title: MiRNA degradation by NS3 of JEV [miRNA]

summary: In order to further determine the je virus (JEV) infection in C57BL / 6 mice after its miRNA levels change, we use the Agilent micrornas chip as a platform, to detect the uninfected group (control group) and the experimental mouse total RNA, it is found that the miRNA levels decrease infection group, and picked out the ten changes obviously micrornas verification, the result is the same.

overall_design: Four week old healthy C57BL / 6 mice were selected. One group was injected with JEV virus as the experimental group. A group of injection medium was used as a control group. After the experimental group showed the corresponding symptoms, the two groups of mice were sacrificed immediately, the brain tissue was separated from the liquid nitrogen and sent to the company for detection of miRNA levels.


title: Cdk1 controls global epigenetic landscape in embryonic stem cells

status: Public on Apr 04 2020

city: Boston

first: Chen

last: Chu

state: MA

address: 450 Brookline Ave, Smith 914

country: USA

institute: Dana-Farber Cancer Institute

type: Genome binding/occupancy profiling by high throughput sequencing

type: Expression profiling by high throughput sequencing

summary: In this study, we found that in ES cells the majority of Cdk1 substrates are localized on chromatin. Cdk1 phosphorylates a large number of proteins involved in epigenetic regulation, including writers and erasers of all major histone marks. High levels of Cdk1 in ES cells phosphorylate and partially inactivate Dot1l, the histone H3 lysine 79 methyltransferase responsible for placing activating H3K79 marks on gene bodies. Decrease of Cdk1 activity during ES cell differentiation de-represses Dot1l, thereby allowing coordinated expression of differentiation genes. These analyses indicate that Cdk1 functions to maintain the epigenetic identity of ES cells.

overall_design: In mouse embryonic stem cells: (1) Thio-ChIP-seq for the Cdk1 substrates-binding DNA; (2) H3K79me2 ChIP-seq upon Cdk1 inhibition; (3) Transcriptome of WT cells, and WT vs. Dot1l KO cells in SL medium and during Wnt3a and activin A-induced differentiation.

first: Wojceich

last: Michowski

first: Piotr

last: Sicinski


title: BAP1 loss triggers DNA methylomic repatterning in highly aggressive Class 2 uveal melanomas [RNA-Seq]

city: Miami

first: Matthew

middle: G.

last: Field

state: FL

address: 1501 NW 10th Avenue

institute: University of Miami

summary: The strong association between BAP1 mutations and highly aggressive Class 2 uveal melanoma (UM) suggests that epigenetic alterations may play a significant role in tumor progression.  Thus, we characterized the impact of BAP1 loss on the DNA methylome in UM.

overall_design: Global DNA methylation was analyzed in 8 Class 1 and 4 Class 2 primary UMs and in 2 different UM cells (92.1, Mel202) engineered to inducibly deplete BAP1 with dox treatment.  For the engineered cell lines, both uninduced and induced cell were analyzed with two replicates of all conditions.

first: J

middle: W

last: Harbour


title: BAP1 loss triggers DNA methylomic repatterning in highly aggressive Class 2 uveal melanomas

type: Methylation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: BAP1 loss triggers DNA methylomic repatterning in highly aggressive Class 2 uveal melanomas [MethylationEPIC]

summary: The strong association between BAP1 mutations and highly aggressive Class 2 uveal melanoma (UM) suggests that epigenetic alterations may play a significant role in tumor progression. Thus, we characterized the impact of BAP1 loss on methylomic repatterning in UM.

overall_design: Global DNA methylation was analyzed in 8 Class 1 and 4 Class 2 primary UMs and in 2 different UM cells (92.1, Mel202) engineered to inducibly deplete BAP1 with dox treatment. For the engineered cell lines, both uninduced and induced cell were analyzed with matched RNA-Seq data.


title: BAP1 loss triggers DNA methylomic repatterning in highly aggressive Class 2 uveal melanomas [BeadChip 450K]


title: Next Generation Sequencing Facilitates Quantitative Analysis of bladder cancer cells (T24) with constitutively active RhoC mutant (Q63E) overexpression and vector control (VEC) Transcriptomes

city: Tianjin

first: Yaxiu

last: Guo

address: 22 Qi Xiangtai Road

department: Immunology

country: China

institute: Tianjin Medical University

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived constitutively active RhoC mutant (Q63E) overexpressed bladder cancer cells (T24) transcriptome profiling (RNA-seq) to quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis
Methods: Bladder cancer cells mRNA profiles of vector(VEC) and RhoC constitutively active mutant (Q63E) stably expressing T24 cells were generated by deep sequencing, in triplicate, using Illumina HiSeqX Ten. The sequence reads that passed quality filters were analyzed at the transcript isoform level with the method: Hisat2 2.1.0 followed by StringTie. qRT–PCR validation was performed using TaqMan and SYBR Green assays
Results: Using an optimized data analysis workflow, we mapped about 50 million sequence reads per sample to the hunam reference genome and identified 209,506 transcripts in the vector(VEC) and constitutively active RhoC mutant (Q63E) transduced bladder cancer cells (T24 cells) with Hisat2 2.1.0 workflow. RNA-seq data confirmed stable expression of known housekeeping genes. Approximately 3% of the transcripts showed differential expression between the vector(VEC) and constitutively active RhoC mutant (Q63E) transduced bladder cancer cells (T24 cells), with a fold change ≥1.5 and p value <0.05. Altered expression of 13 genes was confirmed with qRT–PCR, demonstrating the high degree of sensitivity of the RNA-seq method. Hierarchical clustering of differentially expressed genes uncovered several as yet uncharacterized genes that may contribute to RhoC function in bladder cancer. Data analysis with Hisat2 2.1.0 workflow revealed a significant overlap yet provided complementary insights in transcriptome profiling.
Conclusions: Our study represents the first detailed analysis of constitutively active RhoC mutant (Q63E) overexpressed bladder cancer cells transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell line. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

overall_design: Bladder cancer mRNA profiles of vector (VEC) and constitutively active RhoC mutant (Q63E) transduced T24 cells were generated by deep sequencing, in triplicate, using Illumina HiSeqX Ten.

first: Quan

last: Wang


title: Anti-inflammatory effects of HDL in macrophages predominate over pro-inflammatory effects in atherosclerotic plaques

city: New York

first: David

middle: G

last: Thomas

state: NY

department: Medicine

institute: Columbia University

summary: HDL infusion reduces atherosclerosis in animal models and is being evaluated as a treatment in humans. While some studies have shown anti-inflammatory effects of HDL in macrophages, others have reported pro-inflammatory effects and there is no consensus on underlying mechanisms. Transcriptional profiling reveals that HDL-mediated cholesterol efflux leads to both pro- and anti-inflammatory effects in LPS-stimulated macrophages. While early anti-inflammatory effects reflect reduced TLR4 levels, late anti-inflammatory effects are due to reduced interferon receptor signaling. Pro-inflammatory effects occur late and are ER stress responses mediated by IRE1a/ASK1/p38 MAPK signaling under conditions of marked cholesterol depletion. rHDL infusions in hypercholesterolemic atherosclerotic mice produced moderate anti-inflammatory effects in lesional macrophages without pro-inflammatory gene expression changes suggesting a beneficial therapeutic effect of HDL in vivo.

overall_design: mRNA profiling of BMDM treated with rHDL

first: Alan

last: Tall


title: GR and LSD1/KDM1A-targeted gene activation requires selective H3K4me2 demethylation at enhancers

city: Shanghai

first: Feizhen

last: Wu

state: Shanghai

address: Zhangheng Road 825, Pudong

department: Intelligent Medicine Institute

institute: Fudan Univ, Shanghai, China

summary: KDM1A-mediated H3K4 demethylation is a well-established mechanism underlying transcriptional gene repression, but its role in gene activation is less clear. Here we report a critical function and novel mechanism of action of KDM1A in glucocorticoid receptor (GR)-mediated gene transcription. Biochemical purification of the nuclear GR complex revealed KDM1A as an integral component. In cell-free assays, GR modulates KDM1A-catalyzed H3K4 progressive demethylation by limiting loss of H3K4me1. Similarly, in cells KDM1A binds to most GR binding sites where it removes preprogrammed H3K4me2 but leaves H3K4me1 untouched. Blocking KDM1A catalytic activity prevents H3K4me2 removal, severely impairs GR binding to chromatin, and dysregulates GR-targeted genes. Taken together, these data suggest KDM1A-mediated H3K4me2 demethylation at GRBSs promotes GR binding and plays an important role in glucocorticoid-induced gene transcription, offering a new mechanism contributing to nuclear receptor mediated gene activation.

overall_design:
ChIP-Seq dataset: A549 cell ChIP-seq under treatment with ethanol (vehicle), dexamethasone, or tranylcypromine (TCP). ChIP against GR, KDM1A, H3K4me1,2,3, H3K9me1,2, and H3K27ac.
RNA-Seq dataset: A549 cell RNA-seq under treatment with ethanol (vehicle), dexamethasone.

first: Yujiang

last: Shi

first: Erin

last: Clark

first: Rui

last: Fang


title: Expression data from healthy subjects and patients with M. africanum or M. tuberculosis infection

status: Public on Apr 03 2020

city: Bethesda

first: Sivaranjani

last: Namasivayam

state: Maryland

address: 33 North Drive

institute: National Institutes of Health

summary: A blood transcriptome analysis was performed on a set of healthy subjects and patients infected with M. africanum (MAF) or M. tuberculosis (MTB). All study participants were recruited from Mali.

overall_design: Blood samples were collected from healthy subjects during enrollment and patients at the time of TB diagnosis. RNA was extracted and hybridized on Affymetric micrarrays.

last: Sher

first: Mamoudou

last: Maiga


title: BX795 small inhibitor of TBK1 effect on mouse fibroblast cell line that transfected with pEGFP-N1 plasmid

city: Fuzhou

first: Yajuan

last: Fu

state: Fujian

address: Fujian Normal University,Qishan Campus, No.1 Keji Road, Shangjie, Minhou

department: Biomedical Research Center of South China

institute: Fujian Normal University

summary: Abstract：DNA transfection is widely used in biomedical research. However, transfection efficiency is often the bottleneck of research and gene therapy practices. To explore the mechanism regulating transgene expression, we investigated the possible involvement of the cGAS-STING signaling pathway, which induces type-I interferons in response to cytosolic DNA. We found deletion of cGAS enhances the expression of transfected genes. This enhancement is inversely correlated with the expression of type I interferons and interferon stimulated genes (ISGs). We provide evidence that the interferon responses can suppress expression of transfected genes at the mRNA level. Mechanistically, DNA transfection activates cGAS-STING pathway and induces the expression of the OAS family proteins, leading to the activation of RNaseL and degradation of mRNA derived from transgenes. As a result, administration of chemical inhibitors that block cGAS-mediated signaling cascades improves the expression levels of exogenous genes in multiple cell lines and in primary cells, including T cells. These data suggest that targeting the cGAS-STING pathway can improve transgene expression and this strategy may be applied to gene therapy. Goal：Analysis of mouse fibroblast cell line L929 transfected with pEGFP-N1 plasmid in the presence of DMSO or TBK1 inhibiter (BX795) .  Results provide insight into molecular mechanisms underlying a inhibitor effect of BX795 on DNA-induced cGAS signaling which improves expression of transfected genes. Methods： L929 cells were pretreated with TBK1 inhibitor BX795 or mock treated with DMSO for 1 hour, then transfected with pEGFP-N1 plasmid. There are four groups in this experiment. S1, L929 cells mock-treated; S2, L929 cells transfected with pEGFP-N1 plasmid; S3, L929 treated with 0.5 uM BX795; S4, L929 treated with 0.5 uM BX795 and transfected with pEGFP-N1 plasmid. Each group has three replicates. There are total 12 samples in this experiment. Six hours later, total RNA of 12 samples was extracted using Trizol reagent  from cells according to the manufacturer’s instruction. cDNA library construction and sequencing were performed by BGI Genomics (BGI-SHENZHEN, China) using BGISEQ-500 platform. High-quality reads were aligned to the Mus_musculus reference genome (Mus musculus GRCm38.p5) using Bowtie2 (version:2.2.5, parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200). The expression levels for each of the genes were normalized to fragments per kilobase of exon model per million mapped reads (FPKM) using RNA-seq by Expectation Maximization (RSEM) (version:1.2.12, default parameters). For the identification of differentially expressed genes (DEGs), we used PossionDis, which is developed by BGI Genomics, implementing the passion distribution method. We analyzed up-expression genes in S2  other than S1, S3 and S4.

