title: RNA-seq of zebrafish embryo dorsal forerunner cells lacking Vestigial like 4 like (Vgll4l) or Yes associated protein 1 (Yap1)/ WW domain containing transcription regulator 1 (Wwtr1/Taz) activities

city: Charlottesville

first: Bernard

middle: Victor

last: Thisse

state: VA

address: 1340 Jefferson Park ave

department: Cell Biology

institute: University of Virginia

summary:
Purpose: The goals of this study are to compare control Dorsal Forerunner Cells (DFCs)  transcriptome (RNA-seq) to the one of embryos depleted for either Vgll4l or Yap/Taz (Yap1 and Wwtr1) and to evaluate the transcriptional contribution of these transcription cofactors to the formation of the zebrafish left right organizer
Methods: Knockdown (KD) of Vgll4l and Yap/Taz were performed by injection of morpholinos in Tg(sox17:GFP) embryos at the one cell stage. Single DFCs cluster were dissected out at 90% epiboly. Extraction of Total RNA and cDNA libraries construction were done using SMART-Seq®  v4 Ultra® Low Input RNA Kit for Sequencing from clontech and NEB DNA Ultra library construction kit. Whole genome sequencing was done on illumina Hiseq 2000 sequencer.
Results/Conclusions: Vgll4l and Yap/ Taz play and essential role in the formation of  the left right organizer. They regulate a large number of genes important for differentiation of the organ. They are required for proper expression of major transciprition factors involved in Kupffer vesicle formation as well as for genes involved in ciliogenesis. Both Vgll4l and Yap/Taz  act upstream of major pathways known to regulate the formation of the left right organizer.  Additionally, Vgll4l is required for the spatio-temporal expression of writters and readers of DNA methylation marks (DNA methylation enzymes and methyl CpG binding proteins) during Kupffer's vesicle differentiation

overall_design: Trancriptome of single cluser of control Dorsal Forerunner Cells were compared to the ones of Dorsal Forerunner cells depleted for either Vgll4l or Yap/Taz. Quadrupicates were analyzed for each experimental condtion.

first: Jonathan

last: Fillatre

first: Christine


title: MicroRNA expression in peripheral T-cell lymphomas

status: Public on Sep 19 2019

city: Siena

first: Mohsen

last: Navari

state: SI

address: Via delle Scotte 6

department: Medical Biotechnology

country: Italy

institute: University of Siena

overall_design: MicroRNA expression was assessed in in peripheral T-cell lymphoma cases and normal T-cells using total RNA.

first: Pier

middle: P

last: Piccaluga


title: Peripheral T-cell Lymphoma gene expression profiling

summary: Peripheral T-cell Lymphoma cases along with normal T-cells were subjected to gene expression profiling by means of a DASL array. The cases included both PTCL/NOS and Lennert Lymphoma.

overall_design: Total RNA was extracted from FFPE sample as well as normal T-cells from healthy donors.


title: Development of human brain organoids with functional vascular-like system

city: Montréal

first: Yoshiaki

last: Tanaka

state: Québec

address: 5415 boul. l'Assomption

department: Medicine

country: Canada

institute: Centre de Recherche l'Hôpital Maisonneuve-Rosemont, Université de Montréal

type: Expression profiling by high throughput sequencing

summary: Human cortical organoids (hCOs), derived from human embryonic stem cells (hESCs), provide an excellent platform to study human brain development and diseases in complex 3D tissue. However, current hCOs lack microvasculature, resulting in limited oxygen and nutrient delivery to inner-most parts of hCOs. Previous studies demonstrated that the expression of human ETS variant 2 (hETV2) directly converts human fibroblasts to functional endothelial cells. Here, we engineered hESCs to ectopically express hETV2 to create in vitro vasculature in hCOs, namely vhCOs (vascularized hCOs). hETV2-expressing cells in hCOs contributed to forming a complex vascular network in hCOs. Importantly, the presence of vascularization resulted in enhanced functional maturation of organoids. We found that vhCOs acquired several blood-brain barrier (BBB) characteristics including increased expression of tight junctions, nutrient transporters, and trans-endothelial electrical resistance. Finally, hETV2-induced endothelium supported the formation of perfused blood vessels in vivo. These vhCOs form vasculature that resemble early prenatal brain, and present a robust model to study brain disease in vitro.

overall_design: mRNA profiles of vascularized brain cortical organoids with single-cell level were generated by deep sequencing

first: Bilal

last: Cakir

first: Yangfei

last: Xiang

first: Benjamin

last: Patterson

first: In-Hyun

last: Park


title: Unique regulation of cis-regulatory elements facilitates reacquisition of pluripotency

city: Cambridge

first: Sudhir

last: Thakurela

address: 7 Divinity Avenue

country: USA

institute: HSCRB

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Unique regulation of cis-regulatory elements facilitates reacquisition of pluripotency [ATAC-seq]

summary: Ectopic expression of selected transcription factors enables reprogramming of somatic cells to pluripotency. Despite steady progress in the field the exact molecular mechanisms that coordinate this remarkable transition remain still largely elusive. To better understand the final steps during the acquisition of pluripotency, we optimized an experimental system where cells exit pluripotency and then are systematically challenged to reacquire pluripotency. Using this approach we identify a transient period of deterministic reprogramming during which cells exposed to ectopic transcription factors, but not serum/LIF alone, revert to pluripotency with near 100% efficiency before approaching somatic kinetics (1-2 weeks) and efficiencies (1-2%). Investigation of the transient phase reveals unique molecular dynamics that point to a set of cis-regulatory elements that appear central to facilitating reprogramming. Interestingly, these regions retain an epigenetic signature during in vitro and in vivo differentiation and may act as primary targets of ectopically induced factors during somatic cell reprogramming.

overall_design: In order to better understand reacquisition of pluripotency, we designed an experimental system where differentiation iPSC are systematically challenged to reacquire pluripotency. We performed a comprehensive characterization of differentiation and reacquisition trajectories by RNA-seq,ATAC-seq and ChIP-seq for selected histone modifications.

first: Alexander

last: Meissner


title: Unique regulation of cis-regulatory elements facilitates reacquisition of pluripotency [ChIP-seq]


title: Transcriptome sequencing of HELZ-null HEK293T human cell line generated by CRISPR/Cas9 gene editing

status: Public on Sep 17 2019

city: Schlieren

first: Ramona

last: Weber

address: Wagistrasse 12

department: Institute for Regenerative Medicine

country: Switzerland

institute: University of Zurich

summary: Eukaryotic SF1 helicases have been implicated in various aspects of RNA metabolism, including transcription, processing, translation, and degradation. Nevertheless, until now most human SF1 helicases remain poorly understood. Here, we have functionally and biochemically characterized the role of a putative SF1 helicase termed ‘Helicase with Zinc-finger’, or HELZ. We discovered that HELZ associates with various mRNA decay factors including components of the CCR4-NOT deadenylase complex in human and Drosophila melanogaster cells. The interaction between HELZ and the CCR4-NOT complex is direct and mediated by an extended low-complexity region in the C-terminal part of HELZ. We further reveal that HELZ uses the deadenylase complex to mediate translational repression and decapping-dependent mRNA decay. Transcriptome-wide analysis of HELZ-null cells suggests that HELZ has an important role in the regulation of the expression of genes associated with the development of the nervous system.

overall_design: Two cell types with two biological replicates analysed using RNA-Seq

first: Cátia

last: Igreja


title: Cell differentiation grade determines distinct FOXA2 contributions to the cis-regulatory networks of pancreatic cancer cells [ATAC-seq]

city: Milan

first: Chiara

last: Balestrieri

address: Via Olgettina 58

department: Center for Omics Sciences

institute: IRCCS San Raffaele Scientific Institute

type: Genome variation profiling by high throughput sequencing

summary: Abnormal differentiation contributes to the spectrum of aberrant properties of tumor cells. Differentiation of both normal and tumor cells is controlled by regulatory networks enforced by transcription factors (TFs) involved in lineage specification. Among them, pioneer factors such as FOXA1/2, are able to bind and make accessible naïve chromatin, thus critically contributing to the establishment of gene regulatory networks. Pancreatic ductal adenocarcinoma (PDAC) is characterized by massive heterogeneity, with the coexistence at all disease stages of well- and poorly-differentiated cells with diverging transcriptional networks. We found that FOXA2, a TF controlling pancreas specification, was expressed in both well- and poorly-differentiated PDAC cells, but it controlled distinct gene expression programs and displayed extensively different genomic distributions because of its partnership with TFs expressed in a differentiation grade-specific manner, such as HNF1 and HOXB8/9 in well- and poorly-differentiated cells, respectively. These data suggest that pioneer TFs such as FOXA2 are versatile transcriptional regulators whose broad contribution to the gene regulatory networks of highly heterogeneous cancers such as PDACs, depends on the differential availability of partner TFs expressed in distinct tumor cells.

overall_design: Native chromatin from human pancreatic ductal adenocarcinoma cell lines was tagmented in order to identify accessible sites  and subjected to multiparallel sequencing. Experiments were carried out in  genome edited clonal CFPAC1 cells and their respective control clones.

first: Marta

last: Milan

first: Gioacchino

last: Natoli


title: Comparative evaluation of RNA-Seq library preparation methods for strand-specificity and low input

city: Philadelphia

first: Gregory

middle: Robert

last: Grant

state: PA

address: 3400 Civic Center Blvd.

department: Genetics

institute: University of Pennsylvania

summary: Library preparation is a key step in gene expression quantification. There are considerable advantages to both strand specific sequencing and the ability to sequence samples with very small amounts of starting material. Until recently there was no kit available that allowed both simultaneously. The standard Illumina-TruSeq stranded mRNA Sample Preparation kit requires abundant starting quantity while the Takara Bio-SMART-Seq® v4 Ultra® Low Input RNA kit allows for ultra low starting quantities but sacrifices strand specificity. Recently a kit that can do both, SMARTer® Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian by Takara Bio, has become available. Evaluating the performance and effects of these sample preparation kits is a critical determinant for selecting the appropriate sequencing protocol, but a comprehensive comparison is currently missing. To address this we performed a detailed comparative analysis of sequencing libraries prepared with the three kits. We prepared a set of samples representing two experimental conditions with each kit, allowing for comparison of the kits in a standard realistic differential expression analysis. We find substantial differences in the levels of alignment and differential gene expression. Using differential expression analysis we show that using Pico results in identifying 55% less differentially expressed genes than TruSeq. Nevertheless, using gene pathway enrichment analysis we find similar results for all three kits, indicating that ultimately comparable functional results can be reached.

overall_design: Liver RNA from mice treated with IL-1β or saline. Both treatment conditions have 3 biological replicates.

