title: Rat Rotator Cuff Tear RNASeq

city: Ann Arbor

first: Richard

last: McEachin

state: United States

address: 2800 Plymouth Road

department: DCM&B

institute: University of Michigan

summary: Myosteatosis is the pathological accumulation of lipid that occurs in conjunction with atrophy and fibrosis following skeletal muscle injury or disease. Little is known about the mechanisms by which lipid accumulates in myosteatosis, but many studies have demonstrated the degree of lipid infiltration negatively correlates with muscle function and regeneration. Our goal was to identify biochemical pathways that lead to muscle dysfunction and lipid accumulation in injured rotator cuff muscles, a model that demonstrates severe myosteatosis. Adult rats were subjected to a massive tear to the rotator cuff musculature. After a period of either 0 (healthy control), 10, 30, or 60 days, muscles were prepared for RNA sequencing, shotgun lipidomics, metabolomics, biochemical measures, electron microscopy, and muscle fiber contractility. Following rotator cuff injury, there was a decrease in muscle fiber specific force production that was lowest at 30d. There was a dramatic time dependent increase in triacylglyceride content. Interestingly, genes related to not only triacylglyceride synthesis, but also lipid oxidation were largely downregulated over time. Using bioinformatics techniques, we identified that biochemical pathways related to mitochondrial dysfunction and reactive oxygen species were considerably increased in muscles with myosteatosis. Long chain acyl-carnitines and L-carnitine, precursors to beta-oxidation, were depleted following rotator cuff tear. Electron micrographs showed injured muscles displayed large lipid droplets within mitochondria at early time points, and an accumulation of peripheral segment mitochondria at all time points. Several markers of oxidative stress were elevated following rotator cuff tear. The results from this study suggest that the accumulation of lipid in myosteatosis is not a result of canonical lipid synthesis, but occurs due to decreased lipid oxidation in mitochondria. A failure in lipid utilization by mitochondria would ultimately cause an accumulation of lipid even in the absence of increased synthesis. Further study will identify whether this process is required for the onset of myosteatosis.

overall_design: Rats were subjected to a bilateral full-thickness supraspinatus tear and suprascapular neurectomy. Samples (N=4 per group) were taken at 0 days (unoperated controls), 10 days, 30 days, and 60 days post-injury

first: Jonathan

last: Gumucio

first: Christopher

last: Mendias


title: Inhibition of endothelial Notch signaling attenuates inflammation [ChIP-Seq]

status: Public on Aug 29 2018

city: OSLO

first: Guttorm

last: Haraldsen

state: OSLO

address: Sognsvannsveien 20

department: Department for Pathology

country: Norway

institute: Oslo University Hospital

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Vascular endothelial cells upregulate the Notch ligand Jagged1 in response to inflammatory activation. Here we show that abrogation of endothelial Notch1 signaling impairs induction of key inflammatory target genes. Accordingly, inducible endothelial-targeted knockout of the canonical Notch transcription factor RBPJ reduces inflammation in a murine model of contact hypersensitivity, while overexpression of constitutive active Notch1 has the opposite effect. We show that the proinflammatory role of Notch1 can be attributed to direct genomic priming of the inflammatory landscape involving crosstalk with NF-κB/RelA and selective activation of enhancers associated with Notch-dependent inflammatory genes.  This is the first evidence that canonical Notch signaling supports endothelial activation in response to inflammatory cytokines on the chromatin level.

overall_design: Examination of Notch1, RBPJ, NF-κB/RelA, H3K27ac genomic localization by ChIP-seq, in unstimulated and ILβ1-stimulated human umbilical vein endothelial cells (HUVECs) with and without Notch1 knockdown

first: Lars

last: la Cour Poulsen

first: Reidunn

last: Jetne Edelmann

first: Stig

last: Krüger

first: Rodrigo

last: Diegues-Hurtado

first: Akshay

last: Shah

first: Tor

last: Espen Stav-Noraas

first: Anastasia

last: Renzi

first: Monika

last: Szymanska

first: Junbai

last: Wang

first: Manuel

last: Ehling

first: Rui

last: Benedito

last: Kasprzycka

first: Espen

last: Bækkevold

first: Olav

last: Sundnes

first: Ian

last: Donaldson

first: Kim

last: Midwood

first: Helge

last: Scott

first: Philippe

last: Collas

first: Christian

middle: W

last: Siebel

first: Ralf

middle: H

last: Adams

first: Eirik

last: Sundlisæter

first: Johanna

last: Hol


title: Genome-wide Mapping of Lamin B1 Reveals the Existence of Dynamic and Functional Euchromatin Lamin B1 Domains (eLADs) at the onset of the Epithelial to Mesenchymal Transition

status: Public on Aug 30 2018

city: Barcelona

first: Enrique

last: Blanco

address: Dr. Aiguader 88

department: Gene Regulation, Stem Cells and Cancer

country: Spain

institute: Center for Genomic Regulation (CRG)

type: Expression profiling by high throughput sequencing

summary: Lamins (A/C and B) are type V intermediate filaments and constitute the major cytoskeleton component of nuclei. They are assembled forming a filamentous meshwork that is mainly located between the inner nuclear membrane and the peripheral chromatin in where they form structural and conserved elements called lamin-associated domains (LADs) that cover around 40% of the mammalian genome. However, a small fraction of lamins are also located in the nucleoplasm although is still unclear if represents a fraction that is in transit towards the nuclear membrane, a reservoir for protein turnover or they have specific functions in nuclear organization6. Here we mapped genome-wide the localization of lamin B1 from an enriched euchromatin fraction. Our analysis show for the first time that lamin B1 can be also associated with active euchromatin forming domains of about half a megabase on average in size. These euchromatin lamin B1 domains (eLADs) are constituted by active and accessible euchromatin showed by RNAseq and ATACseq. Importantly, we have analyzed its behavior at the onset of the epithelial to mesenchymal transition (EMT), a cellular transformation process essential during development and reactivated in cancer cells. Our results suggest that eLADs are dynamic and functional during EMT. Finally, Hi-C data during this cellular transformation showed changes in the frequency of chromatin contacts around the TSS in genes enriched in lamin B1 before the generation of new regulatory elements in the mesenchymal state. Taken together, these results demonstrate that not only heterochromatin but euchromatin is organized into lamin domains as well. Moreover, these eLADs are dynamic, functional and essential for chromatin organization and gene regulation during the EMT.

overall_design: List of ChIPseq samples (LaminB1 at 0h/8h/24h), ATACseq samples (at 0h/8h/24h), RNAseq samples (control at 0h/8h/24h and control/LaminB1 knock-down at 0h/8h/24h) and HiC samples (EMT transformation at 0h/8h/24h).

first: Laura

last: Pascual-Reguant

first: Marc

last: Marti-Renom

first: Luciano

last: DiCroce

first: Sandra

last: Peiro


title: The tumor suppressor menin prevents effector CD8 T cell dysfunction by targeting mTORC1-dependent metabolic activation [RNA-seq]

city: Toon

first: Junpei

last: Suzuki

address: Shitukawa

department: Graduate School of Medicine

country: Japan

institute: Ehime University

summary: While menin plays an important role in preventing T-cell dysfunction, such as senescence and exhaustion, the regulatory mechanisms remain unclear. We found that menin prevents the induction of dysfunction in activated CD8 T cells by restricting the cellular metabolism. mTOR complex 1 (mTORC1) signaling, glycolysis, and glutaminolysis are augmented by menin deficiency. Rapamycin treatment prevents CD8 T-cell dysfunction in menin-deficient CD8 T cells. Limited glutamine availability also prevents CD8 T-cell dysfunction induced by menin deficiency, and its inhibitory effect is antagonized by α-ketoglutarate (α-KG), an intermediate metabolite of glutaminolysis. α-KG-dependent histone H3K27 demethylation seems to be involved in the dysfunction in menin-deficient CD8 T cells. We also found that α-KG activates mTORC1-dependent central carbon metabolism. These findings suggest that menin maintains the T-cell functions by limiting mTORC 1 activity and subsequent cellular metabolism.

overall_design: Gene expression in normal conditions CD8T cells (WT-Ctrl and Menin KO-Ctrl) or glutamine deprived conditions CD8 T cells (WT-dGln, Menin KO-dGln CD8 T cells)

first: Masakatsu

last: Yamashita


title: Comparison of methylome data obtained with rPBAT and tPBAT.

status: Public on Aug 28 2018

city: Kashiwa

first: Fumihito

last: Miura

state: Chiba

address: Kashiwanoha 5-1-5

department: Graduate School of Frontier Sciences

institute: The University of Tokyo

type: Methylation profiling by high throughput sequencing

summary: To compare the difference of library preparation protocols for whole-genome bisulfite sequencing, two libraries were prepared from genomic DNA extracted from IMR90 cell with rPBAT and tPBAT. Two and tree lanes of HiSeq X Ten  were assigned for tPBAT and rPBAT libraries, respectively

overall_design: Two libraries for whole-genome bisulfite sequencing were prepared with rPBAT and tPBAT, then the library was loaded on HiSeq X Ten.


title: The tumor suppressor menin prevents effector CD8 T cell dysfunction by targeting mTORC1-dependent metabolic activation

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

overall_design: Refer to individual Series


title: Optimization of the input amount of library for whole-genome bisulfite sequencing on HiSeq X Ten

summary: To know the optimal amount of input library for HiSeq X Ten, the amount of input library was varied. Six lanes of sequencing on HiSeq X Ten was performed.

overall_design: A library for whole-genome bisulfite sequencing was prepared with an improved PBAT protocol, then the library was loaded on HiSeq X Ten.


title: Whole-transcriptome response to wastewater treatment plant and stormwater effluents in the Asian clam, Corbicula fluminea

city: Arcachon

first: Anthony

last: Bertucci

address: Place du Dr Peyneau

country: France

institute: University of Bordeaux

summary:
The increase in human population and urbanization are resulting
in an increase in the volume of wastewater and urban runoff effluents
entering natural ecosystems. These effluents may contain multiple
pollutants to which the biological response of aquatic organisms is still
poorly understood mainly due to mixture toxicity and interactions with
other environmental factors. In this context, RNA sequencing was used to
assess the impact of a chronic exposure to wastewater treatment plant and
stormwater effluents at the whole-transcriptome level and evaluate the
potential physiological outcomes in the Asian clam Corbicula fluminea.
We de-novo assembled a transcriptome from C. fluminea digestive gland and
identified a set of 3,181 transcripts with altered abundance in response
to water quality. The largest differences in transcriptomic profiles were
observed between C. fluminea from the reference site and those exposed to
wastewater treatment plant effluents. On both anthropogenically impacted
sites, most differentially expressed transcripts were involved in
signaling pathways in relation to energy metabolism such as mTOR and
FoxO, suggesting an energy/nutrient deficit and hypoxic conditions. These
conditions were likely responsible for damages to proteins and
transcripts in response to wastewater treatment effluents whereas
exposure to urban runoff might result in immune and endocrine
disruptions.
In absence of comprehensive chemical characterization, the RNAseq
approach could provide information regarding the mode of action of
pollutants and then be useful for the identification of which parameters
must be studied at higher integration level in order to diagnose sites
where the presence of complex and variable mixtures of chemicals is
suspected.

overall_design: 24 samples - From December 2015 to March 2016, 8 specimens were cagged on three sites (a reference site, dowstream a wastewater treatment plant and downstream a urban runoff effluent).