overall_design: mRNA profiles of L929 cell line  transfected with pEGFP-N1 plasmid in the presence of DMSO or BX795

first: Lijun

last: Sun

first: Qi

last: Chen


title: Investigating the role of Foxp1 in murine A20 lymphoma cells

city: Oxford

first: Ling

last: Felce

state: Select State

address: Botnar Research Centre, Windmill Road

department: NDORMS

country: United Kingdom

institute: University of Oxford

summary:
Purpose: to investigate the role of transcription factor Foxp1 in murine A20 lymphoma cells, which can be used as a model for human diffuse large B cell lymphoma
Method: Exons 6 and 7 of Foxp1 were independently targeted using CRISPR/Cas9 editing, and 2 clones from each targeted exon (E6 and E7), showing  depleted Foxp1 isoforms were isolated.
Method: RNA sequencing was conducted on parental A20 cells and CRISPR clones, and differential gene expression was undertaken

overall_design: The mRNA fraction of total RNA from A20 parental cells and two independent CRISPR clones was sequenced in triplicate using Illumina HiSeq4000

first: Suet

middle: L

first: Amanda

middle: P

last: Anderson

first: Shaun

last: Maguire

first: Duncan

middle: M

last: Gascoyne

first: Richard

middle: N

last: Armstrong

first: Kah

middle: K

last: Wong

first: Demin

last: Li

first: Alison

middle: H

last: Banham


title: BRD4 is necessary for epidermal differentiation

city: La Jolla

first: George

last: Sen

state: California

address: 9452 Medical Center Dr.

department: Dermatology

institute: University of California San Diego

summary: BRD4 is an epigenetic reader known to bind to acetylated lysines on histones and transcription factors, and it has been implicated in recruiting transcriptional machinery to promote differentiation gene expression in multiple cellular contexts. This activity is dependant on proper BRD4 localization to active promoters and enhancers, which is dependant on a variety of factors including lineage determining transcription factors (LDTFs). We found BRD4 to be necessary for epidermal differentiation, during which it shares many chromatin binding sites with a variety of epidermal lineage-determining transcription factors (LDTF's). BRD4 also regulates a similar differentiation related transcriptional program with the epidermal LDTF KLF4.

overall_design: Control siRNA (Ambion Silencer Select negative control 4390844), BRD4 siRNA knockdown (Dharmacon D-004937-05), KLF4 siRNA knockdown (Dharmacon: custom sequence) in 3 day differentiated primary keratinocytes, RNA-sequenced in replicates. BRD4 ChIP seq in 3 day differentated primary keratinocytes.

first: Jackson

last: Jones


title: RNA sequencing of sheep infraspinatus muscle after two weeks of tendon release

city: Zurich

first: Martin

last: Flück

address: Lengghalde 5

department: Balgrist Campus

country: Switzerland

institute: University of Zurich

summary: Transcripts were measured in infraspinatus muscle before (PRE) and after 2 weeks of tendon release (POST) in the operated muscle.

overall_design: Three two-year-old female Swiss Alpine sheep were subjected to release of the infraspinatus tendon. Prior to tendon release (PRE) and 2 weeks after tendon release biopsies were collected from the operated infraspinatus muscle. Biopsies were subjected to the characterization of muscle composition and transcript expression.

first: Severin

last: Ruoss

first: Anna

last: Bratus-Neuenschwander

first: Lennart

last: Opitz


title: Global transcriptome analysis identifies a signature for early disseminated Lyme disease and its resolution

city: Valhalla

first: Mary

last: Petzke

address: 15 Dana Road

department: Microbiology and Immunology

institute: New York Medical College

summary: Lyme disease (LD), caused by Borrelia burgdorferi, is the most common tick-borne infectious disease in the United States. We examined gene expression patterns in the blood of individuals with early disseminated LD at the time of diagnosis (Acute LD) and also at approximately 1 month and 6 months following antibiotic treatment. A distinct acute LD profile was observed that was sustained during early convalescence (1 month) but returned to control levels six months after treatment. Using a computer learning algorithm, we identified sets of 20 classifier genes that discriminate LD from other bacterial and viral infections. In addition, these novel LD biomarkers are highly acurate in distinvuishing patients with acute LD from healthy subjects and in discriminating between individuals with active and resolved infecitons.  This computational approach offers the potential for more accurate diagnosis of early dissminated Lyme disease. It may also allow improved monitoring of treatment efficacy and disease resolution.

overall_design: A bioinformatics approach was employed to identify transcriptome alterations in the peripheral blood mononuclear cells of well-characterized human subjects who were diagnosed with early disseminated Lyme disease (LD) based on stringent microbiological and clinical criteria. Transcriptomes were assessed at the time of presentation, and at approximately 1 month (early convalescence) and 6 months (late convalescence) following initiation of an appropriate antibiotic regimen. Comparative transcriptomics identified 335 transcripts, representing 233 unique genes, with significant alterations of at least 2-fold expression in acute or convalescent blood samples from LD subjects relative to healthy donors. Acute phase blood samples from LD subjects had the largest number of differentially expressed transcripts (187 induced, 54 repressed). This transcriptional profile, which was dominated by interferon-regulated genes, was sustained during early convalescence. Six months after antibiotic treatment the transcriptome of LD subjects was indistinguishable from that of healthy controls based on two separate methods of analysis. Return of the LD expression profile to levels found in control subjects was concordant with disease outcome; 82% of subjects with LD experienced at least one symptom at the baseline visit, as compared to 43% at the early convalescence time point and only a single patient (9%) at the six-month convalescence time point. Using the random forest machine learning algorithm, we developed an efficient computational framework to identify sets of 20 classifier genes that discriminated LD from other bacterial and viral infections. These novel LD biomarkers not only differentiated subjects with acute disseminated LD from healthy controls with 96% accuracy, but also distinguished between subjects with acute and resolved (late convalescent) disease with 97% accuracy.

first: Ira

last: Schwartz


title: Endogenous siRNAs promote proteostasis and longevity in germline-less Caenorhabditis elegans

city: Ramat Gan

first: sivan

last: Korenblit

state: - None -

address: Life Sciences Building (212) , mailbox 63, Bar-Ian University

department: Faculty of Life Sciences

country: Israel

institute: Bar-Ilan University

type: Non-coding RNA profiling by high throughput sequencing

summary: How lifespan and the rate of aging are set is a key problem in biology. Small RNAs are conserved molecules that impact diverse biological processes through the control of gene expression. However, in contrast to miRNAs, the role of endo-siRNAs in aging remains unexplored. Here, by combining deep sequencing and genomic and genetic approaches in C.CaenorhabditisC. elegans elegans, we reveal an unprecedented role for endo-siRNA molecules in the maintenance of proteostasis and lifespan extension in germline-less animals. Furthermore, we identify an endo-siRNA-regulated tyrosine phosphatase, which limits the longevity of germline-less animals by restricting the activity of the heat shock transcription factor HSF-1. Altogether, our findings point to endo-siRNAs as a link between germline removal and the HSF-1 proteostasis and longevity-promoting somatic pathway. This establishes a role for endo siRNAs in the aging process and identifies downstream genes and physiological processes that are regulated by the endo siRNAs to affect longevity.

overall_design: glp-1(e2144) and dcr-1(mg375) glp-1(e2144) C. elegans were raised at 25 degrees until day 1 of adulthood. Low molecular RNA fraction was extracted using miRVana miRNA isolation kit (Ambion). Library preparation was done using QsRNA-seq protocol that  mainly captures secondary siRNAs.

first: Moran

middle: C

last: Berkman

first: Shani

middle: B

last: Hemo

first: Alla

last: Fishman

first: Hiba

last: Ben-Asher

first: Ayelet

last: T Lamm

first: Sivan

last: Henis-Korenblit


title: Treehouse compendium of RNA-Seq gene expression data from tumors

city: Santa Cruz

first: Olena

middle: Morozova

last: Vaske

state: CA

address: 1156 High Street

department: MCD Biology Department

institute: UCSC

summary: We uniformly analyze sequence data to generate a resource for comparative gene expression studies

overall_design:
Gene expression data for 11,454 tumor samples gathered from different sources and consistently processed across all samples.

Data pocessing steps were as follows:

Adapters are removed with CutAdapt v1.9 (Martin, 2011)
Reads are  aligned by STAR v 2.4.2a using indices generated from the human reference genome GRCh38 and the human gene models Gencode 23 (Dobin et al., 2013)
RSEM 1.2.25 is used to quantify gene expression (Li and Dewey, 2011).
Gene level expression in TPM is log transformed: log2(TPM+1)

first: Holly

last: Beale

last: Morozova Vaske


title: The clonal and molecular aetiology of Flt3L-mediated ‘emergency’ dendritic cell development

city: Cambridge

first: Luyi

last: Tian

address: 415 main st Cambridge

institute: Broad institute

summary: Flt3 ligand (Flt3L) promotes an increased generation of type 1 conventional dendritic cells (cDC1s), resulting in enhanced immunity against infections and cancer. Here, we employ cellular barcoding to understand how Flt3L regulates single haematopoietic stem and progenitor cell (HSPC) fate. Our results demonstrate that although Flt3L stimulation can recruit some additional cDC1-generating HSPCs, the major contributing factor to higher cDC1 numbers is through enhanced clonal expansion. This selective cDC1 expansion occurs primarily via multi-/oligo-potent clones, without compromising their clonal output to other lineages. We then develop Divi-Seq to simultaneously profile division history, surface phenotype and the transcriptional state of single HSPCs during the early phase of the response. We discover that Flt3L-responsive HSPCs maintain a proliferative ‘early progenitor’-like state, which leads to a selective emergence of CD11c+cKit+ transitional precursors with high cellular output to cDC1s. These findings inform the mechanistic action of Flt3L in natural immunity and immunotherapy.

overall_design:
Mouse HSPCs were CTV labelled and transplanted into non-irradiated recipients, which received PBS or Flt3L treatment for 3 days. Donor-derived cells (CTV+) on day 4 were isolated from recipient bone marrow and index sorted into 384 PCR plate, with library generated using the CEL-seq2 protocol.
Please note that the cells were pooled per plate in the library preparation and the cell barcode annotation is provided.

