel

last: Diamante

first: Elvis

first: Shuai

last: Chan

first: Edward

middle: M

last: Mager

first: Martin

last: Grosell


title: RNA-seq analysis for mRNA expression change in alpha-synclein fibril-treated cultured oligodendrocyte precursor cells

status: Public on Dec 02 2017

city: Kobe

first: Yuichi

last: Ono

state: Hyogo

address: 6-8-2 Minatojima-minamimachi, Chuo-ku

department: Developmental Neurobiology

country: Japan

institute: KAN Research Institute Inc.

summary: Glial cytoplasmic inclusion is the pathological hallmark of multiple system atrophy commonly observed as alpha-synulcien-positive aggregates within oligodendrocytes. We elucidated that preformed alpha-synulcien fibrils triggers multimerization and upsurge of endogenous alpha-synulcien in oligodendrocyte precursor cells which is attributable to insufficient autophagic proteolysis. To assess the functional influence of alpha-synuclein fibrils application on oligodendrocyte precursor cells, RNA-seq analysis was performed. The data revealed  that alpha-synulcien fibrils interfered with numerous protein expressions associated with neuronal support and myelination.

overall_design: mRNA profiles of primary cultured rat oligodendrocyte precursor cells incubated with or without alpha-synuclein fibril for 72 hours were generated by deep sequencing, in triplicate, using Illumina MiSeq.

first: Seiji

last: Kaji

first: Takakuni

last: Maki

first: Yusuke

last: Kinoshita

first: Ryosuke

last: Takahashi


title: Transcriptome-wide characterization of human cytomegalovirus in natural infection and experimental latency

city: Tucson

first: Janko

last: Nikolich-Zugich

state: AZ

address: 1656 E. Mabel St.

institute: University of Arizona

summary:
Abstract: The transcriptional program associated with herpesvirus latency and the viral genes regulating entry into and exit from latency are poorly understood and controversial. Here, we developed and validated a targeted enrichment platform and conducted large-scale transcriptome analyses of human cytomegalovirus (HCMV) infection. We used both an experimental hematopoietic cell model of latency, and cells from naturally infected, healthy human subjects (clinical) to define the breadth of viral genes expressed. The viral transcriptome derived from experimental infection was highly correlated with that from clinical infection, validating our experimental latency model. These transcriptomes revealed a broader profile of gene expression during infection in hematopoietic cells than previously appreciated. Further, using recombinant viruses that establish a non-reactivating, latent-like or replicative infection in CD34+ hematopoietic progenitors (HPCs), we defined classes of low to moderately expressed genes that are differentially regulated in latent vs. replicative states of infection. Most of these genes have yet to be studied in depth. By contrast, genes that were highly expressed, were expressed similarly in both latent and replicative infection.  From these findings, a model emerges whereby low or moderately expressed genes may have the greatest impact on regulating the switch between viral latency and replication. The core set of viral genes expressed in natural infection and differentially regulated depending on the pattern of infection provides novel insight into the HCMV transcriptome associated with latency in the host and a resource for investigating new virus-host interactions underlying persistence.
Significance: Herpesviruses have an extraordinarily complex relationship with their host, persisting for the lifetime of the host by way of a latent infection. Reactivation of replication is associated with significant disease risk, particularly in immunocompromised individuals. We characterize in depth transcriptional profiles of HCMV latency. We show that a broad and concordant viral transcriptome is found in both an experimental model of latency and in asymptomatically infected individuals. We further define genes that are differentially regulated during latent and replicative states-  candidates for key regulators controlling the switch between latency and reactivation. This work will help understand the persistence of complex DNA viruses and provides a path towards developing antiviral strategies to control herpesvirus entry into and exit from latency.

overall_design: We sequenced a total of 49 samples. RNA-seq data sets refer to the following categories: (i) CD34+ HPC samples including mock, 2, 6 and 10dpi (n=30); (ii) Natural infection samples (pooled three samples due to low reads in individual samples). (iii) Fibroblast samples (n=16). We developed target probes (Agilent, SureSelect) to enrich low viral sequences. Our goal is to investigate HCMV transcriptomes in natural infection and experimental latency.

first: Shu

last: Cheng

first: Katie

last: Caviness

first: Jason

last: Buehler

first: Megan

last: Smithey

first: Felicia

last: Goodrum


title: PD-L1 (CD274) overexpression effect on glioblastoma cell line U251

first: Xin Yao

last: Qiu

address: Hangkong Road 13

department: School of Basic Medicine

institute: Huazhong University of Science and Technology

summary: The aim was to identify genes that were influenced by PD-L1 overexpression in glioblastoma cell lines.

overall_design: Glioblastoma cell line U251 was stably transfected with PD-L1 or its vector control via lentivirus infection. Three independent 100-mm dished of U251/PD-L1 or U251/Vec were analyzed.

first: XinYao

first: XiaoQian

last: Chen


title: Dynamic epigenomic landscapes during early lineage specification in mouse embryos

city: Beijing

first: Wei

last: Xie

address: Zhongguancun north street

summary: In mammals, all somatic development originates from lineage segregation in early embryos. However, the dynamics of transcriptomes and epigenomes in concert with initial cell fate commitment remains poorly characterized. Here, we report comprehensive investigation of transcriptomes and base-resolution methylomes for early lineages in peri- and postimplantation mouse embryos. We found allele- and lineage-specific de novo methylation at CG and CH sites, leading to differential methylation between embryonic and extraembryonic lineages at promoters of lineage regulators, gene bodies, and DNA methylation valleys. By determining chromatin architecture using Hi-C across the same developmental period, we showed both global demethylation and remethylation in early development correlate with chromatin compartments. Dynamic local methylation is evident during gastrulation, which revealed maps of putative regulatory elements. Finally, we found that de novo methylation patterning does not strictly require implantation. These data unveiled dynamic transcriptomes, DNA methylomes, and 3D chromatin landscapes during the earliest mammalian lineage specification.

overall_design: Mouse preimplantation, periimplantation and postimplantation embryos were obtained from crosses of C57BL/6N and DBA/2N as well as C57BL/6N and PWK/PhJ. STEM-seq, RNA-seq and Hi-C were performed in these embryos at various stages in development. STEM-seq was also performed on Tet1/2 double knockout embryos and in vitro culture embryos.

first: Yu

last: Zhang

first: Yunlong

last: Xiang

first: Qiangzong

last: Yin

first: Zhenhai

last: Du


title: In vitro modelling of Hypoplastic Left Heart Syndrome (HLHS)

city: Newcastle upon Tyne

first: Majlinda

last: Lako

address: Central Parkway

institute: Newcastle University

summary: We reprogrammed fibroblasts from 5 HLHS patients and 2 controls into iPSCs and differentiated into cardiomyocytes. By comparison of HLHS and control groups we uncovered the developmental, structural and functional defects of HLHS cells. Through high through-put screening, the underlying molecular mechnisms of HLHS ontology was explored.

overall_design: Cardiomyocyte mRNA profiles of normal control and HLHS samples were generated by deep sequencing, in duplicate, using Illumina HiSeq4000.

first: Lyle

last: Armstrong

first: Chunbo

last: Yang


title: Targeting EZH2 in MYCN-amplified Neuroblastoma [RNA-seq]

first: Gabriela

last: Alexe

state: MA

address: 415 Main St.

department: Computational Biology and Bioinformatics

institute: Broad Institute

summary:
Purpose:  Identify new targets in MYCN-amplified Neuroblastoma
Methods: Kelly and LAN-1 neuroblastoma cells were treated in duplicate with 2 uM GSK126 (Excess Biosciences M60071-2) or DMSO for 2 or 5 days. RNA was extracted from cells with the RNeasy Kit (Qiagen). RNA libraries were prepared for sequencing using standard Illumina protocols. The pool of sixteen samples was sequenced on two lanes of an Illumina HiSeq, generating single end reads of 32-76 bp length. Transcript abundance (reads and FPKM scores) at GRCh37/hg19 RefSeq  gene level was computed with the Feature Counts method implemented in the Bioconductor v3.2 Rsubread package (Liao et al., 2014).
Results: Pharmacological suppression of EZH2 inhibited neuroblastoma growth. Transcriptomic analysis revealed that EZH2 serves a PRC2-dependent function in neuroblastoma, repressing neural differentiation. Moreover, EZH2-regulated genes were strongly repressed in MYCN-amplified and high risk primary tumors. These observations demonstrate that MYCN upregulates EZH2 leading to inactivation of a tumor suppressor program in neuroblastoma.
Conclusion: Our study supports testing EZH2 inhibitors in patients with MYCN-amplified neuroblastoma.

overall_design: Treatment of Kelly and LAN-1 neuroblastoma cells in duplicate with  2 uM GSK126 (Excess Biosciences M60071-2) or DMSO for 2 or 5 days.