first: Fabien

last: Pierron

first: Christophe

last: Klopp

first: Patrice

last: Gonzalez

first: Magalie

last: Baudrimont

first: Pierre-Yves

last: Gourves

first: Gauthier

last: Lagarde

first: Clément

last: Pereto

first: Vincent

last: Dufour

first: Alexandra

last: Coynel

first: Helene

last: Budzinski


title: Inhibition of endothelial Notch signaling attenuates inflammation

first: Guttorm

last: Haraldsen

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Androgen receptor functions as transcriptional repressor of Cancer Associated Fibroblast (CAF) activation [ChIP-seq]

city: Biella

first: Paola

last: Ostano

address: via Malta 3

country: Italy

institute: Fondazione Edo ed Elvo Tempia

summary: The age-associated increase of cancer risk has been linked with stromal fibroblast senescence and early steps of Cancer Associated Fibroblast (CAF) activation. Surprisingly little is known about the role of androgen receptor (AR) signalling in this context. We show that AR expression is down-modulated in stromal fibroblasts underlying premalignant skin cancer lesions (actinic keratoses, AK) as well as in CAFs from the three major skin cancer types, squamous (SCC) and basal cell (BCC) carcinomas and melanomas. Decreased AR expression is linked to the concomitant down-modulation of CSL, key effector of canonical Notch signalling and global modulator of chromatin configuration, and it can be counteracted by treatment with BET inhibitors, which reverse CAF activation. Functionally, AR gene silencing in dermal fibroblasts results in p53-dependent senescence and induction of key CAF-effector genes, with AR physically converging with CSL in negative control of these genes. The findings are of functional significance as, in an orthotopic model of skin cancer, dermal fibroblasts with AR loss enhance significantly tumorigenicity of SCC and melanoma cells. As such, the findings establish AR as a novel potential target for stroma-focused cancer prevention and treatment.

overall_design: Chip tagmentation was carried out as in (Kim et al. 2017) using endogenous AR antibody in human dermal fibroblasts (HDFs)

first: Andrea

last: Clocchiatti

first: Soumitra

last: Ghosh

first: Maria-Giuseppina

last: Procopio

first: Luigi

last: Mazzeo

first: Pino

last: Bordignon

first: Sandro

last: Goruppi

first: Giulia

last: Bottoni

first: Mitchell

last: Levesque

first: Reinhard

last: Dummer

first: Victor

last: Neel

first: Berna

middle: C

last: Özdemir

first: Gian

middle: P

last: Dotto


title: Androgen receptor functions as transcriptional repressor of Cancer Associated Fibroblast (CAF) activation [RNA-seq]

overall_design: RNA-seq analysis of two HDFs strains plus/minus AR silencing

last: C. Özdemir


title: Androgen receptor functions as transcriptional repressor of Cancer Associated Fibroblast (CAF) activation


title: Transcriptome analysis of fetal Klinefelter testis tissue samples compared to controls

city: Copenhagen

first: Kristian

last: Almstrup

address: Blegdamsvej 9, Section GR-5064

department: Dept. of Growth and Reproduction

country: Denmark

institute: Rigshospitalet, Copenhagen University Hospital

summary: In humans, the most common sex chromosomal disorder is Klinefelter syndrome (KS), caused by the presence of one or more extra X-chromosomes. The KS patients display a diverse adult phenotype with increased height, gynaecomastia, and hypergonadotropic hypogonadism as the most common symptoms. Men with KS are almost always infertile due to testicular degeneration, which accelerates during puberty. Very few studies investigated when the germ cell loss begins and whether it is caused by dysgenetic fetal development of the testes. We investigated a series of fetal KS testis tissue samples and found a marked reduction in MAGE-A4-positive pre-spermatogonia in the developing KS gonads compared to controls, indicating a failure of the gonocytes to differentiate into pre-spermatogonia. Transcriptome analysis by RNA sequencing of formalin-fixed and paraffin embedded gonads originating from 4 fetal KS samples and 5 age- and cellularity-matched controls revealed 211 differentially expressed transcripts in the fetal KS testis. We found a significant enrichment of upregulated X-chromosomal transcripts and validated the expression of the pseudoautosomal region 1 (PAR1) gene, AKAP17A. Moreover, we found enrichment of long non-coding RNAs in the KS testes (e.g. LINC01569 and RP11-485F13.1). In conclusion, our data indicates that the testicular phenotype observed among adult men with KS is initiated already in fetal life by failure of the gonocyte differentiation into pre-spermatogonia, which could be due to aberrant expression of long non-coding RNAs.

overall_design: Includes a total of 9 samples. 4 fetal Klinefelter and 5 age-matched controls testis samples

first: Sofia

middle: B

last: Winge

first: Marlene

middle: D

last: Dalgaard

first: Jacob

middle: M

last: Jensen

first: Niels

last: Graem

first: Mikkel

last: Schierup

first: Anders

last: Juul

first: Ewa

middle: R

last: Meyts


title: microRNA-seq of TPR50 Tau P301S Transgenic Mouse in different brain regions and time-points

city: Irvine

first: Vivek

last: Swarup

state: CALIFORNIA

address: 3400 Bio Sci 3

department: Neurobiology and Behavior

country: USA

institute: University of California Irvine

type: Non-coding RNA profiling by high throughput sequencing

summary: Purpose: The goal of this study was to assess miRNA expression changes in TPR50 Tau transgenic mice. The mice was backcrossed with 2 divergent mouse strains - DBA and FVB along with the parent C57BL6 strain. The resulting F1 hybrids were used for further analysis.

overall_design: Brain samples from F1 hybrids were isolated and falsh frozen. RNA was isolated using miRNeasy kit and RNA-seq was performed using standard Illumina kit for small RNA sequencing

first: Daniel

last: Geschwind


title: RNA-seq of FACS sorted neurons overexpressing miR-203 in wild-type mice

summary: Purpose: The goal of this study was to assess gene expression changes in neurons overexpressing miR-203 in mouse frontal cortex.

overall_design: Methods: 4-6 mice were infected in frontal cortex using bilateral sterotaxis injection with AAV2/9 either overexpressing miR-203 or scrambled miRNA. The expression of AAV2/9 was restricted to neurons using synapsin promoter. 3 or 6-weeks after infection, cortex was isolated and mononuclear suspension was made using papain digestion kit. GFP+ve neurons were sorted and RNA isolated using Clontech kit and 50bp paired-end libraries were prepared using SMARter Stranded Total RNA V4 ultra low sample prep kit (Clontech). Libraries were then multiplexed and sequenced with HiSeq 4000 instrument (Illumina).

first: Geschwind

last: Daniel. H


title: Genome-wide maps of chromatin state in interferon stimulated cells

city: Sapporo

first: Rui

last: Kamada

address: N10 W8, Kita-ku

department: Department of Chemistry, Faculty of Science

institute: Hokkaido University

summary: We have analyzed epigenetic state of interferon stimulated cells and found that histone H3.3 and H3K36me3 chromatin marks were increased to regulate transcriptional memory.

overall_design: Examination of 6 different histone modifications and RNA polymerase II deposition in 2 cell types.

first: Keiko

last: Ozato


title: Next Generation Sequencing Facilitates Quantitative Analysis of interferon stimulated MEFs Transcriptomes [RNA-Seq]

summary: Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived interferon-stimulated MEF cells transcriptome profiling (RNA-seq).

overall_design: mRNA profiles of interferon stimulated MEF cells derived from H3.3-HA knock-in mice were generated by deep sequencing, using Illumina HiSeq2000


title: Identification of evolutionary conserved gene networks that mediate neurodegenerative dementia


title: Microarray analysis of interferon stimulated bone-marrow derived macrophages Transcriptomes

summary: We used global microarray analysis to identify genes which are regulated by Interferon-gamma stimulation in Bone-marrow derived macrophages.

overall_design: mRNA expression profiles of interferon stimulated bone-marrow deribed macrophages derived from H3.3-HA knock-in mice were generated by macroarray analysis


title: Interferon stimulation creates chromatin marks to establish transcriptional memory


title: RNA-seq of TPR50 Tau P301S Transgenic Mouse in different brain regions and time-points

summary: Purpose: The goal of this study was to assess gene expression changes in TPR50 Tau transgenic mice. The mice was backcrossed with 2 divergent mouse strains - DBA and FVB along with the parent C57BL6 strain. The resulting F1 hybrids were used for further analysis.

overall_design: Brain samples from F1 hybrids were isolated and falsh frozen. RNA was isolated using miRNeasy kit and RNA-seq was performed using unstranded Illumina poly-A library prep kit.


title: The microARN-202 (miR-202) controls female fecundity by regulating oogenesis in medaka

status: Public on Aug 27 2018

city: Rennes

first: Aurelie

last: LE CAM

address: Campus de Beaulieu

department: PHASE

institute: INRA

summary: In fish, female fecundity is tightly linked to the proper completion of oogenesis that takes place in the ovary. These cellular processes have been shown to involve both endocrine and intra-ovarian factors. However, the role of small non-coding miRNAs remains largely unknown. Here, we analyzed the role of miR-202, a miRNA specifically expressed in the vertebrate gonads. We first used fluorescent in situ hybridization to determine the precise cellular expression of miR-202 in the medaka ovary. We then generated a mutant fish line (using CRISPR/Cas9 technology) to determine its role in female fecundity and oogenesis. We performed quantitative image analyses to analyze cellular modifications and a genome-wide transcriptomic approach to analyze gene expression modifications. Our results show that miR-202-5p is predominantly expressed in granulosa cells. In addition, mutant females display a drastically reduced fecundity. Our cellular and molecular analyses of ovaries from mutant females indicate that miR-202 deficiency impairs the early steps of oogenesis/folliculogenesis, which ultimately reduce female fecundity. This provides the first functional evidence that miR-202 is necessary for the female reproductive success, in particular the female fecundity, and shed new light on the regulatory mechanisms that control the early steps of follicular development.

overall_design: Expression profiling of ovary from wild-type female and miR202 knock-out female

first: Stéphanie

last: Gay

first: Jérôme

last: Bugeon

first: Amine

last: Bouchareb

first: Laure

last: Henry

last: Montfort

first: Aurélie

last: Le Cam

first: Julien

last: Bobe

first: Violette

last: Thermes


title: A novel long non-coding RNA HOXC-AS3 mediates tumorigenesis of gastric cancer by binding to YBX1

status: Public on Aug 26 2018

city: nanjing

first: wei

last: de

state: jiangsu

address: longmian da dao

department: Department of Biochemistry and Molecular Biology

country: China

institute: Nanjing Medical University

summary: Recently, increasing evidence shows that long noncoding RNAs (lncRNAs) play a significant role in human tumorigenesis. However, the function of lncRNAs in human gastric cancer remains largely unknown.  By using publicly available expression profiling data from gastric cancer and integrating bioinformatics analyses, we screen and identify a novel lncRNA, HOXC-AS3. HOXC-AS3 is significantly increased in gastric cancer tissues and is correlated with clinical outcomes of gastric cancer. In addition, HOXC-AS3 regulates cell proliferation and migration both in vitro and in vivo. RNA-seq analysis reveals that HOXC-AS3 knockdown preferentially affects genes that are linked to proliferation and migration. Mechanistically, we find that HOXC-AS3 is obviously activated by gain of H3K4me3 and H3K27ac, both in cells and in tissues. RNA pull down-mass spectrometry analysis identifies that YBX1 interacts with HOXC-AS3, and RNA-seq analysis finds a marked overlap in genes differentially expressed after YBX1 knockdown and those transcriptionally regulated by HOXC-AS3, suggesting that YBX1 participates in HOXC-AS3-mediated gene transcriptional regulation in the tumorigenesis of gastric cancer.Together, our data demonstrate that abnormal histone modification-activated HOXC-AS3 may play important roles in gastric cancer oncogenesis and may serve as a target for gastric cancer diagnosis and therapy.

