title: Transcriptome analysis of HeLa cells knocked down for EXT1 or FBXW7 gene expression

status: Public on Sep 25 2020

city: Liège

first: Jean-Claude

last: Twizere

state: Liège

address: CHU - B34 Quartier Hôpital Avenue de l'Hôpital,11

department: Molecular Biology of Diseases

country: Belgium

institute: GIGA Institute

summary: Exostosin-1 (EXT1) is an ER-resident glycosyltransferase known to polymerize heparan sulfate chain by sequential addition of glucuronic acid and N-acetylglucosamine molecules. This reaction results in heavily glycosylated proteoglycans (PG) at the plasma membrane, which form cell-type specific complexes and play vital roles in cell-cell and cell-pathogens interactions, cell growth, plasticity and proliferation in the local tissue environment. We found that EXT1 interact with a number of intracellular proteins including FBXW7 and hypothesized that both proteins cooperate in targeted protein degradation.

overall_design: Examination of transcriptomic differences following knockdown of EXT1 or FBXW7.

first: Sarah

last: Daakour

first: Leon

last: Hajingabo

first: Despoina

last: Kerselidou


title: Single cell RNA-sequencing of murine dermal cells and hindlimb skeletal muscle stromal cells.

status: Public on Sep 29 2020

city: Berkeley

first: Junren

last: Sia

state: California

address: 156 Stanley Hall

department: Bioengineering

country: USA

institute: University of California, Berkeley

type: Expression profiling by high throughput sequencing

summary: Traumatic injury often results in muscle loss and impairment, which is worsened under aged and diseased conditions. Activation of resident stem cells or transplantation of myogenic stem cells can promote muscle regeneration. However, major challenges remain in harvesting sufficient autologous myogenic stem cells and expanding such cells efficiently for muscle regeneration therapies. Here, we identified a chemical cocktail that selectively induced a robust expansion of myogenic stem cells from readily-obtainable dermal cells and from muscle stromal cells. By differential plating and lineage tracing, we showed that Pax7+ cells were the major source for chemical-induced myogenic stem cells (CiMCs). We further performed single-cell RNA sequencing (scRNA-seq) analysis to characterize the transcriptomic profile of CiMCs and demonstrate a specific expansion of myogenic cells from heterogeneous dermal cell population. Upon transplantation into the injured muscle, CiMCs were efficiently engrafted and improved functional muscle regeneration in both adult and aged mice. In addition, CiMC transplantation rescued muscle function in mice with Duchenne muscular dystrophy (DMD). Furthermore, an in situ therapeutic modality using this cocktail was developed by loading the chemical cocktail into injectable nanoparticles, which enabled a sustained release of the cocktail in injured muscle and a local expansion of resident satellite cells for muscle regeneration in adult and aged mice. These findings will lead to the development of novel in vitro and in situ stem cell therapies for effective skeletal muscle repair.

overall_design: Freshly isolated neonatal dermal cells, neonatal dermal cells treated with FR medium for 3 days, adult dermal cells treated with FR medium for 3 days and freshly isolated adult hindlimb skeletal muscle stromal cells were subjected to single cell RNA sequencing. FR medium is 20 μM F, 20 μM R, 50 μg/ml AA, and 50 ng/ml bFGF in high-glucose DMEM containing 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin.

first: Jun

last: Fang

first: Song

last: Li


title: NimbleGen Sequence Capture Array in A549 cells after 125I seed irradiation

status: Public on Oct 23 2020

city: Guangzhou

first: Mingjian

last: Lu

state: China

address: No.78 Hengzhigang Road, Guangzhou ,P.R.China

country: China

institute: State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center (SYSUCC)

summary:
Purpose:To investigate the biological behavior on the invation, proliferation, and apoptosis, and the molecular mechanism of A549 cell which induced by 125I seed irradiation.
Design:The first part cell Experiment: cultured A549 cell in vitro, then divided into 125I seeds group and control group. Using MTT, Transwell experiment, flow cytometric analysis the difference among cell proliferation, invasion, and apoptosis, after 125I seeds different treatment time on the A549 cell. Nimblegen human genome microarray detection to find out the genes expression changes between the two groups. Then screen out target gene, using protein chip technology and western-blot further verified target gene protein expression.

overall_design: Nimblegen whole genome expression microarray detection found 33 differences changing in the signal pathway, and 622 differences changing in genes. According to GO (Gene Ontology) Analysis and abundance of integral (Enrichment Score) Screen out MAPK pathway and MDM2 gene which is closely related to proliferation and apoptosis for further study.

first: Tao

last: Zhang

first: Zhiqiang

last: Mo


title: The Histone Methyltransferase Setd2 Modulates Oxidative Stress to Attenuates Colonic Inﬂammation and Tumorigenesis

city: shanghai

first: min

last: liu

address: huashan road

institute: shanghaijiaotong university

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: Single cell RNAseq reveal covid19 patient immune response

status: Public on Sep 24 2020

city: los angeles

first: Changfu

last: Yao

state: Ca

address: 8700 Beverly Blvd. AHSP Room A9401

department: Lung and Regenerative Medicine Institutes

institute: cedars-sinai medical center

summary: Eighteen patients admitted to CSMC and diagnosed with COVID19 by RT-PCR were stratified into COVID19 mild/moderate, severe, and recovery groups (n=5-6/group). Venous blood was collected into EDTA coated tubes and centrifuged to separate plasma and buffy coat. Plasma was collected and frozen at -80C, and the buffy coat was collected into cryo-preservation media and frozen at -80C.  Recovered cells are sorted for live-dead staining, then  fixed with methanol. Fixed single cells were further captured using 10x chromium Next GEM 3 prime v3.1 kit. Two patients samples from the same group were mixed, captured and sequenced together.

overall_design: single-cell RNA-seq of blood buffy coat from COVID-19 patients.

first: Peter

last: Chen


title: RNA Sequencing of the Androgen-Regulated Transcriptome in Human and Mouse Granulosa Cells

status: Public on Sep 19 2020

city: Rochester

first: Cameron

last: Baker

state: NY

address: 601 Elmwood Ave

institute: University of Rochester

summary: Considering the well-documented importance of androgens in the female reproductive system and particularly in maintenance of the ovarian follicular reserve, follicle growth and granulosa cell proliferation, we hypothesized that activation of the androgen receptor in granulosa cells with DHT induces significant changes in gene transcription. To determine the AR-regulated gene transcriptome in mouse granulosa cells, we treated female mice aged 18 weeks (n=5) with an introperitoneal injection of dihydrotestosterone (DHT, 29 mcg) in a vehicle of 90% sesame oil and 10% ethanol in a total volume of 100 microliters. 18 hours later, granulosa cells were harvested and mRNA was isolated for RNA sequencing. Surprisingly, no genes were differentially expressed in the granulosa cells obtained from DHT-treated compared with vehicle-treated mice. We then assessed the AR-regulated transcriptome in DHT-treated human granulosa-derived KGN cells. After 24 hours of serum starvation, KGN cells were treated with 25 nM DHT or ethanol for 12 hours in five independent experiments, then RNA was extracted for RNA sequencing. In paired analysis to eliminate inter-experimental variability, 173 genes were differentially expressed in DHT-treated compared with vehicle-treated cells. Of these, 125 genes were upregulated by DHT and 48 genes were downregulated by DHT. However, the fold change in expression was very small (ranging from 0.87 to 1.37, DHT vs vehicle). Although these differences were statistically signficant in paired analysis, they are unlikely to be of biological significance due to such small fold changes in expression. We conclude that AR likely has negligible gene-transcription activity in granulosa cells. Importantly, these experiments were not designed to capture any changes in non-coding RNAs.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Granulosa cell mRNA profiles of DHT- versus vehicle-treated mice; mRNA profiles of DHT- versus ethanol-treated KGN cells.

first: Olga

last: Astapova

first: Christina

last: Seger

first: Stephen

middle: R

last: Hammes


title: Increased hippocampal excitability in miR-324-null mice

status: Public on Sep 23 2020

city: NEWCASTLE UPON TYNE

first: David

last: Young

address: Centre For Life

country: United Kingdom

institute: Newcastle University

summary: MicroRNAs are non-coding RNAs that act to downregulate the expression of target genes by translational repression and degradation of messenger RNA molecules. Individual microRNAs have the ability to specifically target a wide array of gene transcripts, therefore allowing each microRNA to play key roles in multiple biological pathways. miR-324 is a microRNA predicted to target thousands of RNA transcripts and is expressed far more highly in the brain than in any other tissue, suggesting that it may play a role in one or multiple neurological pathways. Here we present data from the first global miR-324-null mice, in which increased excitability and interictal discharges were identified in vitro in the hippocampus. RNA sequencing was used to identify differentially expressed genes in miR-324-null mice which may contribute to this increased hippocampal excitability, and 3’UTR luciferase assays revealed that some of these genes are novel direct targets of miR-324. Characterisation of microRNAs that produce an effect on neurological activity, such as miR-324, and identification of the pathways they regulate will allow a better understanding of the processes involved in normal neurological function and in turn may present novel pharmaceutical targets in treating neurological disease.

overall_design: RNA was extracted from the hippocampi of 5 miR-324-null and 5 wild-type mice using the mirVana miRNA Isolation Kit (Thermo Fisher Scientific), following the manufacturer’s protocol to isolate total RNA, and was sequenced using an Illumina NextSeq 500.

first: Dan

middle: J

last: Hayman

first: Tamara

last: Modebadze

last: Charlton

first: Kat

last: Cheung

first: Jamie

last: Soul

first: Yao

last: Hao

first: Hua

last: Lin

first: Colin

middle: G

last: Miles

first: Dimitra

last: Tsompani

first: Robert

middle: M

last: Jackson

first: Michael

middle: D

last: Briggs

first: Katarzyna

middle: A

last: Piróg

first: Ian

last: Clark

first: Matt

last: Barter

first: Gavin

last: Clowry

first: Fiona

middle: E

last: LeBeau


title: SARS-CoV2 infection of iPSC-derived cardiac cells predicts novel cytopathic features in COVID-19 patients

status: Public on Sep 21 2020

city: San Francisco

first: Todd

last: McDevitt

state: CA

address: 1650 Owens St

department: GICD

institute: Gladstone Institutes

summary: Mounting clinical evidence indicates severe pathological consequences from COVID-19 in the heart. Here we examine cardiac susceptibility and response to SARS-CoV-2 using human induced pluripotent stem cell-derived cardiomyocytes, cardiac fibroblasts, and endothelial cells. Of these cell types, SARS-CoV-2 can only productively infect cardiomyocytes, and does so via an endolysosomal mechanism. Transcriptomic profiling of infected cells revealed changes in protein homeostasis and cardiomyocyte contractility, and activation of innate immune response pathways. In addition, we observed a striking pattern of myofibrillar fragmentation, with specific cleavage at the M-line. Numerous cardiomyocytes also lacked nuclear DNA in tissue culture experiments and COVID-19 autopsy specimens. These novel cardiac pathologies induced by SARS-CoV-2 strongly motivate the development of targeted cardioprotective strategies to prevent acute and long-term heart failure in COVID-19 patients.

overall_design: human induced pluripotent stem cells (iPSCs) and iPSC-derived cardiomyocytes, cardiac fibroblasts, and endothelial cells were infected with SARS-CoV-2 and compared with uninfected cells 48 hours after infection, at several multiplicities of infection.