first: Dawn

middle: S

last: Lin

first: Daniela

last: Amann-Zalcenstein

first: Tracey

last: Baldwin

first: Shalin

last: Naik


title: RNA-seq analysis of WT and NCOR1f/f,Cd4Cre in vitro-generated Th17 cells

city: Vienna

first: Wilfried

last: Ellmeier

address: Lazarettgase 19

department: Institute of Immunology

country: Austria

institute: Medical University of Vienna

summary: The differentiation of naïve CD4+ T cells into T helper (Th) subsets is key for a functional immune response and has to be tightly controlled by transcriptional and epigenetic processes. However, the function of cofactors that connect gene-specific transcription factors with repressive chromatin-modifying enzymes in Th cells is yet unknown. Here we determined transcriptional changes in Th17 cells upon deletion of the cofactor NCOR1.

overall_design: mRNA expression profiles of WT and NCOR1f/f,Cd4Cre in vitro-generated Th17 cells were generated by deep sequencing

last: Hainberger


title: RNA-seq analysis of WT and NCOR1f/f,Cd4Cre in vitro-generated Th1 cells

summary: The differentiation of naïve CD4+ T cells into T helper (Th) subsets is key for a functional immune response and has to be tightly controlled by transcriptional and epigenetic processes. However, the function of cofactors that connect gene-specific transcription factors with repressive chromatin-modifying enzymes in Th cells is yet unknown. Here we determined transcriptional changes in Th1 cells upon deletion of the cofactor NCOR1.

overall_design: mRNA expression profiles of WT and NCOR1f/f,Cd4Cre in vitro-generated Th1 cells were generated by deep sequencing


title: Compare transcriptional profile of AXL knockdown cell and AXL wild type cell

city: Stanford

first: Lei

address: 1215 Welch Rd

institute: Stanford's Postdoctoral Scholar programs

summary: We report the comparative investigation of gene expression profiles between genetic inactivation AXL cell and AXL wild type cells in two independent  We found a list of AXL signaling target genes that are important for tumor invasion and angiogenesis.

overall_design: 786-O cell and M62 cell transfected with shSCM and shAXL were selected

first: Yiren

last: Xiao

first: Erinn

last: Rankin


title: RNA-seq analysis of WT and NCOR1f/f,Cd4Cre naive CD4+ T cells

summary: The differentiation of naïve CD4+ T cells into T helper (Th) subsets is key for a functional immune response and has to be tightly controlled by transcriptional and epigenetic processes. However, the function of cofactors that connect gene-specific transcription factors with repressive chromatin-modifying enzymes in Th cells is yet unknown. Here we determined transcriptional changes in naive CD4+ T cells upon deletion of the cofactor NCOR1.

overall_design: mRNA expression profiles of WT and NCOR1f/f,Cd4Cre naive CD4+ T cells were generated by deep sequencing.


title: MiRNA-mediated induction of mesenchymal-to-epithelial transition (MET) between cancer cell types is significantly modulated by inter-cellular molecular variability

city: Atlanta

first: Mengnan

last: Zhang

state: Georgia

address: 315 Ferst Drive

department: School of Biological Sciences

institute: Georgia Institute of Technology

summary: Recent years have witnessed a dramatic increase in our appreciation of the contribution of microRNAs (miRNAs) to cancer onset and progression. As a consequence, there has been growing interest in the development of miRNAs not only as diagnostic biomarkers of cancer but also as a promising new class of therapeutic agents. Over the last several years, our laboratory has focused on analysis of the molecular processes underlying the ability of individual miRNAs to induce mesenchymal-to-epithelial transition (MET) particularly in ovarian cancer. Ectopic over expression of specific miRNAs down regulated during epithelial-to mesenchymal transition (EMT) have previously been reported to induce MET in a variety of cancer cells, thereby reducing metastatic potential and resistance to standard-of-care chemotherapies. Interestingly, the ability of individual miRNAs to induce MET when over expressed in cancer cells is often cancer/cell-type specific. In an effort to better understand the molecular processes underlying this specificity, we examined the molecular and phenotypic responses of three mesenchymal-like cancer cell lines (two ovarian and one prostate) to ectopic over expression of three sequentially divergent miRNAs previously implicated in the EMT/MET process. The ability of these sequentially divergent miRNAs to induce MET in these cells was found to be associated with inherent differences in the starting molecular profiles of the untreated cancer cells and specifically, variability in trans-regulatory controls modulating the expression of genes targeted by the individual miRNAs. While our results support the view that miRNAs have significant potential as cancer therapeutic agents, our findings further indicate that optimal treatments will likely need to be personalized with respect to the molecular profiles of the individual cancers being treated.

overall_design: Ovarian cancer HEY, SKOV3 cells and prostate cancer PC3 cells were transfected with miR-203a, miR-205, and miR-429 for 48 hrs. After transfection, RNA were extracted and microarray gene expression analysises were conducted.

first: Yuehua

last: Wang

first: Lilya

middle: V

last: Matyunina

first: Amber

last: Akbar

first: John

middle: F

last: McDonald


title: shRNA-mediated Myc knockdown and shRNA-mediated knockdown of Myc-induced lncRNA KTN1-AS1 in ST486 Burkitt lymphoma cells

city: Groningen

first: Melanie

last: Winkle

state: Groningen

address: Hanzeplein 1

department: Pathology & Medical Biology

country: Netherlands

institute: UMC Groningen

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

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

overall_design: Refer to individual Series


title: Endogenous siRNAs Promote Proteostasis and Longevity in Germline-less C. elegans

city: Ramat-Gan

first: Hiba

last: Waldman Ben-Asher

address: Ramat-Gan

department: Life-Sciences

summary: How lifespan and the rate of aging are set is a key problem in biology. Small RNAs are conserved molecules that impact diverse biological processes through the control of gene expression. However, in contrast to miRNAs, the role of endo-siRNAs in aging remains unexplored. Here, by combining deep sequencing and genomic and genetic approaches in C. elegans, we reveal an unprecedented role for endo-siRNA molecules in the maintenance of proteostasis and lifespan extension in germline-less animals. Furthermore, we identify an endo-siRNA-regulated tyrosine phosphatase, which limits the longevity of germline-less animals by restricting the activity of the heat shock transcription factor HSF-1. Altogether, our findings point to endo-siRNAs as a link between germline removal and the HSF-1 proteostasis and longevity-promoting somatic pathway. This establishes a role for endo siRNAs in the aging process and identifies downstream genes and physiological processes that are regulated by the endo siRNAs to affect longevity.

overall_design: Two-condition experiment, Wild type (N2) C. elegans vs. dcr-1(mg375) C. elegans, glp-1(e2144) C. elegans vs. dcr-1(mg375) glp-1(e2144) C. elegans. Data from four biological replicates were used for each strain.

first: Moran

last: Cohen Berkman

first: Shani

last: Ben-Hemo

first: Alla

last: Fishman

first: Aylelet

middle: T

last: Lamm

first: Sivan

last: Henis-Korenblit


title: NCOR1 ChIP-seq analysis of WT naive CD4+ T cells

summary: The differentiation of naïve CD4+ T cells into T helper (Th) subsets is key for a functional immune response and has to be tightly controlled by transcriptional and epigenetic processes. However, the function of cofactors that connect gene-specific transcription factors with repressive chromatin-modifying enzymes in Th cells is yet unknown. Here we identified genome-wide binding sites of the cofactor NCOR1 in naive CD4+ T cells by using ChIP-seq.

overall_design: Genome-wide NCOR1 binding peaks in naive CD4+ T cells were identified by combining ChIPmentation (doi:10.1038/nmeth.3542) and next generation sequencing.

first: Daniela


title: Gene expression analysis after shRNA-mediated knockdown of Myc-induced lncRNA KTN1-AS1 in ST486 Burkitt lymphoma cells

summary: The oncogenic transcription factor (c-)Myc is overexpressed in a variety of cancers including subtypes of B cell lymphoma. Here we study long noncoding (lnc)RNAs regulated by Myc, arguing that these lncRNAs may be involved in the very strong effect of Myc on cell proliferation. Using multiple in vitro models and taking into account the kinetics of the response to Myc as well as Myc binding sites we defined two Myc-induced and four Myc-repressed lncRNA candidates. Expression levels of the top Myc-induced lncRNA KTN1-AS1 are low in normal B cell subsets and strongly increased in multiple Myc-positive lymphoma cell lines. In addition, primary lymphoma cases stratified by high or low Myc expression show the expected KTN1-AS1 expression differences. Knockdown of KTN1-AS1 severely impaired the cell growth of multiple Burkitt lymphoma cell lines. Gene expression analysis showed that KTN1-AS1 knockdown affects >300 genes genome wide with a strong enrichment of Myc-target genes involved in metabolism and biosynthesis. In line with this finding, KTN1-AS1 depletion in B cell lymphoma cells caused a substantial decrease of Myc transcript and protein. Thus, our data indicates that KTN1-AS1 overexpression in lymphoma may reinforce high Myc expression at the transcriptional level to activate gene expression programs supporting the high metabolic rate present in lymphoma cells. In conclusion, we  identified a novel positive feedback loop between c-Myc and KTN1-AS1 in B cell lymphoma cells. LncRNAs such as KTN1-AS1, that regulate important oncogenic factors in specific cell types, may open new ways to cancer therapy.

overall_design: Microarray gene expression analysis was performed in ST486 cells infected with 2 individual shRNAs targeting the lncRNA KTN1-AS1 or two non-targeting control shRNAs; samples were harvested at day 4 and day 6 post-infection

first: Klaas

last: Kok

first: Mina

last: Tayari

first: Nathalie

last: Hijmering

first: Annika

last: Seitz

first: Debora

last: de Jong

first: Jasper

last: Koerts

first: Arjan

last: Diepstra

first: Daphne

first: Joost

last: Kluiver

first: Anke

last: van den Berg


title: Expression analysis of mRNA and lncRNA expression levels after shRNA-mediated Myc knockdown in ST486 Burkitt lymphoma cells

first: Melanie

overall_design: Expression of all known mRNAs and >10 000 lncRNAs was assessed in ST486 cells infected with 2 individual anti-Myc shRNAs or a non-targeting control shRNA


title: Transcriptomic characterization of a mixed population of pluripotent stem cell derived cerebellar neuron-like progenitors

city: Chippendale

first: Darya

middle: Pavlovna

last: Vanichkina

state: New South Wales

address: 32 Queen Street

country: Australia

institute: University of Sydney

summary: We set out to ascertain whether it was possible to use PSCs (pluripotent stem cells) to generate a mix of neuronal cell types resembling those in the cerebellum, most notably Purkinje and granule cells. Several groups have previously demonstrated generation of cerebellar-like neuronal cells from murine ESCs (embryonic stem cells), and more recently the Erceg group achieved similar success using human PSCs. Using principles from these studies we successfully induced expression of mid–hindbrain markers EN1 & GBX2 and later MATH1 (a transcription factor which marks rhombic lip/granule cell progenitors) in a mixed neuronal population derived from hPSCs. Further, we show that it is possible to expand these progenitors to produce spontaneously active neuronal cells with morphological similarities to neuronal cells at specific stages of cerebellar development. Based on morphology, electrophysiology, immunohistochemistry and transcriptomic analysis we demonstrate that these cells express behavior, markers and molecular signatures consistent with distinct epochs of cerebellar development spanning from the late embryonic to early postnatal periods. This study describes an in vitro model that provides insight into the early events that drive the formation of the human cerebellum with support from a high-resolution survey of the trancriptomic landscape, including expression of non-coding RNAs and specific transcript isoforms. The generated datasets and accompanying characterization are a valuable resource for researchers to formulate and test hypotheses regarding the molecular players that are involved in the formation of the cerebellum

overall_design: Total RNA-seq profiles of undifferentiated iPS cells and cerebellar neuron-like differentiated cells were generated by deep RNA sequencing, in triplicate, using a HiSeq2500 in Rapid Run mode.