overall_design: RNA-seq analysis of HOXC-AS3 and YBX1 knockdown in one cell type

first: Erbao

last: Zhang

first: Dandan

last: Yin

first: Liang

last: Han

first: Wei

last: De


title: DNA methylomes and RNA transcriptomes in 19-weeks-old CD-1 male epididymal white adipose tissues with or without prenatal exposure to 500 ug/kg/day Bisphenol A

city: Charlestown

first: Toshihiro

last: Shioda

state: MA

address: Building 149 - 7th Floor, 13th Street

department: Center for Cancer Research

institute: MGH Cancer Center

summary: Exposure of mammalian fetuses to endocrine disruptors can increase the risk of adult-onset diseases. For example, we previously showed that exposure of mouse fetuses to bisphenol A (BPA) caused adult-onset obesity. To obtain insights into roles of epigenetic changes in the delayed toxic effects of endocrine disruption, we determined effects of fetal mouse exposure to BPA on genome-wide DNA methylation and mRNA expression in gonadal white adipose tissues by deep sequencing (MBD-seq and RNA-seq), bisulfite pyrosequencing, and real-time qPCR. Pregnant CD-1 mice (F0) were dosed daily with 0, 5, or 500 ug/kg/day BPA during 9-18 dpc, and the weaned F1 animals were fed ad libitum with standard chow until they were sacrificed at 19 weeks old. In the vehicle-exposed F1 animals, fggy promoter showed a clear bimodal pattern of very strong (55-95%) or very weak (5-30%) DNA methylation occurring at nearly equal incidence with no intermediate strength, and promoter hypermethylation completely suppressed mRNA expression. BPA exposure eliminated this naturally occurring dichotomy, shifting fggy promoter towards the hypomethylation state to release transcriptional suppression. Strength of Fggy mRNA expression significantly correlated with increased whole-body weight and gonadal fat weight of males but not females. Bioinformatics studies showed that expression of Fggy mRNA is stronger in mouse white adipose tissues than brown adipose tissues and enhanced in gonadal fat by diet-induced obesity. These observations suggest that prenatal exposure to BPA may disrupt the physiological bimodal nature of epigenetic regulation of fggy in mouse white adipose tissues, possibly contributing to the adult-onset obesity phenotype.

overall_design: Pregnant CD-1 females were exposed to 500 ug/kg/day Bisphenol A or vehicle (oil), and their male fetuses were grown until 19 weeks after birth, when epididymal fat was collected for deep sequencing determination of DNA methylomes (MBD-seq) and RNA transcriptomes (RNA-seq).

first: Julia

middle: A

last: Taylor

first: Shino

last: Mitsunaga

first: Shiomi

last: Yawata

first: Brittany

last: Angle

first: Susan

last: Nagel

first: Frederick

middle: S

last: vom Saal


title: Single cell RNA-sequencing reveals the existence of naïve and primed pluripotency in pre-implantation rhesus monkey embryos [95 cells]

city: Shanghai

first: Denghui

last: Liu

state: Shanghai

address: ShengLi Building, 320 Yueyang Road

institute: CAS-MPG Partner Institute for Computational Biology (PICB)

summary: To explore the dynamic change of transcriptome in pre-implantation of rhesus monkey, we collected single cells for RNA-sequencing.

overall_design: We collected 95 single cells from rhesus monkey early embryos encompassing the stages of 16-cell, early morula, late morula, early blastocyst, middle blastocyst, late blastocyst and hatched blastocyst. 95 single cells were sequenced in total.

first: Xinyi

last: Wang

first: Dajian

last: He


title: Single cell RNA-sequencing reveals the existence of naïve and primed pluripotency in pre-implantation rhesus monkey embryos


title: Unique microglia recovery population revealed by single-cell RNAseq following neurodegeneration

status: Public on Aug 25 2018

city: Freiburg

first: Sagar

address: Hugstetter Straße 55

department: Department of Internal Medicine II

country: Germany

institute: University Medical Center Freiburg

summary: Microglia are brain immune cells that constantly survey their environment to maintain homeostasis. Enhanced microglial reactivity and proliferation are typical hallmarks of neurodegenerative diseases. Whether specific disease-linked microglial subsets exist during the entire course of neurodegeneration, including the recovery phase, is currently unclear. Taking a single-cell RNA-sequencing approach in a susceptibility gene-free model of nerve injury, we identified a microglial subpopulation that upon acute neurodegeneration shares a conserved gene regulatory profile compared to previously reported chronic and destructive neurodegeneration transgenic mouse models. Our data also revealed rapid shifts in gene regulation that defined microglial subsets at peak and resolution of neurodegeneration. Finally, our discovery of a unique transient microglial subpopulation at the onset of recovery may provide novel targets for modulating microglia-mediated restoration of brain health.

overall_design: scRNA-Seq was performed on microglial cells isolated from the ipsilateral and contralateral ventral pons of CX3CR1GFP/wt mice that underwent unilateral facial nerve axotomy at 12 weeks of age. The contralateral ventral pons of un-operated 12-week-old CX3CR1GFP/wt was used as baseline control (Day 0 post nerve transection) for the analysis. Three replicates were used per time point (Day 0, 7 and 30 post axotomy). mCEL-Seq2 protocol was used for single cell sequencing (Hashimshony et al. 2016, Herman et al. 2018).

first: Tuan

middle: L

last: Tay

last: Sagar

first: Dominic

last: Grün

first: Marco

last: Prinz


title: AUXIN RESPONSE FACTOR3 Integrates the Functions of AGAMOUS and Auxin to Repress Cytokinin Biosynthesis and Signaling in Floral Meristem Determinacy

status: Public on Aug 24 2018

first: Renyi

address: 3888 Chenhua Road

department: Bioinformatics

institute: Shanghai Center for Plant Stress Biology

summary: Successful floral meristem (FM) determinacy is critical for the subsequent reproductive development and life cycle. Although phytohormones cytokinin and auxin interact to coordinately regulate many aspects of plant development, whether, if so how, cytokinin and auxin function in FM determinacy remain unclear. Here we show that the homeostasis of cytokinin is critical for the FM determinacy. Auxin promotes the expression of AUXIN RESPONSE FACTOR3 (ARF3) to repress cytokinin activity in FM determinacy. We found that ARF3 represses the expression of the ISOPENTENYLTRANSFERASE (IPT) family genes directly and the LONELY GUY (LOG) family genes indirectly, whose products are enzymes required for cytokinin biosynthesis. Furthermore, ARF3 directly inhibits the expression of ARABIDOPSIS HISTIDINE KINASE4 (AHK4), one of cytokinin receptor genes, to depress cytokinin activity. Genome-Wide Transcriptional Profiling reveals multiple functions of ARF3 in flower development. Consequently, ARF3 controls cell division by regulating cell cycle genes expression through cytokinin. Eventually, we show that AGAMOUS (AG) dynamically regulates the expression of ARF3 and IPTs resulting in coordinated regulation of FM maintenance and termination through cell division. Therefore, our findings reveal the molecular linkage between phytohormones auxin/cytokinin and AG in FM determinacy and shed light on the mechanisms of FM maintenance and termination.

overall_design: mRNA profiles of inflorescences containing stage 6 and younger flowers of ARF3:ARF3-GR arf3-29 treated with DMSO or DEX

first: Xigang


title: Identification of Glucocorticoid-Induced Leucine Zipper (Gilz) gene targets in undifferentiated spermatogonia

city: CLAYTON

first: Robin

middle: Mark

last: Hobbs

state: VIC

address: 27-31 Wright Street

department: Centre for Reproductive Health

country: Australia

institute: Hudson Institute of Medical Research

summary: Sustained spermatogenesis in adult males and recovery of fertility following germ cell depletion are dependent on undifferentiated spermatogonia with self-renewal potential. We have previously demonstrated a critical cell-autonomous role for Gilz in spermatogonial stem cell maintainance and spermatogenesis. To identify genes regulated by Gilz in the male germline, we have isolated undifferentiated spermatogonial cells from tamoxifen treated Gilzflox/flox (Control) and Gilzflox/flox UBC-CreER (TAM-KO) mice that will allow identification of genes mis-expressed upon loss of GILZ.

overall_design: 4 independent sets of Gilzflox/flox (Control) and Gilzflox/flox UBC-CreER (TAM-KO) undifferentiated spermatogonia were isolated by flow sorting from adult mouse testes 7 days after treatment with tamoxifen.

first: Hue

last: La

first: Ai-Leen

last: Chan

first: Julien

last: Legrand


title: Regulators of cellular heterogeneity in basal-like breast cancer influence symmetric versus asymmetric division rates (shRNA targeting)

city: Jerusalem

first: Ittai

last: Ben-Porath

address: Ein-Kerem

department: Department of Developmental Biology and Cancer Research

country: Israel

institute: The Hebrew University Faculty of Medicine

summary: Differentiation events contribute to cellular heterogeneity within tumors and influence disease progression and response to therapy. Here we dissect the mechanisms controlling intratumoral heterogeneity within basal-like breast cancers. We show that cancer cells can transition between a differentiation state related to that of normal luminal progenitors and a state closer to that of mature luminal cells, and that this occurs through asymmetric cell divisions. The Polycomb factor EZH2 and the Notch pathway act to increase the rates of symmetric divisions that produce progenitor-like cells, while the FOXA1 transcription factor promotes asymmetric divisions that reduce the numbers of such cells. Through functional screening, we identified a group of regulators that control cancer cell differentiation state and the relative proportions of tumor cell subpopulations. Our findings highlight the regulation of asymmetric cell divisions as a mechanism controlling intratumoral heterogeneity, and identify molecular pathways that control breast cancer cellular composition.

overall_design: Expression profiles of HCC70 cells expressing shRNAs targeting regulatory factors that influence basal-like cancer cell population composition

first: Roy

middle: Z

last: Granit


title: Quantification of mouse retinal enhancer activity by massively parallel reporter assay

city: St. Louis

first: Joseph

last: Corbo

address: 660 S. Euclid

institute: Washington University School of Medicine

summary: Cone-rod homeobox (CRX) is a paired-like homeodomain transcription factor (TF) and a master regulator of photoreceptor development in vertebrates. The in vitro DNA binding preferences of CRX have been described in detail, but the degree to which in vitro binding affinity is correlated with in vivo enhancer activity is not known. In addition, paired-class homeodomain TFs can bind DNA cooperatively as both homodimers and heterodimers at inverted TAAT half-sites separated by two or three nucleotides. This dimeric configuration is thought to mediate target specificity, but whether monomeric and dimeric sites encode distinct levels of activity is not known. Here, we use a massively parallel reporter assay, CRE-seq, to determine how local sequence context shapes the regulatory activity of CRX binding sites in mouse photoreceptors. We assay inactivating mutations in >1700 TFBSs, and we find that dimeric CRX binding sites act as stronger enhancers than monomeric CRX binding sites. Furthermore, the activity of dimeric half-sites is cooperative, dependent on a strict three-base-pair spacing, and tuned by the identity of the spacer nucleotides. Saturating single-nucleotide mutagenesis of 195 CRX binding sites shows that, on average, changes in TFBS affinity are correlated with changes in regulatory activity, but this relationship is obscured when considering mutations across multiple CREs. Taken together, these results demonstrate that the activity of CRX binding sites is highly dependent on sequence context, providing insight into photoreceptor gene regulation and illustrating functional principles of homeodomain binding sites that may be conserved in other cell types.

overall_design: CRE-seq of mouse retinal explants. 100,000 100-bp target seqeunces were cloned upstream of a photoreceptor promoter (either pRho or pCrx) driving a DsRed reporter harboring CRE-specific 13-bp barcodes in the 3' UTR. This library was electroporated into intact retinas from newborn (P0) mice. Retinas were grown in culture for eight days, at which point RNA and DNA were harvested and barcodes were amplifieid and sequenced to quantify enhancer activity. Each biological replicate consisted of five electroporated retinas, and three biological replicates were performed for each condition (assaying constructs on either pRho or pCrx).

first: Andrew

middle: E

last: Hughes

first: Connie

last: Myers


title: Regulators of cellular heterogeneity in basal-like breast cancer influence symmetric versus asymmetric division rates (Expression profiles)

overall_design: Expression profiles of three cell subpopulations – K18+, K18+K14+ and K18+Vim+ – sorted from the breast cancer cell lines HCC70 and MDA-MB-468


title: Functional Characterization of Diabetes-Induced long non-coding RNA Dnm3os   in Macrophages

status: Public on Aug 23 2018

city: Duarte

first: Rama

last: Natarajan

address: 1500 E Duarte Road

institute: City of Hope

summary:
Objective: Macrophages play key roles in inflammation and diabetic vascular complications. Emerging evidence implicates long noncoding RNAs (lncRNAs) in inflammation, but their role in macrophage dysfunction associated with inflammatory diabetic complications is unclear and was therefore investigated in this study.