first: Juan

last: Pérez-Bermejo

first: Serah

last: Kang

first: Sarah

last: Rockwood

first: Camille

last: Simoneau

last: Joy

first: Gokul

middle: N

last: Ramadoss

first: Ana

middle: C

last: Silva

first: Will

last: Flanigan

first: Huihui

last: Li

first: Ken

last: Nakamura

first: Melanie

last: Ott

first: Bruce

last: Conklin


title: Bi-directional Impacts of Heterotypic Interactions in Engineered 3D Human Cardiac Microtissues Revealed by Single-Cell RNA-Sequencing and Functional Analysis

summary: Technological advancements have enabled the design of increasingly complex engineered tissue constructs, which better mimic native tissue cellularity. Therefore, dissecting the bi-directional interactions between distinct cell types in 3D is necessary to understand how heterotypic interactions at the single-cell level impact tissue-level properties. We systematically interrogated the interactions between cardiomyocytes (CMs) and cardiac non-myocytes in 3D self-assembled tissue constructs in an effort to determine the phenotypic and functional contributions of cardiac fibroblasts (CFs) and endothelial cells (ECs) to cardiac tissue properties. One week after tissue formation, cardiac microtissues containing CFs exhibited improved calcium handling function compared to microtissues comprised of CMs alone or CMs mixed with ECs, and CMs cultured with CFs exhibited distinct transcriptional profiles, with increased expression of cytoskeletal and ECM-associated genes. However, one month after tissue formation, functional and phenotypic differences between heterotypic tissues were mitigated, indicating diminishing impacts of non-myocytes on CM phenotype and function over time. The combination of single-cell RNA-sequencing and calcium imaging enabled the determination of reciprocal transcriptomic changes accompanying tissue-level functional properties in engineered heterotypic cardiac microtissues.

overall_design: 11 samples of different combinations of cardiac cell types at different timepoints were analyzed (Day 0/input: CM+EC, CM+fCF, CM+aCF; Day 7: CM alone, CM+EC, CM+fCF, CM+aCF; Day 30: CM alone, CM+EC, CM+fCF, CM+aCF)

first: Tracy

last: Hookway

first: Oriane

middle: B

last: Matthys

first: David

first: Jessica

last: Sepulveda

first: Reuben

last: Thomas


title: The SBE7 enhancer is active in Shh expressing brain tissue at E10.5

status: Public on Sep 17 2020

city: Edinburgh

first: Robert

last: Hill

address: MRC Human Genetics Unit, Crewe Road South

institute: MRC Human Genetics Unit

summary: Using ATAC-seq, we identified an accessible chromatin region within the Shh expressing cell population of eGFP/Cre-Shh mice, which did not correspond to SBE2-4. This open region displayed high levels of vertebrate conservation, and did not map to a known CTCF site. Further analysis revealed the coordinates of this presumptive active enhancer to correspond to the recently identified SBE7 enhancer.

overall_design: ATAC-seq on GFP positive cell population from entire E10.5 day Shh-GFP mouse head.

first: Zoe

last: Crane-Smith


title: Pharmacological inhibition of the HEG1-KRIT1 interaction

status: Public on Sep 07 2020

city: La Jolla

first: Alexandre

last: Gingras

address: 9500 Gilman Drive

department: Medicine

institute: UCSD

summary: The Krüppel-like Factors 4 and 2 (KLF4/2) are transcription factors and master regulators of endothelial cells (ECs) phenotype and homeostasis. KLF4/2 are important blood-flow-responsive genes within ECs that differentially regulate the expression of factors that confer anti-inflammatory, antithrombotic, and antiproliferative effects in ECs. Genetic inactivation of endothelial HEG1 (Heart of glass) or KRIT1 (Krev interaction trapped protein 1) lead to upregulation of KLF4/2 expression levels. Furthermore, increased expression of thrombomodulin (THBD) and suppression of thrombospondin (THBS1) was ascribed to elevation of KLF4/2 as a result of loss of endothelial KRIT1. Here, we developed a high-throughput screening assay to identify inhibitors of the HEG1-KRIT1 interaction and identified, HEG1-KRIT1 inhibitor 1 (HKi1), as a promising hit inhibitor. The crystal structure of HKi1 bound to the KRIT1 FERM domain confirmed the primary screening results and ultimately led to the identification of a fragment-like inhibitor (HKi3), which occupies the HEG1 pocket producing comparable activity. These findings suggest that these inhibitors block the interaction by competing with the HEG1 for binding to KRIT1 FERM domain. Moreover, our results demonstrate that HKi3 upregulates KLF4/2 gene expression in two types of human ECs. These results reveal that acute pharmacological inhibition of the HEG1-KRIT1 interaction rapidly induces expression of KLF4/2 and their important transcriptional targets thrombomodulin and thrombospondin.

overall_design: HUVECs were cultured in M199 medium (Sigma) supplemented with 10% FBS, 4 U/ml heparin, 3 ng/ml β-EC growth factor (sigma), 4 U/ml heparin, and 100 units/ml penicillin-streptomycin.  HUVECs were treated with a HEG-KRIT1 inhibitor (HKi3) or vehicle control (DMSO) for 24 hours. Four biological replicates were generated for vehicle control conditions and five replicates were generated for HKi3 treatment conditions. Following treatment, total mRNA was extracted, processed, and sequenced on a Illumina HiSeq4000.

first: Brendan

last: Gongol

first: John

last: Shyy


title: Novel lncRNA KILN siRNA knockdown in human aortic smooth muscle cells (HASMCs)

city: Augusta

first: Xiaochun

last: Long

state: GA

address: 1460 Laney Walker Blvd, CL-3004

department: Vascular Biology Center

institute: Augusta University

summary: The goal of this study is to define the transcriptome regulated by novel lncRNA KILN under baseline and proinflammatory conditions

overall_design: We transfected the HASMCs with two individual siRNAs,  siKILN1, siKILN2, and mixture of siKILN1+siKILN2. Cells were then starved overnight followed by the treatment of IL1b (4 ng/ml) for 24 hrs before total RNA extraction for sequencing.

first: Wei

last: Zhang

first: Jinjing

last: Zhao

first: Joseph

last: Miano


title: NFIB induces functional astrocytes from human pluripotent stem cell-derived neural precursor cells mimicking in vivo astrogliogenesis

status: Public on Sep 11 2020

city: Seongbuk-gu

first: Gyu-Bum

last: Yeon

state: Seoul

address: 145, Anam-ro

department: Department of Biodtechnology

country: South Korea

institute: Korea University

summary: The ability to generate astrocytes from human pluripotent stem cells (hPSCs) offers a promising cellular model to study the development and physiology of human astrocytes. However, the extant methods for generating functional astrocytes required long culture periods and remained much ambiguity whether their paradigm follows the innate developmental program. In this report, we provided an efficient and rapid method for generating physiologically functional astrocytes from hPSCs. Overexpressing the nuclear factor IB (NFIB) in hPSC-derived neural precursor cells (NPCs) induced a highly enriched astrocyte population in 2 weeks. RNA sequencing and functional analyses demonstrated progressive transcriptomic and physiological changes in the cells, resembling in vivo astrocyte development. Further analyses substantiated previous results and established the MAPK pathway necessary for astrocyte differentiation. Hence, this differentiation paradigm provides a prospective in vitro model for human astrogliogenesis studies and pathophysiology of neurological diseases concerning astrocytes.

overall_design: RNA-seq time-course analysis of hPSC-derived neural precursor cells (NPCs) overexpressing nuclear factor IB (NFIB).

first: Dae-Sung

last: Kim


title: Transcriptomic analysis of the body wall of farmed sea cucumber Isostichopus badionotus specimens

status: Public on Sep 01 2020

city: MADRID

first: ROBERTO

last: MARTIN-HERNANDEZ

address: CANTOBLANCO

department: BIOSTATISTICS AND BIOINFORMATICS UNIT

country: Spain

institute: IMDEA ALIMENTACION

summary: These data corresponds to RNA-Seq assays obtained from the body wall of farmed I. badionotus juveniles samples. These raw reads were used to evaluate differential gene expression between wild and farmed Isostichopus badionotus specimens. With this aim, a de-novo transcriptome assembled from wild specimens was used as reference. Further information about de-novo assembled transcriptome is available within the BioProject PRJNA639785.

overall_design: Body wall samples from 6 farmed juveniles specimens (captivity).

first: Roberto

last: Martin Hernández

first: Rossana

last: del Pilar Rodriguez Canul


title: Two distinct immunopathological profiles in lungs of lethal COVID-19

status: Public on Sep 02 2020

city: Liestal

first: Ronny

last: Nienhold

address: Mühlemattstrasse 11

department: Institute of Pathology

country: Switzerland

institute: Cantonal Hospital Baselland

summary: Immune responses in lungs of Coronavirus Disease 2019 (COVID-19) are poorly characterized. We conducted transcriptomic, histologic and cellular profiling of post mortem COVID-19 and normal lung tissues. Two distinct immunopathological reaction patterns were identified. One pattern showed high expression of interferon stimulated genes (ISGs) and cytokines, high viral loads and limited pulmonary damage, the other pattern showed severely damaged lungs, low ISGs, low viral loads and abundant immune infiltrates. Distinct patterns of pulmonary COVID-19 immune responses correlated to hospitalization time and may guide treatment and vaccination approaches.

overall_design:
Here we analyzed 34 post mortem lung samples from 16 deceased COVID-19 patients and 9 post mortem lung samples from 6 patients who died from non-infectious causes.
Please note that each processed data file was gnerated from muliptle samples, as indicated in the corresponding sample description field.

first: Yari

last: Ciani

first: Viktor

middle: H

last: Koelzer

first: Alexandar

last: Tzankov

first: Jasmin

last: Haslbauer

first: Thomas

last: Menter

first: Nathalie

last: Schwab

first: Maurice

last: Henkel

first: Veronika

last: Zsikla

first: Niels

last: Willi

first: Werner

last: Kempf

last: Hoyler

first: Mattia

last: Barbareschi

first: Holger

last: Moch

first: Markus

last: Tolnay

first: Gieri

last: Cathomas

first: Francesca

last: Demichelis

first: Tobias

last: Junt

first: Kirsten

last: Mertz


title: Electrophysiological Maturation of Cerebral Organoids Correlates with Dynamic Morphological and Cellular Development

status: Public on Aug 28 2020

city: Columbus

first: Summer

middle: Rose

last: Fair

state: OH

address: 575 Children's Crossroad

department: Institute for Genomic Medicine

institute: Nationwide Children's Hospital

summary: Cerebral organoids (COs) are rapidly accelerating the rate of translational neuroscience based on their potential to model complex features of the developing human brain. Several studies have examined the electrophysiological and neural network features of COs; however, no study has comprehensively investigated the developmental trajectory of electrophysiological properties in whole-brain COs and correlated these properties with developmentally-linked morphological and cellular features. Here, we profiled the neuroelectrical activities of COs over the span of five months with a multi-electrode array (MEA) platform and observed the emergence and maturation of several electrophysiologic properties, including rapid firing rates and network bursting events. To complement these analyses, we characterized the complex molecular and cellular development that give rise to these mature neuroelectrical properties with immunohistochemical and single-cell transcriptomic analyses. This integrated approach underscores the value of COs as an emerging model system of human brain development and neurological disease.

overall_design: Comparison of two organoid culture timepoints.

first: Mark

last: Hester

first: Tracy

last: Bedrosian


title: Gene expression data for tumor and paired adjacent normal tissues from colorectal cancer patients

status: Public on Aug 18 2020

city: Zhuhai

first: Hong-Wei

last: Sun

address: 79 Kangning Road

department: The Affiliated Hospital of Beijing Institute of Technology (Zhuhai People's Hospital)

institute: Beijing Institute of Technology

summary: We have employed whole genome microarray to compare the gene expression profile of tumor tissues and paired adjancent normal colonic tissues from six colorectal cancer patients.