first: Sam

last: Nayler


title: A combinatorial code of transcription factors specifies subtypes of visual motion-sensing neurons in Drosophila

status: Public on Apr 02 2020

city: Martinsried

first: Nikolai

middle: Li-Heng

last: Hoermann

state: Bavaria

address: Am Klopferspitz 18

department: Circuits-Computation-Models

country: Germany

institute: Max Planck Institute of Neurobiology

summary: Direction-selective T4/T5 neurons exist in four subtypes, each tuned to visual motion along one of the four cardinal directions. Along with their directional tuning, neurons of each T4/T5 subtype orient their dendrites and project their axons in a subtype-specific manner. Directional tuning, thus, appears strictly linked to morphology in T4/T5 neurons. How the four T4/T5 subtypes acquire their distinct morphologies development remains largely unknown. Here, we investigated when and how the dendrites of the four T4/T5 subtypes acquire their specific orientations, and profiled the transcriptomes of all T4/T5 neurons during this process. This revealed a simple and stable combinatorial code of transcription factors defining the four T4/T5 subtypes during their development. Changing the combination of transcription factors of specific T4/T5 subtypes resulted in predictable and complete conversions of subtype-specific properties, i.e. dendrite orientation and matching axon projection pattern. Therefore, a combinatorial code of transcription during factors coordinates the development of dendrite and axon morphologies to generate anatomical specializations differentiating subtypes of T4/T5 motion-sensing neurons.

overall_design: Single-cell transcriptomic analysis of T4/T5 subtypes during different developmental stages


title: SUMO and SIM Sites Direct Nuclear Localization of the Zika Virus NS5 Protein  and Regulate Endothelial Cell Transcriptional Responses

city: Stony Brook

first: Jonas

last: Nascimento Conde

address: Life Sciences Building

institute: Stony Brook University

summary: ZIKV NS5 WT expression in human brain microvascular endothelical cells (hBMECs) alters transcriptional responses and downregulate genes related to cell cycle, nucleosome formation and interferon stimulated genes (ISGs).

overall_design: hBMECs were transduced with lentiviral vectors for the expression of ZIKV NS5 WT and the mutants ZIKV NS5 K525R and ZIKV NS5 NLS. After 48h of transduction, total RNA was extracted and submitted to Affymetrix microarray analysis. Mock-transduced cells were used as control.

first: J

last: Conde

first: W

last: Schutt

first: M

last: Mladinich

first: S

last: Young

first: P

last: Hearing

first: E

middle: R

last: Mackow


title: CHOP ARDS Transcriptomic Subtypes (CATS)

city: Philadelphia

first: Nadir

last: Yehya

state: PA

address: 6040A Wood Bldg, 3401 Civic Ctr Blvd

institute: Children's Hospital of Philadelphia

summary:
We aimed to identify endotypes of pediatric acute respiratory distress syndrome (ARDS) using whole blood transcriptomics collected within 24 hours of Berlin ARDS onset in intubated children from CHOP
Affy microarray and cluster analysis

overall_design: 96 children with ARDS, PAXgene collection within 24 hours of ARDS onset; all ARDS, no external control

first: Rui

last: Feng


title: Next Generation Sequencing Facilitates Quantitative Analysis of PHB-knockdown and PHB-knockout Spermatocytes Transcriptomes

city: Shanghai

first: Lingfei

last: Zhang

address: 138 Yixueyuan Road

institute: Shanghai Medical College Fudan University

summary: We analyzed the transcriptomic differences of cultured mouse spermatocytes (GC2 cells) stably transfected with PHB-targeting shRNA (called PHB KD GC2) from those with a control shRNA (called Ctrl GC2). Furthermore, we also analyzed the difference in the transcriptomes of spermatocytes between Phb conditional knock-out and control mice.

overall_design: Examination of mRNAs in Ctrl GC2 cells, PHB KD GC2 cells and spermatocytes from Phb conditional knock-out and control mice. Three biological replicates of each sample were analyzed.

first: Hong

last: Chen


title: RNA-seq of ERINA knockdown T47D cell lines

city: Pittsburgh

first: Yue

last: Wang

state: Pennsylvania

address: 5607 Baum Blvd

institute: UNIVERSITY OF PITTSBURGH

summary: We identified an intergenic lncRNA ERINA (estrogen inducible lncRNA) as a novel lncRNA that is associated with chemo-resistance and highly expressed in multiple cancer types, especially in estrogen receptor (ER) positive breast cancers. Functional characterizations based on RNA-seq analyses established ERINA as an oncogenic lncRNA, because knockdown of ERINA in breast cancer cells inhibits cell cycle progression and tumor cell proliferation in vitro and xenograft tumor growth in vivo.

overall_design: Investigation of gene alterations after knocking down ERINA.

first: Fang

last: Zihui

first: Wang

last: Yue


title: NKp44+ group3 innate lymphoid cells are associated with tumor progression in human colorectal cancer

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

summary: Innate lymphoid cells (ILCs) are the most recently identified lymphocytes that act as critical mediators of intestinal immune response. ILCs have found to be involved in antitumor or tumor-promoting effects depending on tissues in which they react, but their roles in human colorectal cancer (CRC) have not been explored yet.

overall_design: We characterized ILCs in human normal colon and colorectal tumor and investigated whether these cells are implicated in tumor immunity in human CRC.

first: Atsuyo

last: Ikeda

first: Takayuki

last: Ogino


title: Assessment of Viral RNA in Idiopathic Pulmonary Fibrosis Using RNA-seq [nonPoly(A) RNA]

city: New Orleans

first: Qinyan

last: Yin

state: Louisiana

address: 1430 Tulane Ave SL8509

department: Department of Medicine

institute: Tulane University

summary:
Results: We identified sporadic low-level evidence of viral infections in our lung tissue specimens, but did not find a statistical difference for expression of any virus, including EBV, herpesvirus saimiri and HERV-K, between IPF and control lungs. To the best of our knowledge, this is the first publication that employs RNA-seq to assess whether viral infections are linked to the pathogenesis of IPF. Our results do not address the role of viral infection in acute exacerbations of IPF, however, this analysis patently did not support an association between herpes virus detection and IPF.
Conclusions: To the best of our knowledge, this is the first publication that employs RNA-seq to assess whether viral infections are linked to the pathogenesis of IPF. Our results do not address the role of viral infection in acute exacerbations of IPF, however, this analysis patently did not support an association between herpes virus detection and IPF.

overall_design: We investigated the possible association between IPF and viral RNA expression using next-generation sequencing, which has the potential to provide a high degree of both sensitivity and specificity. We quantified viral RNA expression for 740 viruses in 28 IPF patient lung biopsy samples and 20 age-matched controls. Key RNA-seq results were confirmed using Real-time RT-PCR for select viruses (EBV, HCV, herpesvirus saimiri and HERV-K).

first: Michael

middle: J

last: Strong

first: Yan

last: Zhuang

first: Erik

last: Flemington

first: Naftali

last: Kaminski

first: Joao

middle: A

last: de Andrade

first: Joseph

last: Lasky


title: Expression data of wild type and alfa-1 null L3 stage C.elegans with and without food

city: Baltimore

first: Jiou

state: MD

address: 615 N. Wolfe Street

department: Biochemistry and Molecular Biology

institute: The Johns Hopkins University

summary: The objective of this experiment was to determine changes in gene expression upon loss of alfa-1 in C.elegans under well-fed and starvation conditions. The human C9orf72 has an orthologue in C. elegans based on sequence homology, which is the F18A1.6 gene and also recently named as alfa-1 (ALS/FTD-associated gene homolog 1). We analyzed the domain structure of ALFA-1 and found that it shares the same DENN domains as human C9orf72, including the uDENN, cDENN, and dDENN domains. We obtained a mutant strain of the alfa-1 gene, which has a mutant allele (ok3062) of 486 bp deletion and 24 bp insertion in the region of exon 3 and exon 4. To understand the changes in gene expression in the alfa-1 mutant C. elegans, we performed the microarray gene expression profiling experiments under the defined conditions.

overall_design: 16 total samples were analyzed. We compared gene expression levels in wild type N2 C.elegans to alfa-1 null C.elegans under well-fed and starvation condidtions.  There were four replicates for each of four treatments.

first: Yon

last: Ji

first: Janet

last: Ugolino


title: Assessment of Viral RNA in Idiopathic Pulmonary Fibrosis Using RNA-seq [poly(A) RNA]

summary:
We identified sporadic low-level evidence of viral infections in our lung tissue specimens, but did not find a statistical difference for expression of any virus, including EBV, herpesvirus saimiri and HERV-K, between IPF and control lungs. To the best of our knowledge, this is the first publication that employs RNA-seq to assess whether viral infections are linked to the pathogenesis of IPF. Our results do not address the role of viral infection in acute exacerbations of IPF, however, this analysis patently did not support an association between herpes virus detection and IPF.
Conclusions: To the best of our knowledge, this is the first publication that employs RNA-seq to assess whether viral infections are linked to the pathogenesis of IPF. Our results do not address the role of viral infection in acute exacerbations of IPF, however, this analysis patently did not support an association between herpes virus detection and IPF.


title: MGMT enhancer modulates glioma cell sensitivity to temozolomide through long-range regulations of multiple genes

city: Tianjin

first: Bohan

address: NO.94 Weijin Road

institute: Nankai University

summary: Acquired resistance of temozolomide (TMZ) is one of the major obstacle of glioblastoma clinical treatment and the mechanism of TMZ resistance is still not very clear. In the presented research we show that deletion of rs16906252-associated MGMT enhancer in MGMT negative glioma cells induced increase sensitivity to temozolomide and combination of RNA-seq and Capture HiC identified several long-range target genes of rs16906252-associated MGMT enhancer. In addition, HiC data shows alterations of chromatin structures in glioma cells survived from high-dosage TMZ treatment and changes of TADs influence rs16906252-associated MGMT enhancer’s long-range regulations of target genes. Our study suggests rs16906252-associated MGMT enhancer regulates glioma cells’ TMZ sensitivity by long-range regulations of several target genes, which is a novel mechanism of regulation of TMZ sensitivity in glioma cells.

overall_design: MGMT KO glioma cells treated with temozolomide

first: Lei

last: Zhang

first: Wange

last: Lu


title: Beetle horns evolved from wing serial homologs

city: Bloomington

first: David

last: Linz

state: IN

address: Myers Hall 3rd Street

institute: Indiana University

summary: Understanding how novel complex traits originate is a foundational challenge in evolutionary biology. Yet how descent with modification in developmental evolution may lead to morphological innovation remains poorly understood. We investigated the origin of thoracic horns in scarabaeine beetles, one of the most dramatic classes of secondary sexual traits in the animal kingdom. We show that thoracic horns derive from bilateral source tissues, that diverse wing genes are functionally required for instructing this process, and that in the absence of Hox-input thoracic horn primordia transform to contribute to ectopic wings. Once induced, however, the transcriptional profile of thoracic horns diverges markedly from that of wings and other wing serial homologs. Our results provide evidence for the serial homology between thoracic horns and insects wings, and suggest that other insect innovations may similarly derive from wing serial homologs and the concomitant recruitment of diverse genes from outside a wing formation context.