Approach and Results: RNA-sequencing and RT-qPCR demonstrated that a lncRNA Dynamin 3 opposite strand (Dnm3os) is upregulated in bone marrow derived macrophages from type2 diabetic (T2D) db/db mice, diet-induced insulin-resistant mice and diabetic ApoE-/- mice, as well as in monocytes from T2D patients relative to controls. Diabetic conditions (High glucose and palmitic acid) induced Dnm3os in mouse macrophages and THP1 human monocytes. Promoter reporter analysis and chromatin-immunoprecipitation (ChIP) assays demonstrated that diabetic conditions induce Dnm3os via NF-kB activation. RNA-FISH and RT-qPCRs of sub-cellular fractions demonstrated nuclear localization and chromatin enrichment of Dnm3os in macrophages. Stable overexpression of Dnm3os in macrophages altered global histone modifications and upregulated inflammation and immune response genes, and phagocytosis. Conversely, siRNA mediated knockdown of Dnm3os attenuated these responses. RNA pull-down assays with macrophage nuclear lysates identified nucleolin and ILF-2 as protein binding partners of Dnm3os, which was further confirmed by RNA-IP and RNA-FISH-immunofluorescence. Furthermore, nucleolin levels were decreased in diabetic conditions, and its knockdown enhanced Dnm3os-induced inflammatory gene expression and histone H3K9-acetylation at their promoters.

Conclusions: These results demonstrate novel mechanisms involving upregulation of lncRNA Dnm3os, disruption of its interaction with nucleolin, and epigenetic modifications at target genes that promote macrophage inflammatory phenotype in diabetes. The data could lead to lncRNA-based therapies for inflammatory diabetes complications.

overall_design: Performed RNA-seq analysis from stably expressing Dnm3os and Empty Vector (pcDNA 3.1(+) in duplicates in RAW macrophages

first: Sadhan

last: Das

first: Parijat

last: Senapati

first: Marpadga

last: Reddy


title: Chromatin de-condensation by switching substrate elasticity

status: Public on Aug 22 2018

city: Strasbourg

first: Jean-Noel

last: FREUND

address: 3 avenue Molière

institute: Inserm

summary: The mortality in cancer is mostly related to the development of metastases that colonize and comprise the function of vital organs. During the process of dissemination to form metastases, tumor cells face changing environments. Although the consequences of the changes in chemical environment have widely been investigated, much less is known about the effects of the physical changes. We have developed a culture model in which human colon cancer cells have been recurrently grown on soft substrates versus standard rigid substrates. The soft substrates induce several phenotypic changes like the increase of cell motility and the remodeling of chromatin structure. The aim was to investigate, by RNAseq, the changes in global gene expression induced in cells grown on soft versus rigid substrates.

overall_design: Compare gene expression in human colon cancer cells (SW480) grown on soft versus rigid substrate

last: Freund


title: RNAseq data from SCCOHT1 and OVCAR8 ovarian cancer cells treated with BET inhibitors

city: Montreal

first: Michael

last: Witcher

state: QC

address: 3755 Chemin de la Cote Ste-Catherine

country: Canada

institute: Lady Davis Institut

summary: The antitumor activity of bromodomain inhibitors (BETi) has been demonstrated across numerous types of cancer. As such, these inhibitors are currently undergoing widespread clinical evaluation. However, predictive biomarkers allowing the stratification of tumors into responders and non-responders to BETi are lacking. Here, we show significant anti-proliferative effects of BETi in vitro and in vivo against aggressive SCCOHT1 ovarian cancer models lacking the SWI/SNF-related, SMARCA4 protein . Transcriptomic analysis revealed that exposure to BETi potently down-regulated the oncogenic receptor tyrosine kinase HER3 in SCCOHT1 but not in resistant OVCAR8 cells. Repression of this pathway is found to be an important determinant of response to BETi in cells harboring a loss of SMARCA4. Overall, we propose that BETi represent a rational therapeutic strategy in poor prognosis, SMARCA4 deficient cancers.

overall_design: Analysis of mRNA profile of 2 cell lines exposed to DMSO, OTX015 for 4 and 24 hours in duplicate

first: Tatiana

last: Shorstova

first: Maud

last: Marques


title: Chd5 regulates a ribosome biogenesis switch controlling neural cell fate specification

city: Cold Spring Harbor

first: Dong-Woo

last: Hwang

state: NY

address: 1 Bungtown Rd

department: Cancer Center

institute: Cold Spring Harbor Laboratory

summary: Cell fate specification of neural stem/progenitor cells (NSCs) is an intricate developmental process that determines neural cell identity. While transcriptional mechanisms undoubtedly affect this process, translational mechanisms are much less understood. Here we show that deficiency of the chromatin remodeler Chromodomain Helicase DNA binding protein 5 (Chd5) causes transcriptional de-repression of multiple ribosomal subunit genes, increases protein synthesis, and expands the activated stem cell pool leading to perturbation of NSC fate. Compromised H3K27me3 in Chd5 deficient NSCs during early cell fate specification underlies the generation of excessive astrocytes at the expense of neurons at later stages of differentiation. Chd5 expression rescues these cell fate defects while simultaneously reestablishing H3K27me3, and inhibition of the H3K27me3-specific demethylase Utx restores appropriate cell fate specification in NSCs lacking Chd5. These findings define a Chd5-Utx-H3K27me3 axis pivotal in ribosome biogenesis and translation during neurogenesis, consistent with compromised CHD5 being implicated in glioma.

overall_design: mRNA profiles of primary neural/stem progenitor cells (NSCs) of wild type (+/+) and Chd5-/- mice were generated, in duplicate, using Illumina NextSeq 500.

first: Alea

last: Mills


title: Effect of green tea extract on systemic metabolic homeostasis in diet-induced obese mice; based on RNA-sequencing transcriptome profiles

city: Gwangju

first: Ji-Young

last: Choi

address: 30, Chosundae 3-gil, Dong-gu

department: Food and Nutrition

country: South Korea

institute: Chosun University

summary: We investigated the effect of green tea extract on phenotype characteristics and elucidated anti-obesity mechanism based on RNA-seq transcriptomic profiles in an obesity animal model.

overall_design: Total RNA of epididymal adipose tissues and liver were obtained from normal diet, high-fat diet and green tea extract added high-fat diet-fed mice and mRNA expression-associated with lipid, and glucose metabolism was measured.

first: Myung-Sook


title: A Novel Class of MicroRNA Recognition Elements That Function Only in Open Reading Frames

status: Public on Aug 21 2018

city: La Jolla

first: Xiang-Dong

last: Fu

state: CA

address: 9500 Gilman Drive, Room 231

department: CMM

institute: UC San Diego

summary: MicroRNA (miRNA) are well known to target 3’ untranslated regions (3’UTR) in mRNAs to silence gene expression at post-transcriptional levels. Multiple reports have also indicated the capability of miRNAs to target protein-coding sequences (CDS); however, miRNAs have been generally believed to function in a similar mechanism(s) regardless of the location of their action sites. We herein report a class of miRNA recognition elements (MREs) that exclusively function in CDS regions in humans. Through functional and mechanistic characterization of these “unusual” MREs, we demonstrate that CDS-targeted miRNAs require extensive base pairings in the 3’ side rather than the 5’ seed; cause gene silencing in an Argonaute-dependent, but GW182-independent manner; and repress translation by inducing transient ribosome stalling instead of mRNA destabilization. These findings reveal distinct mechanisms and functional consequences for miRNAs to target CDS versus 3’UTR and suggest that CDS-targeted miRNAs may enlist a translational quality control (QC)-related mechanism to regulate translation in mammalian cells.

overall_design: Ago2 eCLIP-seq, RNA-seq, and Ribo-seq w/o miR-17/20a overexpression

first: Kai

last: Zhang

first: Jie

last: Zhou

first: Xiaorong

first: Yu


title: Regulation of cellular heterogeneity and rates of symmetric and asymmetric divisions in triple-negative breast cancer

first: Ittai

last: Ben-Porath

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

overall_design: Refer to individual Series


title: Rapid functional genetics of the oligodendrocyte lineage using pluripotent stem cells

city: Cleveland

first: Paul

last: Tesar

state: Ohio

address: 10900 Euclid Ave.

department: Genetics & Genome Sciences

institute: Case Western Reserve University

summary: Oligodendrocyte dysfunction underlies many neurological disorders but rapid assessment of mutation-specific effects in these cells has been impractical. To enable functional genetics in oligodendrocytes, here we report a highly efficient method for generating oligodendrocytes and their progenitors from mouse embryonic and induced pluripotent stem cells, independent of mouse strain or mutational status. We demonstrate that this approach, when combined with genome engineering, provides a powerful platform for the expeditious study of genotype-phenotype relationships in oligodendrocytes.

overall_design:
Cells were lysed directly in 1 ml of TRIzol (Thermo Fisher) and stored at -80°C. Once all samples were collected, samples were thawed on ice and RNA was separated with chloroform using Phase Lock Gel tubes (5prime). RNA was isolated using the miRNeasy Mini Kit (Qiagen) according to the manufacture’s protocol. One microgram of each sample was then subject to ribosome depletion, fragmented, and library prepared using the TruSeq Stranded Total RNA Kit with Ribo Zero Gold (Illumina) according to the manufacturer’s protocol and indexed using TruSeq adapters. One hundred base pair paired-end reads were generated for each sample on the Illumina HiSeq 2500 (Case Western Reserve University Sequencing Core; Cleveland, OH).