overall_design: Paired fresh tumor and non-tumor tissues obtained from six patients with CRC were used for microarray analysis.

first: Limin

last: Zheng


title: Gene expression data from mouse conventional dendritic cells (cDC) [Batf, Batf3 DKO]

status: Public on Aug 13 2020

city: Saint Louis

first: Sunkyung

last: Kim

state: MO

address: Clinical Science Research Building, 7th Floor, Room 7701A, Campus Box 8118

department: Department of Pathology and Immunology

institute: Washington University School of Medicine

summary: We used microarrays to understand roles of BATF proteins in the regulation of cDC-specific gene expression.

overall_design: Splenic cDCs were sort-purified from WT or Batf–/– Batf3–/– mice for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain gene expression signature that are controlled by BATF proteins for cDC populations.

first: Kenneth

last: Murphy


title: Gene expression data from mouse conventional dendritic cells (cDC) [IRF4,IRF8 DKO]

summary: We used microarrays to detail cDC gene expression program controlled by IRF4 and IRF8.

overall_design: cDCs developed from Irf4–/– Irf8–/– bone marrow (BM) progenitors expressing retroviral Irf4 or Irf8 at low and high levels were sort-purified for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain gene expression signature for cDC populations that are commonly or specifically controlled by IRF4 and IRF8.

first: Tiantian

last: Liu


title: Regulation of islet function and gene expression by prolactin during pregnancy

status: Public on Aug 25 2020

city: Calgary

first: Carol

last: Huang

state: AB

address: 3330 Hospital Dr NW

department: Biochemistry and Molecular Biology

country: Canada

institute: University of Calgary

summary: Pancreatic islets adapt to insulin resistance of pregnancy by up regulating beta-cell proliferation and increase insulin secretion.  Previously, we found that prolactin receptor (Prlr) signaling is important for this process, as heterozygous prolactin receptor-null (Prlr+/-) mice are glucose intolerant, had a lower number of beta cells and lower serum insulin levels than wild type mice during pregnancy. However, since Prlr expression is ubiquitous, to determine its beta-cell-specific effects, we generated a transgenic mouse with a floxed Prlr allele under the control of an inducible promoter, i.e. bPrlR-/- mice, allowing conditional deletion of Prlr from beta cells in adult mice.  In this study, we found that beta-cell-specific Prlr reduction resulted in elevated blood glucose during pregnancy. Similar to our previous finding in mice with global Prlr reduction, beta-cell-specific Prlr loss led to a lower beta-cell mass and a lower in vivo insulin level during pregnancy. However, these islets do not have an intrinsic insulin secretion defect when tested in vitro. Interestingly, when we compared the islet gene expression profile, using islets isolated from mice with global versus beta-cell-specific Prlr reduction, we found differences in expression of genes that regulate apoptosis, synaptic vesicle function and neuronal development. Indeed, islets from pregnant Prlr+/- mice are more susceptible glucolipotoxicity than bPrlR+/- islets. These observations suggest that Prlr has both cell-autonomous and non-cell-autonomous effect on beta cells, beyond its regulation of pro-proliferative genes.

overall_design: A total of 7 samples were included. Heterozygous whole body knock-out mice (N=3) obtained from Jackson Laboratory were used as a reference to compare to conditional Plr deletion in beta pancreatic cells (n=4). (Pdx1CreERTM:PrlR-/- ). Breifly, the confitional ready lines (Tm1a) were obtained from  EUCOMM (The European Conditional Mouse Mutagenesis Program) and generated by breeding with FLPeR mice (The Jackson Laboratories) (Tm1c) and then Pdx1CreERTM mouse (from Mutant Mouse Resource & Research Centers supported by NIH, Stock No.:000350-UCD) (Tm1d). At 3-4 months of age,  heterozygous whole-body and homozyous conditionally deleted Plr knock-out mice were bred to wild-type males and islets were isolated at gestational day 15.

first: Vipul

last: Shrivastava

first: Megan

last: Lee

first: Marle

last: Pretorius

first: Bethany

last: Radford

first: Guneet

last: Makkar


title: Comprehensive analysis of the complexity and heterogeneity of the lncRNAs transcriptome in multiple myeloma

status: Public on Aug 05 2020

city: Pamplona

first: Xabier

last: Agirre

state: Navarra

address: Pio XII, 55

department: Oncology

institute: CIMA

summary: ssRNA-seq analysis of the transcriptional landscape of 38 multiple myeloma patients

overall_design: Bone marrow aspiration specimens from 38 newly diagnosed MM patients were obtained. MM plasma cells were purified by CD138+ positive magnetic separation using AutoMACS system. Total RNA was isolated using TRIzol® Reagent extraction method.

first: Felipe

last: Prosper

first: Teresa

last: Ezponda

first: Arantxa

last: Carrasco-Leon


title: Single-cell transcriptomic phenotyping combined with lineage tracing using paired B cell receptor repertoires identified both persistent antibody-secreting cell as well as memory B cell subsets after immunotherapy.

status: Public on Aug 03 2020

city: New Haven

first: Steven

last: Kleinstein

state: Ct

address: 300 George St.

department: Pathology

institute: Yale University

summary: Disease relevant B cells during post-rituximab (RTX)relapseemerge from the unsuccessfuldepletion of pre-existing B cell clones; single-celltranscriptomic phenotyping combined with lineage tracing using paired B cell receptor repertoires identified both persistent antibody-secreting cell as well as memory B cellsubsets.

overall_design: Examination of gene expression in B-lymphocytes utilizing 10X Genomics single-cell technology, deep sequenced on Illumina NovaSeq.

first: Ruoyi

last: Jiang

first: Kevin

last: O’Connor


title: Leukemia cell of origin influences apoptotic priming and sensitivity to LSD1 inhibition

status: Public on Jul 29 2020

city: New York

first: Richard

last: Koche

state: New York

institute: Memorial Sloan Kettering Cancer Center

summary: Previous studies have established that the cell of origin of oncogenic transformation is a determinant of therapeutic sensitivity. However, the mechanisms governing cell-of-origin-driven differences in therapeutic response have not been delineated. Leukemias initiating in hematopoietic stem cells (HSC) are less sensitive to cytotoxic chemotherapy and express high levels of the transcription factor Evi1 compared to leukemias derived from myeloid progenitors. Here, we compared drug sensitivity and expression profiles of murine and human leukemias initiated in either HSCs or myeloid progenitors to reveal a novel function for Evi1 in modulating p53 protein stability and activity. HSC-derived leukemias exhibit decreased apoptotic priming, attenuated p53 transcriptional output, and resistance to lysine-specific demethylase 1 inhibitors in addition to classical genotoxic stresses. p53 loss-of-function in Evi1low progenitor-derived leukemias induces resistance to LSD1 inhibition. By contrast, Evi1high leukemias are sensitized to LSD1 inhibition by the BH3 mimetic venetoclax, resulting in enhanced apoptosis and greater reductions in disease burden. Our findings demonstrate a cell-of-origin determined novel role for EVI1 in p53 wild-type cancers in reducing p53 function and provide a strategy to circumvent drug resistance in high-risk, chemoresistant EVI1high AML.

overall_design: RNA-seq of bone marrow-derived stem and progenitor cells transformed by MLL-AF9

first: Sheng

middle: F

last: Cai

middle: P

first: Ross

middle: L

last: Levine

first: Scott

last: Armstrong


title: Phenotypic plasticity underlies local invasion and distant metastasis in colon cancer (Single cell RNA-Seq)

status: Public on Jul 23 2020

city: Rotterdam

first: Mathijs

last: Verhagen

address: Doctor Molewaterplein 40

country: Netherlands

institute: Erasmus Medical Center

summary: Phenotypic plasticity and partial EMT underlie local invasion and distant metastasis in colon cancer. CD44highEpCAMhigh and CD44highEpCAMlow single cell RNAseq profiles of colon cancer cell lines HCT116 and SW480.

first: M

last: Teeuwssen

first: A

last: Sacchetti

first: H

last: van de Werken

first: R

last: Fodde


title: Transcriptomes of MCSF- and MUC1-ST-treated monocyte derived human macrophages

status: Public on Sep 24 2020

city: London

last: Beatson

address: Innovation Hub, Cancer Centre, Guys Hospital

department: School of Cancer & Pharmaceutical Sciences

institute: King's College London

summary: RNAseq was used to analyse transcriptomic differences between matched healthy human MCSF-treated macrophages and MUC1-ST-treated macrophages

overall_design:
PolyA RNA analysis of matched monocytes treated with MCSF (50ng/ml every 3 days) or 100ug/ml (day 0) MUC1-ST in serum-free media. Samples run on Illumina HiSeq2500 for 25 cycles

The file 'sample_metadata.xls' (available at the foot of this record) provides additional sample metadata and SRR ID for each raw file included in this study such as sequencing batch ID lane number.

first: Domenico

last: Cozzetto


title: Phenotypic plasticity underlies local invasion and distant metastasis in colon cancer (Bulk RNA-Seq)

summary: Phenotypic plasticity and partial EMT underlie local invasion and distant metastasis in colon cancer. CD44highEpCAMhigh and CD44highEpCAMlow RNAseq profiles of colon cancer cell lines HCT116 and SW480.

overall_design: CD44highEpCAMhigh and CD44highEpCAMlow RNAseq profiles of colon cancer cell lines HCT116 and SW480, in triplicate.


title: Enhancer-promoter interactions in acheiropodia patient's cells

status: Public on Jul 30 2020

first: Nadav

last: Ahituv

address: 1550 4th Street

institute: UCSF

summary: Acheiropodia, congenital limb truncation, is associated with homozygous deletions in the LMBR1 gene around ZRS, an enhancer regulating SHH during limb development. How these deletions leads to this phenotype is unknown. Using whole-genome sequencing, we fine-mapped the acheiropodia-associated region to 12 kb and show that it does not function as an enhancer. CTCF and RAD21 ChIP-seq together with 4C-seq and DNA FISH identify three CTCF sites within the acheiropodia-deleted region that mediate the interaction between the ZRS and the SHH promoter. This interaction is substituted with other CTCF sites centromeric to the ZRS in the disease state. Mouse knockouts of the orthologous 12 kb sequence have no apparent abnormalities, showcasing the challenges in modelling CTCF alterations in animal models due to inherent motif differences between species. Our results show that alterations in CTCF motifs can lead to a Mendelian condition due to altered enhancer-promoter interactions.

overall_design:
Examination of CTCF and RAD21 binding in SHH locus using wild-type and acheiropodia patient cells.   Examination of chromatin structure in SHH locus using wild-type and acheiropodia patient cells.
Please note that each *bw file was generated from both ChIP-seq and INPUT samples, and is linked to the corresponding ChIP-seq sample records.

first: Jingjing

last: Zhao

first: Aki

last: Ushiki

first: Kirsty

last: Jamieson


title: Systems biological assessment of immunity to severe and mild COVID-19 infections

status: Public on Jul 31 2020

city: Atlanta

first: Gregory

middle: K

last: Tharp

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

summary: The recent emergence of COVID-19 presents a major global crisis. Profound knowledge gaps remain about the interaction between the virus and the immune system. Here, we used a systems biology approach to analyze immune responses in 76 COVID-19 patients and 69 age and sex- matched controls, from Hong Kong and Atlanta. Mass cytometry revealed prolonged plasmablast and effector T cell responses, reduced myeloid expression of HLA-DR and inhibition of mTOR signaling in plasmacytoid DCs (pDCs) during infection. Production of pro-inflammatory cytokines  plasma levels of inflammatory mediators, including EN-RAGE, TNFSF14, and Oncostatin-M, which correlated with disease severity, and increased bacterial DNA and endotoxin in plasma in  and reduced HLA-DR and CD86 but enhanced EN-RAGE expression in myeloid cells in severe  transient expression of IFN stimulated genes in moderate infections, consistent with transcriptomic analysis of bulk PBMCs, that correlated with transient and low levels of plasma  COVID-19.