overall_design: This RNAseq project includes eight distinct epidermal regions from O. taurus including: left and right T2 wings as well as five distinct T1 regions: the anterior, posterior, and carinated margin (left and right), the dorso-central prothorax, and the thoracic horn. We further included abdominal support structures from the 3rd-6th abdominal segment (bilateral projections found on the abdominal segments) as well as the dorsal head epidermis. Every tissue possesses six biological replicates, although the carinated margin and T2 wings have an additional six replicates that are derived from left and right tissues from the same individual. The dorsal head epidermis and the dorso-central prothorax are  two tissues we chose to include that, currently, have no published relationship to wings - and thus serve as  contrasts to the other, wing-related tissues.

first: Yonggang

last: Hu

first: Armin

middle: P

last: Moczek


title: Gene expression signatures in 3T3-L1 adipocytes 2, 8 and 20 days after the induction of adipocyte differentiation

status: Public on Apr 01 2020

city: Tokushima-city

first: Masashi

last: Kuroda

state: Tokushima

address: 3-18-15, Kuramoto-cho

institute: Tokushima University

summary: To identify the genes that increase in hypertrophic adipocytes, we have performed DNA microarray analysis in 3T3-L1 adipocytes. Hypertrophic adipocytes were obtained by long-term culture in routine cell culture medium. 2, 8 and 20 days after the induction of adipogenesis, total RNA was isolated.

overall_design: The effects of  adipocyte hypertrophy on gene expression profiles were measured in 3T3-L1 adipocytes.


title: Gene expression signatures in IRF7 overexpressed 3T3-L1 adipocytes

summary: To identify the genes that are regulated by IRF7, we have performed DNA microarray in 3T3-L1 adipocytes differentiated from precursor cells infected with retrovirus empty or carrying IRF7. Plasmids (Empty- and IRF7-pMSCV) were kindly provided from Dr. Eguchi at the Okayama University Graduate School of Medicine, Okayama, Japan [Cell Metab. 2008;7: 86-94.]. Infected 3T3-L1 preadipocytes were selected by puromycin treatment and differentiated into adipocytes. 7 days after the induction of adipogenesis, total RNA was isolated.

overall_design: IRF7-mediated gene expression changes were measured in 3T3-L1 adioocytes at day 7.


title: Estrogen receptor-α expressing neurons in the ventrolateral VMH regulate glucose balance

city: Houston

first: Guangsheng

last: Pei

state: Texas

address: 7000 Fanin

institute: UTHealth

summary:
Background: Brain glucose-sensing neurons detect glucose fluctuations and prevent severe hypoglycemia, but mechanisms mediating functions of these glucose-sensing neurons are unclear.
Methods: We combined mouse genetics, electrophysiology, neural tracing, optogenetics and Patch-RNA-seq to demonstrate how glucose-sensing neurons in the ventrolateral VMH regulate glucose balance.
Results: Here we report that estrogen receptor-α (ERα)-expressing neurons in the ventrolateral subdivision of the ventromedial hypothalamic nucleus (vlVMH) are glucose-sensing neurons to a 5-1-5mM glucose fluctuation, being glucose-inhibited neurons (GI-ERαvlVMH) or glucose-excited neurons (GE-ERαvlVMH). Hypoglycemia activates GI-ERαvlVMH neurons via the anoctamin 4 channel, and inhibits GE-ERαvlVMH neurons through opening the ATP-sensitive potassium channel. Further, we show that GI-ERαvlVMH neurons preferentially project to the medioposterior arcuate nucleus of the hypothalamus (mpARH) and GE-ERαvlVMH neurons preferentially project to the dorsal Raphe nuclei (DRN). Activation of ERαvlVMH-mpARH circuit and inhibition of ERαvlVMH-DRN circuit both increase blood glucose.
Conclusions: Our results indicate that ERαvlVMH neurons detect glucose fluctuations and prevent severe hypoglycemia in mice.

overall_design: Genetically identified single ERα neurons in the vlVMH were first tested for glucoses-sensing features, and then subjected to RNA-seq analyses. Differentially expressed genes were validated through multiple functional assays.


title: An in vitro coculture system of human peripheral blood mononuclear cells with hepatocellular carcinoma-derived cells for predicting drug-induced liver injury

city: Nagoya

first: Shingo

last: Oda

state: Aichi

address: 65 Tsurumai-cho, Showa-ku, Nagoya

institute: Nagoya University Graduate School of Medicine

summary: Preventing clinical drug-induced liver injury (DILI) remains a major challenge because DILI develops via multifactorial mechanisms. Immune and inflammatory reactions are considered important mechanisms of DILI; however, biomarkers from in vitro systems using immune cells have not been comprehensively studied. The aims of this study were 1) to identify promising biomarker genes for predicting DILI in an in vitro coculture model of peripheral blood mononuclear cells (PBMCs) with a human liver cell line, and 2) to evaluate these genes as predictors of DILI using a panel of drugs with different clinical DILI risk. Transcriptome-wide analysis of PBMCs cocultured with HepG2 or differentiated HepaRG cells that were treated with several drugs revealed an appropriate separation of DILI-positive and DILI-negative drugs, from which 12 putative biomarker genes were selected. To evaluate the predictive performance of these genes, PBMCs cocultured with HepG2 cells were exposed to 77 different drugs, and gene expression levels in PBMCs were determined. The MET proto-oncogene receptor tyrosine kinase (MET) showed the highest area under the receiver operating characteristic curve (AUC) value of 0.81 among the 12 genes with a high sensitivity/specificity (85/66%). However, a stepwise logistic regression model using the 12 identified genes showed the highest AUC value of 0.94 with a high sensitivity/specificity (93/86%). Taken together, we established a coculture system using PBMCs and HepG2 cells and selected biomarkers that can predict DILI risk. The established model would be useful in detecting the DILI potential of compounds, in particular those that involve an immune mechanism.

overall_design: Human peripheral blood mononuclear cells (PBMCs) were cocultured with HepG2 or differentialted HeapaRG cells using culture inserts and treated with test drugs. Test drugs included amodiaquine, diclofenac sodium, ketoconazole, levofloxacin, tienilic acid, and trovafloxacin mesylate (DILI-positive) and chloroquine phosphate, ethacrinic acid, ketorolac tromethamine, and mebendazole (DILI-negative) as well as 0.4% DMSO as a control. After a 24 h of incubation (5% CO2 at 37°C), PBMCs were collected and used for RNA extraction.

first: Yuka

last: Uchida

first: Tsuyoshi

last: Yokoi


title: pattern of miR-22 knockout mouse BAT gene expression

city: beijing

first: pengbo

last: lou

address: 2 west Winter Palace road

institute: Agricultural University

summary: To further understand different gene expression of miR-22 knockout mouse BAT and normal BAT, we have employed BAT samples microarray expression profiling as a discovery platform to identify different genes with miR-22 knockout mouse BAT and normal BAT.comparision with normal BAT,significantly upgene is 522 and downgene is 720 in knockout group.

overall_design: 3 control and 3 miR-22 knockout mice BAT samples were flow separated into trizol, the samples were taken to lab on ice, mRNA were extracted with trizol, good quality mRNA were choosen as microarrary analysis in capitalBio technology.

first: Pengbo

last: Lou

first: Zhengquan

last: Yu


title: Expression profiling by high-throughput RNA-sequencing following PGC1β and ERRα knockdown in HCT116 cells

city: Omaha

first: Danielle

last: Frodyma

state: NE

address: Buffet Cancer Center 9.12.379

institute: University of Nebraska Medical Center

summary: The goal of this experiment was to determine differential gene regulation of PGC1𝛽 or ERR𝛼 compared to the control.

overall_design: To identify transcripts that were specifically affected following PGC1β and ERRα knockdown. RNA was isolated using QIAGEN Rneasy kit. Six unstranded (poly A only) RNA samples were sequenced by the UNMC Genomics Core facility using the TrueSeq mRNA protcol.

middle: E

first: Jordan

last: Berg

first: Robert

last: Lewis

first: Kurt

middle: W

last: Fisher


title: Transcriptomic analysis of intestinal tissue of earthworm exposed to Tri-n-butyl phosphate (TnBP)

city: Nanjing

first: Yang

last: Yang

state: Jiangsu

address: 163 Xianlin Avenue

institute: Nanjing University

summary:
Purpose: The objective of this study was to investigate the TnBP-induced intestinal toxicity mechanism on earthworm Eisenia fetida.
Methods: The intestinal tissues of nine earthworms under control and 10 mg/kg TnBP treatments were separately pooled into three replicates (three earthworms per replication) to obtain sufficient amounts of RNA for transcriptomic assessments, using BGISEQ-500. qRT–PCR validation was performed using  SYBR Green assays.
Results: A total of 10,401 contig sequences, mapped to 313 KEGG pathways,were classified. Scatter plots of DEGs based on the results showed that 3786 genes were significantly up regulated and 1084 genes were significantly downregulated at a P-value cut off of 0.01 . Pathway enrichment analysis of DEGs was performed to identify the potential biological functions for the interaction of genes based on the KEGG database. Pathways of the Digestive system were severely affected in the transcriptome dataset for the pathways of Protein digestion and absorption, Salivary secretion, Gastric acid secretion, and Bile secretion disruption. This is in accordance with the intestinal injury results of the digestive tract degradation and the alteration of digestive activities.

overall_design: RNA-seq of earthworm intestinal tissue in control group and in treatment group, both containing three replicates.

first: Mei

last: Li


title: Nanoparticle Uptake in a Spontaneous and Immunocompetent Woodchuck Liver Cancer Model

city: Toronto

first: Jeff

last: Liu

state: Ontario

address: 101 College Street, RM 4-601

department: Princess Margaret Cancer Center

country: Canada

institute: University Health Network

summary: We characterized the identity of hepatic macrophages  from the uninvolved liver of a WHV-positive (area with no visible tumor) tumor bearing woodchuck that take up NPs using RNA-sequencing (RNA-seq). Data from WHV-infected animal from experiment 3.

overall_design: We performed fluorescence activated cell sorting (FACS) analysis on dissociated, live cells from the uninvolved liver (area with no visible tumor) of a WHV-positive tumor bearing woodchuck and sorted into 4 groups: CD14+NP-, CD14-NP-, CD14-NP+, and CD14+NP+. We profiled the molecular signatures of these four cell populations using RNA-seq

first: Lewis

first: Sonya

last: MacParland

first: Gary

middle: D

last: Bader

first: Ian

last: McGilvray


title: Genetic heterogeneity of the Spy1336/R28 – Spy1337 virulence axis in Streptococcus pyogenes and effect on gene transcript levels and pathogenesis

city: HOUSTON

first: Jesus

last: Eraso

state: TX

address: 6670 Bertner

department: Pathology and Genomic Medicine

institute: Methodist Hospital

summary:
Purpose: We used RNA-seq to analyze the transcriptomes of serotype M28 S. pyogenes deletion and SNP isogenic mutants strains. We discovered that changes in the number of T residues in a homopolymeric tract located upstream of the divergently transcribed Spy1336/R28 and Spy1337 genes affected global gene expression and virulence. We performed RNA-seq comparing isogenic mutants grown in vitro containing either 9 or 11Ts, and isogenic deletion mutants, deleted for gene Spy1337, and deleted for both,  Spy1336 and Spy1337.
Methods: We grew isogenic strains in rich media, and collected samples in triplicate at both mid-exponential (ME) and early stationary (ES) phase to perform RNA-seq analysis. Quality of the total RNA, rRNA-depleted RNA, and cDNA libraries was evaluated with RNA Nano, RNA Pico, and DNA high-sensitivity kits (Agilent Technologies, respectively, using an Agilent 2100 Bioanalyzer. For each sample, the cDNA library concentration was measured fluorometrically with Qubit™ dsDNA HS assay kits (Invitrogen). The cDNA libraries were diluted, pooled, and sequenced with an Illumina NextSeq 550 instrument

overall_design: Strains were grown in vitro, in triplicate, and RNA-seq cDNA libraries were generated using Illumina Scriptseq for bacteria.