first: Dimitra

last: Sarantopoulou

first: Soon

middle: Y

last: Tang

first: Emanuela

last: Ricciotti

first: Nicholas

middle: F

last: Lahens

first: Damien

last: Lekkas

last: Schug

first: Xiaofeng

middle: S

last: Guo

first: Georgios

middle: K

last: Paschos

first: Garret

middle: A

last: FitzGerald

first: Allan

middle: I

last: Pack

middle: R


title: Cell differentiation grade determines distinct FOXA2 contributions to the cis-regulatory networks of pancreatic cancer cells


title: RNA Seq analyzed the transcriptional difference between the ICSI and ICAHCI embryo in blastocyst and placenta

city: Shanghai

first: Qing

last: Li

address: 320 Yueyang Road

department: institute of biochemistry and cell biology

country: China

institute: Chinese Academy of Science

summary: Our lab first derived mouse androgenetic haploid embryonic stem cells (AG-haESCs) and demonstrated that AG-haESCs can be used as an “artificial spermatids” to generate gene-edited semi-cloned (SC) mice through intracytoplasmic injection (ICAHCI) into mature oocyte, even though the birth efficiency is very low. Further we proved that H19-DMR and IG-DMR were the main barrier to generate viable mice through androgenetic and parthenogenetic haESCs. More importantly, AG-haESCs mediated SC technology combined with CRISPR-Cas9 is a powerful tool to generate gene-modified mouse models and carry out genetic screening at organismal level. However, it is still not clear how the H19-DMR and IG-DMR coordinately regulate SC embryo development. Here, we found that the H19-DMR and IG-DMR regulate the development of SC embryos in spatio-temporal scales. Firstly, we found that the H19-DMR and IG-DMR are not indispensable for the development of preimplantation of SC embryos. Secondly, H19-DMR is essential for the development of SC embryos in mid-gestation and IG-DMR takes effect in late-gestation. Further, the maintenance of paternal H19-DMR methylation status and deletion of paternal H19 transcription unit play a key role in the structures and transport functions of SC embryo placenta. Importantly, AG-haESCs carrying triple deletions, including H19, H19-DMR and IG-DMR, can further improve the efficiency in generation of viable, normal-size, and fertile mice.

overall_design: For blastocyst, five samples (including ICM and TE) for control (ICSI) and semi-cloned blastocysts (including WT and DKO). For placenta, three samples for control (ICSI) and semi-cloned placentae (including WT, DKO, IG△DMR and H19△13kb)

first: Jinsong

first: Yuanyuan


title: Unique regulation of cis-regulatory elements facilitates reacquisition of pluripotency [RNA-seq]

first: Sudhir

last: Thakurela

first: Alexander

last: Meissner


title: Cell differentiation grade determines distinct FOXA2 contributions to the cis-regulatory networks of pancreatic cancer cells [RNA-seq]

first: Chiara

last: Balestrieri

overall_design: Total RNA from human pancreatic ductal adenocarcinoma cell lines was processed for multiparallel sequencing. Experiments were carried out in genome edited PANC1 cell line (3 FOXA2-deleted CRISPR-Cas9 bulk cell lines and 3 wt bulk) and CFPAC1 cell line silenced  with Control-siRNA, FOXA1 and/or FOXA2 siRNA.

first: Marta


title: Cell differentiation grade determines distinct FOXA2 contributions to the cis-regulatory networks of pancreatic cancer cells [ChIP-seq]

overall_design: Chromatin from human pancreatic ductal adenocarcinoma cell lines was immunoprecipitated with various transcription factor targeting antibodies and subjected to multiparallel sequencing. Experiments were carried out in cells transduced with lentiviral vectors carrying the expression of different transcription factors (CFPAC1 and PANC1 cells) or genome edited clonal CFPAC1 cells, all with their corresponding control cells.

last: Milan

first: Gioacchino


title: Gene expression changes in Neil1 / Neil2 / Neil3 triple knockout mouse teratoma

status: Public on Sep 16 2019

city: Mainz

first: Emil

last: Karaulanov

address: Ackermannweg 4

country: Germany

institute: Institute of Molecular Biology

summary: The bifunctional DNA glycosylases / AP lyases NEIL1 and NEIL2 excise oxidative base damages, but can also enhance the steady-state turnover of thymine DNA glycosylase (TDG) during oxidative DNA demethylation (Schomacher et al. 2016; doi:10.1038/nsmb.3151). The dual role of NEILs in antagonizing base damages and promoting epigenetic gene reactivation prompted us to investigate the consequences of NEIL deficiency during embryonic stem cell differentiation. To account for any possible functional redundancy in the NEIL family, all three paralogs NEIL1, NEIL2 and NEIL3 were inactivated using CRISPR/Cas9 in mouse embryonic stem cells.

overall_design: RNA-seq gene expression profiling in teratomas derived from wildtype and Neil1 / Neil2 / Neil3 triple knockout (TKO) mouse embryonic stem cells (mESCs) in biological triplicates.

first: Dandan

last: Han

first: Lars

last: Schomacher

first: Katrin

middle: M

last: Schüle

first: Medhavi

last: Mallick

first: Michael

middle: U

last: Musheev

first: Laura

last: Krebs

first: Annika

last: von Seggern

first: Christof

last: Niehrs


title: NEIL1 and NEIL2 DNA glycosylases protect neural crest development against mitochondrial oxidative stress

summary: It has become clear that DNA repair factors function not only in the maintenance of genomic integrity but also in active DNA demethylation and epigenetic gene regulation. This dual role raises the question if phenotypic abnormalities resulting from deficiency of DNA repair factors are due to DNA damage or impaired DNA demethylation. Here we investigate the bifunctional DNA glycosylases/lyases NEIL1 and NEIL2, which act in repair of oxidative lesions and in epigenetic demethylation.

sample_organism:
Xenopus laevis
Mus musculus

platform_organism:
Xenopus laevis
Mus musculus


title: Gene expression changes in Neil1, Neil2 and Apex1 single knockout mouse embryonic stem cells prior and during embryoid body differentiation

summary: The bifunctional DNA glycosylases/AP lyases NEIL1 and NEIL2 excise oxidative base damages, but can also enhance the steady-state turnover of thymine DNA glycosylase (TDG) during oxidative DNA demethylation (Schomacher et al. 2016; doi:10.1038/nsmb.3151) probably due to their AP lyase activity during base excision repair (BER). The dual role of NEILs in antagonizing base damages and promoting epigenetic gene reactivation prompted us to investigate the consequences of Neil-deficiency during embryonic stem cell differentiation. For comparison stem cells deficient for Apex1, the bona fide AP endonuclease during BER, were analysed in parallel.

overall_design: RNA-seq gene expression profiling of wildtype, Neil1, Neil2 and Apex1 single knockout mouse embryonic stem cells (mESCs) and embryoid bodies (EBs) derived from them.


title: Demethylation and derepression of genomic retroelements in the skeletal muscles of aged mice

city: Daejeon

first: Byungkuk

last: Min

address: 125 Gwahak-ro, Yuseong-gu

department: Development and Differentiation Research Center

country: South Korea

institute: KRIBB

type: Methylation profiling by high throughput sequencing

summary: Changes in DNA methylation influence the aging process and contribute to aging phenotypes, but few studies have been conducted on DNA methylation changes in conjunction with skeletal muscle aging. We explored the DNA methylation changes in a variety of retroelement families throughout aging (at 2, 20, and 28 months of age) in murine skeletal muscles by methyl-binding domain sequencing (MBD-seq). The two following contrasting patterns were observed among the members of each repeat family in superaged mice: (1) hypermethylation in weakly methylated retroelement copies and (2) hypomethylation in copies with relatively stronger methylation levels, representing a pattern of “regression toward the mean” within a single retroelement family. Interestingly, these patterns depended on the sizes of the copies. While the majority of the elements showed a slight increase in methylation, the larger copies (>5 kb) displayed evident demethylation. All these changes were not observed in T cells. RNA sequencing revealed a global derepression of retroelements during the late phase of aging (between 20-28 months of age), which temporally coincided with retroelement demethylation. Following this methylation drift trend of “regression toward the mean”, aging tended to progressively lose the preexisting methylation differences and local patterns in the genomic regions that had been elaborately established during the early period of development.

overall_design: MBDseq experiments on aged mouse muscles and T-cells, and gene expression analysis of mouse muscles by RNAseq

first: Kyuheum

last: Jeon

first: Myungsun

last: Park

first: Jung Sun

first: Yong-Kook

last: Kang


title: Gene expression profile of cells with unfit Wnt morphogen gradient during cell competition

status: Public on Sep 15 2019

city: Fukuoka

first: Yasuyuki

last: Ohkawa

address: 3-1-1 Maidashi

country: Japan

institute: Medical Institute of Bioregulation

summary: Morphogen signalling forms an activity gradient and instructs cell identities in a signalling strength-dependent manner to pattern developing tissues. However, developing tissues also undergo dynamic morphogenesis, which may produce cells with unfit morphogen signalling and consequent noisy morphogen gradient. Here we show that a cell competition-related system corrects such noisy morphogen gradients. Zebrafish imaging analyses of the Wnt/β-catenin signalling gradient, which acts as a morphogen to establish embryonic anterior-posterior patterning, revealed that unfit cells with abnormal Wnt/β-catenin activity spontaneously appear and produce noise in the gradient. Communication between unfit and neighbouring fit cells via cadherin proteins stimulates apoptosis of the unfit cells by activating Smad signalling and reactive oxygen species production. This unfit cell elimination is required for proper Wnt/β-catenin gradient formation and consequent anterior-posterior patterning. Because this gradient controls patterning not only in the embryo but also in adult tissues, this system may support tissue robustness and disease prevention.

overall_design: β-catCA (constitutive active form of β-catenin)-expressing cells from β-catCA-mosaically introduced or β-catCA ubiquitously-expressing zebrafish early embryos, or cells from uninjected zebrafish embryos were sorted by FACS cell sorter. Total RNAs were extracted and analyzed by RNA-seq.

first: Akieda

last: Yuki

first: Ishitani

last: Tohru

first: Ohkawa

last: Yasuyuki


title: Gene expression changes in stage 23 Xenopus laevis embryos upon Neil2 knockdown

first: Emil

last: Karaulanov

summary: It was shown that neil2 is required for neural crest development in Xenopus (Schomacher et al. 2016; doi:10.1038/nsmb.3151). To gain further insights into the underlying molecular mechanism leading to neural crest defects and microcephaly in neil2 Morpholino injected Xenopus embryos, we performed RNA-seq transcriptome analysis of neil2 Morpholino versus control Morpholino injected embryos.

overall_design: Gene expression profiling by RNA-seq of stage 23 Xenopus laevis embryos injected with either control or neil2 Morpholino antisense oligo

first: Dandan


title: Interleukin 22 mediates interleukin 23-induced pathology in newborn mice by disrupting the function of pancreatic and intestinal cells

status: Public on Sep 14 2019

city: New York

first: Sergio

last: Lira

state: NY

address: 1425 Madison Ave room 12-20

institute: Icahn School of Medicine at Mount Sinai


title: RNA sequencing of pancres tissue of WT and IL23 expression mice (KSR23)

summary: The goal of this study is to check if elevated level of IL-23 and/or its downstream cytokines affect the gene expression in the pancreas of newborn mice. We engineered a mice strain in which the expression of IL-23 was directed to the keratinocytes (KSR23).  The KSR23 mice had normal body weight at birth and much smaller than their control littermates at day 5. KSR23 mice died prematurely (before 15 days of age), but displayed no signs of disease in the skin, intestine, or in other organs examined. To investigate if elevated level of IL-23 and/or its downstreamcytokines could affect body growth, we examined the transcriptome of the the pancreas, which are critical for the processing and absorption of nutrients. Pancreatic mRNA profiles of 5-day-old WT and KSR23 were generated by deep sequencing. The transcriptome of the pancreas of KSR23 mice at P5 differed significantly from that of their control littermates (WT). Kegg pathway analysis showed that several genes involved in pancreatic secretion, were downregulated in the pancreas of KSR23 mice. The pancreatic secretion pathway includes genes encoding several pancreatic enzymes involved in food digestion and genes involved in the secretory pathway. In conclusion, increased expression of IL-23 and/or its down cytokines affects expression of genes in neonatal  pancreas.

overall_design: Pancres mRNA profiles of 5-day old wild type (WT) and IL23 expression mice (KSR23)  were generated by deep sequencing using Illumina Nextseq 500.