overall_design: RNAseq analysis of PBMCs in a group of 17 COVID-19 subjects and 17 healthy controls

first: Prabhu

middle: S

last: Arunachalam

first: Florian

last: Wimmers

first: Chris

last: Mok

first: Mahen

last: Perera

first: Madeleine

last: Scott

first: Thomas

last: Hagan

first: Natalia

last: Sigal

first: Yupeng

last: Feng

first: Laurel

last: Bristow

first: Owen

middle: T

last: Tsang

first: Dhananjay

last: Wagh

first: John

last: Coller

first: Kathryn

last: Pellegrini

first: Dmitri

last: Kazmin

first: Ghina

last: Alaaeddine

first: Wai

last: Leung

first: Jacky

last: Chan

last: Chik

middle: Y

last: Choi

first: Christopher

last: Huerta

first: Michele

last: McCullough

first: Huibin

last: Lv

first: Evan

last: Anderson

first: Srilatha

last: Edupuganti

first: Amit

last: Upadhyay

first: Steve

last: Bosinger

first: Holden

last: Maecker

first: Purvesh

last: Khatri

first: Nadine

last: Rouphael

first: Malik

last: Peiris

first: Bali

last: Pulendran


title: A multivalent signal-transducing model for the DNMT1-mediated maintenance DNA methylation

status: Public on Jul 27 2020

city: Durham

first: Greg

last: Wang

state: NC

address: 3 Genome Court

department: Duke Department of Pharmacology and Cancer Biology  and Duke Cancer Institute

institute: Duke University School of Medicine, and Department of Biochemistry and Biophysics, UNC at Chapel Hill (adjunct)

type: Methylation profiling by high throughput sequencing

summary: Heterochromatin-specific histone modifications frequently coexist with mammalian DNA methylation to orchestrate a repressive chromatin state. However, it remains elusive how these epigenetic modifications crosstalk. Here, we report that the first bromoadjacent homology (BAH1) domain and the replication foci targeting sequence (RFTS) of maintenance DNA methyltransferase DNMT1 function as readers for H4K20me3 and H3K9me3, respectively. Engagements of H4K20me3 by BAH1 and H3K9me3 by RFTS ensure localization of DNMT1 to heterochromatin in cells, and cooperate with the RFTS-ubiquitination readout to allosterically stimulate DNMT1   s methylation activity at both global and focal levels. Strikingly, there is intramolecular crosstalk between the RFTS and BAH1 domains, which profoundly impacts the maintenance of DNA methylation and genomic resistance to radiation damage. Together, our study reveals an    all-in-one    model for DNMT1 in which repressive histone modifications directly influence the cellular landscape of DNA methylation and genomic stability, a process implicative of the DNMT1-related pathogenesis.

overall_design: To examine patterns of maintenance DNA methylation deposited by DNMT1 in cells, we stably transduced either WT or mutant DNMT1 into mouse ES cells with knockout (KO) of DNMT1 (1KO), followed by genome-wide methylation in cells by enhanced reduced representation bisulfite sequencing (eRRBS). eRRBS was carried out side-by-side in three biological replicates of the 1KO rescued lines to generate datasets for across-sample comparisons.

first: Gang

middle: G

first: Sara

last: Grimm


title: Gene expression profiles in rat lung following intratracheal instillation with cellulose nanofibrils and multi-walled carbon nanotubes

status: Public on Jul 09 2020

city: Tsukuba

first: Katsuhide

last: Fujita

address: 16-1 Onogawa

department: Research Institute of Science for Safety and Sustainability

country: Japan

institute: National Institute of Advanced Industrial Science and Technology

summary: To evaluate the biological effects at the transcriptional level of manufactured nanomaterials, whole genome microarray analysis of rat lungs intratracheally instilled with cellulose nanofibrils (CNFs) with different physicochemical properties or multi-walled carbon nanotubes (MWCNTs) were performed.

overall_design: Rats intratracheally instilled with three types of CNFs (CNF1, CNF2, and CNF3), MWCNTs (0.5, 1.0 and 2.0 mg/kg), and their solvents as vehicle control were dissected at 1day, 3 days, 7 days, 30 days, and 90 days post-instillation, and then the lungs were used for microarray analysis.

first: Sawae

last: Obara


title: Dog_CGH_Array on 54 breed and village dogs and one wolf

status: Public on Jul 02 2020

city: Ann Arbor

first: Jeffrey

last: Kidd

state: Michigan

address: 1241 Catherine St

institute: University of Michigan

summary: Comprehensive view of structural variation across dog genomes including mobile elements and nuclear mitochondrial insertions

sample_organism:
Canis lupus
Canis lupus familiaris

overall_design: array CGH on 54 canine blood samples from breed and village dogs and one wolf with reference dog Great Dane Zoey

first: Jeff

first: Amanda

last: Pendleton


title: Fucosyltransferase 4 promotes cancer metastasis via enhancing EGFR/TGFBR signaling network and is associated with poor prognosis in non-small cell lung cancer

status: Public on Jul 15 2020

city: Taipei

first: Hsing-Chen

last: Tsai

address: No.1 Jen Ai road section 1

country: Taiwan

institute: National Taiwan University

summary:
Purpose: Aberrant glycosylation has been known to regulate cancer cell trafficking via promoting intravascular adhesion during metastasis. Clinicopathological studies have also shown a strong correlation between aberrant glycosylation and invasive/metastatic potentials of human cancers. However, the major glycosylation enzymes that drive lung cancer metastases and the signaling networks involved in the process remain incompletely understood.
Methods: Two lung adenocarcinoma cell lines, A549 and CL1-0 cells, with FUT4 overexpression and 81 lung cancer tissues and 19 adjacent lung tissues underwent RNA extraction for RNA-seq analysis.
Results: We identified fucosyltransferase 4 (FUT4) as a strong predictor of patient prognosis from this RNA-seq cohort.
Conclusions: High levels of FUT4 in tumor tissues significantly correlate with poor prognosis in NSCLC patients.

overall_design: FUT4-overexpressed lung cancer cells, NSCLC tumor and adjacent tissue RNA-seq

first: Chong-Jen

last: Yu


title: Dynamics of H3K64 trimethylation on histone core regulates the schizont specific expression of exported proteins in Plasmodium falciparum

status: Public on Jul 18 2020

city: Chennai

first: Arumugam

last: Rajavelu

state: Tamil Nadu

address: Adayar

country: India

institute: IITM

summary: We identified unconventional histone lysine trimethylation mark in the nucleosome core at H3K64 position in human malaria parasite Plasmodium falciparum. Global ChIP analysis was performed using anti-H3K64me3 specific antibody for three major blood stages, i.e. ring, trophozoite and schizont stages to identify the genomic position of the H3K64me3. The sheared chromatin was prepared from highly synchronous P. falciparum culture and subjected for ChIP followed by library preparation from the ChIP DNA and were subjected to sequencing using the HiSeq Illumina platform. H3K64me3 binding sites were determined after sequence alignment and normalization with input sequence. Interestingly, there was a significant reduction in the number of peaks on different chromosomes during multinucleated schizont stage as compared to ring and trophozoite stage. Collectively, this is first study to show that H3K64me3 function as repressor methyl mark during ring and trophozoite stages to regulate the expression of schizont specific export family of proteins in P. falciparum.

overall_design: Global mapping of H3K64me3 mark in all three stages of P. falciparum.

first: Rajavelu

last: Arumugam

first: C

last: Jabeena


title: Acoel single-cell transcriptomics: cell-type analysis of a deep branching organism

city: Fribourg

first: Jules

last: Duruz

state: Fribourg

address: Ch. du Musée 10

department: Biology

institute: University of Fribourg

summary: Bilaterian animals display a wide variety of cell types, organized into defined anatomical structures and organ systems, which are mostly absent in pre-bilaterian animals. Xenacoelomorpha are an early branching bilaterian phylum displaying an apparently relatively simple anatomical organization that have greatly diverged from other Bilaterian clades. In this study, we use whole-body single-cell transcriptomics on the acoel Isodiametra pulchra to identify and characterize different cell types. Our analysis identifies the existence of at least 11 major cell-type categories in acoels all contributing to the main biological functions of the organism: metabolism, locomotion and movements, behavior, defense and development. Interestingly, while most cell clusters express core fate markers shared with other animal clades, we also describe a surprisingly large numbers of clade-specific marker genes, suggesting the emergence of clade-specific common molecular machineries functioning in distinct cell types. Together, these results provide novel insight into the evolution of bilaterian cell-types and open the door to a better understanding of the origins of the bilaterian body plan and their constitutive cell types.

overall_design: Single-cell transcriptomics of Isodiametra pulchra hatchlings

first: Cyrielle

last: Kaltenrieder

first: Peter

last: Ladurner

first: Rémy

last: Bruggmann

first: Pedro

last: Martìnez

first: Sprecher

last: Simon


title: Differential gene expression of neutrophils that lack lymphotoxin beta receptor identifies a metabolic gene signature

status: Public on Aug 01 2020

city: La Jolla

first: Thomas

last: Riffelmacher

address: 9420 Athena Circle

institute: La Jolla Institute for Immunology

summary: Isolating Neutrophils from mouse blood, we employed bulk RNAseq and DE gene expression analysis to determine pathways that are regulated downstream of LTBR in neutrophils.

overall_design: Blood neutrophils were isolated from adult control and LTBR-deficient mice and cultured in the presence or absence of inflammatory cytokines as indicated in methodology section.


title: Adipocytes Fail to Maintain Cellular Identity During Obesity Due to Reduced PPARg Activity and Elevated TGFβ-SMAD Signaling

status: Public on Jul 05 2020

city: Boston

first: NORC

last: Boston

state: MA

address: 3 Blackfan Circle, CLS0733

institute: Beth Israel Deaconess Medical Center

summary: Obesity due to overnutrition causes adipose tissue dysfunction, serving as a critical pathological step on the road to Type 2 diabetes (T2D) and other metabolic disorders. Here, we performed an unbiased investigation into the fundamental molecular mechanisms by which adipocytes transition to an unhealthy state during obesity. We fed NuTRAP (Nuclear tagging and Translating Ribosome Affinity Purification) mice crossed with Adipoq-Cre with chow or high fat diet (HFD) for 10 weeks and determined adipocyte-specific transcriptomic profiles by RNA-seq, active promoter and enhancer activities by H3K27ac ChIP-seq, and the PPARg cistrome by ChIP-seq. We also assessed the impact of the PPARg agonist rosiglitazone (Rosi) on gene expression and cellular state of adipocytes from HFD-fed mice. We used bioinformatic approaches to find transcriptional pathways and performed functional studies using shRNA-mediated loss-of-function approaches in 3T3-L1 adipocytes. Adipocytes from HFD-fed mice exhibited reduced expression of adipocyte markers and metabolic genes while showing enhanced expression of myofibroblast marker genes involved in cytoskeletal organization, accompanied by the formation of actin filament structures within the cell. PPARg binding was globally reduced in adipocytes after HFD feeding, and Rosi restored the molecular and cellular phenotypes of adipocytes associated with HFD feeding. SMAD binding motifs were over-represented in HFD-induced promoters and enhancers, while TGFb1 expression was elevated in adipose tissues after HFD feeding. TGFb1 treatment of mature 3T3-L1 adipocytes induced gene expression and cellular changes similar to those seen after HFD in vivo, and knockdown of Smad3 blunted the effects of TGFb1. Our data demonstrate that adipocytes fail to maintain cellular identity after HFD, acquiring characteristics of a myofibroblast-like cell type through reduced PPARg activity and elevated TGFb-SMAD signaling. This cellular identity crisis may serve as a fundamental mechanism that drives functional decline of adipose tissues during obesity.