first: Kimberly

last: Stegmaier


title: BioProject PRJNA381064: Convergent origination of a Drosophila-like dosage compensation mechanism in a reptile lineage (Allelic Gene Expression in Anolis carolinensis, bulk tissue RNA-seq)

city: Lausanne

first: Diego

last: Cortez

address: Rue de Lausanne

country: Switzerland

institute: Univerity of Lausanne - CIG

summary: In order to rule out the presence of imprinted X inactivation in A. carolinensis females we generated RNA-seq data from brain, heart, kidney, liver, ovary and genome sequence data from kidney.

overall_design: Call of heterozygous SNPs of exonic regions in genomic DNA (kidney); call of expressed (allelic) SNPs from brain, heart, kidney, liver, and ovary of the same specimen.

first: Henrik

last: Kaessmann

first: Francesco

last: Lamanna

first: Madapura

last: Pradeepa


title: Targeting EZH2 in MYCN-amplified Neuroblastoma [ChIP-seq]

summary:
Purpose:  Identify new targets in MYCN-amplified Neuroblastoma
Methods:  ChIP-Seq experiments were performed on Kelly and LAN-1 neuroblastoma cells by using the following antibodies:  anti-EZH2 (Cell Signaling 5246S); anti-H3K27me3 (Millipore 07-449); anti-H3K4me3 (Abcam ab8580). We evaluated the global EZH2 PRC2-dependence by identifiying direct genome-wide target genes for EZH2,  H3K27me3 and H3K4me3.
Results: We found that EZH2 serves a PRC2-dependent function in neuroblastoma, repressing neuronal differentiation. Moreover, EZH2-regulated genes were strongly repressed in MYCN-amplified and high-risk primary tumors.
Conclusion: Our study supports testing EZH2 inhibitors in patients with MYCN-amplified neuroblastoma.

overall_design: Examination of the global EZH2 PRC2-dependence  by identifiying direct genome-wide target genes for EZH2, H3K27me3 and H3K4me3.


title: Transcriptome data of pears treated with Meyerozyma guilliermondii and sterile distilled water

status: Public on Dec 01 2017

city: Zhenjiang

first: Xiangfeng

last: Zheng

state: Jiangsu

address: 301, Xuefu Road

department: Food school

institute: Jiangsu university

summary: Meyerozyma guilliermondii, which was isolated from pears by our laboratory, M. guilliermondii had a significant effect on the induction of several defense-related genes compared to the control. It revealed the defense response mechanism of pears by transcriptomics, and investigated the function of more defense-related genes in pears.

overall_design: Pears treated with sterile distilled water (CK) and pears treated with Meyerozyma guilliermondii (Y)

first: Hongyin

first: Yuan

last: Yan


title: Hypothalamic transcriptome of Spraque Dawley rat at postnatal day 10 exposed to maternal high fat diet or control diet

city: Waurn Ponds

first: Sanna

last: Barrand

state: VIC

address: 75 Pigdon Rd

department: Faculty of Health, School of Medicine

country: Australia

institute: Deakin University

summary: We have compared hypothalamic transcriptome of rat offspring exposed to maternal high fat diet or control diet

overall_design: Examination transciptional differences between maternal high fat diet offspring and maternal control diet offspring

first: S

first: T

last: Crowley

first: R

middle: J

last: Wood-Bradley

first: K

last: De Jong

first: J

last: Armitage


title: Whole transcriptome and miRNAome analysis of porcine muscle tissue in the terms of muscle growth and development

city: Balice

first: Kacper

last: Zukowski

address: Krakowska 1 Street

country: Poland

institute: National Research Institute of Animal Production

summary:
Purpose: The aim of present research was to identify genes potentially related with muscle growth in pig
Methods: RNA-seq analysis was performed on longissimus lumborum samples collected from 13 pigs representing two sire-line breeds – Pietrain and Hampshire.  Base on dissection data, pigs were selected from a larger population in terms of weight of loin muscle to obtain the most extreme groups in each breed The cDNA libraries were constructed form 300 ng of total RNA with the use TruSeq RNA Sample Prep Kit v2 kit (Illumina) according to the protocol. The quantification of obtained libraries was performed on Qubit 2.0 (Invitrogen, Life Technologies) and TapeStation 2200 (D1000 ScreenTape; Agilent). The RNA-seq was performed in 101 single-end cycles on HiScanSQ platform (Illumina) with the use of ruSeq SR Cluster Kit v3- CBOT-HS and TruSeq SBS Kit v 3 - HS (Illumina).  Each library was sequences in 4 technical replications. The DEGs were detected using DESEq2 software and validation was performed by qPCR.
Results: RNA-seq approach allowed to identify 627 and 416 DEGs between pig groups with different loin weight (pvalue <0.05; fold change≤1.5) for Pietrain and Hampshire; respectively. Next, the comparison of obtained genes sets showed 43 genes identified in both breeds. The Gene Ontology analysis (Panther software) confirmed that detected genes were involved in regulation of metabolic process (18 genes), developmental growth or skeletal system development (PCOLCE; BBS2; TBX2; RBBP6; ATAF5). According to David software these genes belong to PI3K-Akt signaling, Focal adhesion and ECM-receptor interaction pathways.
Conclusions: Obtained results allow to propose the panel of genes, which can be related with porcine muscle growth and development. Such analysis can be the basis of future research in terms of identification of candidate genes related with important production traits in pigs.

overall_design: The muscle (longissimus dorsi) transcriptome sequencing was performed for 13 samples collected form pigs representing two breeds - Pietrain and Hampshare, using Illumina HiScan SQ in 101 single-end cycles and in 4 technical repetitions repetitions.

first: Katarzyna

last: Ropka-Molik

first: Klaudia

last: Pawlina

last: Żukowski

last: Piórkowska

first: Grzegorz

last: Żak

first: Natalia

last: Derebecka

first: Joanna

last: Wesoły


title: RNA-seq and small RNA-seq analysis of N2 wildtype and mir-71(n4115) C. elegans during aging

city: New Haven

first: Sachi

last: Inukai

state: Connecticut

address: 219 Prospect St

institute: Yale University

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

overall_design: Refer to individual Series


title: Genome-wide mapping of decay factor-mRNA interactions in yeast identifies nutrient responsive transcripts as targets of the deadenylase Ccr4

city: University Park

first: Joseph

middle: C.

last: Reese

state: PA

address: North Frear Laboratory

department: Biochemistry and Molecular Biology

institute: The Pennsylvania State University

summary: The Ccr4-Not complex is a major regulator of stress responses that controls gene expression at multiple levels, from transcription to mRNA decay. Ccr4, a core subunit of the complex, is the main cytoplasmic deadenylase in Saccharomyces cerevisiae, however its mRNA targets have not been mapped on a genome-wide scale. Here we describe a genome-wide approach, RNA immunoprecipitation-high throughput sequencing (RIP-seq), to identify the RNAs bound to Ccr4, and two proteins that associate with it, Dhh1 and Puf5. All three proteins were preferentially bound to lowly abundant mRNAs, most often at the 3’ end of the transcript. Furthermore, Ccr4, Dhh1 and Puf5 are recruited to mRNAs that are targeted by other RNA-binding proteins that promote decay, mRNA transport and inhibit translation.  Although Ccr4-Not regulates mRNA transcription and decay, Ccr4 recruitment to mRNAs correlates better with decay rates, suggesting it imparts greater control over transcript abundance through decay. Ccr4-enriched mRNAs are refractory to control by the other deadenylase complex in yeast, Pan2/3, suggesting a division of labor between these deadenylation complexes. Finally, Ccr4 and Dhh1 associate with mRNAs whose abundance increases during nutrient starvation and those that fluctuate during metabolic and oxygen consumption cycles, which explains the known genetic connections between these factors and nutrient utilization and stress pathways.

overall_design: Genome-wide characterization of the RNA-protein interactions of Ccr4, Dhh1 and Puf5 in yeast, in triplicate using SOLiD sequencing.

first: Jason

last: Miller

first: Liye

last: Zhang

first: Haoyang

last: Jiang

first: Yunfei

last: Li

first: B

last: Pugh

middle: C


title: Deep sequencing of small RNAs from whole nematode C. elegans during aging

summary: MicroRNAs (miRNAs) have been implicated in gene regulation in many complex processes, including aging. Moreover, expression levels of many miRNAs are altered during aging, though we know little about the mechanisms that regulate this process. To address these issues, we investigated the network of regulatory factors that interact with miRNAs during aging. We found miR-71, a known promoter of normal lifespan, to be an especially important regulator of alg-1/Argonaute. Here we show that increased ALG-1 expression in aging mir-71 loss-of-function mutants was associated with an increased global miRNA abundance and deregulation of mRNA expression. Further, variability in gene expression and lifespan are diminished in mir-71 mutants. Thus, miR-71 appears to promote normal lifespan by directly repressing the expression of alg-1 and indirectly regulating miRNA expression levels and noise. Our findings demonstrate the broad impacts of miRNAs on gene regulation during aging.

overall_design: Small RNA profiles from Day 0 adulthood and Day 5 adulthood C. elegans nematodes. 12 total samples, in biological triplicate at each time point from wildtype control (N2) and mir-71(n4115) strains. Generated using Illumina HiSeq 2500.