Samples include mESC derived oligodendrocyte progenitor cells (OPCs) from four different wildtype mouse strains at 0 hr, 24, hr, 48 hr, and 72 hr after treatment with thyroid hormone T3 (n = 4 biological replicates per time point). Two additional samples include mutant OPCs (shiverer and MYRF knockout 'delMYRF') at 72 hr time point.

first: Angela

last: Lager

middle: J


title: TempO-Seq S1500+ Platform Gene Expression of Rat Liver Mode of Action Samples

city: RTP

first: Pierre

middle: Robert

last: Bushel

state: NC

department: Biostatistics and Computational Biology Branch

institute: NIEHS

summary: Using the TempO-Seq rat S1500+ platform we performed  gene expression analysis of using 63 purified RNA samples from the livers of rats exposed to controls or chemicals that fall into one of five modes of action (MOAs): constitutive androstane receptor/pregnane X receptor (CAR/PXR) activation, aryl hydrocarbon receptor (AhR) activation, peroxisome proliferator-activated receptor-alpha (PPARA) activation, cytotoxicity or DNA damage.  The TempO-Seq data generated was used to compare to gene expression data acquired from the same samples run on Affymetrix microarays (GEO: GSE47875) and Illumina RNA-Seq (GEO: GSE55347, SRA:SRP039021).

overall_design: Male Sprague-Dawley rats (aged 6–8 weeks and weighing 200–260 g) were dosed once daily in triplicate for 3, 5, or 7 days, depending on the test chemical, and livers were harvested 24 hours after the last dose.  MOA samples, preparation of them and RNA extraction  are as previously described (Wang et al., 2014, PMID: 25150839).  For each of the five MOAs there were three test chemicals.

first: Scott

last: Auerbach

first: Richard

last: Paules


title: RNAseq of wildtype and deletion mutants (H3.V KO, H4.V KO, H3.V/H4.V KO)

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

institute: ZB MED - Information Centre for Life Sciences

summary: RNA was extraced from wildtype and deletion mutants and a comparative analysis of gene expression was performed using DESeq2.

overall_design: Total RNA from 45 million cells was extracted in triplicates, spiked with a synthetic RNA control. RNA was depleted for rRNA using custom-made anti-rRNA oligonucleotides that hybridize to the target RNAs and are subsequently digested with RNAseH. RNA was reverse transcribed into cDNA and libraries for Illumina sequencing were constructed. We aimed at 15 million reads for each replicate. Comparative expression analysis was performed using DeSeq2.

first: Laura

last: Müller

first: T

middle: N

last: Siegel

middle: U


title: RNA-seq Analysis of MoBHLH6-dependent Genes in Magnaporthe oryzae 70-15

city: Hangzhou

first: Jianping

last: Lu

state: Zhejiang

address: 866 Yuhantang Road

department: College of Life Sciences

institute: Zhejiang University

summary:
Purpose: The goals of this study are to find out the genes regulated directly or indirectly by bHLH protein MoBhlh6 (Crf1) by RNA-seq in the rice blast fungus
Methods: Mycelial mRNAs of the wild type strain 70-15, ΔMobhlh6 incubated in H2O at 25˚C for 4 h, in triplicate independently for each strain, were extracted and isolated by RNeasy Plant mini kit (QIAGEN) and AMPure XP beads (Beckman). RNA-sequencing libraries were constructed using NEBNext RNA sample preparation kit (NEB). Samples were sequenced in a 1 x 100 nt way on Illumina Hiseq2500 instrument using TruSeq PE Cluster Kit v3 - cBot - HS (Illumina) and TruSeq SBS Kit v3-HS (Illumina).The M. oryzae genome database (MG8) (www.broadinstitute.org) was used as a reference gene database. Genome-wide transcript levels of genes were quantified in fragments per kilobase of exon model per million mapped reads (FPKM) (Trapnell 2010). Gene Ontology (GO) enrichment analyses for differentially expressed genes were performed using hypergeometric test with topGO, and p-values were adjusted with Bonferroni for multiple testing (Alexa 2006). And we selected FDR < 0.05 as enrichment terms.
Results and Conclusions: We identified 3603 genes regulated by MoBhlh6 through RNA-seq.

overall_design: Mycelial mRNA profiles of wild type strain 70-15 (WT), ΔMobhlh6 incubated in H2O for 4 h were generated, in biologic triplicate, by Illumina Hiseq2500 in a 1 x 100 nt way

first: Jian

first: Hui

last: Cao

first: Li

first: Peng

middle: Y

last: Huang

first: Fu

middle: C

last: Lin


title: Effect of influenza infection on genome structure in human primary cells [Hi-C]

first: Max

last: Chang

address: 9500 Gilman Drive

institute: University of California, San Diego

summary: Hi-C was used to profile changes in the genome structure of human primary cells at multiple time points in response to infection with active and UV-inactivated H5N1 influenza virus. Human tracheobronchial epithelial cells (HTBE) and monocyte-derived macrophages (MDM) were used. The Influenza A/Vietnam/1203/04 (H5N1) HALo mutant virus is an attenuated H5N1 virus generated from wild-type Influenza A/Vietnam/1203/04 (H5N1) virus as described in Steel, J., et al. J Virol. 2009 Feb; 83(4):1742-53.

overall_design: Human tracheobronchial epithelial cells and monocyte-derived macrophages, obtained from multiple donors, were infected with active and UV-inactivated H5N1 influenza. Samples were collected in duplicate at 6, 12, and 18 hours post-infection for Hi-C analysis, along with time-matched uninfected controls.

first: Christopher

last: Benner

first: Sven

last: Heinz

first: Matthew

last: Urbanowski

first: Lars

last: Pache

first: Megan

last: Shaw

first: Randy

last: Albrecht

first: Adolfo

last: Garcia-Sastre


title: Tomato plants increase their tolerance to low temperatures in a chilling acclimation process entailing comprehensive transcriptional and metabolic adjustments

city: Pozuelo de Alarcón

first: Manuel

last: Pineiro

state: Madrid

address: Autopista M-40, Km 38

institute: Centro de Biotecnologia y Genomica de Plantas (CBGP)

summary: Most crops are from tropical origin and, consequently, chilling sensitive. However, some tropical plants, are able to augment their chilling tolerance in response to suboptimal growth temperatures. Yet, the molecular and physiological mechanisms underlying this response still remain unclear. Here, we demonstrate that tomato plants can develop a chilling acclimation response and document the comprehensive transcriptomic and metabolic adjustments leading to the increase in chilling tolerance.

overall_design: Transcriptomic profiling through RNAseq of tomato plants exposed to suboptimal growth temperature (10C) for 0, 3, 24 and 48h

first: Javier

last: Barrero-Gil

first: Raúl

last: Huertas

first: José

last: Rambla

first: Antonio

last: Granell

first: Julio

last: Salinas


title: Rejuvenation and conversion of skin fibroblasts for immune modulation and bone and cartilage repair in vivo

status: Public on Aug 20 2018

first: Kunshan

last: Zhang

address: 389 Xincun Road

department: Stem cell Translational Research center

institute: Tongji Hospital, Tongji University

summary: Mesenchymal stem cells (MSCs) exist in many tissues and have emerged as promising candidates for therapeutic interventions. While MSCs may be used to reverse aging, they themselves also age. For example, bone marrow-derived MSCs from old individuals are known to have reduced ability to produce bone and cartilage cells, while biased towards making adipose tissues, hence aged bone marrow are referred to as "yellow marrow". Here we report, using step-wise treatment with different "cocktails" of small molecules, we turned old skin fibroblasts into much younger MSC-like cells (MSC-LCs), which reversed many aging features including shortened telomere as well as reduced proliferation potentials and differentiation bias. Moreover, MSC-LCs manifest potent effects in bone and cartilage repair in vivo. MSC-LCs also demonstrated strong immune modulatory functions both in vitro and in vivo during liver damage repair. Taken together, our study demonstrated that old skin fibroblasts could be reprogrammed to acquire youth and harbor huge therapeutic values.

overall_design: 54 samples were analyzed by RNA-seq.

first: Yanjiao

last: Li

first: KunShan

first: Jiaoni

last: Cheng

first: Yaolong

last: Wang

first: Jie

last: Liu

first: Orion

last: Fan

first: Xingfei

last: Wu

first: Pengfei

last: Bao

first: Qiong

last: Bai

first: Congtao

last: Yu

first: Hailiang

first: Zhaoxia

last: Ma

first: Xinpei

last: Gao

first: Lirong

first: Jinxue

first: Change

first: Daiping

first: Bin

last: Jiang

first: Fangyun

last: Chen

first: Shu

last: Liang

first: Qi

last: Gu

first: Zhuowei

first: Zhaojie

first: Kunhua

first: Yi

last: Sun

first: Min

last: Hu


title: RNA sequencing of lncRNAs knockdown in human pancreatic cancer cell lines

city: New York

first: Luis

last: Arnes

state: New York

address: 1130 St Nicholas avenue

department: Biomedical Informatics

institute: Columbia University

summary: We report the transcriptome changes that result from the transient knockdown of FAM83H-AS1 in Aspc1 cells and transient knockdown of LINC00673 in Panc1 cells.

overall_design: Total RNA extracted 48 hour after transfection with targeting and control siRNAs. Libraries were prepared from total RNA (RIN>8) with the TruSeq RNA prep kit (Illumina) and sequenced using the HiSeq2500 (Illumina) instrument. Reads were mapped to the human genome (UCSC/hg19) using Tophat (version 2.0.4) with 4 mismatches and 10 maximum multiple hits. Significantly differentially expressed genes were calculated using DESeq2.

first: Zhaoqi

first: Kenneth

middle: P

last: Olive

first: Raul

last: Rabadan

first: Jiguang


title: Specific control of Arabidopsis BAK1- and SERK4-regulated cell death by protein glycosylation

city: College Station

first: Libo

last: Shan

state: Texas

address: Norman Borlaug Center 136, TAMU2123

department: Department of Plant Pathology and Microbiology

institute: Texas A&M University

summary: Among 24,572 detectable transcripts , we identified 3637 genes showed significant differential expression genes (cut-off: fold change≥2,  FDR<0.1), with 1920 genes showing induced and 1717 reduced expression in the bak1-4/serk4-1 double mutant compared to WT plant.

overall_design: RNA-seq analysis was performed with 10-day-old seedlings of WT and bak1-4/ser4-1. Two independent repeats were performed for RNA-seq analysis. For each repeat, equal amount of RNA from two biological replicates was pooled together for RNA-seq library construction. RNA-seq library preparation and sequencing were carried out on an Illumina HiSeq 2500 platform with single end reads.

first: Marcos

middle: V

last: de Oliveira

first: Guangyuan

last: Xu

first: Bo

last: Li

first: Xiangzong

last: Meng

first: Xin

first: Aline

last: Intorne

first: Abbey

last: Babinat

first: Gonçalo

last: de Souza Filho

first: Ping

last: He


title: An intrinsic tumor-suppression mechanism mediated by steroid hormone in Drosophila

city: Basel

first: Tommy

middle: Beat

last: Schlumpf

state: Basel-Stadt

address: Mattenstrasse 26

department: D-BSSE

country: Switzerland

institute: ETH Zürich

summary: Polycomb group (PcG) proteins are evolutionarily conserved epigenetic regulators that mediate histone modifications and suppress target gene expression, therefore establish and maintain cellular memory during development1-3.  Deregulation of PcG genes is associated with various human cancers, but the mechanisms are incompletely understood4.  Polyhomeotic (Ph), one of the Drosophila PcG proteins, can act as a tumor suppressor in larval imaginal discs5, 6.  Cells mutant for ph overgrow and give rise to neoplastic tumors during larval development6.  Here we report an intrinsic tumor-suppression mechanism mediated by the steroid hormone ecdysone in Drosophila.  During metamorphosis, ecdysone transforms tumorigenic ph mutant cells into non-tumorigenic cells, thereby suppressing the malignant growth in adult flies.  We demonstrate ecdysone exerts its function by inducing the expression of microRNA lethal-7 (let-7), which suppresses its target gene chinmo, to inhibit the tumorigenic growth of ph mutant cells.  Furthermore, we show let-7 can also suppress the overgrowth of brain tumors in brain tumor (brat) mutant flies, indicating this intrinsic mechanism is functional in different tissues to suppress neoplastic growth.  As let-7 is highly conserved among metazoans, our findings will be relevant for mechanistic studies and therapeutic applications in human cancers.