first: James

middle: M

last: Musser

first: Priyanka

last: Kachroo


title: Transcriptomic programming of human CD8+ T cells. By pDCs and cDC2s jin the context of DC-based cancer vaccines

city: Nijmegen

first: Jessie

middle: van

last: Buggenum

address: Heyendaalseweg 135

institute: Radboud University

summary: Cancer vaccines utilizing naturally circulating dendritic cell (DC) subsets, such as plasmacutoid DCs (pDCs) and type 2 convential DCs (cDC2s), have demonstrated their potential as a therapy.  For melanoma in recent clinical trials. These DC vaccines aim to. human. DC subsets on the. T cell transcriptional program, which. forms the. molecular. basis. of an. antitumor. T cell response, is. poorly understood. In. this study,  we investigated the eraly gene expressionsignature of CD8+ T. cells following.  stimulation by pDCs or cDC2s. in. a culture system that mimics. the. current protocol of primary DC-based cancer vaccines. Our results demonstrate that pDCs and cDC2s induce a remarkably similar transcriptomic profile in CD8_ T cells, which. is tailored for increased effector function, survival and sensitivity. towards secondary signals. Nonetheless,  differences between pDC- and cDC2-induced T cell gene expression signatures encompass genes with a role in proliferation, cytolytic capacity and differentiation. Combining both DC subsets results in a T cell. transcriptomic program that. is very. similar to. the program induced by. pDCs alone. The results suggest that the. choice of DC subsets for use in cancer vaccines impacts the induced antitumor CD8+ T cell response.

overall_design:
Cd8 Tcells and DC subtypes were isolated from blood from 3 donors
Antigen: NY-ESO-1 peptide (SLLMWITQV)

first: Johannes

last: Textor


title: Methylation Sequencing  data of MII oocytes fromTet2-ko and WT mice

first: Mo

last: Gou

address: China, Tianjin, Nankai University

type: Methylation profiling by high throughput sequencing

summary: We analysed 3~4 repeats of 3 groups of mouse MII oocytes  including  2-month-old WT,  2-month-old Tet2-KO, 11-month-old WT to find Tet2 function on female mice fertility.

overall_design: 3~4 repeats of 20 samples of mouse MII oocytes, 10 oocytes each sample

first: H

last: Wang

first: L

first: M


title: Hiltonol and pRNA stimuli induce an immune activating profile in the transcriptomics of cDC1s

summary: 8 ligand), and compared these samples to unstimulated counterparts. Both methods, RNA-seq and microarray, gave very similar results and showed that Hiltonol and pRNA lead to almost identical changes in the transcriptome of cDC1 mDCs. A gene ontology (GO) term analysis suggested that these changes were mainly related to activation and maturation pathways, including induction of type I IFN and IL-12 transcription, while pathways related to adverse effects or cell damage were not strongly affected. The combination of both reagents in the DC cultures gave a very similar result as compared to either stimulus alone, suggesting no synergistic effect. Together, our results indicate that both stimuli are potent clinical grade adjuvants with comparable effects to mature cDC1 mDCs within an immunogenic profile in short-term cultures suitable to be used in immunotherapy.

overall_design:
BDCA3 were isolated from blood from 3 donors, 4 treatments were tested
Stimulus 1: Hiltonol
Stimulus 2: pRNA


title: Estrogen receptor alpha signaling establishes a sexually dimorphic regulatory node of energy expenditure

city: Los Angeles

first: John

middle: Edward

last: van Veen

state: CA

address: 610 Charles E young Dr

department: Integrative Biology and Physiology

institute: UCLA

summary: Estrogen receptor a (ERa) signaling in the ventromedial hypothalamus (VMH) contributes to energy homeostasis by modulating physical activity and thermogenesis. However, the precise neuronal populations involved remain undefined. Using single-cell RNA transcriptomics and in situ hybridization, we describe six neuronal populations in the mouse VMH. ERa is enriched in populations showing sex biased expression of reprimo (Rprm), tachykinin 1 (Tac1), and prodynorphin (Pdyn). Female biased expression of Tac1 and Rprm is patterned by ERa-dependent repression during male development, whereas male biased expression of Pdyn is maintained by circulating testicular hormone in adulthood. Chemogenetic activation of ERa+ VMH neurons stimulates heat generation and movement in both sexes. However, silencing Rprm gene function increases core temperature selectively in females and ectopic Rprm expression in males is associated with reduced core temperature. Together these findings reveal a role for Rprm in temperature regulation and ERa in the masculinization of neuron populations that underlie energy expenditure.

overall_design: Single cell RNA sequencing of cells in the mouse ventromedial hypothalamus. N = 3 male and 3 female mice sacrificed on post-natal day 10, and FACS purified

first: Laura

last: Kammel

first: Patricia

last: Bunda

first: Michael

last: Shum

first: Michelle

last: Reid

first: Megan

last: Massa

first: Douglas

last: Arneson

first: Jae

last: Park

first: Zhi

last: Zhang

first: Alexia

last: Joseph

first: Haley

last: Hrncir

first: Marc

last: Liesa

first: Arthur

last: Arnold

first: Xia

first: Stephanie

last: Correa


title: A long noncoding RNA, LOC157273, is the effector transcript at the chromosome 8p23.1-PPP1R3B metabolic traits and type 2 diabetes risk locus

city: Cambridge

first: Alisa

last: Manning

state: MA

address: 75 Ames Street

department: Metabolism Program

institute: Broad Institute

summary: Genome wide association studies (GWAS) identified a chromosome 8 locus associated with fasting glucose (FG), insulin (FI) and lipid levels that is located near PPP1R3B (a gene which encodes the catalytic subunit of a serine/threonine protein phosphatase that promotes hepatic glycogen storage upon insulin signaling). The lead SNP rs4841132 lies in a long non-coding RNA (lncRNA) LOC157273, 175 kb away and is not in linkage disequilibrium with PPP1R3B. Our analysis of the FANTOM consortium data shows LOC157273 is expressed only in hepatocytes. We hypothesized that LOC157273 is the causal candidate that acts upstream of PPP1R3B to regulate FG and FI. Human whole transcriptome sequencing was performed to understand which other genes undergo changes in expression levels upon silencing of LOC157273.

overall_design: RNA was extracted from human hepatocytes from a single human donor (Life Technologies donor ID HU8200-A) after siRNA knockdown (or control conditions) in three biological replicates.

first: Leonard

last: Lipovich

middle: K


title: Between-generation phenotypic and epigenetic stability in a clonal snail

city: Pullman

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

summary: Epigenetic variation might play an important role in generating adaptive phenotypes by underpinning within-generation developmental plasticity, persistent maternal effects of the environment (e.g., trans-generational plasticity), or heritable epigenetically based polymorphism.  These adaptive mechanisms should be most critical in organisms where sources of variation are limited.  Consequently, using a clonally reproducing freshwater snail (Potamopyrgus antipodarum), we examined the plasticity of an adaptive phenotype (shell shape) and of DNA methylation between generations by experimentally manipulating the current-speed environment in the lab.  By comparing three generations of lab-reared snails with reference field populations, we showed that habitat-specific adaptive shell shape is stable across one generation, and adaptively responds gradually over two subsequent generations. We also showed that DNA methylation specific to high-current environments was stable across one generation. Together these observations suggest that shell shape variation is at least in part determined by transgenerational plasticity and that DNA methylation provides a potential mechanism.

overall_design: River snails were collected from tributary spring stream of the Snake River at Ritter Island (42.7439°N, 114.8420°W). For the transgenerational observations of shell shape, 5 iso-female lines were initiated. After the first generation reproduced, snails were photographed under a dissecting microscope and their tissue was harvested for analysis of DNA methylation. The second and third generations were raised under the same conditions and shell shapes were measured after females were reproductive.

first: Mark

last: Smithson

first: Jennifer

last: Thorson

first: Ingrid

last: Sadler-Riggleman

first: Daniel

last: Beck

last: Dybdahl


title: RNA Sequencing of wild type and RNA polymerase mutant (rpoCA494V) strains of Escherichia coli

city: Bengaluru

first: Aswin

middle: Sai Narain

last: Seshasayee

state: Karnataka

address: GKVK campus Bellary road

country: India

institute: National Centre for Biological Sciences

summary: RNA Sequencing of wild type Eschrichia coli and a RNA polymerase mutant isolated from deep stationary phase

overall_design: RNA polymerase mutation rpoCA494V is introduced in different genetic backgrounds of E.coli and pairwise comparison between mutant and wild type strains have been done in each different backgrounds. Cells were grown overnight in rich media (LB) and Whole RNA fraction isolated in stationary phase

first: Pabitra

last: Nandy

first: Savita

last: Chib

middle: S


title: Lesional and non-lesional skin gene-expression profiles from Phase-3 clinical trials of Brodalumab

city: New York

first: Mayte

last: Suarez-Farinas

state: NY

address: 1425 Madison Ave, L2-70C, Box 1077,

institute: Mount SinaiSchool of Medicine

summary:
IL-17 antagonists induce impressive clinical benefit in psoriasis, but it is unknown too what extent cellular and molecular characteristics of psoriasis are suppressed by a clinically relevant dose and schedule of any IL-17 antagonist.
Examine the effects the IL-17A receptor antagonist brodalumab, on the clinical and molecular characteristics of psoriasis, including IL-17 dependent gene-sets.

overall_design: A subset of 116 patients enrolled in three Phase-3 randomized clinical trials (AMAGINE-1,2,3) participated in a mechanistic sub-study where punch biopsies were collected for lesional and non-lesional skin between baseline and 12 weeks. The biopsy cohort included moderate-to-severe psoriasis patients treated with 140mg (n=46), 210mg (n=41) brodalumanb or placebo (n=29), 844 samples total. Affymetrix arrays were used to evaluate the treatment-induced changes in the expression profile of lesional skin.