overall_design: Adipoq-NuTRAP mice fed chow or high fat diet were used for adipocyte-specific transcriptomic and epigenomic analysis.

first: Roh

last: Hyun

first: Rosen

last: Evan


title: Crtc1 deficiency aggravates fat accumulation in the white adipose tissue

status: Public on Sep 05 2020

city: Shenzhen

first: Zhihua

last: Wang

address: No. 12, Langshan Road, Xili Street, Nanshan District, Shenzhen

department: Shenzhen Key Laboratory of Cardiovascular Disease

institute: Fuwai Hospital Chinese Academy of Medical Sciences, Shenzhen

summary: Obesity is described as excessive fat accumulation that drives the development of glucose and lipid metabolism disorders, which is linked to multiple diseases. Crtc1, known as a transducer to regulate Creb activity, plays an important role in several basic physiological functions. Previous studies have shown visible hyperappetite and obesity in Crtc1 knockout (Crtc1-/-) mice. To investigate the effect of Crtc1 on fat accumulation in different organs, we generated Crtc1-/- mice by CRISPR/Cas9 system and regarded Crtc1+/+ as control under the normal feeding conditions. Compared with Crtc1+/+ mice, Crtc1-/- mice exhibited increase of bodyweight which was resulted from the abnormal expansion of white adipocyte. In addition, Crtc1-/- mice were more prone to hyperglycemia and dyslipidemia, supported by the levels of plasma glucose and FABP4. The results of RNA-seq and qRT-PCR in liver and epididymal white adipose tissue (eWAT) showed that the fat accumulation caused by Crtc1 deletion was mainly related to the lipid metabolism of adipose tissue, not liver. Moreover, the up-regulation of lipid metabolism in eWAT induced by Crtc1 deficiency was closely related to the up-regulation of Pparγ signaling pathway. Our findings suggested that endogenous Crtc1 had a protective role in obesity development and Crtc1 deficiency aggravates the progression of fat accumulation and related co-morbidities, which introduced a new insight for treatment of obesity.

overall_design: 12 weeks old male Crtc1-/- mice and Crtc1+/+ mice were euthanatized by cervical dislocation. A piece of liver and eWAT were used to extracted RNA according to the manufacturer's instructions. Transcriptome sequencing of RNA was completed by Beijing Genomics Institution (BGI). Two independent biological replicate samples were sequenced for each group.

first: Yimeng

last: Hu

first: Jian

last: Lv

first: Yu

last: Fang

first: Qiang

last: Luo

first: Yuan

last: He

first: Lili

last: Li

first: Mingxia

last: Fan


title: Ectopic Osx+ Cells Affect Tumor Growth

status: Public on Aug 13 2020

city: St. Louis

first: Roberto

last: Civitelli

state: Missouri

address: 660 S. Euclid Ave.

department: Bone and Mineral Diseases

institute: Washington University St. Louis

summary: Tumor growth and metastases are dependent on interactions between cancer cells and the local environment. Expression of the cell-cell adhesion molecule N-cadherin (Ncad) is associated with highly aggressive cancers, and its expression by osteogenic cells has been proposed to provide a molecular “dock” for disseminated tumor cells to establish pre-metastatic niches within the bone.  Contrary to expectations, the breast cancer cells were able to form tumors in bone and to induce osteolysis in Cdh2-cKO as well as in control mice. Notably, subcutaneous tumors grew larger in Cdh2-cKO relative to control littermates. Cell tracking experiments using the Ai9 reporter revealed the presence of Osx+ and Ncad+ cells in the stroma of extra-skeletal tumors and in a small population of lung cells, a frequent site of breast cancer metastasis. Gene expression analysis by RNAseq of CD45- Osx+ cells isolated from extra-skeletal tumors revealed alterations of pro-tumorigenic signaling pathways in Cdh2-cKO cells relative to control Osx+ cells.  Also surprisingly, we find Osx+ cells present in the circulation, and the majority of tumor-associated and circulating Osx+ cells express the hematopoietic marker CD45, have a phenotypic profile resembling that of tumor infiltrating myeloid and lymphoid populations, but with higher expression of lymphocytic immune suppressive genes. Our results indicate that Osx marks distinct tumor promoting CD45- and CD45+ populations and challenge the dogma that osteogenic and hematopoietic markers are mutually exclusive. They also show that Ncad in CD45- Osx+ cells is not necessary for the establishment of bone metastases, but in extra-skeletal tumors it regulates pro-tumorigenic support by the microenvironment.

overall_design: Profiling mRNA expression in Osx+ cells (CD45+ and CD45-) isolated from the stromal component of subcutaneous tumors grown in Cdh2-cKO and wild type mice

first: Roberta

last: Faccio

first: Francesca

last: Fontana

first: Biancamaria

last: Ricci


title: Expression date from mouse Hepatocytes

status: Public on Jul 16 2020

city: Funabashi

first: Shota

last: Okuyama

state: Chiba

institute: Toho University

summary:
The fields of drug discovery and regenerative medicine require large numbers of adult human primary hepatocytes. For this purpose, it is desirable to use hepatocyte-like cells (HLCs) differentiated from human pluripotent stem cells. To develop an efficient HLCs induction method, we constructed a red fluorescent reporter, CYP3A7R, in which DsRed is placed under the transcriptional regulation of CYP3A7 coding for a human fetus-type P450 enzyme. We created transgenic mice using mouse embryonic stem cells (mESCs) carrying a CYP3A7R transgene.
CYP3A7R mESCs were used to optimize the HB-LC induction procedure. These induction conditions were applied to TT2F mESC and matured to HLC. To confirm the similarity of the highly expressed genes in these HLCs, Genechip analysis was used to compare them to transgenic mice FL and AL.

overall_design: The gene expression of the HLCs generated in this study was confirmed by comparison. Comparisons were made with HLCs (day-41 of differentiation), transgenic mouse fetal liver (E18.5: embryonic 18.5-day old fetus) and adult liver (6W: 6-week old mouse).

first: Masako

last: Tada


title: Human Bacille Calmette-Guérin vaccination elicits trained immunity via the hematopoietic progenitor compartment

status: Public on Jun 30 2020

city: Bonn

first: Branko

last: Cirovic

address: Carl-Troll Str 31

country: Germany

institute: LIMES

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

overall_design: Refer to individual Series


title: Human Bacille Calmette-Guérin vaccination elicits trained immunity via the hematopoietic progenitor compartment  [bone marrow]

summary: Induction of trained immunity by human Bacille-Calmette-Guérin (BCG) vaccination is implicated in the beneficial heterologous effects of the vaccine, but the underlying mechanisms remain elusive. We performed global transcriptome analysis of sorted progenitors from bone marrow before (D0) and 90 days after vaccination (D90). BCG vaccination induced transcriptomic myeloid priming of the hematopoietic stem and progenitor cell (HSPC) compartment marked by the upregulation of myeloid and granulocytic pathways alongside the induction of transcription factors connected to myeloid cell function, namely Hepatocyte Nuclear Factors (HNF). These findings are corroborated by higher granulocyte numbers in BCG-vaccinated infants, HNF1-related SNP variants correlating with immune training and elevated serum levels of the HNF1 target gene SERPINA1. Taken together, we reveal a transcriptomic reprograming of HSPCs and peripheral monocytes as a trait of in vivo BCG-induced trained immunity.

overall_design: mRNA profiles of sorted hematopoietic stem and progenitor cells (HSPC, i.e. pooled HSC & MPP) from human bone marrow. Sample collection was performed before and 90 days after vaccination from the same individuals (n=15 for BCG-vaccinated individuals, n=5 for placebo-treated individuals) resulting in a total of 39 transcriptomic profiles (one sample (Donor 9 D0) was identified as outlier and excluded).

first: Charlotte

last: de Bree

first: Simone

last: Picelli

first: Kristian

last: Händler

first: Katrin

last: Klee

first: Joachim

last: Schultze

first: Mihai

last: Netea

first: Andreas

last: Schlitzer


title: Human Bacille Calmette-Guérin vaccination elicits trained immunity via the hematopoietic progenitor compartment [PBMC]

overall_design: Fresh peripheral blood mononuclear cells (PBMCs) are enriched (Ficoll) from the same healthy volunteers before (D0) and three months after (D90) vaccination with BCG. mRNA profiles were generated from PBMCs cultured in the presence of C.albicans (Ca) for 24 h.


title: Identification of endothelial derived factors that promote metastasis III

status: Public on Jun 29 2020

first: Bernardo

last: Tavora

state: NY

address: 1230 York Ave

institute: The Rockefeller University

summary: To identify endothelial-derived factors that may instructively drive cancer metastasis, we generated a new mouse model that allows endothelial-specific ribosomal tagging. We crossed the RiboTag (Rpl22fl/flHA) mice with the endothelial inducible Cre line Cdh5(PAC)-CreERT2 mice. Endothelial derived ribosome-associated mRNA-sequencing was performed from highly metastatic B16F10 and poorly metastatic B16F0 tumours.

overall_design: Immunoprecipitation and RNASeq of RNA bound to monoclonal dsRNA-specific antibody J2 in highly versus poorly metastatic mouse tumour cell lines.

first: Hani

last: Goodarzi

first: Sohail

last: Tavazoie


title: Perinatal exposure to lead and DEHP change DNA methylation profile in mouse liver and blood

status: Public on Jul 01 2020

first: Siyu

last: Liu

state: MI

address: 100 Washtenaw avenue

department: Bioinformatics

summary:
Purpose: Then goal of this study id to investigate the effects of perinatal lead  (32 ppm in maternal drinking water) and DEHP (25 mg per kg of chow) exposure on liver and blood DNA methylation in both PND21 and 5-month male and female mice.
Methods: Enhanced reduced-representation bisulfite sequencing (ERRBS) was used to assess DNA methylation in PND21 and 5-month old DEHP-exposed, lead-exposed and control mice. Sex-specific differential methylaton analysis by DEHP and lead exposure was conducted using MethylSig R package.
Results: We observed hundreds to thousands of stably modified, sex-specific differentially methylated regions in blood and liver of DEHP-exposed and lead-exposed animals at both PND21 and 5 months.

overall_design: A total of 151 DNA methylation profiles of PND21 and 5-month mouse blood and liver with DEHP exposure, lead exposure or no exposure, measured by Enhanced Reduced Representation Bisulfite Sequencing (ERRBS)

first: Dana

last: Dolinoy

first: Maureen

last: Sartor

first: Laurie

last: Svoboda

first: Kai

last: Wang

first: Kari

last: Neier

first: Christine

last: Rygiel

first: Tamara

last: Jones

first: Raymond

last: Cavalcante

first: Claudia

last: Lalancette

first: Zing

last: Tsai

first: Justin

last: Colacino


title: Identification of endothelial derived factors in highly metastatic tumours


title: Identification of endothelial derived factors that promote metastasis II

overall_design: Analysis of endogenous retroviral elements (ERV) abundance and differentially expressed ERVs in total RNA and cell free RNA extracted from highly versus poorly metastatic mouse tumour cell lines or conditioned media.