overall_design: Two replicates each of Ph505 tumor tissue was sequenced at 4 weeks, 8 weeks and 14 weeks. During this time it was cultured in adult fly abdomen and piece of it was transplanted once a week to a new host. This data was compared to three control replicates of wild type eye discs from which the tumor originally derives. Additionally tumor tissue from flies that did eclose was analyzed in triplicates to contrast it to larvae stage tumor and wild type tissue

first: Yanrui

last: Jiang

first: Makiko

last: Seimiya

first: Renato

last: Paro


title: Examination and comparsion of exosomes isolated under hypoxia vs normoxia

city: Los angeles

first: Xiangming

last: Ding

address: 650 Charles E Young Dr S, Los Angeles, CA 90095

institute: UCLA

summary: RNA sequencing of extracted RNA from exosomes

overall_design:
Examination and comparison of exosomes isolated under hypoxia vs normoxia
contributor: UCLA genomic core


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and YTHDF2 KD human umbilical cord blood CD34+ cell Transcriptomes

status: Public on Aug 17 2018

city: Kansas City

first: Madelaine

last: Gogol

state: MO

address: 1000 E. 50th Street

department: Computational Biology Core

institute: Stowers Institute

summary: RNA-seq analysis were performed with total RNA extracted from wt and YTHDF2 KD human UCB CD34+ cells.

overall_design: Three replicates of wt and three of YTHDF2 knockdown RNA-seq

first: Zhenrui

middle: M


title: Transcriptome profiles of POM121-knockout prostate cancer cell lines

city: Dallas

first: Yujin

last: Hoshida

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

summary: Nucleoporins are major constituents of nuclear pore complexes, molecular conglomerates embedded within the nuclear envelope that participate in bidirectional trafficking between nucleus and cytoplasm, chromatin silencing and organization, and transcriptional regulation . This functional vantage point is of utmost importance for fundamental cell processes such as intracellular signaling, cell migration, DNA repair and cell division, all of which can be impaired when the molecular identity of the NE and nuclear pore complex is compromised, as seen in cancer. Here we identify a nucleoporin POM121 as a key regulator of proliferation, tumourigenesis, and survival in chemoresistant prostate cancer. Mechanistically, POM121 regulates nuclear transport of specific survival-conferring transcription factors (MYC and E2F1) and androgen receptor that have been previously linked with advanced stages of prostate cancer. POM121-mediated deregulation of nucleocytoplasmic transport occurs through its interaction with Importin β, which serves as a pharmacological target that decreases tumour growth, sensitizes the tumor cells to standard chemotherapy, and improves survival of patient-derived xenograft mice. These results indicate that nuclear pore complex represents a novel mechanism of chemoresistance, which can be therapeutically targetable in aggressive prostate cancer.

overall_design: POM121 gene was knockout by siRNA in 2 prostate cancer cell lines, and transcriptome profiling was performed using RNA-Seq.

first: Veronica

last: Rodriguez-Bravo

first: Josep

last: Domingo-Domenech

first: Hadassa

last: Hirschfield


title: YTHDF2 irCLIP-seq

summary: We performed irCLIP-seq to determine the mRNA targets of YTHDF2 in mouse hematopoietic progenitor cell line HPC-7

overall_design: Three replicates of irCLIP-seq mouse hematopoietic stem cells.


title: Single-allele chromatin interactions identify regulatory hubs in dynamic compartmentalized domains [Hi-C]

city: Oxford

first: A Marieke

last: Oudelaar

address: John Radcliffe Hospital

department: MRC Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

summary: The genome is organized into self-interacting chromatin domains containing genes and the cis-regulatory elements controlling their expression. How these domains form and how elements within them interact is unknown. We have developed Tri-C, a sensitive, high-resolution Chromosome Conformation Capture (3C) approach to identify concurrent chromatin interactions in single cells. Combining Tri-C with conventional 3C and polymer modeling, we show that, rather than folding into stable pre-formed loops, self-interacting domains form dynamic compartmentalized chromatin structures, delimited by CTCF/Cohesin boundaries. Within these tissue-specific domains, all regions of chromatin contact each other, but preferential structures are formed in which multiple enhancers and promoters interact simultaneously. Flanking CTCF/Cohesin-bound elements are excluded from these interactions and form distinct structures. These observations are best explained by a dynamic loop extrusion mechanism and subsequent stabilization of enhancer-promoter interactions, rather than the current view of long-range interactions occurring via the formation of discrete pre-formed chromatin loops.

overall_design: Two replicates of C57BL/6 mice erythroid cells from phenylhydrazine treated spleen, sequenced with Hi-C , and analyzed to give an intra-chromosomal interaction matrix.

first: A

first: Yu

last: Liu

first: Ron

last: Schwessinger

first: Jelena

last: Telenius

first: Job

last: Dekker

first: Jim

middle: R

last: Hughes


title: Single-allele chromatin interactions identify regulatory hubs in dynamic compartmentalized domains [Tri-C]

summary: The genome is organized into self-interacting chromatin domains containing genes and the cis-regulatory elements controlling their expression. How these domains form and how elements within them interact is not fully understood. We have developed Tri-C, a sensitive, high-resolution Chromosome Conformation Capture (3C) approach to identify concurrent chromatin interactions in single cells. Combining Tri-C with conventional 3C and polymer modeling, we show that, rather than folding into stable pre-formed loops, self-interacting domains form dynamic compartmentalized chromatin structures, delimited by CTCF/Cohesin boundaries. Within these tissue-specific domains, all regions of chromatin contact each other, but preferential structures are formed in which multiple enhancers and promoters interact simultaneously. Flanking CTCF/Cohesin-bound elements are excluded from these interactions and form distinct structures. These observations are best explained by a dynamic loop extrusion mechanism and subsequent stabilization of enhancer-promoter interactions, rather than the current view of long-range interactions occurring via the formation of discrete pre-formed chromatin loops.

overall_design: Tri-C is a new 3C-based technique that can analyze multi-way interactions. It combines 3C library preparation (NlaIII restriction enzyme) with oligonucleotide capture enrichment for viewpoints of interest and the fragments they interact with. The capture step has been optimized to capture two or more interacting fragments with high efficiency. We have used this to analyze the 3D structure of the murine alpha and beta globin loci in active primary erythroid cells and inactive ES cells.


title: Single-allele chromatin interactions identify regulatory hubs in dynamic compartmentalized domains

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

overall_design: Refer to individual Series


title: Transcriptome Analysis of Cucumber (Cucumis sativus L.) Leaves Under Chilling Stress

city: Shenyang

first: Zhiyong

institute: Shenyang Agriculture University

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of gene expression profiles of cucumber under short-term chilling stress. The goals of this study are to transcriptome analysis of cucumber leaves under chilling stress.

Methods: mRNA profiles of seedlings exposed to an air temperature of 6°C in the absence of light at 0, 2, 6, and 12 h were generated by deep sequencing, in triplicate, using Illumina Hiseq platform. The reference genome and gene model annotation files were downloaded from the genome website （http://cucurbitgenomics.org/）. An index of the reference genome was built using Bowtie v.2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v.2.0.12. qRT–PCR validation was performed using SYBR Green assays.

Results: A total of 55.7 million clean reads was generated. Based on the threshold values of absolute value of log2 ratio ≥ 1 and FDR ≤ 0.05, a total of 2113 DEGs was identified at three time points (2, 6, and 12 h). A total of 30 genes was detected at all time points. The number of DEGs increased with time. In total, 100 TFs from 22 families in three subsets were detected. And 19 kinase families were identified in three subsets. The DEGs identified by RNA sequencing were confirmed by qRT-PCR analysis, indicating that the data were reliable.  These findings provide information that can be useful for investigating the molecular mechanisms underlying the response to chilling stress in cucumber and other plants.

Conclusions: The results presented here reveal changes in the transcriptome profile of cucumber in response to chilling stress. Exposure to a low temperature induced genes involved in hormone regulation, lipid metabolism, and photosynthesis, including NAC, WRKY, AP2/ERF, ERD, MYB as well as zinc finger TFs and protein kinases such as receptor-like protein kinase, MAPK, and CDK. Most TFs were upregulated whereas CDKs were downregulated. These findings provide information that can be useful for investigating the molecular mechanisms underlying the response to chilling stress in cucumber and other plants.

overall_design:
mRNA profiles of seedlings exposed to an air temperature of 6°C in the absence of light at 0, 2, 6, and 12 h were generated by deep sequencing, in triplicate, using Illumina Hiseq platform.

Raw data are not available for GSM3048831, GSM3048837 or GSM3048839 due to file corruption.

first: Xueling

last: Ye


title: H3K27me3 marked genes in primary hippocampal neurons

city: Hong Kong

first: Siu Yuen

last: Chan

address: 21 Sassoon Road

department: Paediatrics & Adolescent Medicine

country: Hong Kong

institute: University of Hong Kong

summary: ChIP-seq in wildtype and Tspyl2 loss-of-function hippocampal neurons to define H3K27me3 marked genomic regions

overall_design: Hippocampal primary neurons were collected from wildtype and Tspyl2 loss-of-function embryos at E16.5 and cultured in Neurobasal Medium with 1 % FBS and B27 supplement for 14 days. Two samples of each genotype were used. SRA Study accession is SRP065154 and BioProject accession is PRJNA299542.

first: Hang

first: Siu


title: RHBDF2 in Stromal Fibroblasts Mediates TGF-b Signal and Enhances Cancer Cell Invasion via Intercellular Cross-Talk

city: Singapore

first: Tannistha

last: Nandi

address: 60 Biopolis Street, Genome, #02-01

department: Cancer Therapeutics & Stratified Oncology

country: Singapore

institute: Genome Institute of Singapore

summary: Cancer-associated fibroblasts (CAFs) existing in tumor stroma play a crucial role in tumor progression. Here, we show that stromal fibroblasts near cancer cells are likely to display up-regulated RHBDF2 expression caused by chronic stimulation from pro-inflammatory cytokines. RHBDF2 promotes both the cleavage of type I transforming growth factor (TGF)-b receptor, through tumor necrosis factor α converting enzyme activation, and the motility of CAFs upon stimulation with TGF-b1. High-motility CAFs can consequently assist cancer cell invasion. Furthermore, the expression profiles of these cytokines are significantly associated with poor prognosis in gastric cancer (GC) patients. These findings highlight the underlying mechanism whereby cancer cells take advantage of CAFs to acquire invasiveness.