first: Frank

last: Slack


title: Engineered Nanointerfaces for Microfluidic Isolation and Molecular Profiling of Tumor-specific Extracellular Vesicles

city: Boston

first: David

middle: T

last: Ting

address: 149 E 13th street

department: Cancer Center

institute: Massachusetts General Hospital

summary: Tumor-EVs were captured on a nanostructured interface through immunoaffinity immobilization in a microfluidic channel containing herringbone (HB) structure for efficient mixing (EVHB-Chip).  Processing serum and plasma samples from glioblastoma multiforme (GBM) patients, isolated tumor EVs were analyzed using next-generation RNA sequencing analysis, and identified genes specific to glioblastoma as well as transcripts that are hallmarks for the four genetic subtypes of disease (e.g., classical, mesenchymal, neural, and pro-neural).

overall_design: Plasma or serum isolated from 13 GBM patients than run through the EVHB-Chip coated with antibodies.(EGFR, EGFRvIII, PDGFR) Isolated Evs analysed using next-generation RNA sequencing analysis.

first: Eduardo

last: Reátegui

first: Kristan

last: van der Vos

first: Charles

last: Lai

first: Mahnaz

last: Zeinali

first: Nadia

last: Atai

first: Berent

last: Aldikacti

first: Frederick

last: Floyd Jr.

first: Aimal

last: Khankhel

first: Vishal

last: Thapar

first: Fred

last: Hochberg

first: Lecia

middle: V

last: Sequist

first: Brian

last: Nahed

first: Bob

last: Carter

first: Mehmet

last: Toner

first: Leonara

last: Balaj

first: Xandra

middle: O

last: Breakefield

first: Shannon

last: Stott


title: Deep sequencing of poly(A)-selected RNAs from whole nematode C. elegans during aging

first: Sachi

last: Inukai

overall_design: RNA profiles (poly(A)-selected RNA) from Day 0 adulthood and Day 5 adulthood C. elegans nematodes. 12 samples total, in biological triplicate at each time point from wildtype control (N2) and mir-71(n4115) strains. Generated using Illumina HiSeq 2500.

first: Frank

last: Slack


title: Genome-wide maps of DNase I sensitivity in normoxic and hypoxic cells

city: Singapore

first: Henry

last: Yang

address: 28 Medical Drive

country: Singapore

institute: Cancer Science Institute of Singapore

summary: We report genome-wide maps of DNase I sensitivity in normoxic and hypoxic cells to provide information on changes in chromatin status in response to oxygen availability.

overall_design: Examination of 1 cell type (neuroblastoma) under 3 different oxygen conditions.

first: Norio

last: Suzuki

first: Nikola

last: Vojnovic

first: Kian

last: Lee

first: Katarina

last: Gradin

first: Lorenz

last: Poellinger


title: Single cell RNA-seq of mouse brain vascular transcriptomes

city: Uppsala

first: L.

last: He

address: Dag Hammarskjölds Väg 20

institute: Uppsala University

summary: By analyzing thousands of vascular single cell transcriptomes from adult mouse brain, we provide molecular definitions of the principal vascular (endothelial and mural cells), and vascular-associated cell classes.

overall_design: We used four different transgenic mouse reporter lines with fluorescent expression in different populations of vascular cells, Cldn5(BAC)eGFP mice that strongly labels brain endothelial cells, mice doubly positive for Pdgfrb(BAC)eGFP and NG2dsRed, in which brain vascular mural cells express both markers whereas each single marker are expressed also in other, non-overlapping cell types, and Pdgfra-H2BGFP that we found labeled a perivascular population of cells distinct from mural cells and astrocytes, in addition to the known labeling of cells of the oligendendrocyte lineage.   We chose to focus our efforts to adult mice 10 to 19 weeks old in order to primarily define fully differentiated and quiescent vascular cells and we chose a methodology based on fluorescence-activated cell sorting (FACS) into 384-well plates followed by the SmartSeq2 methodology for the generation and sequencing of full length polyadenylated cDNAs

first: Michael

last: Vanlandewijck

first: Liqun

first: Maarja

last: Mäe

first: Johanna

last: Andrae

first: Christer

last: Betsholtz


title: Novel Targeting of Transcription and Metabolism in Glioblastoma

city: Bethesda

first: Jing

last: Wu

state: Maryland

address: 9030 Old Georgetown Rd

department: Center for Cancer Research

institute: National Cancer Institute, NIH

summary:
Purpose: Glioblastoma (GBM) is highly resistant to treatment, largely due to disease heterogeneity and resistance mechanisms. We sought to investigate a promising drug that can inhibit multiple aspects of cancer cell survival mechanisms and become effective therapeutics for GBM patients.

Experimental Design: To investigate TG02, an agent with known penetration of the Blood-Brain Barrier, we examined the effects as single agent and in combination with temozolomide, a commonly used chemotherapy in GBM. We utilized human GBM cells and a syngeneic mouse orthotopic GBM model, evaluating survival and the pharmacodynamics of TG02.  Mechanistic studies included TG02-induced transcriptional regulation, apoptosis and RNA sequencing in treated GBM cells as well as the investigation of mitochondrial and glycolytic function assays.

Results: We demonstrated that TG02 inhibited cell proliferation, induced cell death, and synergized with temozolomide in GBM cells with different genetic background but not in astrocytes. TG02-induced cytotoxicity was blocked by the overexpression of phosphorylated CDK9, suggesting a CDK9-dependent cell killing. TG02 suppressed transcriptional progression of anti-apoptotic proteins, and induced apoptosis in GBM cells. We further demonstrated that TG02 caused mitochondrial dysfunction and glycolytic suppression and ultimately ATP depletion in GBM. A prolonged survival was observed in GBM mice receiving combined treatment of TG02 and temozolomide. The TG02-induced decrease of CDK9 phosphorylation was confirmed in the brain tumor tissue.

Conclusions: TG02 inhibits multiple survival mechanisms and synergistically decreases energy production with temozolomide, representing a promising therapeutic strategy in GBM, currently under investigation in an ongoing clinical trial.

overall_design: The RNA sequencing was carried out to analyze the profile of RNA expression following 0.1% of DMSO (control), TG02, TMZ, and TG02/TMZ treatment, in duplicate, in GSC923 cells.

first: Yu-Ting

last: Su


title: The intracellular mediators of the BMP pathway SMAD1/5 bind the Imprinting Control  Regions through interaction with the ZFP57/KAP1 complex and contribute to maintain their  DNA methylation and H3K9me3 in mouse embryonic stem cells

status: Public on Dec 07 2017

city: Naples

first: Marco

last: Cammisa

state: Naples

address: Via Castellino Pietro, 111

country: Italy

institute: Institute of Genetics and Biophysics "A. Buzzati Traverso" (IGB-ABT)

summary: We report that SMAD1/5 bind the ICRs by interacting with the ZFP57/KAP1 complex and that this is necessary for the proper maintenance of methylation imprints in mESCs

overall_design: Examination of SMAD1/5 occupancy in Zfp57 -/- mESCs compared to the wild-type

first: Harpreet

last: Kukreja

first: Andrea

last: Oneglia

first: Basilia

last: Acurzio

first: Vincenzo

last: Riso

first: Zahra

last: Anvar

first: Angela

last: Sparago

first: Valentina

last: Citro

first: Annalisa

last: Fico

first: Susana

last: de Sousa Lopes

last: Riccio


title: Integration host factor and LuxR synergistically bind DNA to coactivate quorum-sensing genes in Vibrio harveyi.

city: Bloomington

first: Julia

last: van Kessel

state: IN

address: 1001 E 3rd Street

department: Biology

institute: Indiana University

summary: LuxR is the master quorum sensing regulator in Vibrio harveyi. This transcription factor controls the expression of over 600 genes to coordinate group behaviors. In order to understand how LuxR regulates transcription we identified a co-regulator, integration host factor (IHF). In this study we performed RNA-seq to show that the LuxR and IHF regulons overlap significantly.

overall_design: Wild-type, ΔluxR, ΔihfA ΔihfB strains were grown at 30 °C to OD600 = 1.0. RNA was extracted and prepared from three biological replicates of each strain. cDNA libraries were created and sequenced for differential gene expression analysis.

first: Ryan

last: Chaparian

first: Stephen

last: Olney

first: Christine

last: Hustmeyer

first: Dean

last: Rowe-Magnus


title: FOX and ETS family transcription factors regulate the pigment cell lineage in planarians

city: Portland

first: Bret

last: Pearson

state: OR

address: 3181 SW Sam Jackson Park Rd., BRB Room 305

department: Pediatrics

institute: Oregon Health and Science University

summary: Many pigment cells acquire unique structural properties and gene expression profiles during animal development. The underlying differentiation pathways have been well characterized in cells formed during embryogenesis, such as the neural crest-derived melanocyte. However, much less is known about the developmental origins of pigment cells produced in adult organisms during tissue homeostasis and repair. Here we report a lineage analysis of ommochrome- and porphyrin-producing cells in the brown, freshwater planarian Schmidtea mediterranea. Using an RNA-sequencing approach, we identified two classes of markers expressed in sequential fashion when new pigment cells are generated during regeneration or in response to pigment cell ablation. We also report roles for FOXF-1 and ETS-1 transcription factors, as well as an FGF Receptor-like molecule, in the specification and maintenance of this cell type. Together, our results provide the first insight into mechanisms of adult pigment cell development in the strikingly colorful Platyhelminthes phylum.