first: Lili

last: Chen

first: Valentina

last: Strohmeier

first: Zhengxiang

last: He

first: Madhura

last: Deshpande

first: Glaucia

middle: C

last: Furtado


title: RNA sequencing of Jejunum of WT and IL23 expression mice (KSR23)

summary: The goal of this study is to check if elevated level of IL-23 and/or its downstream cytokines affect the gene expression in the jejunum of newborn mice. We engineered a mice strain in which the expression of IL-23 was directed to the keratinocytes (KSR23). The KSR23 mice had normal body weight at birth and much smaller than their control littermates at day 5. KSR23 mice died prematurely (before 15 days of age), but displayed no signs of disease in the skin, intestine, or in other organs examined. To investigate if elevated level of IL-23 and/or its downstreamcytokines could affect body growth, we examined the transcriptome of the the intestine, which are critical for the processing and absorption of nutrients. Jejunum mRNA profiles of 5-day-old WT and KSR23 were generated by deep sequencing. The transcriptome of the Jejunum of KSR23 mice at P5 differed significantly from that of their control littermates (WT). Several genes were differentially expressed, including IL-22, and genes that are downstream of it such as Reg3 genes and digestive enzymes also produced by the jejunum. Kegg pathway analysis of WT and KSR23 jejunum indicated that genes involved in protein digestion and absorption such as chymotrypsinogen B1 (Ctrb1), trypsinogen (Prss1), trypsin (Tyr5 and Tyr4), caboxypeptidase a1 (Cpa1) and chymotrypsin-like elastase family member 3b (Cela3b), were downregulated in the intestine of KSR23 mice. Transcriptome analysis also showed decreased expression of several genes involved in the regulation of the very low-density lipoprotein particle pathway (VLDL). These particles regulate fat and cholesterol release into the bloodstream. Together, these results indicate that systemic expression of IL-23, and other cytokines, correlated with significant transcriptional changes in genes that regulate food processing in the intestine.

overall_design: Jejunum mRNA profiles of 5-day old wild type (WT) and IL23 expression mice (KSR23)  were generated by deep sequencing using Illumina Nextseq 500.


title: Gene Expression Changes from E-Cigarette Exposure During Early Pregnancy

status: Public on Sep 12 2019

city: Chapel Hill

first: Kathleen

last: Caron

state: NC

address: 111 Mason Farm Road, CB7545

department: Cell Biology and Physiology

institute: University of North Carolin

summary: Electronic nicotine delivery system (E-Cigarette) use is prevalent among pregnant women. We examined whether E-Cigarette exposure impairs implantation. RNA microarray was performed on day 4.5 pseudopregnant mice exposed to E-Cigarettes or sham during each day of pregnancy.

overall_design: C57BL/6J dams primed with E-Cigarette or sham were mated to vasectomized males. The presence of a copulatory plug was recorded as day 0.5 and pseudopregnant mice were exposed to E-Cigarette or sham for each day of pregnancy until euthanasia on the morning of day 4.5. Each sample represents one mouse with 4 samples exposed to sham versus 4 samples exposed to E-Cigarettes.

first: Margeaux

last: Wetendorf


title: IL-33 blockade impacts mediators of persistence and exacerbation in a model of chronic airway inflammation

status: Public on Sep 13 2019

city: Tarrytown

first: Wei Keat

last: Lim

address: 777 Old Saw Mill River Rd

institute: Regeneron Pharmaceuticals

summary:
Summary: Blocking IL-33 signaling ameliorates inflammation, tissue remodeling and preserves lung function in a model of persistent and exacerbating airway disease.
Background: Severe inflammatory airway diseases are associated with inflammation that fails to resolve, leading to structural changes and an overall environment primed for exacerbations.
Objective: We sought to identify and inhibit pathways that perpetuate this heightened inflammatory state, as this could lead to therapies that allow for a more quiescent lung, less predisposed to symptoms and exacerbations.
Methods: Using prolonged exposure to house dust mite (HDM) in mice, we developed a mouse model of persistent and exacerbating airway disease characterized by a mixed inflammatory phenotype.
Results: We show that lung IL-33 drives inflammation and remodeling beyond the type 2 response classically associated with IL-33 signaling. IL-33 blockade with an IL-33 neutralizing antibody normalized established inflammation, and improved remodeling of both the lung epithelium and lung parenchyma. Specifically, IL-33 blockade normalized persisting and exacerbating inflammatory endpoints, including eosinophilic, neutrophilic and ST2+ CD4+ T cell infiltration. Importantly, we identified a key role for IL-33 in driving lung remodeling, as anti-IL-33 also reestablished the presence of ciliated cells over mucus producing cells and lowered myofibroblast numbers, even in the context of continuous allergen exposure, resulting in improved lung function.
Conclusion: Overall, this study shows that elevated IL-33 drives a self-perpetuating amplification loop that retains the lung in a state of lasting inflammation and remodeled tissue, primed for exacerbations. Thus, IL-33 blockade may ameliorate symptoms and prevent exacerbations by quelling persistent inflammation and airway remodeling.

overall_design:
Using prolonged exposure to house dust mite (HDM) in mice, we developed a mouse model of persistent and exacerbating airway disease characterized by a mixed inflammatory phenotype.
HDM4wk:  mouse exposed to house dust mite (HDM) for 4 weeks with no antibody treatment.
HDM15wk:  mouse exposed to house dust mite (HDM) for 15 weeks with no antibody treatment.
HDM15wk_Iso:  mouse exposed to house dust mite (HDM) for 15 weeks with isotype control treatment.
HDM15wk_antiIL33:  mouse exposed to house dust mite (HDM) for 15 weeks with anti-IL-33 antibody treatment.

first: Jeanne

last: Allinne

first: George

last: Scott

first: Wei

first: Dylan

last: Birchard

first: Jonas

last: Erjefält

first: Caroline

last: Sandén

first: Li-Hong

last: Ben

first: Amit

last: Agrawal

first: Navneet

last: Kaur

first: Jee

middle: H

last: Kim

first: Vishal

last: Kamat

first: Wen

last: Fury

first: Tammy

last: Huang

first: Neil

last: Stahl

middle: D

last: Yancopoulos

first: Andrew

middle: J

last: Murphy

first: Matthew

last: Sleeman

first: Jamie

last: Orengo


title: RNA interactions are essential for proper CTCF function

first: Ricardo

last: Saldana-Meyer

address: 522 First Avenue

department: Biochemistry and Molecular Pharmacology

institute: NYUMC - HHMI

summary: The function of the CCCTC-binding factor (CTCF) in the organization of the genome has become an important area of investigation, but the mechanisms by which CTCF dynamically contributes to genome organization are not clear. We previously discovered that CTCF binds to large numbers of endogenous RNAs, promoting its self-association. In this regard, we now report two independent features that disrupt CTCF association with chromatin: inhibition of transcription and disruption of CTCF-RNA interactions through mutations of two of its 11 zinc fingers which are not required for CTCF binding to its cognate DNA site: zinc finger-1 (ZF1) or -10 (ZF10). These mutations alter gene expression profiles as CTCF mutants lose their ability to form chromatin loops and thus, the ability to insulate chromatin domains as well as mediate CTCF long-range genomic interactions. Our results point to the importance of CTCF-mediated RNA interactions as a structural component of genome organization.

overall_design: In this experiment with characterized mESC under transcriptional inhibition or Rnase digestion using Chip-Seq and 5C experiments. As well as rescue cell lines where endogenous CTCF was depleted and a mutant CTCF was expressed using ChIP-Seq, RNA-Seq, scRNA-Seq and Hi-C

last: Saldaña-Meyer

first: Danny

last: Reinberg


title: SUFU and SPOP mediated downregulation of Hh signaling promotes pancreatic beta-cell differentiation through the regulation of organ-specific stromal niche signals

city: Toronto

first: Tae-Hee

state: Ontario

address: 686 Bay St.

department: Development and Stem Cell Biology

institute: The Hospital for Sick Children

summary:
Purpose: Human Embryonic Stem Cell (hESC)-derived insulin-producing beta cells offer a promising cell-based therapy for diabetes. However, efficient hESC to beta cell differentiation has proven difficult, possibly due to the lack of cross-talk with the appropriate mesenchymal niche. To define organ-specific niche signals, we isolated pancreatic and gastrointestinal stromal cells and analyzed their transcriptomes during development.
Methods: mRNA profiles from E13.5 mice were generated from mesenchymal cells dissected from wild-type (WT)  intestine, stomach, pancreas and mutant Sufu-/- Spop -/- pancreatic mesenchyme, in duplicate, by illumina HiSeq 2500. Reads were aligned to the mm10 assembly and unambiguously mapping reads were analyzed at the gene level for differential expression between tissue types alignment using STAR and differential analysis using DESeq2.
Results: Using our workflow, we mapped about 30 million reads per sample to mm10. Differential expression (DE) analysis identified over 900 significantly differentially expressed genes between WT pancreatic mesenchyme and gastrointestinal mesenchymes, and over 1100 genes differentially expressed between WT and mutant pancreatic mesenchyme. Our findings reveal the importance of tightly-regulated Hh signaling in the pancreatic mesenchyme. In vivo inactivation of mesenchymal Hh signaling leads to annular pancreas, and stroma-specific activation of Hh signaling via loss of Hh  regulators, Sufu and Spop, impairs pancreatic growth and beta cell genesis. Genetic rescue and transcriptome analyses show that these Sufu and Spop knockout defects occur through GLI2-mediated activation of gastrointestinal stromal signals such as Wnt ligands. Importantly, inhibition of Wnt signaling in organoid and hESC cultures significantly promotes insulin-producing cell generation, revealing the requirement for organ-specific regulation of stromal niche signals.

overall_design: mRNA profiles from E13.5 mice were generated from mesenchymal cells dissected from wild-type (WT)  intestine, stomach, pancreas and mutant Sufu-/- Spop -/- pancreatic mesenchyme, in duplicate, by Illumina HiSeq 2500

first: Cristina

last: Nostro


title: RNA-sequencing in plasmacytoid dendritic cells from patients with primary Sjogren's syndrome (pSS), non-Sjogren's sicca (nSS), and healthy donors (HC)

status: Public on Sep 11 2019

city: Utrecht

first: Aridaman

last: Pandit

address: Heidelberglaan 100

country: Netherlands

institute: University Medical Center Utrecht

summary: We here provide the first in-depth molecular analysis of pDCs from patients with pSS and nSS in comparison to HC. We isolated circulating pDCs from two independent cohorts of patients and controls (each n=31) and performed RNA-sequencing, after which data-driven networks and modular analysis were used to identify signatures of robustly reproducible transcriptional “signatures” of dysregulated differential and co-expressed genes. Four reproducible gene signatures were identified that indicated pDC activation. Comparison with in vitro activated pDCs showed that pSS pDCs have higher expression of many genes also upregulated upon pDC activation. In all transcriptional analyses, nSS patients formed an intermediate group in which some patients were molecularly similar to pSS patients. Our data provide in-depth characterization of the aberrant regulation of pDCs from patients with nSS and pSS and substantiate their perceived role in the immunopathology of pSS, supporting studies that target pDCs, type-I IFNs, or IFN-signalling in pSS.