first: Lewis

last: Tomalin

first: Chris

last: Russell

first: Sandra

last: Garcet


title: Transcriptomic profiles of host epithelial cells in response to actin rearrangement induced by atypical enteropathogenic Escherichia coli

city: Dallas

first: Fernando

middle: Henrique

last: Martins

address: 6000 Harry Hines Blvd, NL4.110H

department: Microbiology

institute: University of Texas Southwestern Medical Center

summary: Atypical enteropathogenic Escherichia coli (aEPEC) is amongst the leading causes of diarrheal disease worldwide. The colonization of the gut mucosa by aEPEC results in actin pedestal formation at the site of bacterial attachment. This cytoskeletal rearrangement is triggered by the interaction between the bacterial adhesin intimin and its receptor Tir, which is translocated through the type three secretion system, to the host cell. While some aEPEC require tyrosine phosphorylation of Tir and recruitment of the host Nck to trigger actin polymerization, certain aEPEC strains, whose Tir is not phosphorylated, rely on the effector EspFu for efficient actin remodeling. To understand how the host responds to these different actin polymerization signaling pathways, we analyzed gene expression changes in epithelial cells infected with pedestal-forming aEPEC strains using high-throughput RNA sequencing (RNA-seq).

overall_design: RNA-Seq was performed on HeLa cells infected for 6 hours with aEPEC strains which trigger actin rearrangement via Tir:Nck (KOct2), Tir:EspFu (BA320) or both pathways (KOct1), as well cells infected with a strain which does not induce robust actin polymerization (KO). Uninfected cells (mock infected) were also processed as control. Each of five conditions was performed in duplicates, resulting in a total of ten samples.

middle: H

first: Ashwani

last: Kumar

first: Chao

last: Xing

first: Vanessa

last: Sperandio

first: Waldir

last: Elias


title: Single Cell RNA-Seq profiling human embryonic kidney cortex cells [H14w]

first: Guilherme

last: de Sena Brandine

address: 1050 Child's Way

department: Quantitative and Computational Biology

institute: University of Southern California

summary: To characterize the cellular diversity in the human kidney cortical nephrogenic niche we dissociated cells from the cortex and performed 10X Genomics single-cell RNA sequencing.

overall_design: Identifying cell types and nephrogenic programs in the developing human kidney

first: Andrew

last: Ransick

first: Albert

last: Kim

last: De Sena Brandine

first: Nils

middle: O

last: Lindstrom

last: McMahon


title: Impact of TNF receptor superfamily member costimulation on the transcriptome of in vitro CD3/CD28 activated mouse Tregs

city: Paris

first: Benoit

last: Salomon

address: 8 rue de la Croix-Jarry

department: Inserm DR6

country: France

institute: BioPark

summary: Activated Foxp3+ regulatory T cells (Tregs) express several TNF receptor superfamily (TNFRSF) members. Here, we analyzed the transcriptome of purified Tregs that were activated with anti-CD3 and anti-CD28 mAbs, IL-2 and with or without agonists of TNFR2, 4-1BB, DR3 and OX40 for 18h and 36h. Triggering these TNFRSF in Tregs induces similar changes in gene expression patterns, suggesting that they engage common signal transduction pathways. Among them, we identified a major role of canonical NF-κB.

overall_design: Bulk RNA-Seq on purified in vitro activated Tregs.

first: Martina

last: Lubrano di Ricco

middle: L


title: MRTF-A promotes angiotensin II-induced inflammatory response and aortic dissection in mice

city: Kurume

first: Hiroki

last: Aoki

state: Fukuoka

address: 67 Asahimachi

department: Cardiovascular Research Institute

institute: Kurume University

summary: Aortic dissection (AD) is a major cause of acute aortic syndrome with high mortality due to the destruction of aortic walls. Although recent studies indicate the critical role of inflammation in the disease mechanism of AD, it is unclear how inflammatory response is initiated. Here, we demonstrate that myocardin-related transcription factor A (MRTF-A), a signal transducer of humoral and mechanical stress, plays an important role in pathogenesis of AD in a mouse model. A mouse model of AD was created by continuous infusion of angiotensin II (AngII) that caused dilation of thoracic aorta in 1 day and AD in 4 days. Systemic deletion of Mrtfa gene resulted in a marked suppression of AD development. Transcriptome and gene annotation enrichment analyses revealed that AngII infusion for 1 day caused pro-inflammatory and pro-apoptotic responses before AD development, which were suppressed by Mrtfa deletion. AngII infusion for 1 day induced pro-inflammatory response, as demonstrated by expressions of Il6, Tnf , and Ccl2, and apoptosis of aortic wall cells, as detected by TUNEL staining, in an MRTF-A-dependent manner. Furthermore, pharmacological inhibition of MRTF-A by CCG-203971 during AngII infusion prevented AD development, indicating that acute suppression of MRTF-A is effective in preventing the aortic wall destruction. These results indicate that MRTF-A transduces the stress of AngII challenge to the pro-inflammatory and pro-apoptotic responses, ultimately leading to AD development. Intervening this pathway may represent a potential therapeutic strategy.

overall_design: Gene expression was examined for aortic tissues from WT and MRTF-A KO mice with and without 1 day AngII infusion.

first: Sohei

last: Ito

first: Michihide

last: Nishihara

first: Satoko

last: Ohno

first: Aya

last: Furusho

first: Saki

last: Hirakata

first: Norifumi

last: Nishida

first: Makiko

last: Hayashi

first: Koichiro

last: Kuwahara

first: Yoshihiro

last: Fukumoto


title: Grafting changed silicon metabolism and expression of bloom-forming related genes of cucumber pericarp

city: Tai'an

first: Zhao

last: Sheng

state: Shandong

address: No.61 Daizong street

department: College of Horticultural Science and Engineering

institute: Shandong Agricultural University

summary: Cucumber (Cucumis sativus L.) is an economically important vegetable cultivated all over the world. Grafting can produce bloomless or sparse-bloom cucumber, which is welcomed by increasing consumers. Bloom granule is tine glandular hair, which is hard and rare studied on its formation and related genes. Mutifunctional RNA-seq is a recently developed analytical approach for transcriptome profiling via high-throughput sequencing and has been recently applied to a wide variety of organisms, which provide us reliable technical means detect bloom formation and related genes. In this study, we chose a cucumber inbred line (Shannong No.5) and two pumpkin rootstock lines as materials, and constructed four tested cucumbers, grew plants in “Yamazaki cucumber nutrient solution formula” prepared by deionized water, treated plants with or without 1.7mM potassium silicate 2 hours before collecting pericarp. Each treatment were duplicated twice.16 cDNA libraries were constructed from pericarp of a cucumber inbred line (own-rooted cucumber), C/C (self-grafted cucumber), M/C (More bloom, cucumber grafted onto “3225” rootstock) and L/C(Less bloom, cucumber grafted onto “3212” rootstock). We obtained 17,215,769~17,529,047 high quality reads, and 18,804~19,358 genes from each sample. All reads can be mapped to the cucumber genome (Version 2). By RPKM comparing, we got 38 comparing combinations with differentially expressed genes (DEGs), obtained 38 significantly expressed combinations by FDR≤0.001 and the absolute value of log2Ratio≥1 as the thresholds. These results suggest that there are many differences and genes expression mode among effects of grafting or added silicon. This study addresses a preliminary analysis and offers a foundation for future genomic research in the bloom formation of cucumber.

overall_design: Own-rooted cucumber,self-grafted cucumber and cucumber grafted onto two pumpkin rootstock lines, cultivated by deionized water nutrient solution with 1.7mM silicon added or not; RNA-Seq on cucumbers pericarp, analyse the data, and get differencially expressed genes

first: Wang

last: Hui

first: WEI

last: Min

first: WANG

last: Xiu-feng

first: SHI

last: Qing-hua

first: YANG

last: Feng-juan


title: Primed to naïve-like conversion of the common marmoset embryonic stem cells

city: Tokyo

first: Seiji

last: Shiozawa

address: 35 Shinanomachi, Shinjuku-ku

institute: Keio University, School of Medicine

summary: Mammalian pluripotent stem cells are thought to exist in two states: naïve and primed states. Generally, unlike those in rodents, pluripotent stem cells in primates including humans are regarded as being in the primed pluripotent state. Recently, several groups reported the existence of naïve pluripotent stem cells in humans. In this study, we report the conversion of primed state embryonic stem cells from common marmoset, a New World monkey, to the naïve state by using transgenes. The cells showed typical naïve state features including dome-like colony morphology, growth factor requirement, gene expression profile, X chromosome activation state, and energy metabolic status. Moreover, interspecies chimeric embryo formation ability with mouse embryos was increased in the naïve state. This technique can be applied in basic medical research using non-human primates such as preclinical use of naïve pluripotent stem cells and generating genetically modified primates.

overall_design: RNA-seq of cjESCs and epiblast of early embryos.

first: Hideyuki

last: Okano


title: Effect of DMHF (2,5-dimethyl-4-hydroxy-3(2H)-furanone) inhalation on gene expression in Rat brain

city: Aomori

first: Yuji

last: Nakai

state: Aomori

address: 2-1-1, Yanagawa

department: Institute of Regional Innovation

institute: Hirosaki University

summary:
Background: 2,5-Dimethyl-4-hydroxy-3(2H)-furanone (DMHF) is one of the major odor compounds generated by the Maillard reaction. We previously reported that the inhalation of DMHF decreased systolic blood pressure via the autonomic nervous system in rats. The autonomic nervous system is also closely related to appetite regulation. The present study investigated the effects of DMHF on dietary intake and gene expression.
Results: The inhalation of DMHF increased the dietary intake of rats during the feeding period. However, body weight gain was suppressed after six weeks of feeding. A DNA microarray analysis showed that DMHF altered gene expression associated with feeding behavior and neurotransmission in the rat brain.  Conclusion: DMHF inhalation promotes appetite and changes gene expression in rats. Furthermore, phenotypic changes may regulate neurotransmission and appetite at the mRNA level in addition to controlling the autonomic nervous system.

overall_design: Six-week-old Wistar rats were purchased from CLEA Japan Inc. (Tokyo, Japan). Rats were housed in plastic cages in an animal room at 22 ± 2℃ and 50 ± 10% humidity under an artificial lightning system of 12-h light and 12-h darkness (lights on from 08:00 to 20:00). Rats were housed for a week to acclimate to the environment, and were able to access water and chow diets ad libitum during the experimental period. Rat brains were obtained for the DNA microarray analysis after the inhalation of DMHF. A 5-mL aliquot of distilled water (control) or DMHF was deposited into a two-neck flask; air was pumped into one neck and the vapor phase from the flask was ejected from the other. After 5 min of DMHF inhalation, rats were left to stand for 10 min and then sacrificed. The inhalation of DMHF was performed before the circadian rhythm dark period.

first: Issei

last: Yokoyama

last: Suzuki

first: Motoko

last: Ohata

first: Yusuke

last: Komiya

first: Jun

last: Nagasao

first: Keizo

last: Arihara


title: Loss of Down syndrome critical region-1 causes cholesterol-metabolic dysfunction leading to corneal opacity

first: Shogo

last: Yamamoto

address: 4-6-1 Komaba, Megro-ku

department: Research Center for Advanced Science and Technology

institute: The University of Tokyo

summary: To elucidate the molecular mechanisms behind corneal angiogenesis in Dscr-1-/- mice, we performed microarray analysis using intact corneas from B6, Dscr-1-/- mice, ApoE-/- mice,  Dscr-1-/- and ApoE-/- double null mutant mice and sutured corneas from B6, Dscr-1-/- and Dscr-1 Tg mouse.

overall_design: Expression data of intact corneas from B6, Dscr-1-/- mice, ApoE-/- mice,  Dscr-1-/- and ApoE-/- double null mutant mice and sutured corneas from B6, Dscr-1-/- and Dscr-1 Tg mouse. Total RNA of dissected intact and sutured corneas from each mouse was used.