overall_design: RNA deep sequencing (RNAseq) was performed on wildtype (WT) animals as well as fully depigmented animals (8 days of depigmentation by light exposure) and partially repigmented animals (1, 2 and 8 days of repigmentation in the dark on starved animals). Experiments were performed in biological-triplicate but mixed in equal amounts prior to sequencing, sequenced to a depth of ~40 million reads per sample, and multiplexed on an Illumina HiSeq2500 with 50 base pair, single-end reads. 75 genes of interest were identified based on high 8 day WT:depigmented fold change. Raw scRNAseq data (including stem cells, neurons, gut, epithelial, muscle and parapharyngeal cells) were obtained from the NCBI Sequence Read Archive (SRA:PRJNA276084) and the NCBI Gene Expression Omnibus (GEO:GSE79866) (Molinaro and Pearson, 2016; Wurtzel et al., 2015). Reads were aligned to the SmedASXL transcriptome assembly under NCBI BioProject PRJNA215411 using bowtie2 (Langmead and Salzberg, 2012) with 15 bp 3’ trimming.

first: Xinwen

last: He

first: Nicole

last: Lindsay-Mosher


title: Migratory CD11b+ conventional dendritic cells induce T follicular helper cell dependent antibody responses

city: Farmington

first: Marina

last: Yurieva

address: 10 Discovery dr

department: Computational Sciences

institute: Jackson Laboratory

summary: T follicular helper (Tfh) cells are a subset of CD4+ T cells that promote antibody production during vaccination. Conventional dendritic cells (cDCs) efficiently prime Tfh cells; however, conclusions regarding the nature of the cDC responsible for instructing Tfh cell differentiation have differed between recent studies. We found that these discrepancies might exist, in part, due to the unusual sites used for immunization in murine models, which differentially bias which DC subsets access antigen. We used intranasal immunization as a physiologically relevant route of exposure that we show delivers antigen to all tissue DC subsets. Using a combination of mice in which the function of individual DC subsets is impaired and different formulations of antigen delivery, we determined that CD11b+ migratory type 2 conventional DCs (cDC2s) are necessary and sufficient for Tfh induction. DC-specific deletion of the guanine nucleotide exchange factor DOCK8 resulted in an isolated loss of CD11b+ cDC2 but not CD103+ cDC1 migration to lung-draining lymph nodes. Impaired cDC2 migration or development in DC-specific Dock8 or Irf4 knockout mice, respectively, led to reduced Tfh cell and antibody development, whereas loss of CD103+ cDC1s in Batf3-/- mice did not. Loss of cDC2-mediated Tfh responses was associated with impaired antibody-mediated protection from live influenza virus challenge. We show that migratory cDC2s uniquely carry antigen into the sub-anatomic regions of the lymph node where Tfh cell priming occurs, the T-B border. This work identifies the DC responsible for Tfh cell-dependent antibody responses, in particular when antigen dose is limiting or is encountered at a mucosal site, which could ultimately inform the formulation and delivery of vaccines.

overall_design: RNA-seq of CD11b+ and CD103+ dendritic cells from the mediastinal lymph nodes

first: J

middle: K

last: Krishnaswamy

first: U

last: Gowthaman

first: B

last: Zhang

last: Mattsson

first: L

last: Szeponik

first: D

last: Liu

first: R

last: Wu

first: T

last: White

first: S

last: Calabro

last: Xu

first: M

last: Collet

last: Alsén

first: P

last: Fogelstrand

last: Yrlid

first: W

last: Heath

middle: N

last: Mueller

first: Adam

last: Williams

first: Stephanie

last: Eisenbarth


title: Hippocampus and hypothalamus RNA-sequencing of WFS1-deficient mice [hypothalamus]

city: Perth

first: Sulev

last: Koks

state: Western Australia

address: 90 South Street

department: Centre for Molecular Medicine and Innovative Therapeutics

institute: Murdoch University

summary: Wolfram syndrome is caused by mutations in the WFS1 gene. WFS1 protein dysfunction results in a range of neuroendocrine syndromes and is mostly characterized by juvenile-onset diabetes mellitus and optic atrophy. WFS1 has been shown to participate in membrane trafficking, protein processing and Ca2+ homeostasis in the endoplasmic reticulum.  In the present study we aimed to find the transcriptomic changes influenced by Wfs1 in the hypothalamus and hippocampus using RNA-sequencing. We used WFS1-deficient mice as a model system to analyze the changes in transcriptional networks.  The number of differentially expressed genes between hypothalami of WFS1-deficient (Wfs1KO) and wild-type (WT) mice was 43 and between hippocampi 311 with False Discovery Rate (FDR) <0.05. In hypothalamus of Wfs1KO mice one of the most upregulated genes was Avpr1a whilst Avpr1b was significantly upregulated in hippocampus. Trpm8 was the most upregulated gene in the hippocampus of Wfs1KO mice. The functional analysis revealed significant enrichment of networks and pathways associated with protein synthesis, cell-to-cell signaling and interaction, molecular transport, metabolic disease and nervous system development and function.   In conclusion, the transcriptomic profiles of WFS1-deficient hypothalamus and hippocampus do indicate the activation of degenerative molecular pathways causing the clinical occurrences typical to Wolfram syndrome.

overall_design: 12 samples: three genotypes, 4 individuals in each genotype

first: Marilin

last: Ivask

first: Sander

last: Pajusalu

first: Ene

last: Reimann

last: Kõks


title: Hippocampus and hypothalamus RNA-sequencing of WFS1-deficient mice


title: Powerdress Mediated Histone Deacetylation Is Essential For Thermomorphogenesis In Arabidopsis Thaliana

city: Melbourne

first: Avilash

last: Singh Yadav

state: Victoria

address: Innovation Walk 18, Monash University Clayton Campus

department: School of Biological Sciences

institute: Monash University

summary: We report POWERDRESS (PWR), a SANT domain containing protein known to facilitate the deacetylation of lysine rich residues of histone H3 by HISTONE DEACETYLASE 9 (HDA9), to play key role in temperature induced growth in Arabidopsis thaliana. Mutations in PWR showed severe attenuation in high temperature associated phenotypes viz., temperature-induced hypocotyl elongation, petiole elongation and early flowering. The study involved analysing the impact of the loss of PWR on the transcriptome in response to changes in ambient temperature. About one hundred 6 day old seedlings of wild type (Col-0) and pwr-2 mutant (in Col-0 background) were grown at 23 °C in short days (SD) photoperiod in growth chambers (GR-36, Percival Scientific, Canada). Half of the samples were then shifted to 27°C under short day photoperiod. Total RNA was extracted from whole seedlings grown at 23 °C and 27°C after two hours. Two biological replicates were used for Col-0 and pwr-2 samples. RNA was extracted using Isolate II RNA plant kit (Bioline Pty Ltd, Australia). RNA-Seq libraries were generated on Illumina HiSeqTM 2000 platform using paired-end sequencing of 90 bp in length at BGI-Shenzen (Beijing Genomics Institute). Gene expression analysis was performed using DESeq2 (v1.14.1) differential expression analysis pipeline.

overall_design: Comparison of the transcriptome of 6 day old seedlings of Col-0 (WT) and pwr-2 mutants (in Col-0 background) grown at 23°C and shifted to 27°C for 2 hrs. Whole seedlings for RNA extraction were collected from   23°C and  27°C after two hours.

first: Celine

last: Tasset

middle: S

last: Yadav

first: Sridevi

last: Sureshkumar

first: Rupali

last: Singh

first: Lennard

last: van der Woude

first: Maxim

last: Nekrasov

first: David

last: Tremethick

first: Martijn

last: van Zanten

first: Sureshkumar

last: Balasubramanian


title: RNA-seq analysis of activated plasmacytoid dendritic cell subsets after viral infection

city: Paris

first: Violaine

last: Saint-André

address: 26 rue d'Ulm

country: France

institute: Institut Curie

summary: Hematopoiesis generates cell diversity through evolutionarily-determined differentiation programs defined at steady-state conditions. Here, we show that peripheral innate immune activation can generate cell diversity and functional specialization during the activation process. We found that activation of steady state human plasmacytoid pre-dendritic cells (pDCs) with a single microbial stimulus induced their differentiation into three phenotypically, morphologically, and functionally distinct subsets, in the absence of cell division: P1 (PD-L1+CD80-), P2 (PD-L1+CD80+) and P3 (PD-L1-CD80+). Different stimuli induced variable proportions of the subsets, suggesting that steady state pDC are multipotent. P1-pDCs display a plasmacytoid morphology and strong specialization on IFN production, whereas P3-pDCs adopt a dendritic morphology and adaptive immune functions. P2-pDCs have an intermediate functional profile. We found that a P1-pDC phenotype is present in human autoimmune diseases associated to type I IFN production as lupus and psoriasis, supporting their pathophysiological relevance. We propose that peripheral innate activation represents a differentiation mechanism to generate subsets diversity and functional complementarity in human pDCs.