title: TOP2B binding and enzymatic activity on promoters and introns modulates multiple oncogenes in human gliomas

status: Public on Jun 25 2020

first: Junfei Zhao

last: Zhao

address: 1130 St. Nicholas Ave

institute: Columbia University


title: Identification of endothelial derived factors that promote metastasis I

overall_design: RNASeq and differential gene expression analysis of the tumor endothelium in highly versus poorly metastatic tumors by endothelial cell specific ribosomal tagging in Rpl22fl/flHA;Cdh5(PAC)-CreERT2 mice


title: Single cell RNA sequencing of human high-grade serous ovarian cancer (HGSC) cells and human immortalized fallopian tube epitheilal (FTE) cells

status: Public on Jun 15 2020

city: Omaha

first: Adam

middle: R

last: Karpf

state: NE

address: S 42nd &, Emile St

institute: UNMC

summary: The goal of this experiment was to generate scRNA-seq data for human HGSC cells and human FTE cells.  FTE is the progenitor cell type for HGSC.

overall_design: Determination of RNA transcriptomes in OVCAR8 (HGSC) and FT282-C11 (FTE) cell lines

first: Mustafa

last: Albahrani


title: Heterogeneity of alveolar macrophages in fungal infections [single-cell RNA-seq]

status: Public on Jun 08 2020

first: Mari

last: Shinohara

department: Immunology

institute: Duke University School of Medicine

summary: Alveolar macrophages have hetergenous response to Cryptococcus at single-cell level

overall_design: Total CD45+ lung cells were isolated from either naïve or 9-hour post Cryptococcus-infected mice. Alveolar macropahges were classified using an automated reference-based annotation appoach based on similiarity to bulk RNA-sequencing data of relevant immune populations from the ImmGen database

first: Shengjie

last: Xu-Vanpala

first: M

last: Deerhake


title: Development of gene expression signatures for vein graft restenosis following vascular grafting

status: Public on Jun 16 2020

city: Chengdu

first: JIAYU

last: SHEN

state: Sichuan

address: GuoXue Alley 37#

institute: West China Hospital, Sichuan University

summary: To further development of our gene expression approach to cardiovascular disease, we have employed microarray expression profiling as a discovery platform to identify genes with the potential to distinguish the therapeutic target of the vein graft restenosis following coronary artery bypass grafting. Vein graft samples were obtained from model rats which received external jugular vein-carotid bypass grafting at different postoperative timepoints (n=3/group; day 7, 14 and 28, respectively). Vein samples were also obtained from control rats without vascular grafting (n=3/group; day 0). Time-dependent gene expression profiles were described with microarray analysis. Expression of three lncRNA-mRNA pairs (AF062402-Src, BC091437-Edg1 and BC166461- Mcam) from this signature were quantified in the same RNA samples by real-time PCR, confirming the accuracy of the microarray data.

overall_design: Gene expression profiles were identified at day 7, 14 and 28 after the establishment of external jugular vein-carotid bypass model in experimental rats and at day 0 in control rats without receiving surgery. Three independent experiments were performed at each time (day 7, 14 and 28) after surgery.

first: Jiayu

last: Shen

first: Hongwei

last: Zhang


title: Novel Dopamine Receptor 3 Antagonists Inhibit the Growth of Primary and Temozolomide Resistant Glioblastoma Cells

city: Huntsville

first: Sara

last: Cooper

state: AL

address: 601 Genome Wau

institute: HudsonAlpha Institute

summary: In a study focused on the role dopamine receptor 3, we completed RNA-sequencing of D456 and JX39, glioblastoma xenograft lines after SRI-21979 or dmso treatment

overall_design: RNA-sequencing after temozolomide treatment in D456 and JX39 neuroblastoma cell lines

middle: J

first: Anita

last: Hjelmeland


title: TOP2B binding and enzymatic activity on promoters and introns modulates multiple oncogenes in human gliomas [ChIP-seq]

city: New York

summary: We investigated the contribution of TOP2B to transcriptional modulation in gliomas given the variable expression of this helicase across tumors, and its emerging role in  epigenetic regulation of transcription. We mapped the genomic location of TOP2B, and identified distinct sites of native binding and enzymatic activity across human glioma cell lines and human tumor specimens. TOP2B was active in a subset of promoters and introns, and its inhibition led to downregulation of these genes. We investigated the contribution of TOP2B to transcriptional modulation in gliomas given the variable expression of this helicase across tumors, and its emerging role in  epigenetic regulation of transcription. We mapped the genomic location of TOP2B, and identified distinct sites of native binding and enzymatic activity across human glioma cell lines and human tumor specimens. TOP2B was active in a subset of promoters and introns, and its inhibition led to downregulation of these genes.

overall_design: We performed ChIP-seq (Chromatin immunoprecipitation and sequencing) for TOP2A and TOP2B to investigate its genomic localization in proneural glioma genotypes TS543 and BT142 and two mesenchymal glioma cell lines SNB19 and 0777A. To analyze the contribution of TOP2B on gene expression we treated cells with the TOP2 inhibitor ICRF193 10Um for 5hrs followed by RNA-seq. 20 TS543 samples (10 untreated; 10 treated), 12 BT142 samples (5 untreated; 7 treated) were included in the study.

middle: M

last: Sonabend

first: Junfei


title: Active transcription and Orc1 drive chromatin association of the AAA+ ATPase Pch2 during meiotic G2/prophase

status: Public on Jun 14 2020

city: Dortmund

first: Richard

last: Cardoso da Silva

state: North Rhine Westfallen

department: Mechanistic Cell Biology

institute: Max Planck Institute of Mol Physiol


title: Active transcription and Orc1 drive chromatin association of the AAA+ ATPase Pch2 during meiotic G2/prophase [ChIP-Seq]

summary: Pch2 is an AAA+ protein that controls DNA break formation, recombination and checkpoint signaling during meiotic G2/prophase. Chromosomal association of Pch2 is linked to these processes, and several factors influence the association of Pch2 to euchromatin and the specialized chromatin of the ribosomal (r)DNA array of budding yeast. Here, we describe a comprehensive mapping of Pch2 localization across the budding yeast genome during meiotic G2/prophase. Within non-rDNA chromatin, Pch2 associates with a subset of actively RNA Polymerase II (RNAPII)-dependent transcribed genes. Chromatin immunoprecipitation (ChIP)- and microscopy-based analysis reveals that active transcription is required for chromosomal recruitment of Pch2. Similar to what was previously established for association of Pch2 with rDNA chromatin, we find that Orc1, a component of the Origin Recognition Complex (ORC), is required for the association of Pch2 to these euchromatic, transcribed regions, revealing a broad connection between chromosomal association of Pch2 and Orc1/ORC function. Ectopic mitotic expression is insufficient to drive recruitment of Pch2, despite the presence of active transcription and Orc1/ORC in mitotic cells. This suggests meiosis-specific ‘licensing’ of Pch2 recruitment to sites of transcription, and accordingly, we find that the synaptonemal complex (SC) component Zip1 is required for the recruitment of Pch2 to transcription-associated binding regions. Interestingly, Pch2 binding patterns are distinct from meiotic axis enrichment sites (as defined by Red1, Hop1 and Rec8). This suggests that although Pch2 is linked to axis/SC-directed recruitment and function, the chromosomal population of Pch2 described here is not directly associated with chromosomal axis sites. In line with this observation, interfering with the pool of Pch2 that associates with active RNAPII transcription does not lead to effects on the chromosomal abundance of Hop1, a known axial client of Pch2. We thus report characteristics and dependencies for Pch2 recruitment to meiotic chromosomes, and reveal an unexpected link between Pch2, SC formation, chromatin and active transcription.

overall_design: 3X-FLAG Pch2 wild type and 3X-FLAGPch2-E399Q (samples collected at 4h in SPO medium) binding sites were identified by ChIP-seq in triplicate using a Illumina HiSeq 3000 platform

last: da Silva

first: María

middle: A

last: Villar-Fernández

first: Gerben

last: Vader


title: Transcriptomic analysis of adipose and muscle of dairy calves supplemented with 5-hydroxytryptophan

status: Public on Jun 05 2020

city: Madison

first: Francisco

last: Peñagaricano

state: Wisconsin

address: 1675 Observatory Drive

department: Animal and Dairy Sciences

institute: University of Wisconsin-Madison

summary: Serotonin is a monoamine that regulates processes such as energy balance and immune function. Manipulating this pathway in growing dairy calves could promote growth and development by modulating functions and signaling pathways within key organs. In this study, we characterized the adipose and muscle transcriptome of pre-weaned calves with increased serotonin bioavailability through the elucidation of differentially expressed genes.

overall_design: Holstein bull calves (21d old) were fed milk replacer (8 L/d) supplemented with saline (CON, n=4) or 5-hydroxytryptophan (5HTP, n=4) for 10 d. Calves were euthanized on d 10 to harvest adipose and muscle tissue for RNA-Sequencing.

first: Jimena

last: Laporta

last: Peñagaicano


title: Multiple roles of H2A.Z in regulating promoter chromatin architecture in human cells (RNA-seq)

status: Public on Jun 01 2020

city: TALLAHASSEE

first: LAUREN

last: COLE

state: Florida

address: 319 STADIUM DR

institute: FLORIDA STATE UNIVERSITY

summary: We employed an MNase-Transcription Start Site Sequence Capture method to map and determine the accessibility of all nucleosomes, including those that contain H2A.Z, at high coverage for all human Pol II promoters. We uncovered unexpected features of nucleosomal organization in epithelial cells and following transition to a mesenchymal and malignant state. In contrast to the prevailing model, we observe many different types of active and inactive promoter structures that differ in their nucleosome organization and sensitivity to MNase digestion. Further, we found that  H2A.Z has an important role in the assembly of repressed promoters into an inaccessible state. Finally, we uncovered a new promoter type in which a stable H2A.Z nucleosome occupies the TSS of an active promoter.

overall_design: RNA-seq in MCF10A and MCF10A-CA1a cells

first: Jonathan

last: Dennis

first: David

last: Tremethick

first: Lauren

last: Cole

first: Sebastian

last: Kurscheid


title: Heterogeneity of alveolar macrophages infected by Cryptococcus neoformans

city: Durham

first: Mari

last: Shinohara


title: Inheritance and reprogramming of non-CG methylation at satellite DNA repeats

status: Public on May 26 2020

city: Darlinghurst

first: Ozren

last: Bogdanovic

state: NSW

address: 384 Victoria Street

department: Genomics and Epigenetics

country: Australia

institute: Garvan Institute of Medical Research

summary: In vertebrates, DNA methylation predominantly occurs at CG dinucleotides however, widespread non-CG methylation (mCH) has been reported in mammalian embryonic stem cells and in the brain. In mammals, mCH is found at CAC trinucleotides in the nervous system, where it is associated with transcriptional repression, and at CAG trinucleotides in embryonic stem cells, where it positively correlates with transcription. Moreover, CAC methylation appears to be a conserved feature of adult vertebrate brains. Unlike any of those methylation signatures, here we describe a novel form of mCH that occurs in the TGCT context within zebrafish mosaic satellite repeats. TGCT methylation is inherited from both male and female gametes, remodelled during mid-blastula transition, and re-established during gastrulation in all embryonic layers. Moreover, we identify DNA methyltransferase 3ba (Dnmt3ba) as the primary enzyme responsible for the deposition of this mCH mark. Finally, we observe that TGCT-methylated repeats are specifically associated with H3K9me3-marked heterochromatin suggestive of a functional interplay between these two gene-regulatory marks. Altogether, this work provides insight into a novel form of vertebrate mCH and highlights the substrate diversity of vertebrate DNA methyltransferases.