overall_design: RNA-sequencing in primary circulating plasmacytoid dendritic cells from patients with pSS, nSS, and HC. Two cohorts of n=31 each are included (discovery and replication), no duplicates samples

first: Maarten

last: Hillen

first: Sofie

middle: L

last: Blokland

first: Sarita

last: Hartgring

first: Cornelis

last: Bekker

first: Eefje

last: van der Heijden

first: Nila

last: Servaas

first: Marzia

last: Rossato

first: Aike

last: Kruize

first: Joel

last: van Roon

first: Timothy

last: Radstake


title: Therapeutic targeting of Notch signaling and immune checkpoint blockade in a spontaneous, genetically-heterogeneous mouse model of T-cell acute lymphoblastic leukemia

status: Public on Sep 10 2019

first: Qi

last: Zhao

address: 777 Old Saw Mill River Road

institute: Regeneron Pharmaceuticals Inc

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

overall_design: Refer to individual Series


title: Exome sequencing of thymus transplantation based spontaneous murine T cell acute lymphoblastic leukemia (T-ALL) model

summary: We adapted a spontaneously-arising, genetically-heterogeneous, thymic transplantation-based murine model of T-ALL, recapitulating key histopathological and genetic features of the human disease, to the preclinical testing of targeted and immune-directed therapies.

overall_design: Wild-type thymus-derived  T-ALL samples  were subjected to exome sequencing

first: Jie

last: Gao


title: Intragenomic variability and extended sequence patterns in the mutational signature of ultraviolet light

city: Gothenburg

first: Martin

last: Boström

address: Medicinaregatan 9A

country: Sweden

institute: University of Gothenburg

summary: Mutational signatures can reveal properties of underlying mutational processes and are important when assessing signals of selection in cancer. Here we describe the sequence characteristics of mutations induced by ultraviolet (UV) light, a major mutagen in several human cancers, in terms of extended (longer than trinucleotide) patterns as well as variability of the signature across chromatin states. Promoter regions display a distinct UV signature with reduced TCG>TTG transitions, and genome-wide mapping of UVB-induced DNA photoproducts (pyrimidine dimers) showed that this may be explained by decreased damage formation at hypomethylated promoter CpG sites. Further, an extended signature model encompassing additional information from longer contextual patterns improves modeling of UV mutations, which may enhance discrimination between drivers and passenger events. Our study presents a refined picture of the UV signature and underscores that the characteristics of a single mutational process may vary across the genome.

overall_design: Genome-wide mapping of CPDs in A375 melanoma cells exposed to UVB as well as untreated control cells using a modified CPD-seq protocol

first: Markus

last: Lindberg

first: Kerryn

last: Elliott

first: Erik

last: Larsson


title: Habenular Tcf7l2 links nicotine addiction to diabetes

first: Zichen

last: Wang

address: 1468 Madison Ave

department: Pharmacological Sciences

summary: Nicotine contained in tobacco smoke increases blood glucose levels in humans, and the risk of developing diabetes is dramatically increased in habitual smokers. Little is currently known about how nicotine increases blood glucose levels or the relevance of this action to either the persistence of the smoking habit or the pathophysiology of diabetes in smokers. Here, we show that the diabetes-associated gene Tcf7l2 is highly expressed in the medial habenula (mHb), where it regulates the function of local nicotinic acetylcholine receptors. We find that Tcf7l2 mutant (Tcf7l2mut) rats consume far greater quantities of nicotine than wild-type rats. Similarly, CRISPR-mediated cleavage of wild-type Tcf7l2 in the mHb increases nicotine intake in mice. Polysynaptic tracing identified a connection from the mHb to the pancreas, and nicotine-induced activation of the mHb elevates blood glucose. This effect is mimicked by chemogenetic stimulation of the mHb and blocked by Tcf7l2 knockdown in mHb. A history of nicotine consumption elevates circulating levels of the pancreas-derived hormones glucagon and insulin and precipitates diabetes-like dysregulation of blood glucose homeostasis in wild-type rats, whereas Tcf7l2mut rats are resistant to these actions of nicotine. Our findings suggest that Tcf7l2 regulates the stimulatory actions of nicotine on the habenula-pancreas axis, linkings the addictive properties of nicotine to its diabetes-promoting actions.

overall_design: RNA-Seq is performed in three brain regions, including medial habenula (mHb), Interpeduncular nuclear (IPn) and dorsal hippocampus (dHIP), from wild-type and Tcf7l2 mutant rats.

first: Alexander

last: Duncan

first: Avi

last: Ma'ayan

first: Paul

last: Kenny


title: Gene expression profiling of human gastric tumour cells (HGT-1) harboring genotype I human norovirus replicons

first: Frederic

last: Sorgeloos

address: Addenbrookes Hospital, Hills Road

department: Pathology

country: United Kingdom

institute: University of Cambridge

summary: Gene expression analysis of GI human norovirus (HuNoV) replicon in human gastric tumor cells (HGT-NV), IFN-cured population of replicon-harboring HGT-1 cells (HGT-Cured) and wild-type parental HGT-1 cells (HGT) to provide insight into the cellular factors promoting human norovirus replication in vitro.

overall_design: Quadruplicates of HGT-1 cells haboring GI HuNoV replicon were compared side by side with IFN-cured populations of replicon-harboring cells and with wild-type parental cells.

first: Sabastine

last: Arthur

first: Myra

last: Hosmillo

first: Ian

last: Goodfellow


title: Alpha-ketoglutarate links p53 to cell fate during tumor suppression

status: Public on Sep 09 2019

first: Richard

last: Koche

state: New York

institute: Memorial Sloan Kettering Cancer Center

summary: The tumor suppressor p53 is mutated in the majority of human cancers, including pancreatic ductal adenocarcinoma (PDAC)1,2. Wild-type p53 accumulates in response to cellular stress and acts to regulate the expression of genes that influence cell fate and constrain tumorigenesis2. p53 also can modulate cellular metabolism3, though it remains unclear how the metabolic effects of p53 influence tumor suppression or whether the metabolic consequences of p53 loss play a role in disease maintenance. Here, we show that restoring endogenous p53 function in cancer cells derived from a mouse model of PDAC driven by oncogenic Kras and a regulatable p53 short hairpin RNA (shRNA) rewires glucose and glutamine metabolism to support the accumulation of the metabolite alpha-ketoglutarate, an obligate substrate for several enzymes that regulate chromatin methylation. p53 restoration induces transcriptional programs characteristic of pre-neoplastic differentiation, an effect that can be partially recapitulated by addition of cell permeable alpha-ketoglutarate. Consequently, enforcing alpha-ketoglutarate accumulation in p53 deficient cells by inhibiting expression of oxoglutarate dehydrogenase (Ogdh), the enzyme that consumes alpha-ketoglutarate in the tricarboxylic acid cycle, reduces tumor-initiating capacity and promotes tumor differentiation in vivo. In both mouse and human pancreatic cancer, decreasing levels of the alpha-ketoglutarate-dependent chromatin modification 5-hydroxymethylcytosine (5hmC) marks progression from prenoplastic to de-differentiated malignant lesions. p53 restoration or Ogdh suppression promotes accumulation of 5hmC specifically in differentiated tumor cells in vivo. Together, these results nominate alpha-ketoglutarate as an effector of p53-mediated tumor suppression that promotes pre-neoplastic differentiation and suppresses malignant progression.

overall_design: ATAC-sequencing of mouse PDAC cell lines in control, p53 on, or aKG setting

first: John

last: Morris IV

first: Lydia

middle: W

last: Finley

first: Scott

last: Lowe


title: Gene expression analysis of the impact of TDP-43 knockout in human cells.

city: New Haven

first: Shawn

middle: Michael

last: Ferguson

state: CT

address: 295 Congress Ave

institute: Yale School of Medicine

summary:
Purpose:  The goal of this stuydy was to apply  transcriptome profiling (RNA-seq) to human cells that either express or which lack the TDP-43 protein.
Methods: mRNA profiles of TDP-43 KO HeLa cells and "rescued" TDP-43 KO cells wherein a wildtype TDP-43 transgene was re-expressed at endogenous levels  were generated by deep sequencing, in triplicate,  on Illumina’s HiSeq 2500 using 2x70bp paired-end reads, generating 104.4-128.2 million reads (52.2-64.1 million pairs) per sample. . The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat2 followed by Cufflinks Cuffmerge and Cuffdiff to define transcripts and establish their abundance and  finally to perform differential gene expression analysis, using the assembled known plus novel transcripts .
Results: Using an optimized data analysis workflow, we mapped approximately 50-60 million reads per sample to the human genome (build hg19) and identified transcripts whose abundance differed between the TDP-43 KO versus "rescued" conditions.
Conclusions: Our study presents a detailed analysis of the impact of the knockout of TDP-43 on the transcriptome of a human cell line. The results reported here should provide a framework for defining transcripts whose abundnace and splicing are regulated by TDP-43.

overall_design: Examination of the transcriptome of human cells that lack and which express TDP-43.


title: BRG1 attenuates colonic inflammation and tumorigenesis through autophagy-dependent oxidative stress sequestration

city: shanghai

first: min

last: liu

address: huashan road

institute: shanghaijiaotong university

summary: We report that BRG1, an ATPase subunit of the SWI/SNF chromatin remodeling complex, was required for the homeostatic maintenance of colonic epithelial cells (IECs) to prevent the inflammation and tumorigenesis. Consistent with the reduced BRG1 expression in IBD patients, adult mice with IEC ablation of BRG1 developed spontaneous colitis and exhibited increased susceptibility to mutagen-induced tumor growth. Conversely, BRG1 overexpression protected the mice from DSS-induced epithelial damage and subsequent oncogenesis. Mechanistically, BRG1 emerged as a key regulator that directly governs the transcription of Atg16l1, Ambra1, Atg7 and Wipi2, which are important for autophagosome biogenesis. Thus, defective autophagy in BRG1-deficient IECs resulted in excess reactive oxygen species (ROS), which led to the defects in cellular apoptosis and barrier integrity.

overall_design: ChIP assays of two-month-old Brg1F/F and Brg1IEC-AKO IECs were generated by deep sequencing

first: Min

last: Liu

first: Tongyu

last: Sun


title: A single cell reference map for human blood and tissue T cell activation

first: Hanna

middle: Mendes

last: Levitin

address: Department of Systems Biology 3960 Broadway, Lasker 203A

department: Department of Systems Biology

institute: Columbia University Medical Center

summary: Human T cells coordinate adaptive immunity by localization in diverse tissue sites, though blood T cells are the most readily studied.  We investigated the functional responses of T cells isolated from human lungs (LG), lymph nodes (LN), bone marrow (BM), and blood to TCR-stimulation using single-cell RNA-seq. We defined cellular states for resting T cells including signatures that differentiate tissue and blood T cells and employed new factorization methods to identify activation states conserved across tissues, including an IFN-response activation state in CD4+T cells and distinct effector states specific to CD8+T cells. We demonstrate how this high-resolution map can be used to assess the origin and functional state of T cells in disease by projecting scRNAseq profiles of tumor-associated T cells from multiple cancers, revealing CD8 T cells that co-express markers of exhaustion, activation, and proliferation, and a lack of activated CD4 T cells. Our results establish a high-dimensional reference for human T cell homeostasis and function in multiple sites, from which to probe T cell dysfunction in disease.

overall_design: Single-cell RNA-sequencing of control and and anti-CD3/anti-CD28 stimulated T cells from human lung, lymph node, bone marrow and blood.