overall_design: 15 samples: medium (control condition), ex-vivo, P1, P2 and P3, each from 3 healthy donors. Ex-vivo plasmacytoid dendritic cells from the blood of healthy human donors were treated for 24h with influenza virus. Treated cells were sorted as P1, P2, and P3 subsets depending on surface markers: P1 (PD-L1+CD80-), P2 (PD-L1+CD80+) and P3 (PD-L1-CD80+). Non-treated control cells correspond to  pDCs  kept in medium.

first: Solana

middle: G

last: Alculubre

first: Maxime

last: Wery

first: Antonin

last: Morillon

first: Vassili

last: Soumelis


title: Myc and YAP roles in the control of the cell cycle [MEF RNA-seq pharmacological treatment]

city: milano

first: stefano

last: campaner

address: via adamello 16

department: Center for Genomic Science

institute: fondazione Istituto italiano di tecnologia

summary: Expression profiling by RNA-seq

overall_design: RNAseq analysis serum starved Mouse embryonic fibroblasts expressing MycER (activated by OHT) and mutant YAP2S (YAPS127/381A),  treated with Y27632.

first: Stefano

last: Campaner

first: Marieta

last: Caganova

first: Elisa

last: Donato

first: Ottavio

last: Croci


title: Precision genome editing using synthesis-dependent repair of Cas9-induced DNA breaks

city: Baltimore

first: Daniel

last: Goldman

address: 725 N. Wolfe St.

department: Molecular Biology and Genetics

institute: Johns Hopkins School of Medicine

summary: The RNA-guided DNA endonuclease Cas9 has emerged as a powerful new tool for genome engineering. Cas9 creates targeted double-strand breaks (DSBs) in the genome. Knock-in of specific mutations (precision genome editing) requires homology-directed repair (HDR) of the DSB by synthetic donor DNAs containing the desired edits, but HDR has been reported to be variably efficient. Here, we report that linear DNAs (single and double-stranded) engage in a high-efficiency HDR mechanism that requires only ~35 nucleotides of homology with the targeted locus to introduce edits ranging from 1 to 1000 nucleotides. We demonstrate the utility of linear donors by introducing fluorescent protein tags in human cells and mouse embryos using PCR fragments. We find that repair is local, polarity-sensitive, and prone to template switching, characteristics that are consistent with gene conversion by synthesis-dependent strand-annealing (SDSA). Our findings enable rational design of synthetic donor DNAs for efficient genome editing.

overall_design: The genomic lamin locus is probed for template switching between two donor repair templates after repair of a Cas9-induced DNA break

first: Alexandre

last: Paix

first: Andrew

last: Folkmann

first: Heather

last: Kulaga

first: Michael

last: Grzelak

first: Dominique

last: Rasoloson

first: Supriya

last: Paidemarry

first: Rachel

last: Green

first: Randall

last: Reed

first: Geraldine

last: Seydoux


title: Targeting EZH2 in MYCN-amplified Neuroblastoma

city: Cambridge

first: Gabriela

last: Alexe

address: 415 Main St.

institute: Broad Institute

overall_design: Refer to individual Series


title: Super-Enhancers Promote Transcriptional Dysregulation in  Nasopharyngeal Carcinoma [ChIP-seq]

first: Phillip

middle: H

last: Koeffler

address: 14 Medical Drive

institute: Cancer Science Institute

summary: Nasopharyngeal carcinoma (NPC) is an invasive cancer with particularly high  incidence in Southeast Asia and Southern China. The pathogenic mechanisms of NPC,  particularly those involving epigenetic dysregulation, remain largely elusive,  hampering the clinical management of this malignancy. To identify novel druggable  targets, we carried out an unbiased high-throughput chemical screening and observed  that NPC cells were highly sensitive to cyclin-dependent kinases (CDKs) inhibitors,  especially THZ1, a covalent inhibitor of CDK7. THZ1 demonstrated pronounced  anti-neoplastic activities both in vitro and in vivo. An integrative analysis using both  whole-transcriptome sequencing (RNA-Seq) and chromatin-immunoprecipitation  sequencing (ChIP-Seq) pinpointed oncogenic transcriptional amplification mediated  by Super-Enhancer (SE) as a key mechanism underlying the vulnerability of NPC  cells to THZ1 treatment. Further characterization of SE-mediated network identified  many novel SE-associated oncogenic transcripts, such as BCAR1, F3, LDLR,  TBC1D2 and a long non-coding RNA, TP53TG1. These transcripts were highly and  specifically expressed in NPC, and functionally promoted NPC malignant phenotypes.  Moreover, DNA-binding motif analysis within the SE segments suggest that several  transcription factors (including ETS2, MAFK and TEAD1) may help establish and  maintain SE activity across the genome. Our data together established the landscape  of SE-associated oncogenic transcriptional network in NPC, which can be exploited  for the development of more effective therapeutic regimen for this disease.

overall_design: ChIP seq for histone modifications in three NPC cell lines – C666-1, HK1 and HNE1

first: Jiang

last: Juan

first: Yan-Yi

last: Jiang

first: Anand

last: Mayakonda

first: Moli

last: Huang

first: Ling-Wen

last: Ding

first: Han

last: Lin

first: Feng

last: Yu

first: Kwok

last: Loh

first: Jeffrey

last: Tyner

first: De-Chen

first: H


title: Super-Enhancers Promote Transcriptional Dysregulation in  Nasopharyngeal Carcinoma [RNA-seq]

overall_design: RNA-seq in three NPC cell lines – C666-1, HK1 and HNE1


title: Single cell RNA sequencing of peanut-responsive T cells

city: NEW YORK

first: Cecilia

last: Berin

state: NY

address: 1470 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

summary: Peanut-responsive T cells from peanut allergic subjects were identified and selected based on CD154 expression after stimulation of peripheral blood mononuclear cells with crude peanut extract for 18h. As controls, polyclonally activated CD4+ T cells from peanut allergic subjects were selected. Additional controls included CD4+CD25+CD127- Tregs from peanut allergic or healthy controls. Single cells were obtained using the C1 system from Fluidigm, and a barcoded library constructed. Sequencing (Illumina) was performed using 100 nt paired end reads. Data on a total of 431 cells was available. The goal of the study was to understand the heterogeneity of the peanut-specific T cell response.

overall_design: 212 peanut-responsive T cells from 5 peanut allergic subjects, 122 polyclonally activated T cells from 3 peanut allergic subjects, and 97 Tregs from 4 peanut allergic and 4 healthy controls were obtained.

first: Chiang

last: David

first: Chen

last: Xintong

first: Jones

last: Stacie

first: Wood

last: Robert

first: Sicherer

last: Scott

first: Burks

last: Wesley

first: Leung

last: Donald

first: Agashe

last: Charuta

first: Grishin

last: Alexander

first: Dawson

last: Peter

first: Davidson

last: Wendy

first: Newman

last: Leah

first: Sebra

first: Merad

last: Miriam

first: Sampson

last: Hugh

first: Losic

last: Bojan

first: Berin

last: Cecilia


title: De novo transcriptome of the cosmopolitan dinoflagellate Amphidinium carterae to identify genes with biotechnological interests

city: Verona

first: Massimo

last: Delledonne

address: Strada le Grazie 15

institute: Universita' degli Studi di Verona

summary: Dinoflagellates are phytoplanktonic organisms found in both freshwater and marine habitats. They are often studied because related to harmful algal blooms responsible for impacts on ecosystem functioning, economic damages for aquaculture and fishery industries and/or deleterious impacts for human health. In addition they are also known to produce bioactive compounds, such as for the treatment of cancer or beneficial effects for the treatment of Alzheimer’s disease. The dinoflagellate Amphidinium sp. is a cosmopolitan dinoflagellate species known to produce both cytotoxic and beneficial compounds. However, several studies reported that environmental changes (e.g. nutrient starvation, UV radiation and ocean acidification) may alter this production. The aim of this study was to sequence the full transcriptome of the dinoflagellate Amphidinium carterae in both nitrogen- starved and -repleted culturing conditions (1) to evaluated its response to nitrogen starvation, (2) to look for possible polyketide synthases (PKSs), involved in the synthesis of various compounds, in this studied clone, (3) if present, to evaluate if nutrient starvation can influence PKS activity, (4) to test strain cytotoxicity on human cells and (5) to look for other possible enzymes/proteins of biotechnological interest.

overall_design: The dinoflagellate A. carterae was cultured in two conditions, i.e. Nitrogen-starved or -repleted (control) conditions. Cells were harvested at the end of the stationary phase and used for RNA extraction. Triplicate samples of both conditions were sequenced and differential expression analysis was performed. In addition, enzymes with biotechnological interest were identified.