overall_design: Enzymatic methylation sequencing (EM-seq): 24hpf (n=10 embryos / sample, n=2 samples); Reduced Representation Bisulfite sequencing (RRBS): 48hpf (n=10 embryos / sample, n=2 samples / condition); Whole Genome Bisulfite Sequencing (WGBS): 72h larvae (n=10 embryos / sample, n=2 samples / condition) and adult tissues (n=2 samples).

first: Sam

middle: E

last: Ross

first: Allegra

last: Angeloni

first: Michael

last: Geng


title: Characterizing gene expression patterns in Basal Cell Carcinomas and Squamous Cell Carcinomas

status: Public on May 08 2020

city: Indianapolis

first: Jiali

last: Han

state: Indiana

address: 1050 Wishard Blvd.Health Sciences Building, RG 5112

department: Department of Epidemiology

institute: Indiana University School of Public Health

summary: Expression profiling by high-throughput sequencing of tumor tissues and adjacent tissues.

overall_design: Gene expression profiling of BCCs, SCCs and the adjacent tissues.

first: Hongji

last: Dai

first: Jingwu

last: Xie

first: Sheng

last: Liu

first: Jun

last: Wan


title: Ursolic acid regulates  inflammatory cell infiltration to prevent ulcerative colitis

status: Public on May 16 2020

city: Hangzhou

first: Mingqian

last: Li

address: Gucui Road 234

institute: Tongde hospital of Zhejiang Province

summary: Total RNA was isolated from 3 colonic tissues of each treatment group using the Qiagen RNeasy kit following the manufacturers' protocol. RNA samples with good quality control (RIN values>8) were sequenced using Hiseq-2500 by Novogene. Ursolic acid (UA), Dextran sulfate sodium (DSS)."Con" group stands for normal group, "DSS" group stands for DSS induced group, "UA_DSS" group stands for UA Preventive DSS induced group, "DSS_UA" group stands for UA Treatment DSS induced group.

overall_design: Examination of 12 colon tissues of 4 different treatment groups

first: Qinsong

last: Sheng

first: Kequn

last: Chai


title: Interactions of gene expression, alternative splicing, and DNA methylation in determining nodule identity

status: Public on May 22 2020

city: Knoxville

first: Sarbottam

last: Piya

state: Tennessee

address: 2431 Joe Johnson Dr.

department: Plant Science

institute: University of Tennessee

summary: Profiling the transcriptome, spliceome, and methylome of developing soybean nodules reveals insights into their associations that may configure transcriptome complexity and proteome diversity

overall_design: Genome wide transcriptome analysis of soybean root and nodules in triplicate at three different stages of nodule development.

first: Tarek

last: Hewezi


overall_design: Refer to individual Series


title: Human Bacille Calmette-Guérin vaccination elicits trained immunity via the hematopoietic progenitor compartment [ATAC-seq]

first: Branko

last: Cirovic

overall_design: Healthy individuals were vaccinated with BCG and peripheral blood was taken from the same individuals before (D0) and three months (D90) after vaccination. CD14+ monocytes were enriched (MACS) from the mononuclear cell fraction and subjected to ATACseq.

first: Charlotte

last: de Bree

first: Simone

last: Picelli

first: Kristian

last: Händler

first: Katrin

last: Klee

first: Joachim

last: Schultze

first: Mihai

last: Netea

first: Andreas

last: Schlitzer


title: Inhibitor of Differentiation 4 (ID4) represses myoepithelial differentiation of mammary stem cells through its interaction with HEB

status: Public on May 07 2020

first: Alexander

last: Swarbrick


title: HEB ChIP-seq in ID4 knockdown Comma-Dβ mammary epithelial cells

summary: We performed ChIP-seq for the E-protein transcription factor HEB in ID4 knockdown mammary epithelial cells to determine how ID4 affects HEB DNA binding.

overall_design: HEB ChIP-seq in cells treated with siRNA targeting ID4 were compared with cells treated with non-targeting (NT) siRNA control. 3 biological replicates were performed.

first: Holly

last: Holliday

first: Daniel

last: Roden


title: HEB and histone mark ChIP-seq in Comma-Dβ mouse mammary epithelial cells

summary: The goal of this study was to determine the genome wide binding sites of the E-protein transcription factor HEB in mammary epithelial cells, and to delineate the chromatin context of these regions. ChIP-seq for HEB, H3K4Me3, H3K27Ac, and H3K27Me was performed in Comma-Dβ cells in quadruplicate.

overall_design: Examination of 1 transcription factor and 3 histone modificiations in Comma-Dβ cells. 4 biological replicates.


title: Sex dependent compensatory mechanisms to preserve blood pressure homeostasis in PGI2 receptor deficient mice

city: Philadelphia

first: Gregory

middle: Robert

last: Grant

state: PA

address: 3400 Civic Center Blvd.

department: Genetics

institute: University of Pennsylvania

summary: Inhibitors of microsomal prostaglandin E synthase-1 (mPges-1) are in the early phase of clinical development. Deletion of mPges-1 in mice confers analgesia, restrains atherogenesis and fails to accelerate thrombogenesis, while suppressing prostaglandin (PG) E2, but increasing biosynthesis of prostacyclin (PGI2). In hyperlipidemic mice, this last effect represents the dominant mechanism by which mPges-1 deletion restrains thrombogenesis, while suppression of PGE2 accounts for its anti-atherogenic effect. However, the impact of mPges-1 depletion on blood pressure (BP) in this setting remains unknown. To address how differential effects on PGE2 and PGI2 might modulate salt-evoked BP responses in the absence of mPges-1, we generated mice lacking the I prostanoid (Ipr) receptor or mPges-1 on a hyperlipidemic background caused by deletion of the low density lipoprotein receptor (Ldlr). Here, mPges-1 depletion significantly increased the BP response to salt loading in male Ldlr-/- mice, whereas, despite the direct vasodilator properties of PGI2, Ipr deletion suppressed it. Furthermore, combined deletion of the Ipr abrogated the exaggerated BP response in male mPges-1-/- mice. Suppression of PGE2 biosynthesis was enough to explain the exaggerated BP response to salt loading by either mPges-1/Ldlr depletion or by an MPGES-1 inhibitor in mice expressing human mPGES-1. However, the lack of a hypertensive response to salt in Ipr-deficient mice was attributable to reactive activation of the atrial natriuretic peptide (ANP) pathway. Interestingly, these unexpected BP phenotypes were not observed in female mice fed a high salt diet. This is attributable to the protective effect of estrogen in Ldlr-/- mice and in Ipr-/- /Ldlr-/- mice. Thus, estrogen compensates for a deficiency in PGI2 to maintain BP homeostasis in response to high salt in hyperlipidemic female mice. In males, by contrast, augmented formation of ANP plays a similar compensatory role, restraining hypertension and oxidant stress in the setting of Ipr depletion. In male mice, depletion of Lactobacilius in the gut microbiome coincided with a reduction in their fecal product, indole-3-lactic acid and plasma levels of indoxyl sulfate/ tryptophan. These metabolites act via the Aryl Hydrocarbon Receptor to restrain inflammation and oxidative stress and their depletion may augment salt induced hypertension in males. Hyperlipidemic males on a high salt diet might be at risk of a hypertensive response to mPGES-1 inhibitors.

overall_design: RNA-seq expression analysis of 52 samples across mouse kidney medulla and atria in Ldlr knockout and Ipr/Ldlr double-knockout (DKO). Kidney: 8 male Ldlr KO and 8 male Ipr/Ldlr DKO. Atria: 9 female Ldlr KO, 9 female Ipr/Ldlr DKO, 9 male Ldlr KO, and 9 male Ipr/Ldlr DKO.

first: Soon

last: Tang

first: Hu

last: Meng

first: Seán

last: Anderson

first: Dimitra

last: Sarantopoulou

first: Soumita

last: Ghosh

first: Nicholas

last: Lahens

first: Katherine

middle: N

last: Theken

first: Emanuela

last: Ricciotti

first: Elizabeth

last: Hennessy

first: Vincent

last: Tu

first: Kyle

last: Bittinger

first: Aalim

last: Weiljie

first: Garret

last: FitzGerald


title: RNA-seq of FACS-enriched mammary subpopulations (basal, luminal progenitor, mature luminal) from WT and ID4 knockout mice

first: Alexander

last: Swarbrick

summary: The goal of this study was to determine the genes regulated by ID4 in mammary epithelial subpopulations. Basal, luminal progenitor, and mature luminal mammary epithelial subpopulations were FACS-sorted from adult mice that were either WT or ID4 KO in quadruplicate. RNA-seq and differential gene expression analysis was performed.

overall_design: Mammary glands were pooled from 4-8 WT or ID4 KO female adult (10-12 week) mice at estrus and digested into a single cell suspension. Live lineage negative CD24+CD29hiCD61+ basal, CD24+CD29loCD61+ luminal progenitor and CD24+CD29loCD61- mature luminal cells were isolated by FACS and RNA was extracted for RNA-seq. 4 biological replicates were performed.

first: Chia-Ling

last: Chan


title: PCR cycles affect gibbs free energy bias

status: Public on May 06 2020

first: Tim

last: Reddy

state: North carolina

address: CIEMAS, Room 2347 101 Science Drive

institute: Duke university

summary: We amplified DNA fragments randomly sheared from PER1 BAC library with four different PCR cycles (3, 6, 12, and 18 cycles). We report the effect of Gibbs free energy bias to coverage significantly increases with additional number of PCR cycles, especially for fragments with high Gibbs free energy (usually corresponding to low GC content).

overall_design: Examination of gibbs free energy bias in fragments amplified with different PCR cycles

first: Young-Sook

last: Kim

first: Graham

middle: D

last: Johnson


title: Hypermethylation and reduced expression of Gtl2, Rian and Mirg at the Dlk1-Dio3 imprinted locus as a marker for poor developmental potential of mouse embryonic stem cells

status: Public on May 01 2020

city: CAMBRIDGE

first: William

middle: Henry

last: Colledge

address: Dowing Street

institute: University of Cambridge

summary: Mouse embryonic stem cells (ESCs) have played a crucial role in biomedical research where they can be used to elucidate gene function through the generation of genetically modified mice. A critical requirement for the success of this technology is the ability of ESCs to contribute to viable chimaeras with germ-line transmission of the genetically modified allele. We have identified several ESC clones that cause embryonic death of chimaeras at mid to late gestation stages. These clones had a normal karyotype, were pathogen free and their in vitro differentiation potential was not compromised. Chimaeric embryos developed normally up to E13.5 but showed a significant decrease in embryo survival by E17.5 with frequent haemorrhaging. We investigated the relationship between the ESCs transcriptional and epigenomic state and their ability to contribute to viable chimaeras. RNA sequencing identified four genes (Gtl2, Rian, Mirg and Rtl1as) located in the Dlk1-Dio3 imprinted locus that were expressed at lower levels in the compromised ESC clones and this was confirmed by qRT-PCR. Bisulphite sequencing analysis showed significant hypermethylation at the Dlk1-Dio3 imprinted locus with no consistent differences in methylation patterns at other imprinted loci. Treatment of the compromised ESCs with 5-azacytidine reactivated stable expression of Gtl2 and rescued the lethal phenotype but only gave low level chimaeras.