first: Peter

last: Szabo

last: Mendes Levitin

first: Michelle

last: Miron

first: Mark

middle: E

last: Snyder

first: Takashi

last: Senda

first: Jinzhou

last: Yuan

first: Yim

last: Cheng

first: Erin

last: Bush

first: Pranay

last: Dogra

first: Puspa

last: Thapa

first: Donna

last: Farber

last: Sims


title: Gene expression profile of thymus transplantation based spontaneous murine T cell acute lymphoblastic leukemia (T-ALL) model

status: Public on Sep 07 2019

first: Qi

last: Zhao

overall_design: Wild-type thymus-derived T-ALL samples, Notch3 knockout thymus-derived T-ALL samples, and controls were subjected to RNA sequencing

first: Jie

last: Gao


title: Distinct transcriptional roles for Histone H3-K56 acetylation during the cell cycle

city: Montpellier

first: Marta

last: Radman-Livaja

address: 1919 route de Mende

department: IGMM

country: France

institute: CNRS

summary: Dynamic disruption and reassembly of promoter-proximal nucleosomes is a conserved hallmark of transcriptionally active chromatin.  Histone H3-K56 acetylation (H3K56Ac) enhances these turnover events and promotes nucleosome assembly during S phase. Here we sequence nascent transcripts to investigate the impact of H3K56Ac on transcription throughout the yeast cell cycle. Strikingly, we find that H3K56Ac is a genome-wide activator of transcription. H3K56Ac has a major impact on transcription initiation, but it also appears to promote elongation and/or termination. In contrast, H3K56Ac represses promiscuous transcription that occurs immediately following replication fork passage, in this case by promoting efficient nucleosome assembly.  We also detect a stepwise increase in transcription as cells transit S phase and enter G2, but this response to increased gene dosage does not require H3K56Ac. Thus, a single histone mark can exert both positive and negative impacts on transcription that are coupled to different cell cycle events.

overall_design: We have mapped changes in nucleosome positions on newly replicated DNA in a timecourse after genome replication. We have used Micrococcal Nuclease footprinting of cross linked chromatin to determine nucleosome positions and EdU (ethylene deoxy uridine) to mark nascent DNA strands. EdU incorporated into nascent DNA strands was biotinylated with Click chemistry and nascent DNA strand fragments were subsequently isolated using Streptavidin coated magnetic beads.

first: Salih

last: Topal

first: Pauline

last: Vasseur

first: Craig

last: Peterson


title: Identification of miRNA-mRNA regulatory network for Human Atrial Aging [mRNA]

status: Public on Sep 06 2019

city: Beijing

first: Yan

last: Yao

address: No 2 Anzhen Road

institute: Beijing Anzhen Hospital

summary: We report an integrative analysis of miRNA-seq and mRNA-seq to identify miRNAs, genes, and miRNA-mRNA interactions for human atrial aging (AA). We found that seven miRNAs (4 upregulation and 3 downregulation) and 42 genes (23 upregulation and 19 downregulation) show differential expression between older samples and younger samples in human right atrial tissues. Pearson correlation analysis identified 114 pairs of putative miRNA-mRNA interactions for AA. Pathway enrichment analysis identified three important pathways including rhythmic process, senescence and autophagy in cancer, and positive regulation of cytokine biosynthetic process. Our study revealed novel miRNA-mRNA interaction networks and signaling pathways for AA, providing novel insights into the development of human AA. This dataset includes data generation and processing steps for the mRNA-seq data generated from twelve SR samples.

overall_design: Right atrial appendages from twelve patients who received aortic valve replacement were subjected to miRNA-seq and RNA-seq. All the patients were in sinus rhythm (SR) and stratified by age into four groups (SR40, SR50, SR60, and SR70). Four age groups were matched by baseline demographic and clinical features. Differential expression analysis was carried out to identify miRNAs and genes for human AA using program edgeR. This dataset includes data generation and processing steps for the mRNA-seq data generated from twelve SR samples.


title: Transcriptomics analysis of amphotericin B and lactoferrin drug synergy in Cryptococcus neoformans H99

status: Public on Sep 08 2019

city: Sydney

first: Chi Nam Ignatius

last: Pang

state: NSW

address: School of Biotechnology and Biomolecular Sciences, UNSW Australia

department: The NSW Systems Biology Initiative

country: Australia

institute: The University of New South Wales

summary: Invasive fungal infections (IFIs) are difficult to treat. Few effective antifungal drugs are available and many have problems with toxicity, efficacy and drug-resistance. To overcome these challenges, existing therapies may be enhanced using more than one agent acting in synergy. Previously, we have found amphotericin B (AMB) and the iron chelator, lactoferrin (LF), were synergistic against Cryptococcus neoformans and Saccharomyces cerevisiae. This study investigates the mechanism of AMB+LF synergy using RNA-seq in Cryptococcus neoformans H99.

overall_design: We extracted mRNA from C. neoformans treated with i) AMB only (0.06 µg/mL), ii) LF only (2 µg/mL), iii) a combination of AMB + LF (0.06 µg/mL and 2 µg/mL, respectively) or iv) corresponding matching untreated controls. ID20 (inhibition of cell growth by 20%) was chosen as the time point for RNA isolation from all treatments, as at this point cells are stressed but there should be few confounding effects of cell death, allowing a direct comparison among treatments. The ID20 for AMB of 60 minutes, and AMB-LF of 50 minutes. The same incubation times were applied to each of the matched control samples. RNA-seq data were generated using Illumina HiSeq 2000 and Illumina NextSeq 500 with biological triplicates multiplexed and randomized across two sequencing lanes. Using EdgeR, we identified differentially expressed genes by comparing AMB treatment with the matched control. We also compared AMB + LF treatment with its matched control.

first: Yu-Wen

last: Lai

first: Chi

first: Leona

middle: T

last: Campbell

first: Sharon

last: Chen

first: Dee

last: Carter

first: Marc

last: Wilkins


title: Stat6 occupancy profiling by high throughput sequencing from wild-type(WT) or Trim24-deficient(Trim24-KO) mouse peritoneal macrophages stimulated with IL-4 for 1 hour .

first: Tao

last: Yu

state: Shanghai

address: 320 Yueyang Road

institute: Chinese Academy of Science

summary: To identify the potential genes that regulated by Trim24 through Stat6 DNA binding activity, we immunoprecipitated chromatin from WT or Trim24-KO macrophages stimulated with IL-4, and analyzed the precipitated DNA with deep sequencing (ChIP-Seq).

overall_design: To exam the difference of Stat6 DNA binding in WT and Trim24-KO macrophages,the chromatin of mouse macrophages stimulated for 1 hour with IL-4 was prepared and followed by ChIP-Seq analysis by Active Motif, Inc. using the antibody against Stat6.

first: Yichuan

last: Xiao


title: Chronic inflammation directs an olfactory stem cell functional switch from neuroregeneration to immune defense (bulk RNA-Seq)

city: Baltimore

first: Andrew

middle: P.

last: Lane

state: Maryland

address: 855 N Wolfe Street, Room 540

department: Department of Otolarynology

institute: Johns Hopkins School of Medicine

summary: Although the olfactory mucosa possesses long-lived horizontal basal stem cells (HBCs) and remarkable regenerative capacity, the function of human olfactory neuroepithelium is significantly impaired in the setting of chronic rhinosinusitis. Here we used RNA sequencing to analyze the transcriptional profile of mouse HBCs in a chronic inflammatory milieu. Global gene expression analysis in inflamed HBCs reveals broad upregulation of NF-κB-regulated cytokines and chemokines accompanied by enhancement of “stemness”-related transcription factors. Our results provide evidence of basal stem cells as direct participants in the progression of chronic inflammation and identify a concomitant functional switch away from neuroregeneration.

overall_design: GFP+ HBCs from Krt17-EGFP; Cyp2g1-rtTA; TRE-TNF mice after 6 weeks of tissue-specific temporally-controlled olfactory inflammation were collected by FACS. GFP+ HBCs from Krt17-EGFP mice were isolated as normal control. The HBC mRNA transcriptional profile was analyzed by bulk RNA sequencing.

first: M

first: R

last: Reed

first: A

middle: P


title: Expression data from wild-type and TIF1a-knockout mouse macrophages stimulated with or without mouse IL-4(20ng/mL) for 6 h.

summary: We conducted gene expression profile analysis by using wild-type and TIF1a-knockout peritoneal macrophage.Analysis revealed the most prominent different expression of genes altered in macrophages upon IL-4 stimulation were associated with marker genes of alternative macrophage.

overall_design: Genome-wide expression profiling of wild-type and TIF1a-knockout mouse macrophages stimulated with or without mouse IL-4(20ng/mL) for 6 h were generated by RNA-sequencing analysis.


title: Expression data from wild-type peritoneal macrophages (termed WTPM) non-treated (NT) or stimulated for 6 h with mouse IL-4.

summary: We conducted gene expression profile analysis by using wild-type peritoneal macrophages(termed WTPM).Scatter diagram revealed the most prominent different expression of genes altered in macrophages upon IL-4 stimulation were associated with M2 macrophage and Trims genes.

overall_design: Genome-wide expression profiling of wild-type macrophages(WTPM) non-treated (NT) or stimulated for 6 h with IL-4 were generated by RNA-sequencing analysis


title: Expression data from WT and Trim24-deficient tumor-associated macrophage(TAM) sorted from B16 bearing mouse

summary: We conducted gene expression profile analysis by using CD45+ CD11b+ F4/80+ TAM sorted from WT or Trim24-deficient B16 bearing mouse.Scatter diagram revealed the most prominent different expression of genes altered in TAM were associated with M2 genes.

overall_design: Genome-wide expression profiling of WT and Trim24-deficient TAM sorted from B16 bearing mice by RNA-sequencing analysis.


title: Identification of miRNA-mRNA regulatory network for Human Atrial Aging [miRNA]

type: Non-coding RNA profiling by high throughput sequencing

summary: We report an integrative analysis of miRNA-seq and mRNA-seq to identify miRNAs, genes, and miRNA-mRNA interactions for human atrial aging (AA). We found that seven miRNAs (4 upregulation and 3 downregulation) and 42 genes (23 upregulation and 19 downregulation) show differential expression between older samples and younger samples in human right atrial tissues. Pearson correlation analysis identified 114 pairs of putative miRNA-mRNA interactions for AA. Pathway enrichment analysis identified three important pathways including rhythmic process, senescence and autophagy in cancer, and positive regulation of cytokine biosynthetic process. Our study revealed novel miRNA-mRNA interaction networks and signaling pathways for AA, providing novel insights into the development of human AA. This dataset includes data generation and processing steps for the miRNA-seq data generated from twelve SR samples.

overall_design: Right atrial appendages from twelve patients who received aortic valve replacement were subjected to miRNA-seq and RNA-seq. All the patients were in sinus rhythm (SR) and stratified by age into four groups (SR40, SR50, SR60, and SR70). Four age groups were matched by baseline demographic and clinical features. Differential expression analysis was carried out to identify miRNAs and genes for human AA using program edgeR. This dataset includes data generation and processing steps for the miRNA-seq data generated from twelve SR samples.


title: The U-box family genes in Medicago truncatula: key elements in response to salt, cold, and drought stresses

status: Public on Sep 04 2019

city: Nanchang

first: Jianbo

last: Song

state: Jiang Xi

address: Department of Biochemistry and Molecular Biology, College of Science, Jiang Xi Agricultural University, Nanchang 330045, China

institute: Jiang Xi Agricultural University

summary: The ubiquitination pathway regulates growth, development, and stress responses in plants, and the U-box protein family of ubiquitin ligases has important roles in this pathway. Here, 64 putative U-box proteins were identified in the Medicago truncatula genome. In addition to the conserved U-box motif, other functional domains, such as the ARM, kinase, KAP, and WD40 domains, were also detected. Phylogenetic analysis of the M. truncatula U-box proteins grouped them into six subfamilies, and chromosomal mapping and synteny analyses indicated that tandem and segmental duplications may have contributed to the expansion and evolution of the U-box gene family in this species. Using RNA-seq data from M. truncatula seedlings subjected to three different abiotic stresses, we identified 33 stress-inducible plant U-box genes (MtPUBs). Specifically, 25 salinity-, 15 drought-, and 16 cold-regulated MtPUBs were detected. Among them, MtPUB10, MtPUB17, MtPUB18, MtPUB35, MtPUB42, and MtPUB44 responded to all three stress conditions. Expression profiling by real-time PCR was consistent with the RNA-seq data, and stress-related elements were identified in the promoter regions. The present findings strongly indicate that U-box proteins play critical roles in abiotic stress response in M. truncatula.