overall_design: 11 matched normal and cancer fibroblast cell lines from diffused type gastric cancer and normal samples

first: Takatsugu

last: Ishimoto

first: Patrick

last: Tan


title: Plasma transcriptome profiling in patients with chronic kidney disease and end-stage renal disease

status: Public on Aug 16 2018

city: Taipei

first: Kai-Chien

last: Yang

address: No.1, Sec. 1, Jen-Ai Rd, 1150R

department: Graduate Institute and Department of Pharmacology

country: Taiwan

institute: National Taiwan University

summary: Cardiovascular disease is the major cause of morbidity and death in patients with chronic kidney disease (CKD) and end-stage renal disease (ESRD). Patients with CKD and ESRD are at high risk for myocardial dysfunction, ischemia and heart failure. The mechanisms linking impaired renal function and increased risk for cardiovascular diseases, however, remain elusive. In addition, conventional therapeutics proven effective in reducing cardiovascular events in general population fail to provide similar benefits in uremic patients. There is a clear need to identify novel mediators of cardiovascular complications in uremic patients to provide insights into the pathogenesis, to tailor clinical care based on cardiovascular risks, and to develop new therapeutic strategies.  It has become increasingly clear that the transcription of the eukaryotic genome is far more pervasive and complex than previously appreciated. While the expression of messenger RNAs (mRNAs) and microRNAs (miRNAs) account for only ~1% of all transcribed species, up to 90% of the mammalian genome is transcribed as long non-coding RNAs (lncRNAs), a heterogeneous group of non-coding transcripts longer than 200 nucleotides. LncRNAs have been shown to be functional and involved in specific physiological and pathological processes through epigenetic, transcriptional and post-transcriptional mechanisms. While the roles of lncRNAs in human diseases including cancer and neurodegenerative disorders are beginning to emerge, it remains unclear how lncRNA regulation contributes to cardiovascular complications in patients with renal dysfunction.   In this proposal, we seek to apply next-generation sequencing technology to investigate circulating (plasma) lncRNA expression in control subjects and in patients with CKD and ESRD. We will test the hypothesis that circulating lncRNA expression signature can reflect the underlying kidney disease states in patients with CKD and ESRD. In addition, we will determine if circulating lncRNA expression signature could be a sensitive and specific biomarker to predict adverse cardiovascular events in patients with ESRD.

overall_design: During the initial exploratory phase, plasma total RNA was isolated from 48 study subjects (28 ESRD, 8 CKD and 12 controls), followed by amplicon-based RNA sequencing (AmpliSeq TranscriptomeTM, Thermo Fisher), which allows simultaneous quantification of 20812 human transcripts, including 2228 lncRNAs. Differential expression analyses following RNASeq identified lncRNAs that were altered with ESRD, compared to control/CKD, as well as lncRNAs that were linked to adverse CV outcomes in uremic patients. The prognostic role of plasma lncRNAs in patients with ESRD were then validated in an independent cohort of 111 subjects.

first: Chin-Hsien

last: Lin

first: Chun-Fu

last: Lai


title: Single-allele chromatin interactions identify regulatory hubs in dynamic compartmentalized domains [Capture-C]

first: A Marieke

overall_design: Capture-C combines 3C library preparation with oligonucleotide capture for the desired viewpoint restriction fragments. Experiments were performed in biological triplicates of primary erythroid and ES cells.

first: A


title: Transgenerational inheritance of DNA hypomethylation in Daphnia magna in response to salinity stress.

city: Aveiro

first: João

middle: André

last: Barbosa

address: Campus Universitário de Santiago

department: Biology Department

country: Portugal

institute: University of Aveiro

summary: Epigenetic mechanisms have been found to play important roles in environmental stress response and regulation. These can, theoretically, be transmitted to future unexposed generations, yet few studies have shown persisting stress-induced transgenerational effects, particularly in invertebrates. Here, we focus on the aquatic microcrustacean Daphnia, a parthenogenetic model species, and its response to salinity stress. Salinity is a serious threat to freshwater ecosystems and a relevant form of environmental perturbation affecting freshwater ecosystems. We exposed one generation of D. magna to high levels of salinity (F0) and found that the exposure provoked specific methylation patterns that were transferred to the three consequent non-exposed generations (F1, F2 and F3). This was the case for the hypomethylation of six protein-coding genes with important roles in the organisms’ response to environmental change: DNA damage repair, cytoskeleton organization and protein synthesis. This suggests that epigenetic changes in Daphnia are particularly targeted to genes involved in coping with general cellular stress responses. Our results highlight that epigenetic marks are affected by environmental stressors and can be transferred to subsequent unexposed generations. Epigenetic marks could therefore prove to be useful indicators of past or historic pollution in this parthenogenetic model system. Furthermore, no life history costs seem to be associated with the maintenance of hypomethylation of across unexposed generations in Daphnia following a single stress exposure.

overall_design: Comparison of DNA methylation patterns between non-exposed and exposed daphnids to NaCl. Three replicates were established for each non-exposed and exposed cultures.

first: Jana

last: Asselman

first: Joana

last: Pereira

first: Guilherme

last: Jeremias

first: Sérgio

last: Marques

first: Fernando

last: Gonçalves

first: Karel

last: De Schamphelaere

first: Filip

last: Van Nieuwerburgh

first: Dieter

last: Deforce


title: Expression data from young and aged BMSCs

status: Public on Aug 15 2018

city: changsha

first: CHANGJUN

last: LI

address: 87# Xiangya Road

department: Department of Endocrinology, Endocrinology Research Center

institute: Xiangya Hospital of Central South University

summary:
Bone marrow mesenchymal stem cells (BMSCs) differentiate into various mature cell types, including adipocytes and osteoblasts, which is determined by genetic, molecular mediators and local microenvironment. With age, BMSCs become inclined to undergo differentiation into adipocytes rather than osteoblasts, resulting in an increased number of adipocytes and a decreased number of osteoblasts, causing osteoporosis. The dysregulated the gene expression in BMSCs during aging were analyzed.
We used microarrays to detail the global programme of gene expression duing aing in BMSCs.

overall_design: BMSCs isolated from Young (3 Month-old) and aged (18 month-old) mice were selected for RNA extraction and hybridization on Affymetrix microarrays. The population of Sca-1+CD29+CD45–CD11b– BMSCs were sorted for experiments.

first: Chang-Jun

last: Li

first: Ye

last: Xiao

first: Xiang-Hang

last: Luo


title: Sequencing facilitates quantitative analysis of transcriptomes in wild type and Lrp6-knockdown cells

city: ShangHai

first: Yuan

last: Tianyou

address: No.1239,SiPing road,YangPu District

institute: tongji university

summary:
Purpose: The goals of this study are to determine the LRP6-mediated splicing regulation, and cellular transcriptomes from rat and human are analysised by deep sequencing.
Methods: The mRNA profiles of WT and LRP6 KD were generated by deep sequencing, using Illumina HiSeq 4000. And the transcript isoform difference betwwen the two group were analysied by bioinformation, Semiquantitative PCR was performed to identify the analysis result.
Results and conclusions: We detected a substantial number of Lrp6 loss-induced AS events, and up to nearly 50 of them were exon-skipped. A gene ontology analysis of the conserved LRP6-driven network showed enrichment for ninety-four genes encoding proteins mainly involved in cellular and metabolic processes . Among them, a decade of genes with LRP6-dependent isoform expression showed identical splicing patterns on the exon level across species. The RNA sequencing results were further verified by Semiquantitative PCR. We conclude that LRP6 could regulate mRNA splicing.

sample_organism:
Homo sapiens
Rattus norvegicus

platform_organism:
Homo sapiens
Rattus norvegicus

overall_design: Examination of  different transcriptome in 3 cell types

first: Wang

last: Shiyi


title: Effect of SGC0946 and SGC0649 on CD4+ T cells under Th1 polarizing conditions

city: Clayton

first: Sebastian

last: Scheer

address: 15 Innovation Walk

institute: Monash University

summary: Comparison between naïve CD4+ mouse T cells and either bona fide IFNg+ and IFNg- CD4+ T cells after culturing under Th1 polarizing conditions in the presence of either the epigenetic probe SGC0946 or SGC0649

overall_design: 3 naïve biological replicates (CD4+ CD44- CD62L+), 3 biological replicates of enriched CD4+ T cells that were polarized for 4 days under Th1 polarizing conditions and FACS sorted for bona fide IFN-g+ (YFP-reporter+) or IFN-g- (YFP-reporter-) cells in the presence of 1 µM of either SGC0946 or SGC0649

first: Kirill

last: Tsyganov


title: Transcription elongation regulates genome 3D structure

city: La Jolla

first: Christopher

last: Benner

state: California

address: 9500 Gilman Dr. MC 0640

department: Medicine

institute: University of California, San Diego (UCSD)

summary: How transcription affects genome organization in the nucleus is poorly understood. Analyzing  influenza A virus (IAV)-infected human macrophages, we observe rapid reorganization of  chromatin interactions. These changes occur where IAV NS1 protein-induced global inhibition of transcription termination leads to read-through transcription for hundreds of kilobases past the ends of highly transcribed genes.  In these read-through regions, RNA polymerase II induces cohesin displacement from CTCF sites at loop anchors, leading to disrupted chromatin interactions and decompaction. Conversely, transcription elongation inhibition allows cohesin to accumulate at previously transcribed CTCF sites and to mediate chromatin looping and compaction. Data from non-viral stimuli indicates that transcription generally regulates cohesin and genome organization within gene bodies. Additionally, transcription into heterochromatin regions switches them from the inert (B) to the permissive (A) chromatin compartment and enables transcription factor binding. Our data indicate that transcription elongation by RNA polymerase II remodels genome architecture in vivo.

overall_design: Analysis of transcription, epigenetics, and chromatin structure during influenza A virus (IAV) infection in macrophages and during expression of IAV NS1 protein in THP-1 cells treated with IFNb, Pam3csk4, dexamethasone, and/or flavopiridol

first: Sven

last: Heinz

first: Max

last: Chang

first: Lorane

last: Texari

first: Michael

last: Hayes

first: Matthew

last: Urbanowski

first: Ninvita

last: Givarkes

first: Alexander

last: Rialdi

first: Kris

last: White

first: Randy

middle: A

last: Albrecht

first: Lars

last: Pache

first: Ivan

last: Marazzi

first: Adolfo

last: García-Sastre

first: Megan

middle: L

last: Shaw


title: Genome-wide transcriptome profile in response to expression of ectopic MYC proteins [RNA-seq]

city: Lebanon

middle: David

last: Cole

state: NH

address: One Medical Center Drive

department: Genetics

institute: Geisel School of Medicine at Dartmouth

summary: We report the application of RNA-seq digital expression analysis to determine overall expression changes in cells responding to exogenous MYC expression. We found that as a result of expressing several different versions of MYC including a minimal MYC protein, expression of all active genes was amplified linearly in all samples. This suggests that presence of the DNA-binding domain and Myc Box II are sufficient to rescue one of Myc's major phenotypes.

overall_design: Examination of overall cellular expression changes due to Myc by comparing cells with deleted Myc to cells containing Myc, MycN, or minimal Myc.

first: Dustin

last: Elwood

first: Charles

last: Lin

middle: D


title: Functional genomic and transcriptomic analysis of amphioxus and the origin of vertebrate genomic traits [RNA-Seq]

city: Sevilla

first: Juan

middle: J.