overall_design: RNA-seq of 4 ESC clones with compromised developmental potential and 3 control ESC clones; 3 biological replicates were analysed for each ESC clone

first: Maria

last: Schacker

first: Yi-Han

last: Chen

first: Melanie

last: Eckersley-Maslin

first: Richard

last: Snaith

middle: H


title: Next Generation Sequencing Facilitates Quantitative Analysis of Negative control/si-PDLIM3/si-PDLIM5/si-LMO7 Transcriptomes

status: Public on May 30 2020

first: HAORONG

last: HE

address: No. 211 Huimin Road

department: Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province

institute: Sichuan Agricultural University

summary: The PDZ-LIM superfamily member is present in the nucleus of many cells and  consists of one PDZ domain at the N-terminus and one or more LIM domains at the  C-terminus. The family includes 10 genes, of which PDLIM3, PDLIM5 and LMO7 genes  have been shown to promote mouse myoblast differentiation and participate in the  regulation of skeletal muscle growth and development. To explore whether chicken  PDLIM3, PDLIM5 and LMO7 genes have the same function, this study explored the  expression of these genes in the before and after birth of chicken,  and after the chicken skeletal muscle satellite cells cultured in vitro interfered with the  expression of these genes. The proliferation and differentiation of  satellite cells were finally analyzed by transcriptome sequencing. The molecular  pathways involved in the regulation of cell proliferation and differentiation were  analyzed. The main results are as follows:  Transcriptome sequencing revealed that the differentially expressed genes of  chicken skeletal muscle satellite cells interfering with PDLIM3 gene expression were  mainly enriched in cGMP-PKG, Oxytocin, MAPK, Tight junction and other signaling  pathways, and involved in cytoskeletal protein binding, actin binding, muscle tissue  regeneration and development, adhesion and other functions. Transcriptome sequencing revealed that compared with the control group, the  differentially expressed genes of chicken skeletal muscle satellite cells that interfered  with PDLIM5 gene expression were mainly enriched in signaling pathways such as  Tight junction, Oxytocin, p53, MAPK, and involved in myocyte production and  muscle contraction. Muscle cell differentiation, and participate in cytoskeletal protein  binding, actin cytoskeleton formation, actin and actin binding.

overall_design: mRNA profiles of si-PDLIM3, si-PDLIM5, si-LMO7 and negative control satellite cells

first: Haorong

last: He

first: Huadong

last: Yin

first: Xueke

last: Yu


title: Cytokine-sensing primary enhancer cluster launches secondary enhancers to activate multi-gene locus [ChIP-seq]

status: Public on Jun 04 2020

city: Bethesda

first: Michaela

last: Willi

address: 9000 Rockville Pike

department: NIDDK

institute: NIH

summary: Enhancer clusters are platforms occupied at high-density by the transcription machinery to activate lineage-specific genes. However, it is not clear yet whether they are merely a collection of conventional enhancers or represent unique and new types of regulatory elements. Specifically, the question remains whether they activate additional enhancer programs in multigene loci. We addressed this issue in the mouse mammary gland, where genes are highly activated during pregnancy. We identify a 300kb multi-gene locus with twenty-one regulatory elements, including a cytokine-dependent primary enhancer cluster (PEC). Using genome editing in combination with ChIP-seq, RNA-seq and 3C-technologies, we show that the PEC initiates the activation of lineage-specific genes through contacting and activating secondary enhancers. This new framework of enhancer clusters indicates a hitherto unrecognized hierarchy of regulation by which a PEC activates genes via regulating secondary enhancers.

overall_design: ChIP-seq for STAT5A, GR, NFIB, RNA Pol II, H3K27ac and H3K4me3 in the mammary tissues of wild type, and mutant mice,at day one, day 6 and 18 of pregnancy. Mutant mice carry enhancer deletions at Csn1s2b and Csn3, but also single and combined deletions of one enhancer cluster in the casein locus  (single deletions: enhancer element one, two and four; combined deletions: one and two together, and a complete deletion of the cluster)

first: Hye

last: Lee


title: Genome-wide maps of chromatin state in A375 cells or in normal or USP7 knockdown A375 cells .

city: Beijing

first: Lin

last: Shan

address: 10 You’anmen Outer West 1st Street

institute: Capital Medical University

summary: ChIP-seq experiments were performed in normal or USP7 knockdown A375 cells with specific antibodies against USP7, EZH2, H3K27me3 and H2BK120ub1. Consistent with our expectations, the analysis of ChIP-seq data showed that USP7 loss-of-function led to obviously reduction in USP7, EZH2 and H3K27me3 around the USP7-specific peaks, but an upregulation in H2BK120ub1. This study gave us a new understanding that USP7 is required for EZH2 loading and H3K27 trimethylation.

overall_design: Examination of the change of the indicated protein densities around the USP7 specific peaks after knockdown of USP7

first: Dongxue

last: Su


title: Effects of the Levonorgestrel-containing Intrauterine Device, Copper Intrauterine Device, and Levonorgestrel-Containing Oral Contraceptive on the Endometrial and Cervical Transcriptomes Offer Insights into Mechanisms of Action of Intrauterine Devices

status: Public on Apr 29 2020

city: San Francisco

first: Deepak

last: Srivastava

state: CA

address: 1650 Owens St

institute: J David Gladstone Institutes

summary: The contraceptive effectiveness of intrauterine devices has been attributed in part to effects of a foreign body reaction on the endometrium.  We performed this study to identify compare the effects on the endometrial transcriptome of intrauterine devices and combined oral contraceptives, to better understand their mechanisms of action. We collected endometrial and cervical biopsies from women using the levonorgestrel-intrauterine device, copper intrauterine device or levonorgestrel-containing combined oral contraceptives, and from women not using contraceptives (control group). Transcriptional profiling was performed with Affymetrix arrays, Principal Component Analysis and the bioconductor package limma. Pathway analysis was performed using EnrichR and Reactome 2016. In endometrial samples from copper intrauterine device users (n=13), there were no genes with statistically significant differential expression compared to controls (n=11), whereas in levonorgestrel-intrauterine device users (n=11), 2509 genes were significantly dysregulated and mapped onto several immune and inflammatory pathways. In combined oral contraceptive users (n=12), 133 genes were significantly dysregulated and mapped predominantly onto pathways involving regulation of metal ions.  Both levonorgestrel-intrauterine device and combined oral contraceptive use were associated with significant downregulation of members of the metallothionein gene family. In cervical samples, none of the groups showed statistically significant differential gene expression compared to controls. In conclusion, hormonal and copper intrauterine devices differ significantly in their effects on the endometrial transcriptome, with endometrium from copper intrauterine device users being indistinguishable from luteal phase endometrium. These results suggest that the contraceptive mechanisms of intrauterine devices are unlikely to rely on a common pathway involving a foreign body reaction in the endometrium.

overall_design: Cross-sectional study using cervical and endometrial samples from 4 groups of women: controls  not on hormonal or intrauterine contraceptives (n=12), copper intrauterine device users (cuIUD, n=14), combined oral contraceptive users (COC, n=14),  and levonorgestrel-intrauterine device users (LNG-IUD, n=12),

first: Karen

last: Smith-McCune

first: Reuben

last: Thomas

first: Sarah

last: Averbach

first: Dominika

last: Seidman

first: Margaret

last: Takeda

first: Linda

last: Giudice

first: Sahar

last: Houshdaran


title: Single cell RNA sequencing of CD42+ and CD42- iHPC in RUNX1 haploinsufficiency

status: Public on Apr 23 2020

first: Brian

last: Estevez

state: Pennsylvania

address: 3615 Civic Center Blvd

department: Pediatrics

institute: Children's Hospital of Philadelphia

summary: To gain insights into the global and local transcriptomic changes underlying defective production of CD42a+ iHPCs in RUNX1+/-, we performed scRNA SEQ on sorted CD42a- and CD42a+ iHPCs from L1 and L1-C. There were on average 11,328 reads per cell with an average of 2,081 genes expressed. To identify and analyze distinct subpopulations in the control and RUNX1+/- iHPCs, dimension reduction was performed and cell clustering was visualized using uniform manifold approximation and projection (UMAP)

overall_design: Examination of gene expression in 6 sorted samples from control  (1 CD42- and 1 CD42+) and RUNX1 haploinsufficient (2 CD42- and 2 CD42+) iHPCs based on CD42 expression.

first: Mortimer

last: Poncz


title: Transcriptome analysis of Streptococcus mutans fluoride-resistant (FR) strain

city: Busan

first: Jeong Nam

last: Kim

address: Biology Building 402, Busandaehang-ro, 63beon-gil 2, Geumjeong-gu

department: Microbiology

institute: Pusan National University

summary: RNA-seq was performed to examine the overall gene expression in a S. mutans FR strain and to identify potential genes that can mainly contribute to the generation of a fluoride resistance in S. mutans. Using RNA-seq technique, the differentially expressed genes that are implicated in phenotypic changes of the FR strain were studied.

overall_design: Comparative analysis of the S. mutans wild-type strain with the fluoride-resistant strain

first: Hyeon-jeong

first: Jeong


first: Sarbottam

last: Piya

overall_design: Genome wide methylome analysis of soybean root and nodules in triplicate at three different stages of nodule development.

first: Tarek

last: Hewezi


title: Spatiotemporal single-cell RNA sequencing of developing chicken hearts identifies interplay between cellular differentiation and morphogenesis

status: Public on Apr 28 2020

city: Ithaca

first: Iwijn

last: De Vlaminck

state: New York

address: Weill Hall, 237 Tower Road

department: Meinig School of Biomedical Engineering

institute: Cornell University

summary: Single-cell RNA sequencing is a powerful tool to study developmental biology but does not preserve spatial information about tissue morphology and cellular interactions. Here, we combine single-cell and spatial transcriptomics with algorithms for data integration to study the development of the chicken heart from the early to late four-chambered heart stage. We create a census of the diverse cellular lineages in developing hearts, their spatial organization, and their interactions during development. Spatial mapping of differentiation transitions in cardiac lineages defines transcriptional differences between epithelial and mesenchymal cells within the epicardial lineage. Using spatially resolved expression analysis, we identify anatomically restricted expression programs, including expression of genes implicated in congenital heart disease. Last, we discover a persistent enrichment of the small, secreted peptide, thymosin beta-4, throughout coronary vascular development. Overall, our study identifies an intricate interplay between cellular differentiation and morphogenesis.

overall_design: Spatially-resolved RNA-seq with high-throughput time-course scRNA-seq to study the gene expression, interactions, and regulatory programs that drive fetal development of the chicken hearts.

first: Madhav

last: Mantri

first: Gaetano

last: Scuderi

first: Roozbeh

last: Nassab

first: Jonathan

last: Butcher


title: Excision repair hotspots of UV-induced DNA damage in the human genome

status: Public on Apr 09 2020

city: Athens

first: Wentao

last: Li

state: GA

address: 500 D. W Brooks Drive

department: Environmental Health Science

institute: University of Georgia

summary: We recently developed high-throughput sequencing approaches, eXcision Repair sequencing (XR-seq) and Damage-seq, to generate genome-wide mapping of DNA damage formation and excision repair, respectively, with single-nucleotide resolution. Here, we adopted time-course XR-seq data to profile UV-induced excision repair dynamics, paired with Damage-seq data to quantify the overall induced DNA damage. We identified genome-wide repair hotspots that are subject to exemplified amount of repair very soon after UV irradiation. We show that such repair hotspots do not result from hypersensitivity to DNA damage and are thus not damage hotspots. We find that the earliest repair occur preferentially in promoters and enhancers from open-chromatin regions. The repair hotspots are also significantly enriched for frequently interacting regions and super-enhancers, both of which are hotspots for local chromatin interactions. We further extend the interrogation of chromatin organization to DNA replication timing and conclude that early-repair hotspots are enriched for early-replication domains. Collectively, we report genome-wide early-repair hotspots of UV-induced damage, in association with chromatin states and epigenetic compartmentalization of the human genome.

overall_design: Determination of repair hotspots and coldspots of UV-induced DNA damage in the human genome.

first: Yuchao

last: Jiang

first: Laura

last: Lindsey-Boltz

first: Yuchen

last: Yang

first: Yun

first: Aziz

last: Sancar