overall_design: RNA-seq in Medicago truncatula


title: Change in cellular mRNA expression caused by US7 or US8

status: Public on Sep 05 2019

city: seoul

first: areum

last: park

address: 50, Yonsei-ro, Seodaemun-gu, Seoul, Republic of Korea

institute: immune

summary:
HCMV glycoproteins US7 and US8 target the innate immune response.
We used microarrays to detail the global programme of gene expression and identified to down-regulated genes by US7 or US8.

overall_design: We stimulated HCMV-permissive human foreskin fibroblast (HFF) cells expressing hemagglutinin (HA)-tagged US7 (HA-US7) or US8 (HA-US8) with dsDNA  for RNA extraction and hybridization on Affymetrix microarrays.

first: Areum

last: Park

first: Taeyun

middle: A

last: Lee


title: Establishment of chronic typhoid infection in a mouse carriage model involves a Type 2 immune shift and T and B cell recruitment to the gallbladder

city: Columbus

first: John

last: Gunn

state: Ohio

address: 700 Children’s Drive

department: Center for Microbial Pathogenesis

institute: Abigail Wexner Research Institute at Nationwide Children’s Hospital

summary: Typhoid fever, caused primarily by Salmonella enterica serovar Typhi (S. Typhi), is a life-threatening systemic disease responsible for significant morbidity and mortality worldwide. 3-5% of individuals infected with S. Typhi become chronic carriers due to bacterial persistence in the gallbladder. We have demonstrated that Salmonella forms biofilms on gallstones to establish gallbladder carriage. However, an in-depth molecular understanding of chronic carriage in the gallbladder, from the perspective of both the pathogen and host, is poorly defined. To examine the dynamics of the gallbladder in response to Salmonella infection, we performed transcriptional profiling in the mouse gallbladder at early (7 day) and chronic (21 day) time points. RNA-Seq revealed a shift from a Th1 pro-inflammatory response at 7 days post infection (DPI) towards an anti-inflammatory Th2 response by 21 DPI, characterized by increased levels of immunoglobulins and the Th2 master transcriptional regulator, GATA3. Additionally, bioinformatic analysis predicted the upstream regulation of characteristic Th2 markers including IL-4 and Stat6. Immunohistochemistry and FACS analysis confirmed a significant increase in lymphocytes, including T and B cells, at 21 DPI in mice with gallstones. Interestingly, Salmonella-specific CD4 T-cells were ten-fold higher in the gallbladder of mice with gallstones at 21 DPI. We speculate that the biofilm state allows Salmonella to resist the initial onslaught of the Th1 inflammatory response, while yet undefined events influence a switch in the host immunity towards a more permissive Type 2 response, enabling the establishment of chronic infection.

overall_design: 48 male 129X1/SvJ mice were fed a lithogenic diet (1% cholesterol and 0.5% cholic acid (Envigo/Harlan Laboratory, IN, USA)) for 8 weeks, half were injected intraperitoneally (IP) with PBS (mock infection control) and half were inoculated IP with a dose of 2x10e4 CFUs of S. Typhimurium. Half the mice from each group were sacrificed at 7 DPI and the remaining half at 21 DPI. At both time points gallbladders were removed and flash frozen in dry ice for RNA extraction, gallbladders from 3 animals were pooled to make one sample. Only RNA samples that met quality standards were sequenced.

first: Juan

middle: F

last: González

first: Jonathan

last: Kurtz

first: David

last: Bauer

first: Regan

last: Hitt

first: James

last: Fitch

first: Amy

last: Wetzel

first: Krista

last: La Perle

first: Peter

last: White

last: McLachlan

middle: S


title: Transcriptome profiling of derived-hepatocyte progenitors from human iPSCs with nanoCAGE

city: Tokyo

first: Stéphane

last: Poulain

address: Fw-203, 4-6-1, Komaba, Meguro-ku

department: Institute of Industrial Science

institute: The University of Tokyo

summary: We investigated the human induced pluripotent stem cells (hiPSCs) during a sequential in vitro step-by-step differentiation into hepatocyte-like cells (HLCs) using nanoCAGE, a method for promoters, transcription factors, and transcriptome analysis.

overall_design: Analysis of the transcriptome profiles of cultured cells at the 4 different steps of the differentiation protocol.

first: Charles

last: Plessy

first: Éric

last: Leclerc

first: Yannick

last: Tauran

first: Myriam

last: Lereau-Bernier

first: Mathieu

last: Danoy

first: Marie

last: Shinohara

first: Bertrand-David

last: Segard

first: Sachi

last: Kato

first: Taketomo

last: Kido

first: Atsushi

last: Miyajima

first: Yasuyuki

last: Sakai


title: Rare mutations in the complement regulatory gene CSMD1 are associated with male and female infertility

city: Beaverton

first: Don

last: Conrad

state: OR

address: 505 NW 185th Avenue, Mail Code L584

department: Division of Genetics, Oregon National Primate Research Center

institute: Oregon Health & Science University

summary: Infertility in men and women is a common and complex genetic trait with shared biological bases between the sexes. We performed a series of rare variant analyses across 73,185 women and men to identify genes that contribute to primary gonadal dysfunction and identified CSMD1 as a strong candidate in both sexes. CSMD1 is a complement regulatory protein on chromosome 8p23. In order to interpret and support our genetic findings, we performed detailed transcriptomic and protein-based experiments which found CSMD1 enriched at the germ-cell/somatic-cell interface in both male and female gonads. We then performed a battery of tests on Csmd1 knockout mice. Knockout males show increased rates of infertility, and present testes with severe histological degeneration and significantly increased deposition of complement C3 protein. Knockout females show significant reduction in ovarian quality and breeding success, as well as impaired branching of the mammary glands.  Furthermore, double knockout of Csmd1 and C3 leads to an unexpected and non-additive reduction in breeding success, suggesting that CSMD1 and the complement pathway play an important role in the normal postnatal development of the gonads in both sexes.

overall_design: RNA-seq of mouse whole ovaries, whole testes, and FACS purified germ cell subpopulations

first: Arthur

last: Lee


title: IRF2 is a master regulator of human keratinocyte stem cell fate [ChIP-seq]

status: Public on Sep 03 2019

city: Houston

middle: Yang

last: Lin

state: TX

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

summary: Resident adult epithelial stem cells maintain tissue homeostasis by balancing self-renewal and provision of differentiated cells. Human epidermal keratinocytes retain stem cell potential in vitro but this is highly variable and lost over time suggesting extrinsic and intrinsic regulation.   Transcription factor-controlled regulatory circuitries govern cell identity and are sufficient to induce pluripotency or transdifferentiate cell types. We asked whether transcriptional circuitry also governs phenotypic changes within a given cell type by comparing human primary keratinocytes with intrinsically high versus those with low stem cell potential.   Using integrated chromatin and transcriptional profiling, we implicate the transcription factor IRF2 as antagonistic to stemness and show that it binds to and regulates active cis-regulatory elements at interferon response and antigen presentation genes. CRISPR-KD of IRF2 in keratinocytes with low stem cell potential is sufficient to increase self-renewal, migration and epidermis formation.   These data demonstrate that transcription factor regulatory circuitries, in addition to maintaining cell identity, control plasticity within cell type and offer potential for therapeutic modulation of cell function.

overall_design: ChIP-seq for BRD4 and H3K27ac in human primary keratinocytes with either low (O or LSCP-HK) or high (Y or HSCP-HK) stem cell potential.

first: Nicolas

last: Mercado

first: Felix

last: Lohmann

middle: Y

first: Susan

last: Kirkland


title: Conversion of Sox2-Dependent Merkel Cell Carcinoma to a Differentiated Neuron-like Phenotype by T Antigen Inhibition

city: PITTSBURGH

first: Yulong

last: Bai

state: Pennsylvania

address: Public Health Building, 130 De Soto St,, 3121

department: Human Genetics

institute: University of Pittsburgh

summary: Keratinocyte-cocultured Merkel cell carcinoma cell line (MCC) CVG-1 cells transduced with contorl shRNA (shCtrl) and viral T antigen targeting shRNA (shpanT) were sequenced using the 10x Genomics platform in order to analyze transcriptional changes associated with MCC cancer cell differentiation into neuron-like cells on a single cell level.

overall_design: scRNAseq of two samples of keracinocyte-cocultured CVG-1 cells transduced with shpanT and CVG-1 cells with shCtrl.

first: Masahiro

last: Shuda

first: Hyun

last: Park


title: Identification of miRNA-mRNA regulatory network for Human Atrial Aging

first: Yan

last: Yao

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

overall_design: Refer to individual Series


title: IRF2 is a master regulator of human keratinocyte stem cell fate

first: Charles


title: IRF2 is a master regulator of human keratinocyte stem cell fate [RNA-seq]

overall_design: RNA-seq in human primary epidermal keratinoctyes with either low (O or LSCP-HK) or high (Y or HSCP-HK) stem cell potential


title: IRF2 is a master regulator of human keratinocyte stem cell fate [ChIPmentation]

overall_design: ChIPmentation for IRF2-HA (using HA epitope) in human primary keratinocytes engineered with stable IRF2 knockdown and doxycycline inducible IRF2-HA expression


title: X chromosome domain architecture regulates Caenorhabditis elegans lifespan but not dosage compensation

city: San Francisco

first: Elphege

last: Nora

state: CA

address: 555 Mission Bay Blvd S

department: CVRI

institute: UCSF


title: IRF2 is a master regulator of human keratinocyte stem cell fate  [ATAC-seq]

overall_design: ATAC-seq in human primary epidermal keratinocytes with either low (O or LSCP-HK) or high (Y or HSCP-HK) stem cell potential


title: Transcriptomic analysis of senescent cells and liver treated with Cardiac glycosides

city: London

first: Gopuraja

last: Dharmalingam

address: Faculty of Medicine, Imperial College, Hammersmith Hospital Campus

department: Epigenetics section

institute: MRC London Institute of Medical Sciences

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: NLRP3 inflammasome in fibroblasts links tissue damage with inflammation in breast cancer progression and metastasis

status: Public on Sep 02 2019

city: Tel Aviv

first: Metsada

last: Pasmanik-Chor

address: Ramat Aviv

department: Biology

country: Israel

institute: Tel Aviv University

summary:
Global gene expression of spontaneous breast tumors developed in transgenic mice at different time course (FVB/N-MMTV-PyMT: model of spontaneous mammary carcinoma. Lin EY et al.,Am J Pathol. 2003 Nov;163(5):2113-26.
Cancer-Associated Fibroblasts (CAFs) are highly abundant in the microenvironment of breast tumors.  CAFs were shown to orchestrate tumor-promoting inflammation in multiple malignancies, including  breast cancer. However, the molecular pathways that govern the inflammatory role of CAFs are poorly  characterized. In this study we found that fibroblasts can sense damage-associated molecular  patterns (DAMPs), and in response activate the NLRP3 inflammasome pathway, resulting in  instigation of pro-inflammatory signaling and secretion of IL-1β. This upregulation was evident in  CAFs in mouse and in human breast carcinomas. Moreover, CAF-derived inflammasome signaling  facilitated mammary tumor growth and lung metastasis, which was attenuated when NLRP3 or IL-1β  were specifically ablated. Functionally, CAF-derived inflammasome promoted tumor progression and  metastasis by modulating the tumor microenvironment towards an immune suppressive milieu and  by upregulating the expression of adhesion molecules on endothelial cells. Thus, our findings  elucidate a novel mechanism by which CAFs promote breast cancer progression and lung metastasis,  by linking the physiological tissue damage response of fibroblasts with tumor-promoting inflammation.