first: Lauritano

last: Chiara

first: Adrianna

last: Ianora


title: Transcriptome-wide analysis of the RNA content of purified Nanoblades

city: Lyon

first: Emiliano

last: Ricci

address: 46 allée d'Italie

department: Centre International de Recherche en Infectiologie

institute: INSERM

summary: Programmable nucleases have enabled rapid and accessible genome engineering in eukaryotic cells and living organisms. However, their delivery into target cells can be technically challenging when working with primary cells or in vivo. Using engineered murine leukemia virus-like particles loaded with Cas9/sgRNA ribonucleoproteins (“Nanoblades”), we were able to induce efficient genome-editing in cell lines and primary cells including human induced pluripotent stem cells, human hematopoietic stem cells and mouse bone-marrow cells. Transgene-free Nanoblades were also capable of in vivo genome-editing in mouse embryos and in the liver of injected mice. Nanoblades can be complexed with donor DNA for “all-in-one” homology-directed repair or programmed with modified Cas9 variants to mediate transcriptional up-regulation of target genes. Nanoblades preparation process is simple, relatively inexpensive and can be easily implemented in any laboratory equipped for cellular biology.

overall_design: Virus-like particles were purified on a sucrose cushion. Total RNA was extracted using Trizol and fragmented to ~100 nucleotides and used as input for cDNA library preparation. PCR-amplified libraries were sequenced on the Hiseq2500 platform (Illumina)


title: 22Rv1 in vivo progression model

city: Taipei

first: Chin-Hsien

last: Tsai

state: Others

address: Nan-Kang

department: ABRC

country: Taiwan

institute: Academia Sinica

summary:
Purpose: Even in last stage of metastatic castration-resistant prostate cancer, androgen receptor (AR) signaling remains active.To derive high metastatic prostate cancer (PCa), we labeled AR-positive but castration-resistant 22Rv1 PCa cells with luciferase gene (22Rv1-Luc2) and these cells were orthotopically implanted in mouse prostate for spontaneous progression.
Methods:  2 × 10^5 of luciferase-expressing 22Rv1 cells (22Rv1-Luc2) cells were implanted in the anterior prostate of nude mice. After 12-14 weeks, the host mice were necropsied and the metastases from lumbar lymph nodes and primary tumors were dissected under laminar flow. Tumor tissues were minced using sterile scalpels and further digested with Collagenase D for 1 h. The lymph node metastatic cancer cells, named 22Rv1-M1, were orthotopically reimplanted in nude mice. At 12 weeks, the secondary metastases were isolated in the lumbar lymph nodes and designated as 22Rv1-M2 cells. Suspension of 1 × 10^6 22Rv1-M2 cells in DPBS was injected into nude mice through the tail vein, and mice developed metastases (22Rv1-M3) after 6 week. This procedure was repeated once to attain the 22Rv1-M4.
Results: 22Rv1-derived metastatic cell lines exhibit increased in vitro and in vivo invasion activity as the progression from 22Rv1 to M4. Transcriptomic analysis of genome-wide gene expression in the M4 tumors reveal the unique gene expression profile compared to 22Rv1 tumors.
Conclusions: Transcriptomic data provide the gene network for decoding the mechanism of PCa metastasis.

overall_design: Transcriptomic profiles of the 22Rv1-Luc2 cells, 3 individual 22Rv1-derived tumor samples and 3 individual 22Rv1-M4-derived tumor samples were sequenced using RNAseq. SRA Study accession:SRP108867; BioProject accession: PRJNA389750

first: Pei-Wen

last: Hsiao


title: Cockayne syndrome A and B proteins regulate the transcription arrest upon genotoxic stress through a ubiquitin/proteasome degradation process (RNA-seq)

city: Illkirch

first: Tao

last: YE

address: 1 rue Laurent Fries

institute: IGBMC (CNRS/INSERM/UDS)

summary: The rare genetic disease Cockayne syndrome (CS) results in mutations in CSA and CSB. Upon UV irradiation, RNA synthesis was arrested: RNA-seq showed 70% of down-regulated genes in common between CSA and CSB deficient cells. ATF3, the product of an immediate early gene was overexpressed and bound to its CRE/ATF site to inhibit its responsive genes. ChIP experiments showed that CSA/CUL4A/DDB1 together with CSB and MDM2, target ATF3. In vivo and in vitro experiments showed that ATF3 was ubiquitilated by a concerted action of CSA and MDM2 ubiquitin-ligases and was further eliminated by the proteasome concomitantly with the recruitment of RNA polymerase II to restart transcription. In CS cells, dysfunctional CSA or CSB were unable to assemble the ubiquitin/proteasome complex, thereby maintaining the ATF3-dependent transcription arrested. Though, in addition to their function in DNA repair, CSA and CSB might thus regulate the timing of DNA binding factors on its specific target site via the ubiquitin/proteasome machinery.

overall_design: Examination kinetic of 8 samples including CS3BE, CSA, CS1AN, and CSB in 0, 8 and 24 hours, in wild type and CSB mutant cell lines.

first: Alexey

last: Epanchintsev

last: Ye

first: Jean-Marc

last: Egly


title: Cockayne syndrome A and B proteins regulate the transcription arrest upon genotoxic stress through a ubiquitin/proteasome degradation process (ChIP-seq)

overall_design: Examination kinetic of 18 samples including ATF3, PolII, CSA, CSB, MDM2, PSMB5 and PSMD1 in 0, 8 and 24 hours, in wild type and CSB mutant cell lines.

first: Federico

last: Costanzo


title: Transcriptional changes in pancreatic cancer cells associated with gemcitabine resistance

first: Meghan

middle: Morrison

last: Joly

address: Sears Lab, CLSB 4N079, Oregon Health & Science University 2730 SW Moody Ave

department: Molecular and Medical Genetics

summary: The goal of this study was to determine the transcriptional changes in pancreatic cancer cells after treatment with gemcitabine.

overall_design: HPAFII cells were treated with PBS or Gemcitabine for 72 hours. RNA was harvested from 3 independent, experimental replicates per treatment group.

first: Rosalie

last: Sears


title: Inhibition of TGFβRI as a therapy for GATA4 deficient lung cancers

city: Beijing

first: huanwei

last: huang

address: 7 Science Park Rd., ZGC life science park

institute: NIBS

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


title: Activation of the STING-dependent type I interferon response reduces microglial reactivity and neuroinflammation

city: Palo Alto

first: Liana

middle: Nicole

last: Bonanno

state: California

address: 3801 Miranda Ave, Bldg 100 Rm D3-111

department: Neurology

institute: Stanford University

summary: RNA-sequencing analysis of cerebellar microglia from PBS or GCV treated WT or STING goldenticket mice with Experimental Autoimmune Encephalomyelitis (EAE).

overall_design: Mice were induced with EAE and  GCV treatment started on Day 3 after induction. Mice from each group were sacrificed and microglia isolated when PBS treated mice reached a score of 2 or more.

first: Vidhu

last: Mathur

first: Benoit

last: Lehallier

first: Tony

last: Wyss-Coray


title: Bighead is a Wnt antagonist secreted by the Xenopus Spemann organizer that promotes Lrp6 endocytosis

city: Los Angeles

first: Edward

last: De Robertis

state: CA

address: 615 Charles E. Young Drive South

department: Biological chemistry

institute: HHMI/UCLA

summary: The Xenopus laevis embryo has been subjected to almost saturating screens for molecules specifically expressed in dorsal Spemann organizer tissue. In this study, we performed high-throughput RNA sequencing of ectodermal explants, called animal caps, which normally give rise to epidermis. We analyzed dissociated animal cap cells that, through sustained activation of MAPK, differentiate into neural tissue. We also microinjected mRNAs for Cerberus, Chordin, FGF8, BMP4, Wnt8, and Xnr2, which induce neural or other germ layer differentiations. The searchable database provided here represents a valuable resource for the early vertebrate cell differentiation. These analyses resulted in the identification of a gene present in frog and fish, which we call Bighead. Surprisingly, at gastrula, it was expressed in the Spemann organizer and endoderm, rather than in ectoderm as we expected. Despite the plethora of genes already mined from Spemann organizer tissue, Bighead encodes a secreted protein that proved to be a potent inhibitor of Wnt signaling in a number of embryological and cultured cell signaling assays. Overexpression of Bighead resulted in large head structures very similar to those of the well-known Wnt antagonists Dkk1 and Frzb-1. Knockdown of Bighead with specific antisense morpholinos resulted in embryos with reduced head structures, due to increased Wnt signaling. Bighead protein bound specifically to the Wnt coreceptor lipoprotein receptor-related protein 6 (Lrp6), leading to its removal from the cell surface. Bighead joins two other Wnt antagonists, Dkk1 and Angptl4, which function as Lrp6 endocytosis regulators. These results suggest that endocytosis plays a crucial role in Wnt signaling.