last: Tena

address: Univ. Pablo Olavide, Ctra. Utrera km1

country: Spain

institute: CABD/CSIC

summary: What genomic changes led to the origin of vertebrates remains a mystery. On the one hand, animal evolution is thought to be driven mostly by changes in the cis-regulatory regions of a shared conserved and toolkit of developmental genes. On the other hand, vertebrates experienced two rounds of whole genome duplication (WGD) that increased their gene repertoire, particularly of regulatory genes controlling embryo development. To shed light into the origin and evolution of the vertebrate regulatory genome, we have generated an unprecedented transcriptomic and epigenomic resource for the non-duplicated genome of the European amphioxus, a closely related invertebrate chordate. These data include RNA-seq for more than 35 developmental stages and adult tissues, CAGE-seq, ChIP-seq, bisulphite-seq and ATAC-seq for several developmental stages and adult tissues. By comparing these data sets with equivalent novel and previously available data for various vertebrate species, especially zebrafish, we uncovered multiple conserved and vertebrate-specific regulatory landmarks. We first identify a conserved chordate phylotypic stage, a developmental period in which different chordate species show the highest gene expression similarity. We also shed light on the origin of enhancer demethylation in vertebrates, by identifying, for the first time in an invertebrate species, differentially methylated enhancers. Furthermore, we show that conserved clusters of co-expressed and tissue-specific genes display similar enrichments for cis-regulatory motifs between amphioxus and vertebrates. Finally, we study the impact of vertebrate WGDs on the evolution of gene regulation, providing the first genome-wide quantitative assessment of sub-functionalization and neo-functionalization processes after the vertebrate WGDs; changing the way in which these evolutionary mechanisms have been traditionally understood.

sample_organism:
Branchiostoma lanceolatum
Danio rerio
Oryzias latipes

overall_design: RNA-seq assays in different developmental stages of european amphioxus, zebrafish and medaka

first: Jon

last: Permanyer

first: Demian

last: Burguera

first: Hector

last: Escriva

first: Stéphanie

last: Bertrand

first: Lorena

last: Buono

last: Martínez-Morales

first: Manuel

last: Irimia


title: m6A-seq mapping of mouse hematopoietic stem/progenitor cells

first: Madelaine

last: Gogol

summary: We performed m6A-seq analysis with sorted mouse LT-HSC, ST-HSC and MPPs.

overall_design: Two replicates of three cell types were analyzed with m6A-seq, with an input for each IP.

first: Zhenrui

last: Li


title: m6A-seq mapping of human umbilical cord blood hematopoietic stem/progenitor cells

summary: We performed m6A-seq analysis with CD34+ human umblilical cord blood HSPCs

overall_design: Three replicates of CD34+ HSPCs were analyzed with m6A-seq, with an input sample for each.


title: Prediction of ribosomal elongation rate from ribosome profiling data

status: Public on Aug 18 2018

city: Cleveland

first: Jeff

last: Coller

address: 10900 Euclid Ave., Wood Bldg.  W113

department: Center for RNA Science and Therapeutics

institute: Case Western Reserve University School of Medicine

summary: We leverage a model statistical framework coupled with high resoluation ribosome profiling data to produce robust estimates of per-codon elongation rates in yeast.

overall_design: Codon-level Ribosome Profiling Analysis

first: Najwa

last: Al-Husaini

first: Gavin

last: Hanson

first: T

middle: J

last: Sweet


title: Hematopoietic stem cell expansion through suppression of YTHDF2-mediated m6A-marked mRNA decay


title: Epigenome Mapping in pancreatic cancer cells

city: LOS ANGELES

first: MARINA

last: KOUTSIOUMPA

address: 650 Charles E. Young Dr South, CHS 33-315

department: MEDICINE

summary: Genome binding/occupancy profiling of H3K4me1 and H3K4me3 upon KMT2D depletion was performed by Illumina NextSeq500 using single‐end 75bp protocol.

overall_design: Chromatin fragments, derived from siControl and siKMT2D (using 2 different siRNAs) treated cells, were immunoprecipitated with antibodies against Anti-Histone H3 (mono-methyl K4) and Anti-Histone H3 (tri-methyl K4). After purification of DNA from cell lysate by functionalized magnetic particles, libraries for next generation sequencing were prepared and analyzed using standard procedures.

first: Dimitrios

last: Iliopoulos

first: Marina

last: Koutsioumpa


title: Single cell RNA sequencing of interneurons of the mouse dorsolateral striatum II

city: Stockholm

first: Sten

last: Linnarsson

address: Scheeles väg 1

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

summary: In order to investigate age-dependent mRNA expression in mouse striatal interneurons, we performed single cell RNA-seq on FACS-isolated fluorescently labeled cells from the dorsal striatum of two mouse lines, 5ht3aEGFP or Lhx6cre::R26R-tdTomat,  from either P21-26 or P55-76 animals. We included the ventricular side of the striatum that contains adult born neuroblasts destined for the olfactory bulb.

overall_design: 3417 single cells isolated from the mouse dorsal striatum.

first: Ana

middle: B

last: Munoz-Manchado

first: Amit

last: Zeisel

first: Jens

last: Hjerling-Leffler


title: Functional genomic and transcriptomic analysis of amphioxus and the origin of vertebrate genomic traits [ATAC-Seq]

first: Juan

last: Tena

platform_organism:
Branchiostoma lanceolatum
Danio rerio
Oryzias latipes

overall_design: ATAC-seq assays in different developmental stages of european amphioxus, zebrafish and medaka

first: Elisa

middle: d

last: la Calle-Mustienes

first: Ignacio

last: Maeso

first: Sandra

last: Jiménez-González

first: Ensieh

last: Faharani

first: Panos

last: Firmpas

first: José

last: Gömez-Skarmeta


title: Gene expression in BMSCs isolated from NONMMUT002667 gene KO mice and wildtype control mice

first: CHANGJUN

last: LI

summary: LncRNA-NONMMUT002667 was idenified in BMSCs during aging. To identify the downstream molecules that mediate NONMMUT002667 induced BMSC location alteration, we FACS-sorted BMSCs from NONMMUT002667-KO mice and WT mice and performed a gene expression profile microarray.

overall_design: Sca-1+ CD29+ CD45− CD11b−BMSCs from NONMMUT002667-KO mice and WT mice were sorted and performed a gene expression profile microarray.

first: Chang-Jun

last: Li

first: Ye

last: Xiao

first: Xiang-Hang

last: Luo


title: Differential RNASeq of human bronchial epithelial cells stimulated with RIG-I ligand SLR14

city: New Haven

first: Ellen

middle: Flescher

last: Foxman

state: CT

address: 330 Cedar St.

department: Laboratory Medicine

institute: Yale University

summary: The purpose of this study was to assess transcriptome changes in primary human airway epithelial cells following stimulation with RIG-I ligand.

overall_design: MRNA profiles were generated from primary human airway epithelial cells at rest or following stimulation with RIG-I ligand.

first: Yong

last: Kong

first: Akiko

last: Iwasaki


title: Regulation of fiber-specific actin expression by the Drosophila SRF ortholog Blistered

city: Kennesaw

first: Anton

last: Bryantsev

state: GA

address: 370 Paulding Ave.

institute: Kennesaw State University

summary: Gene expression in the indirect flight muscles was evaluated by Illumina next-gen sequencing under normal conditions and in response to a genetic knockdown of Blistered (bs), a fly homolog of Serum Response Factor.

overall_design:
Progeny of the following crosses were used: 1151-Gal4 x w1118 (control) and 1151-Gal4 x bs[KK108659] (bs knockdown).
For each sample (either control or knockdown), indirect flight muscles (IFMs) were dissected from 4 young females in 1M sucrose and immediately dissolved in the solubilizing buffer provided by RNeasy RNA purification kit (Qiagen). Total RNA was extracted following the kit manufacturer’s protocol, including 15-min on-column DNAse I digestion. 100-200 ng of purified total RNA were submitted for sequencing at the Sulzberger Genome Center (Columbia University, New York). At the Center mRNA transcripts were enriched by poly-A pull-down using TrueSeq RNA prep kit (Illumina) and ~30 millions of single-end, 100-bp reads were produced per each sample by Illumina HiSeq2000 instrument.
The post-run analysis was performed on the web-based platform Galaxy (usegalaxy.org). Transcript quantification was done by Salmon tool (doi:10.1101/021592) that used reference transcriptome and gene coordinates from D. melanogaster 6.21 genome release. Comparative analysis between control and knockdown samples was done by DEseq2 (doi:10.1186/s13059-014-0550-8).

first: Ashley

last: DeAguero

first: Richard

last: Cripps


title: Comparison of cultured and sand fly-derived promastigotes by means of RNA-Seq

city: MADRID

first: PEDRO

middle: JOSÉ

last: ALCOLEA ALCOLEA

address: Ramiro de Maeztu, 9

department: CENTRO DE INVESTIGACIONES BIOLÓGICAS

institute: CONSEJO SUPERIOR DE INVESTIGACIONES CIENTÍFICAS

summary: A laboratory colony of Phlebotomus perniciosus sand flies was maintained. Sand flies were infected with cultured Leishmania infantum promastigotes in stationary phase. Ten infected sand flies were dissected after 5 days and promastigotes within the gut pooled. The cells were immediately washed in PBS once and lysed in TRIzol reagent (Life Technologies). RNA isolation was completed according to the manufacturer's instructions, obtaining 63ng. RNA-seq libraries were generated using the spliced leader sequence for second strand synthesis (Cuypers et al., 2017; Haydock et al., 2015), thus allowing for specific amplification of sequences from L. infantum promastigotes, thus avoiding contamination with material from the sand fly gut. Single-end sequencing was performed in an Illumina HiSeq2500 instrument and data analysis was conducted using bowtie2, samtools, featureCounts and Geneious. The main findings are: i) substantial differences in differential gene expression between sand fly-derived (sfPro) and cultured (acPro) promastigotes; and ii) over-expression of genes involved in metacyclogenesis in sfPro vs. acPro, including gp63 genes, autophagy genes, etc.

overall_design: Spliced-leader RNA-seq (SL-Seq). PRJNA290068

first: Pedro

last: Alcolea

first: Gowthaman

last: Ramasamy

first: Ana

last: Alonso

first: A

last: Sur

first: C

last: Paisie

first: Aarthi

last: Sekar

first: Loren

last: Baugh

first: Ricardo

last: Molina

first: Maribel

last: Jiménez

first: Vicente

last: Larraga

first: Peter

last: Myler


title: Global loss of epigenetic and transcriptional fidility defines a subclass of cancer with immunotherapy resistance [RCC]

city: Cincinnati

first: Kakajan

last: Komurov

address: 3333 Burnet Ave

department: Experimental Hematology and Cancer Biology

institute: Cincinnati Children's Hospital Medical Center

summary: We report that some cancers have extensive loss of epigenetic and transcriptional fidelity, characterized widespread spurious transcription and mRNA processing defects (Loss of transcriptional fidelity: LTF+). LTF impairs transcriptional elongation and imposes a highly specific molecular phenotype where pathways regulated by long genes, such as those involved in inflammatory response are consistently impaired in LTF+ tumors. Accordingly LTF blunts inflammatory response and confers resistance to immune mediated anti-tumor attack, and correlates with poor response to immunotherapeutic drugs in renal cell carcinoma and melanoma patients. We show that genetic or chemical perturbation of gene body histone methylation or of transcriptional elongation can recapitulate LTF-like phenotype, imposing resistance to immune-mediated anti-tumor mechanisms in-vitro and in-vivo.

overall_design: Paired end  poly A selected RNAseq was performed on RNA extracted from 1-10 micro meter thickness OCT embedded renal clear cell carcinoma (RCC) tumors obtained from University of Cincinnati Tumor Bank. Expression profiling of these samples was used to identify LTF+ samples in an independent cohort.

first: Navneet

last: Singh

first: Vishnu

last: Modur

first: Vakul

last: Mohanty

first: Kwangmin

last: Choi

first: Yunzhu

last: Dong

first: Xiaoting

last: Chen

first: Kashish

last: Chetal

first: Nancy

last: Ratner

first: Nathan

last: Salomonis

first: Matthew

middle: T

last: Weirauch

first: Susan

last: Waltz

first: Edith

last: Janssen

first: Gang

last: Huang

first: Lisa

last: Privette-Vinnedge