overall_design: 11 Samples (arrays) were performed.

first: Nour

last: Ershaid

first: Yoray

last: Sharon

first: Hila

last: Doron

first: Yael

last: Raz

first: Ophir

last: Shani

first: Leonor

last: Leider-Trejo

first: Amir

last: Ben-Shmuel

first: Muhammad

last: Yassin

first: Adit

last: Ben-Baruch

first: Ron

last: Apte

first: Neta

last: Erez


title: A large pool of actively cycling progenitors orchestrates self-renewal and injury repair of an ectodermal appendage

city: Vilnius

first: Rapolas

last: Zilionis

state: LT

address: Sauletekis av 7

department: Life Sciences Center

country: Lithuania

institute: Vilnius University

summary: The classical model posits that a small number of quiescent stem cells (SCs) gives rise to proliferating transit-amplifying cells before terminal differentiation. However, recent evidence indicates that some tissues house multiple progenitor pools with distinct proliferative and differentiation potentials. Resolving the identity and spatial organization of these populations is therefore a fundamental requirement for understanding tissue renewal. Here, using a combination of single-cell RNA sequencing (scRNAseq), mouse genetics, and tissue injury approaches, we uncovered cellular hierarchies and mechanisms underlying the maintenance and repair of the ever-growing mouse incisor, an ectodermal appendage model system that requires high cell turnover for its homeostasis and quick healing capability. We found that during homeostasis, a group of actively cycling epithelial progenitors generates both the enamel-producing ameloblasts and the adjacent non-ameloblast cell layers, which were previously proposed to be quiescent SCs. Upon injury, transient adjustments to the proliferation kinetics of dental epithelial progenitor cells compensated for cell loss. Injury repair was also supported by direct conversion of supporting Notch1-expressing cells to ameloblasts. Our elucidation of epithelial SC identity, position, and function thus provides a mechanistic basis for the homeostasis and repair of a fast-turnover ectodermal appendage and illustrates how a cycling progenitor pool confers considerable epithelial plasticity during tissue renewal.

overall_design: Single cell RNA sequencing of mouse incisor growth region EPCAM+ cells under two conditions: 1) homeostasis (5 mice pooled into one sample); 2) 3-days post-injury with 5- fluorouracil (5 mice pooled into one sample).

first: Amnon

last: Sharir

first: Pauline

last: Marangoni

first: Mian

last: Wan

first: Tomas

last: Wald

first: Jimmy

last: Hu

first: Kyogo

last: Kawaguchi

first: David

last: Castillo-Azofeifa

first: Leo

last: Epstein

first: Kyle

last: Harrington

first: Pierfrancesco

last: Pagella

first: Thimios

last: Mitsiadis

first: Chris

last: Siebel

first: Allon

middle: M

last: Klein


title: Transcriptomic analysis of senescent cells treated with Cardiac glycosides

first: Gopuraja

last: Dharmalingam

summary: IMR90 ER:RAS cells were treated with 4OHT to induce senescence. 6 days later they were treated with Vehicle, Ouabain or Digoxin for 16 or 36h and collected he cells were collected for total mRNA analysis. Minus (Cell not treated with 4OHT), Plus (Cell treated with 4OHT and vehicle), Plus C (On to pof the aforementiones treatments, cells were treated with Caspase inhibitors O/N)

overall_design: 12 conditions were examined

first: Nicolas

last: Herranz

first: Ana

last: Guerrero

first: Jesus

last: Gil


title: SLC19A1 transports immunoreactive cyclic dinucleotides

status: Public on Sep 01 2019

city: Berkeley

last: Raulet

address: 485 Life Sciences addition

department: Molecular and Cell Biology

institute: University of California Berkeley

summary: The accumulation of DNA in the cytosol serves as a key immunostimulatory signal associated with infections, cancer and genomic damage. Cytosolic DNA triggers immune responses by activating the cGAS/STING pathway. The binding of DNA to the cytosolic enzyme cGAMP synthase (cGAS), activates its enzymatic activity, leading to the synthesis of a second messenger, cyclic[G(2’,5’)pA(3’,5’)] (2’3’-cGAMP). 2’3’-cGAMP, a cyclic dinucleotide (CDN), activates the protein ‘stimulator of interferon genes’ (STING), which in turn activates the transcription factors IRF3 and NF-κB promoting the transcription of genes encoding type I interferons and other cytokines and mediators that stimulate a broader immune response. Exogenous 2’3’-cGAMP produced by malignant cells and other CDNs, including CDNs produced by bacteria and synthetic CDNs used in cancer immunotherapy, must traverse the cell membrane to activate STING in target cells. How these charged CDNs pass through the lipid bilayer is unknown. Here we used a genome-wide CRISPR interference screen to identify the reduced folate carrier SLC19A1, a folate-organic phosphate antiporter, as the major transporter for CDNs. CDN uptake and functional responses are inhibited by depleting SLC19A1 from human cells and enhanced by overexpressing SLC19A1. In both human cell lines and primary cells ex vivo, CDN uptake is inhibited by folates, as well as two medications approved for treatment of inflammatory diseases, sulfasalazine and the antifolate methotrexate. The identification of SLC19A1 as the major transporter of CDNs into cells has implications for the immunotherapeutic treatment of cancer, host responsiveness to CDN-producing pathogenic microorganisms, and potentially in certain inflammatory diseases.

overall_design: the human monocytic cell line THP-1 expressing dCas9-BFP-KRAB, the genome-wide CRISPRi library v2, and a cyclic dinucleotide (CDN) reporter construct was stimulated with the CDNs cGAMP or RR-S2 CDA. Cells were sorted in replicate based on CDN reporter expression: low reporter expression, high reporter expression, and a unsorted population (background control)

first: Rutger

last: Luteijn

first: Shivam

last: Zaver

first: Benjamin

middle: G

last: Gowen

first: Stacia

last: Wyman

first: Nick

last: Garelis

first: Liberty

last: Onia

first: Sarah

last: McWhirter

first: George

last: Katibah

first: Jacob

last: Corn

first: Joshua

last: Woodward

middle: H


title: Transcriptomics analysis of the livers of old mice treated with Ouabain

summary: Methods: Liver mRNA profiles of 7 weeks old wild-type (WT) and 24 months old mice treated with Vehicle or Ouabain (1mg/Kg)

overall_design: A cohort of 16 female mice 21-22 months old were treated with Vehicle or Ouabain (1mg/Kg) for 12 weeks. Mice were treated 4 times a week on Weeks 0,3,6,9 and 12. Therefore they rested from tretament 2 weeks before a new round of treatment. Mice were culled 3 days after last round of treatment


title: Global gene expression profiling in HepaRG cells exposed to TCDD for 24 h

city: Brno

first: Jirina

last: Prochazkova

address: Kralovopolska 135

department: Cytokinetics

country: Czech Republic

institute: Institute of Biophysics CAS

summary:
Comparison of expression profiles detected inundifferemtitated HepaRG cells exposed to DMSO, TCDD for 24h.
The aryl hydrocarbon receptor (AhR) activation has been shown to stimulate proliferation, promote apoptosis or alter differentiation of adult rat liver progenitors.    We investigated the impact of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD)-mediated AhR activation on a human model of bipotent liver progenitors, undifferentiated HepaRG cells.                                                                                We used both intact undifferentiated HepaRG cells, and HepaRG cells with silenced Hippo pathway effectors, YAP1 and TAZ, which play key role(s) in tissue specific  progenitor cell self-renewal and expansion, including liver, cardiac or respiratory progenitors.

overall_design: Control DMSO-treated HepaRG cells compared with HepaRG cells exposed to TCDD 10 nM.

first: Jiri

last: Klema

first: Jan

last: Vondracek


title: Gene expression profiles of MLL-AF9 leukemia cells treated with DS-5272

status: Public on Aug 31 2019

first: Yasutaka

last: Hayashi

address: 4-6-1 Shirokanedai, Minato-ku

department: Division of Cellular Therapy, Advanced Clinical Research Center

institute: Institute of Medical Science, The University of Tokyo

summary: To assess the molecular changes induced by p53 activation in MLL-AF9 leukemia, we examined gene expression profiles of vehicle- or DS-5272-treated MLL-AF9 cells by RNA-sequence analysis.

overall_design: DS-5272 was orally administered to leukemic mice 24 hours before collecting leukemia cell. Leukemia cells were sampled from bone marrow and isolated using cell sorter before RNA extraction.

first: Susumu

last: Goyama

first: Akiko

last: Matsumoto

first: Satoshi

last: Yamasaki

first: Tatsuhiro

last: Shibata

first: Toshio

last: Kitamura


title: Gene expression profiles of mESCs

city: beijing

first: zhao

middle: xue

last: tong

address: chaoyang District

institute: beijing institute of genomics

summary: The 24th recoverable satellite of China was designed specifically for experiments on microgravity physics and space life science that are collectively referred to as the SJ-10 programme. We participated in the SJ-10 programme using Rad9-/- mESCs and corresponding wild-type mESCs as study models, comparing the gene expression profiles of these models after 1 day or 5 days of culture in space to those of their counterparts on the ground

overall_design: We had 8 cell samples in total, which were designated as Space_R9wt_D1, Space_R9wt_D5, Space_R9del_D1, Space_R9del_D5, Ground_R9wt_D1, Ground _R9wt_D5, Ground _R9del_D1, Ground_R9del_D5

first: Lili

last: An

first: Yanming

last: Li

first: Yingjun

last: Fan

first: Ning

last: He

first: Fanlei

last: Ran

first: Hongzhu

last: Qu

first: Yanqiu

last: Wang

first: Xuetong

last: Zhao

first: Chen

last: Ye

first: Yuanda

last: Jiang

first: Xiangdong

last: Fang

first: Haiying

last: Hang


title: CXCR5+PD-1+ follicular helper CD8 T cells control B cell tolerance

status: Public on Aug 30 2019

city: Milwaukee

first: Robert

last: Burns

state: Wisconsin

address: 8727 W Watertown Plank Rd

institute: Blood Research Institute, Versiti


title: Gene expression profile of OSSL_325096 treated myeloma cells

city: Kumamoto

first: Yutaka

last: Okuno

state: Kumamoto

address: 1-1-1 Honko, Chuo Ku

department: Department of Hematology

institute: Kumamoto university of Medicine

summary: OSSL_325096 is a compound that acts as p97/VCP inhibitor and induces apoptosis in myeloma cells. Therefore, we treated KMS12PE and KMS11 myeloma cell lines with OSSL_325096 or DMSO and compare gene expression levels to elucidate the mechanisms of apoptosis.

overall_design: We treated KMS12PE and KMS11 myeloma cell lines with 1 μM OSSL_325096 or DMSO. RNA was extracted and purified using Trizol reagent (Thermo Fisher Scientific) and an RNeasy Mini Kit (Qiagen). Primary RNA-sequencing was performed by Novogene (Beijing, China). Raw sequence data was mapped to hg19 and expression values were determined as RPKM using Biomedical Genomics Workbench 5 software (QIAGEN Bioinformatics, Venlo, Netherlands). Then gene expression levels in two myeloma cell lines were compared using Biomedical Genomics Workbench 5 software.