overall_design: A genome-wide study of the effects of vavious growth factors and dissociation on animal caps of Xenopus laevis

first: Yi

last: Ding

first: Gabriele

last: Colozza

first: Eric

middle: A

last: Sosa

first: Yuki

last: Moriyama

first: Samantha

last: Rundle

first: Lukasz

last: Salwinski


title: Transcriptome profile of vegetative and cyst cells states of Azospirillum brasilense sp7

city: Bloomington

first: Elizabeth

middle: Ann

last: Malinich

address: 212 S Hawthorne Dr Rm313

institute: Indiana University

summary: We report the differences in the transcriptome profile (as measured by RNA seq) of vegetative versus encysted cell states of A. brasilense.

overall_design: RNA-seq of cyst and vegetative (3 biological replicates) colonies of A. brasilense sp7

first: Carl

last: Bauer


title: The global transcriptome analysis in the time course of hESC-derived cardiac differentiation

city: los angeles

first: matteo

last: pellegrini

address: 610 charles young drive east

institute: UCLA

summary: We analyzed the global transcriptome signature over the time course of the cardiac differentiation from hESC by RNA-seq. We characterized the genome-wide transcriptome profile of 5 distinct stages; undifferentiated hESC (day 0), mesodermal precursor stage (hMP, day 2), cardiac progenitor stage (hCP, day 5), immature cardiomyocyte (hCM14) and hESC-CMS differentiated for 14 additional days (hCM28). While the stem cell signature decreases over the five stages, the signatures associated with heart and smooth muscle development increase, indicating the efficient cardiac differentiation of our protocol.

overall_design: Five different temporal samples, two replicates for only first four samples day 0 through day 15

first: Haruko

last: Nakano

first: Herman

last: Pappoe

first: Marco

last: Morselli

first: Kai

last: Fu

first: Matteo

last: Pellegrini

first: Atsuishi


title: Inhibition of TGFβRI as a therapy for GATA4 deficient lung cancers [ChIP-seq]

first: huanwei

last: huang

summary: GATA4 is frequently epigenetically silenced in lung cancers. However, the impact of GATA4 inactivation on tumorigenesis and related therapeutic strategy remain to be determined. Through the genome-wide screening of tumor suppressing transcription factors, we demonstrate that GATA4 functions as an essential tumor suppressor in lung cancer in vitro and in vitro. Interestingly, ectopic GATA4 expression resulted in cellular senescence. Mechanistically, GATA4 up-regulates multiple miRNAs (miRNA-32, miRNA-301b, miR-320a, and miR-590) targeting TGFB2 mRNA and causes ensuing downregulation of WNT7B level to induce senescence. TGFBRI inhibitor synergizes with MEK1/2 inhibitor to promote lung cancer regression in Kras G12D/GATA4-/- mouse models. Decreased GATA4 level in clinical specimens negatively correlates with WNT7B or TGFB2 level and is significantly associated with poor prognosis.

overall_design: Investigate GATA4 binding sequences by ChIP-seq

first: Liang

last: Chen

first: Lei

last: Gao

first: Huanwei

last: Huang


title: Glucose inhibits cardiac maturation through nucleotide biosynthesis

summary: In summary, we discovered (1) that glucose dose-dependently inhibits cardiac maturation in vitro and in vivo, (2) that the maturation-inhibitory effect is dependent on nucleotide biosynthesis via the PPP, (3) that the developing heart accomplishes glucose deprivation condition by limiting the glucose uptake at late gestational stages during normal embryogenesis, and (4) that perturbation of the glucose deprivation in gestational diabetes affects natural cardiomyocyte maturation and potentially contributes to congenital heart disease.

overall_design: Three different samples, three replicates each

first: Itsunari

last: Minami

first: Daniel

last: Braas

first: Xiuju

last: Wu

first: Laurent

last: Vergnes

first: Xueqin

last: Ding

first: Adam

middle: Z

last: Stieg

first: James

last: Gimzewski

first: Peter

last: Clark

first: Karen

last: Reue

first: Aldons

last: Lusis

first: Bernard

last: Ribalet

first: Siavash

last: Kurdistani

first: Heather

last: Christofk

first: Norio

last: Nakatsuji


title: RNA-seq analysis comparing WT, Rad21 MO and CTCF MO zebrafish embryos at stages (2.5, 3.3, 4.5, 5.3, 10 hpf) pre and post ZGA (zygotic genome activation)

city: Dunedin

first: Michael

last: Meier

address: 1st Floor Hercus Building, Dunedin School of Medicine, Great King Street

department: Pathology

country: New Zealand

institute: University of Otago

summary:
Methods: Triplicate RNA samples from morphologically stage-matched embryos were sequenced to compare expression profiles over time. Strand-specific libraries were prepared using the TruSeq stranded total RNA-ribozero kit (Illumina) and 100-bp paired-end sequencing was performed to depth of 10 million reads per library on an Illumina HiSeq 2000.
Methods: On average, 19 million 100 bp paired-end reads per library were generated. These were then adapter and quality trimmed using cutadapt and SolexaQA. Each sequencing data set was independently mapped to the zebrafish genome with a bowtie2 index generated from Danio_rerio.Zv9.70 (Ensembl) downloaded from Illumina’s iGenomes collection. Zebrafish genome danRer7was used to provide known transcript annotations from Ensembl using TopHat2 (version 2.0.9) with the following options: “tophat2 --GTF genes.gtf --library-type fr-firststrand -p 24 --mate-inner-dist -8 --mate-std-dev 6 zv9” (on average, 75.38% reads mapped uniquely to the genome). Transcriptomes were assembled with Cufflinks (version 2.2.0) using options: ‘cufflinks -p 32 --GTF genes.gtf’ and differential expression analysis between control and knockdown embryos was performed using Cuffdiff. A FDR corrected p-value of 0.05 was applied as the cut off to identify differentially regulated transcripts
Results: We could show that MO assisted depletion of Rad21 and CTCF affected the transcriptional profiles of embryos in different ways.

overall_design: mRNA profiles of  (2.5, 3.3, 4.5, 5.3, 10 hpf) wild type (WT) and morpholino depleted Rad21 MO (Rad21) and CTCF MO (CTCF) embryos were generated by deep sequencing, in triplicate, using Illumina HiSeq 2000.

first: Julia

last: Horsfield


title: Hydroxymethylcytosine in mouse intestinal differentiation [RNA-Seq]

first: Chandra

last: Chilamakuri

address: Robinson Way

institute: Cancer Research UK Cambridge Institute

summary: The discovery of cytosine hydroxymethylation (5-hmC) as a mechanism that potentially controls DNA methylation changes typical of neoplasia prompted us to investigate its behavior in colon cancer. 5-hmC is globally reduced in proliferating cells such as colon tumors and the gut crypt progenitors, from which tumors can arise. Here, we show that colorectal tumors and cancer cells express Ten-Eleven Translocation (TET) transcripts at levels similar to normal tissues. Genome-wide analyses show that promoters marked by 5-hmC in normal tissue, and those identified as TET2 targets in colorectal cancer cells, are resistant to methylation gain in cancer. In vitro studies of TET2 in cancer cells confirm that these promoters are resistant to methylation gain independently of sustained TET2 expression. We also find that a considerable number of the methylation gain-resistant promoters marked by 5-hmC in normal colon overlap with those that are marked with poised bivalent histone modifications in embryonic stem cells. Together our results indicate that promoters that acquire 5-hmC upon normal colon differentiation are innately resistant to neoplastic hypermethylation by mechanisms that do not require high levels of 5-hmC in tumors. Our study highlights the potential of cytosine modifications as biomarkers of cancerous cell proliferation.

overall_design: Four biological replicates were analysed per cell type purified by flow cytometry using the CD24 marker and depletion of CD45 and Ulex lectin positive cells. See Wong et al. NatCellBiol 2012 Mar 4;14(4):401-8 or Buczacki et al. Nature 2013 Mar 7;495(7439):65-9. CD24Mid are also referred to as CD24low in the manuscript.

first: Santiago

last: Uribe-Lewis

first: Suraj

last: Menon

first: Silvia

last: Halim


title: Mucin Acts as a Nutrient Source and a Signal for the Differential Expression of Genes Coding for Cellular Processes and Virulence Factors in Acinetobacter baumannii

city: Oxford

first: Luis

last: Actis

state: OH

address: 700 E. High St.

department: Microbiology

institute: Miami University

summary: The capacity of Acinetobacter baumannii to persist and cause infections depends on its interaction with abiotic and biotic surfaces, including those found on medical devices and host mucosal surfaces. However, the extracellular stimuli affecting these interactions are poorly understood. Based on our previous observations, we hypothesized that mucin, a glycoprotein secreted by lung epithelial cells, particularly during respiratory infections, significantly alters A. baumannii’s physiology and its interaction with the surrounding environment. Biofilm, virulence and growth assays showed that mucin enhances the interaction of A. baumannii ATCC 19606T with abiotic and biotic surfaces and its cytolytic activity against epithelial cells while serving as a nutrient source. The global effect of mucin on the physiology and virulence of this pathogen is supported by RNA-Seq data showing that its presence results in the differential transcription of 427 predicted protein-coding genes. The reduced expression of ion acquisition genes and the increased transcription of genes coding for energy production together with the detection of mucin degradation indicate that this host glycoprotein is a nutrient source. The increased expression of genes coding for adherence and biofilm biogenesis on abiotic and biotic surfaces, the degradation of phenylacetic acid and the production of an active type 6 secretion system further supports the role mucin plays in virulence. Taken together, our observations indicate that A. baumannii recognizes mucin as an environmental signal, which triggers a response cascade that allows this pathogen to acquire critical nutrients and promotes host-pathogen interactions that play a critical role in the pathogenesis of bacterial infections.