first: Masashi

last: Muramatsu

first: Suguru

last: Nakagawa

first: Tsuyoshi

last: Osawa

first: Takashi

last: Minami


title: Transcriptome analysis of methylparaben treated H1299 lung carcinoma cells

city: Seoul

first: Jung-Woong

last: Kim

address: 84 Heuksuk-ro Dongjak-ku

department: Life Science

country: South Korea

institute: Chung-Ang University

summary:
Purpose: finding differential transcripts usage in environmentally harzardous chemical, methylparaben
Methods: transcriptome analysis by the RNA-seq via mRNA pull-down
Results: We found that methylparaben increases cellular toxicity in H1299 cells. Also, over thousands of retained intron events were detected from the RNA-seq analysis.
Conclusions: Methylparaben increases cytotoxic effects in H1299 cells through the caspase-3 pathway and changes the context of trascript through the splicing regulation mechanisms.

overall_design: H1299 cells were treated with methylparaben and all experiments were duplicated.


title: Investigate the gene expression profiles of oral sublingual DC and macrophage subsets

first: Yue

last: Yang

state: Tokyo

institute: Tokyo medical and dental university

summary: Oral mucosa has a potential to maintain immunological homeostasis since little severe inflammation happens in the continuous antigen exposure in the oral cavity. SLIT applied for the allergen-specific immune suppression is performed by repeated antigen (Rpt Ag)-painting to sublingual mucosa (SLM). Among a series of immune cells at submucosa, heterogeneous DC/MF subsets contribute to the orchestration of mucosal immune responses. Previously, We found that Rpt Ag-painting to SLM exhausted typical CD11c+ DCs and induced round-type Macrophage-like CD206hi cells.  In this study, we defined three major DC/Macrophage fraction in SLM after Rpt Ag-painting by the expressions of several surface molecules. Fraction 1 (Fr-1): CD206- CD11c+ F4/80lo; Fraction 2 (Fr-2): CD206- CD11c- F4/80+ and Fraction 3 (Fr-3): CD206hi CD11clo F4/80+. Microarray analyses revealed that total of 7282 up-regulated and 7389 down-regulated genes in Fr-3 were enriched compared with Fr-2, respectively. Genes in Fr-3 preferentially expressed molecules related to homeostatic process and negative regulation of T cell activation. Furthermore, new B7 family of immune checkpoint molecules express significantly higher on Fr-3. When we checked the expressions of genes related to M2 MF, Fr-3 cells preferentially express fizz1, aldh1a1 and aldh1a2 but not Ym-1 and arginase-1 compared to in vivo induced M2-like cells. These results indicate that Fr-3 has distinct features compared with M2 like cells and may has T cell regulation potential. Functional investigation imply that CD206hi cell dominant status induces suppression of Ag-specific T cell responses. In conclusion, these results suggest that CD206hi cells from SLM involved in immune tolerogenic inducement by expressing new B7 family molecules and modulate T cell immune responses.

overall_design: 6 Samples were sequenced: Fr-1, Fr-2 and Fr-3 cells were sorted from sublingual mucosa (SLM) of BALB/c mice painted FITC twice to SLM.(n=2 replicates per fraction from independent experiments.)

first: Shigenori

last: Nagai

first: Miyuki

last: Azuma


title: scRNA-seq of human vitiligo reveals a multi-step process of disease progression

city: Worcester

first: Kyle

last: Gellatly

address: 368 Plantation Street

institute: University of Massachusetts Medical School

summary: Comparison of neonatal foreskin (NFS) cultured melanocytes treated with phosphate buffered saline (PBS), Dimethyl sulfoxide (DMSO), or interferon-gamma (IFNg)

overall_design: RNA-seq on cultured melanocytes treated with DMSO, PBS, or IFNg

first: James

last: Strassner


title: Single cell sequencing facilitates the identification of colonic epithelial Tcf4 Lin-  stem cells that give rise to absortive and secretory precursor populations.

city: Salt Lake City

first: Mario

middle: R.

last: Capecchi

state: UT

address: 15 North 2030 East

institute: University of Utah

summary: We report the Single Cell analysis of Tcf4 Lin- cells isolated from the mouse colon.

overall_design: Isolation and single cell sequencing of Tcf4 Lin- cells to define the Tcf4 Lin- populations within the colon

first: Melinda

last: Angus-Hill

first: Tim

last: Mosbruger

first: Annika

middle: V

last: Thorpe

first: Saher

last: Hammoud


title: Transcriptional profile of WT, p53 -/- and p53R172H esophageal cells

city: Boston

first: Mirazul

last: Islam

address: D857A, Dana Farber Cancer Institute, 44 Binney St. Boston MA

department: Medical Oncology

institute: DFCI

summary: We report different transcriptional profiles of WT, p53-/- and p53R172H cells derived from mouse esophagi. P53-/- and p53R172H expressing mice were treated with 4NQO to enhance tumor formation.

overall_design: Gene expression analysis of 2 WT, 2 p53 -/-, and 3 p53R172H cell lines

first: Anil

last: Rustgi

first: Ashley

last: Lento


title: Expression data from murine RAW264.7 macrophages

city: Frederiksberg

first: Laura

middle: J

last: Myhill

address: Dyrlægevej 100

country: Denmark

institute: University of Copenhagen

summary: We aimed to determine the effect of inulin and Trichuris suis soluble product (TsSP) on inflammatory gene expression in LPS-induced macrophages.

overall_design: RAW 264.7 macrophages were stimulated in the presence of inulin plus or minus helminth products, then stimulated with LPS. Then, incubated for 6 hours at 37°C, 5% CO2.


title: Identification of transcriptome changes associated with toxic effects of methanolic coal dust extract on fish early life stage by RNASeq

city: Iquique

first: Angelica

last: Guerrero Castilla

address: Avda Arturo Prat #2120

country: Chile

institute: Universidad Arturo Prat

summary: We report the transcriptional changes associated with toxic effects of methanolic coal dust extract on normal zebrafish development. Early exposure of wild type embryos at 4 hpf to coal dust extract led to 3 groups of malformed phenotypes - tail deformity (P1), deformed yolk (P2) and smaller embryos with extruded yolks (P3). RNAseq of each phenotypic group revealed changes in genes involved in xenobiotic metabolism, intermediate filament composition, oxidation-reduction processes, calcium ion binding, focal adhesion and the ECM-receptor interaction pathway.

overall_design: Determination of transcriptional changes in 24 hpf wild type zebrafish embryos exhibiting 3 different phenotypes (P1,P2,P3) that resulted from exposure to methanolic coal dust extract at 4 hpf

first: Imelda

middle: T

last: Sandoval

last: Guerrero-Castilla


title: Cardiac ReductomiRs: Identification of Novel Nrf2-Dependent microRNAs as Post-Transcriptional Regulators of Myocardial Gene Expression

city: Stanford

first: Mark

middle: Emile

last: Pepin

address: 870 Quarry Road

department: Cardiovascular Medicine

institute: Stanford University

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

overall_design: Refer to individual Series


title: Next Generation Sequencing of TMAO (Trimethylamine N-oxide)-treated Cardiac Transcriptomes

city: Niigata

first: Yohko

last: Yoshida

address: 1-757, Asahimachi-dori, Chuo-ku

institute: Niigata University

summary: To investigate the mechanism how TMAO deteriorates cardiac dysfunction in murine left ventricular pressure overload model, we performed RNA-seq analysis with cardiac tissue from TMAO-treated mice.

overall_design: Cardiac mRNA profiles of 13-weeks old wild type mice treated with TMAO for 2 weeks were generated by RNA-seq using Illumina NextSeq500.

first: Goro

last: Katsuumi


title: An epigenetic map of malaria parasite development from host to vector

city: London

first: Kathrin

last: Witmer

address: Imperial College Road

department: Life Sciences

institute: Imperial College London

summary: Chromatin state has not been investigated in many other Plasmodium species, strains or life cycle stages, yet. Here, we used ChIP-seq to profile heterochromantin and euchromatin occupancy in P. berghei parasites as they progress through the life cycle. Additionally, we performed RNAseq of the same stages in triplicate to complete the dataset. Collectively, the generated heterochromatin, euchromatin and transcription profiles provide a detailed catalogue of epigenetic regulation in the P. berghei parasite as it progresses through the life cycle.

overall_design: In total, we sequenced 12 ChIP-seq samples (4 HP1-ChIP-seq samples, 4 H3K9ac-ChIP-seq samples, 4 inputs) generated from chromatin from three different Plasmodium berghei lines (2.33, 820 and 507), and four different stages (asexual blood stage, female and male gametocyte and ookinete) and we sequenced 12 RNA-seq samples of the same stages from the same lines in triplicates (3 asexual blood stages, 3 female gametocytes, 3 male gametocytes, 3 ookinetes) and used gDNA as a control for the RNA-seq protocol (mixed asexual blood stages, line 2.33).

first: Sabine

middle: A

last: Fraschka

first: Dina

last: Vlachou

first: Richárd

last: Bártfai

first: George

last: Christophides


title: Characterization of human BRAF mutated melanoma cells that persist after PLX4032 treatment

city: Buenos Aires

first: Florencia

middle: Paula

last: Madorsky Rowdo

address: Av. Patricias Argentinas 435

country: Argentina

institute: Fundación Instituto Leloir

summary: We performed RNA-seq in parental MEL-XY3 melanoma cells (JM9) and in MEL-XY3 SUR cells obtained in vitro after 5 week treatment with PLX4032 (JM7)

overall_design: Transcriptome profile of 2 melanoma cell lines

last: Madorsky

first: Marcela

last: Barrio

first: José

last: Mordoh


title: RNA deep sequencing data of the whole transcriptomes of the wild-type and furA triple mutant strains of Mycobacterium smegmatis MC2 155

city: Busan

first: Jungwook

last: Park

address: Pusan National University, 2, Busandaehak-ro 63beon-gil, Geumjeong-gu, Busan 609-735, Korea

institute: Pusan National University

summary: To identify the FurA regulon in Mycobacterium smegmatis MC2 155, we constructed a furA triple mutant with deletion of three furA paralogous genes (MSMEG_6383, MSMEG_3460, and MSMEG_6253) and profiled the transcriptomes of the wild-type and furA triple mutant strains. Differentially expressed genes were identified pair-wisely by means of the edgeR package in R language. 742 genes were differentially expressed in the furA triple mutant compared to the wild-type strain.

overall_design: Six libraries constructed: Each three replicates of furA mutant strain and wild-type in Mycobacterium smegmatis MC2 155

first: Ha-Na

last: Lee

first: Hyun-Hee

first: Young-Su

last: Seo

first: Jeong-Il

last: Oh


title: PRMT1-mediated FLT3 arginine methylation promotes FLT3-ITD+ Acute Myeloid Leukemia maintenance

city: Duarte

first: Xin

last: He

address: 1500 E Duarte Rd

country: USA

institute: City of Hope

summary:
We want to obtain FLT3-ITD gene signature. To do so, we transduced  CB CD34+ cells  with mock or FLT3-ITD vectors and performed RNA sequencing (RNA-Seq).
Two Groups: Group1: CB CD34+ cells transduced with mock vector; Group2: CB CD34+ cells transduced with FLT3-ITD vector;

overall_design: Expression profiling data in FLT3-ITD+ Cord blood cells were compared to corresponding control mock transduced cells by RNA-seq technology

first: Ling

last: Li