first: Nao

last: Nishimura

first: Mohamed

middle: O

last: Radwan

first: Masayuki

last: Amano

first: Eri

last: Fujii

first: Hironori

last: Hayashi

first: Shinya

last: Endo

first: Shikiko

last: Ueno

first: Nina

first: Hiro

last: Tatetsu

first: Hiroyuki

last: Hata

first: Yoshinari

last: Okamoto

first: Masami

last: Otsuka

first: Hiroaki

last: Mitsuya

first: Matsuoka

last: Masao


title: CXCR5+PD-1+CD8+ T cells are a novel T helper cell sublineage and are negatively regulated by Stat5 [scRNA-Seq]

summary: Many autoimmune diseases are characterized by the production of autoantibodies. The current view is that CD4+ Tfh cells are the main subset regulating autoreactive B cells. Here, we discover a distinct novel CXCR5+PD1+ Tfh subset of CD8+ T cells whose development and function are negatively regulated by Stat5. These CD8+ Tfh cells regulate the GC B cell response and control autoantibody production. Deficiency of Stat5 in CD8+ T cells leads to an increase of CD8+ Tfh cells, resulting in the breakdown of B cell tolerance and autoantibody production. CD8+ Tfh share similar gene signatures with CD4+ Tfh and require CD40L/CD40 and TCR/MHCI interactions to deliver help to B cells. Our study highlights the diversity of follicular T cell subsets that contribute to the breakdown of B-cell tolerance

overall_design: Splenic CXCR5+PD-1+CD8+ T cells were sorted from LCMV-infected  Stat5+/+CD8Cre and Stat5fl/-CD8Cre mice (Armstrong, day8) or from Stat5+/+CD8CreIgHELsHEL and Stat5fl/-CD8CreIgHELsHEL mice, and subjected to sc-RNA-seq analysis.

first: Yuhong

last: Chen

first: Mei

last: Yu

first: Yongwei

last: Zheng

first: Renren

last: Wen

first: Demin

last: Wang


title: Distinct transcriptional roles for Histone H3-K56 acetylation during the cell cycle

status: Public on Aug 29 2019

city: Worcester

first: Salih

last: Topal

state: MA

address: 373 Plantation Street

institute: UMass Medical School

summary: H3K56Ac is a genome-wide activator of transcription. H3K56Ac has a major impact on transcription initiation, but it also appears to promote elongation and/or termination. In contrast, H3K56Ac represses promiscuous transcription that occurs immediately following replication fork passage, in this case by promoting efficient nucleosome assembly.  There is stepwise increase in transcription as cells transit S phase and enter G2, but this response to increased gene dosage does not require H3K56Ac. Thus, H3K56ac can exert both positive and negative impacts on transcription that are coupled to different cell cycle events.

overall_design: Native elongating transcript sequencing (NET-seq) in rtt109∆, H3K56R and ASF1-AA; TT-seq, 4sU-seq and RNA-seq in rtt109∆; Nascent chromatin avidin pull down (NChAP) in rtt109∆

first: Craig

middle: L

last: Peterson


title: MeCP2-E1 isoform is a dynamically expressed, weakly DNA-bound protein with different protein and DNA interactions compared to MeCP2-E2

status: Public on Aug 27 2019

city: Vancouver

first: Martin

last: Hirst

state: British Columbia

address: 2125 East Mall

department: Microbiology and Immunology

institute: University of British Columbia

summary: In this study we report differences between MeCP2 isoforms (DNA binding ability, degradation rates and genomic binding) that reflect non-overlapping functions of the 2 proteins.

overall_design: ChIP seq of MeCP2 isoforms E1 and E2in mice frontal cortexes euthanized at 2 different times of the day (12 a.m. and 12 p.m.)

first: Alexia

last: Martinez de Paz

first: Leila

last: Khajavi

first: Helene

last: Martin

first: Rafael

last: Claveria-Gimeno

first: Susanne

last: tom Dieck

first: Manjinder

last: Cheema

first: Jose

last: Sanchez-Mut

first: Malgorzata

last: Moksa

first: Annaïck

last: Carles

first: Nick

last: Brodie

first: Taimoor

last: Sheikh

first: Melissa

last: Freeman

first: Evgeniy

last: Petrotchenko

first: Christoph

last: Borchers

first: Erin

last: Schuman

first: Matthias

last: Zytnicki

first: Adrian

last: Velazquez-Campoy

first: Olga

last: Abian

first: Manel

last: Esteller

first: John

last: Vincent

first: Cecile

last: Malnou

first: Juan

last: Ausio


title: RNA-seq analysis of control and ZC3H18-depleted ovarian cancer cells

city: Rochester

first: Daniel

middle: Rothschild

last: OBrien

state: MN

address: 200 First St. SW

institute: The Mayo Clinic

summary: We report the differential gene expression in control versus ZC3H18-depleted OVCAR-8 cells

overall_design: Examination of mRNA profiles in two-independent ZC3H18 siRNA-transfected OVCAR-8 cells compared to control luciferase siRNA transfected cells. Three technical replicates per sample.

first: Karnitz

last: Larry

first: Kanakkanthara

last: Arun


title: Targets mediated microRNA arm-imbalance promotes gastric cancer progression

status: Public on Aug 28 2019

city: Beijing

first: Xu

middle: jia

last: yue

address: NO.3 Dongdan street, Beijing

institute: Peking Union Medical College

summary:
Two miRNA arms from the same precursor, miR-574-5p and miR-574-3p, were reversely expressed and played exact opposite role in gastric cancer progression. miR-574-5p/-3p ratio was also strongly correlated with higher TNM stages and shorter survival of patients. The increase of miR-574-5p/-3p ratio, or the arm-imbalance of miR-574 was due to the dynamic expression of their highly complementary targets in gastric carcinogenesis. The arm imbalance of miR-574 in turn strongly contributed to and further promoted gastric cancer progression.
Conclusion: Our findings indicated that targets mediated miR-574 arm-imbalance contributed to gastric cancer progression. Re-modification of the miR-574-targets homeostasis may represent a realistic approach for gastric cancer prevention and therapy.

overall_design: Uncover the driving force of miR-574 arm-imbalance in gastric carcinogenesis and their intrinsic physiological effects in gastric cancer progression

first: Zhengyi

last: Zhang

first: Jingnan

last: Pi

first: Dongling

last: Zou

first: Xiaoshuang

last: Wang

first: Jiayue

last: Xu

first: Yanni

last: Ma

first: Dong

first: Jia

last: Yu


title: Gene expression changes after depletion of Cyclin F and atypical E2Fs in HeLa cells.

city: Utrecht

first: Bart

last: Westendorp

address: Uppsalalaan 8

department: Molecular Health Sciences

institute: Utrecht University

summary: Using RNAi technology, Cyclin F, E2F7+8, or the combination of all proteins in were knocked down HeLa cells.  The goal was to study which gene expression programmes are altered by cyclin F depletion in G2/M cells. Furthermore, we had performed experiments suggesting that cyclin F mediates degradation of the atypical E2F repressor proteins E2F7 and E2F8. Therefore we investigated using combinatorial knockdown if additional depletion of E2F7/8 rescues gene expression changes caused by cyclin F. Our resuilts show that cyclin F depletion downregulates expression hundreds of E2F target genes, which could be prevented by additional E2F7/8 depletion.

overall_design: Cells were harvested 48 hours after transfection. Final concentration of each individual siRNA was 10 nM. Nocodazole (250 ng/mL) was added during the last 16 hours to collect all cells in G2/M-phase. Per time point we used 4 biological replicates. Control cells received a scrambled siRNA.


title: Lin28b controls a neonatal to adult switch in B cell positive selection

city: Lund

first: Jonas

last: Ungerback

address: Klinikgatan 26

department: Division of Molecular Hematology

institute: Lund University

summary: The ability of B-1 cells to become positively selected into the mature B cell pool, despite being  weakly self-reactive, has puzzled the field since its initial discovery. Here, we explore changes  in B cell positive selection as a function of developmental time by exploiting a link between  CD5 surface levels and the natural occurrence of self-reactive B cell receptors (BCRs) in BCR  wildtype mice. We show that the heterochronic RNA-binding protein Lin28b potentiates a  neonatal mode of B cell selection characterized by enhanced overall positive selection and the  developmental progression of CD5+ immature B cells in particular. Importantly, Lin28b  achieves this through amplifying the CD19/PI3K/c-Myc positive feedback loop and ectopic  Lin28b expression restores both positive selection and mature B cell numbers in CD19–/– adult  mice. Thus, the temporally restricted expression of Lin28b alters the rules for B cell selection  during ontogeny through modulating tonic signaling. We propose that this neonatal mode of B  cell selection represents a cell intrinsic cue to accelerate the de novo establishment of the  adaptive immune system and incorporate a layer of natural antibody mediated immunity  throughout life.

overall_design: BM cells from tet-Lin28b or WT mice fed DOX food for 2 weeks; or 3d old neonatal Lin28b wild-type, heterozygous or knockout mice

first: Stijn

last: Vanhee

first: Giorgia

last: Montano

first: Hugo

last: Åkerstrand

last: Ungerbäck

first: Joan

last: Yuan


title: RNAseq of souble factors in RPE cells from Cryba1 conditional knockout (cKO) mice

status: Public on Aug 26 2019

city: Pittsburgh

first: Sayan

last: Ghosh

state: PA

address: 4401 Penn Avenue

department: Ophthalmology

institute: University of Pittsburgh

summary: The study was aimed at understanding the expression of known neutrophil regulating factors in the retinal pigment epithelium (RPE) cells with increasing age in a mouse model (Cryba1 cKO, mice lacking gene which codes for beta A3/A1-crystallin protein only in the RPE cells) of age-related macular degeneration

overall_design: The samples are RPE cells harvested from the mouse eyes from control (Cryba1 floxed/WT) and Cryba1 cKO animals at 5 months and 10 months old

first: Debasish

last: Sinha


title: Hair follicle stem cells (HF-SCs) can initiate psoriasis-like disease in mice

status: Public on Aug 23 2019

city: Madrid

first: Osvaldo

last: Graña

state: Comunidad de Madrid

address: C/ Melchor Fernández Almagro, 3

department: Structural Biology

country: Spain

institute: CNIO

summary: Using lineage-tracing in a well-established psoriasis-like mouse model with inducible epidermal deletion of c-Jun and JunB, we found that mutant HF-SCs survive and express a broad group of pro-inflammatory cytokines, whereas mutant inter-follicular epidermal cells (IFE) disappear over time. Mutant HF-SCs initiate epidermal hyperplasia and skin inflammation by priming neighboring non-mutant epidermal cells to acquire a psoriasis-like phenotype. To explore the molecular mechanisms that govern the behavior of these distinct mutant and non-mutant HF-SCs and IFE cell populations during psoriasis-like disease, RNA sequencing analyses of sorted GFP+, Tomato+ HF-SCs and b-KCs from DKO*-mT/mG mice.

overall_design: Whole-genome transcriptomic analysis was performed by Next-Gen RNA-sequencing in four groups of psoriatic-like epidermal subpopulations: MutantGFP, non-mutantTom basal keratinocytes, mutantGFP and non-mutantTom hair follicle stem cells were purified from the ears of three independent psoriatic-like DKO* mice after 7 days of tamoxifen induction. RNA-seq was also performed in control basal keratinocytes and hair follicle stem cells from the ears of three Control-mT/mG mice.

first: Nuria

last: Gago-López

last: Grana

first: Guillermo

last: Martín-Serrano

first: Erwin

last: Wagner