overall_design: RNAseq of Acinetobacter baumannii ATTC19606T, grown in the presence or absence of mucin, was performed for triplicate samples on an Illumina MiSeq platform.

first: Brock

last: Arivett

first: Emily

last: Ohneck


title: Effects of WCE herbal extract on hormone-refractory PC-3 tumors

first: Chin-Hsien

last: Tsai

summary:
Purpose: Androgen-deprivation therapy is the standard treatment for prostate cancer but fails in hormone-refractory prostate cancer. The anti-inflammatory plant Wedelia chinensis is rich in luteolin, apigenin, and wedelolactone that act synergistically to suppress androgen receptor activity in prostate cancer. Here, we evaluated the systemic antitumor effects of a standardized and effect-optimized Wedelia chinensis herbal extract (WCE) on hormone-refractory prostate cancer.

Methods: Hormone-refractory PC-3 orthotopic tumor mouse models were orally administered with WCE. The tumor transcriptomes were studied using RNA sequencing and Ingenuity Pathway Analysis to identify the molecular mechanisms.

Results: WCE significantly attenuated tumor growth and metastasis in orthotopic PC-3 xenografts. Transcriptomic analysis of genome-wide gene expression in the tumors revealed that WCE suppressed the expression of HIF1α, IKKα/β phosphorylation, and the downstream cytokines/chemokines.

Conclusions: A standardized preparation of Wedelia chinensis improved prostate cancer therapy through repressing NFκB-mediated cytokine expression in tumor cells and modulating the inflammatory tumor microenvironment. These data suggest that WCE functions through immunomodulation and has potential application as an adjuvant agent for the treatment of castration-resistant prostate cancer.

overall_design: mRNA profiles of tumor xengrafts were generated by  sequencing in 3 individual tumor samples from mice with vehicle treatment and 3 individual tumor samples from WCE-treated mice  SRA Study accession: SRP108551; BioProject accession: PRJNA389147

first: Pei-Wen

last: Hsiao


title: Super-Enhancers Promote Transcriptional Dysregulation in  Nasopharyngeal Carcinoma

city: Singapore

first: Phillip

last: Koeffler

overall_design: Refer to individual Series


title: Next Generation Sequencing for Quantitative Expression Analysis of Wild Type and Nrf1 deficient Liver Transcriptomes from Regular Diet (RD) or High Cholesterol Diet (CholD) fed mice

status: Public on Nov 30 2017

city: Boston

first: Scott

last: Widenmaier

address: 665 Huntington Avenue

department: Genetics and Complex Diseases

institute: Harvard TH Chan School of Public Health

summary:
Purpose: Next-generation sequencing (NGS) for systematic analysis to discover Nrf1-dependent cellular pathways involved in defending liver against the stress of cholesterol excess.
Methods: Liver mRNA profiles of 9-12-old wild-type (WT in fastq files; flox in paper) and liver Nrf1 deficient (KO in fastq files; L-KO in paper) mice were generated by deep sequencing, in triplicate or quadruplicate, using Illumina HiSeq2500. The sequence reads that passed quality filters were analyzed at the transcript level with TopHat followed by Cufflinks. qRT–PCR validation of selected target genes was performed using SYBR Green assays.
Results: We mapped sequence reads to the mouse genome (build mm10) and identified greater than 10,000 transcripts in the liver of WT and KO mice. RNA-seq data revealed a role for Nrf1 in regulating inflammation, lipid metabolism, and sterol metabolism in response to a cholesterol challenge.
Conclusion: Our study reveal Nrf1 as a guardian of cholesterol homeostasis and a core component of adaptive responses to excesses in cellular cholesterol.

overall_design: Liver mRNA profiles of 9-12 week old wild type (WT) and Nrf1 KO mice were generated by deep sequencing, in triplicate or quadruplicate, using Illumina HiSeq2500.

first: Gokhan

last: Hotamisligil


title: TRIM28 and novel interacting KRAB-ZNFs preserve self-renewal of human pluripotent stem cells through H3K9me3 and DNA methylation mediated repression of pro-differentiation genes

first: Ayush

last: Raman

address: 75 Ames St

department: Epigenomics Program

institute: Broad Institute of MIT and Harvard

summary: Reprogramming to induced pluripotent stem cells (iPSCs) and differentiation of pluripotent stem cells (PSCs) are primarily regulated by epigenetic machinery. Tripartite motif protein 28 (TRIM28), a universal mediator of Krüppel-associated box domain zinc fingers (KRAB-ZNFs), is known to regulate both processes, however exact mechanism and identity of participating KRAB-ZNF genes remains unknown. Here, using a novel reporter system, we first showed that TRIM28/KRAB-ZNFs alter DNA methylation patterns in addition to H3K9me3 to cause gene repression during reprogramming. Next, using several expression datasets, we identified novel KRAB-ZNFs (ZNF114, ZNF483 and ZNF589) in the human genome that regulate pluripotency. Mechanistically, we demonstrated that these KRAB-ZNFs directly alter gene expression of important developmental genes by modulation of H3K9me3 and DNA methylation on their promoters. In summary, TRIM28 employs novel KRAB-ZNFs to evoke epigenetic silencing of its target differentiation genes by H3K9me3 and DNA methylation.

overall_design:
Identification of the targets repressed by pluripotency-specific KRAB-ZNFs. ChIP-seq analysis focused on genome-wide binding profile of the pluripotency-specific KRAB-ZNFs (ZFP57, ZNF114, ZNF483 and ZNF589). RNA-seq analysis included three experiments: comparison of the gene expression profile between fibroblasts and induced pluripotent stem cells derived from them, analysis of gene expression changes during reprogramming of the fibroblasts with and without TRIM28 knockdown and analysis of gene expression changes in hESCs and iPSCs upon trim28 knockdown. In the latter analysis, pluripotent stem cells cultured without FGF to trigger differentiation were also tested.
------------------------------------
This represents the ChIP-seq component only.

first: Maciej

last: Wiznerowicz

first: Kunal

last: Rai

first: Urszula

last: Oleksiewicz

first: Katarzyna

last: Kulcenty


title: Early Changes In B Cell Subsets Predict Risk Of Autoimmunity Following Combination Immune Checkpoint Blockade

status: Public on Nov 29 2017

city: New Haven

first: Kavita

last: Dhodapkar

address: 333 Cedar Street

institute: Yale

summary: We report changes in B cells in patients treated with combination immune checkpoint blockade (CCB; anti-CTLA4 and anti-PD1)

overall_design: We examine CD19+ sorted B cells before and after CCB therapy

first: Madhav


title: Distinct roles of Hand2 in developing and adult autonomic neurons

status: Public on Nov 28 2017

city: Mainz

first: Abhijeet

last: Pataskar

address: Ackermannweg 4

institute: Institute of Molecular Biology

summary: Purpose: Analyze the function of the transcription factors Hand2 and Gata3 in adult sympathetic neurons by induced knockout and RNAseq analysis

overall_design: Method and Result: Hand2flx/del::DbhCreERT2 (referred to as mutant) and Hand2flx/+::DbhCreERT2 (referred to a control) were injected for 10 days with tamoxifen to activate Cre. Animals were killed, sympathetic ganglia (SCG+Stellate) collected and processed for RNA isolation and RNAseq (Stanzel et al., 2016). Gata3flx/flx::DbhCerERT2 (mutant) and Gata3flx/+::DbhCreERT2 (controls) were treated as Hand2 animals. 16 ganglia from 4 mice were pooled for Hand2 mutant and controls and Gata3 controls. As only rudimentary ganglia were present in Gata3 mutant mice (Tsarovina et al., 2010) ganglia from 8 mice were pooled. The specific effects of the Hand2 knockout are decribed in Stanzel et al., 2016. The analysis of ganglion rudiments in the Gata3 knockout revealed that Gata3 was not reduced, indicating that the remaining cells had escaped the knockout.

first: Hermann

last: Rohrer

first: Konstantina

last: Tsarovina


title: RNA-seq analysis of Lactobacillus at acidic stress

city: Seoul

first: kucsbl

last: submitter

state: Seoul

address: Anamdong 5-ga, Seongbuk-gu

department: Department of Biotechnology

country: South Korea

institute: Korea University

summary: To understand transcriptional regulation of probiotic bacteria under acidic condition, RNAseq analysis was carried out over different growth conditions

overall_design: Comparison of acidic (pH4) and neutral (pH7) conditions by differentially expressed genes

first: In-Geol

last: Choi

first: Sejong

last: Oh