title: Activation of the VEGFC/VEGFR3 pathway induces cancer immune escape through tumor-associated lymphatic vessels and macrophages in colorectal cancer

city: Milano

first: Luca

last: Massimino

state: MI

address: Via Olgettina, 58

department: Gastroenterology

country: Italy

institute: Ospedale San Raffaele

summary: Colorectal cancer (CRC) is one of the major causes of cancer-related death in Western countries and is associated with increased numbers of lymphatic vessels (LVs) and tumor-associated macrophages (TAMs). The VEGFC/VEGFR3 pathway is regarded as the principal inducer of lymphangiogenesis and it contributes to metastases; however, no data are available on its role during CRC development. We found that both VEGFC and VEGFR3 were upregulated in human non-metastatic CRC, with VEGFR3 localising on both LVs and TAMs. We further proved in different preclinical models of CRC, that VEGFC/VEGFR3 axis can shape both LECs and TAMs to synergically inhibit anti-tumor immunity and promote primary CRC growth. VEGFR3-directed therapy could be envisioned for the treatment of non-metastatic CRC.

overall_design: n=8 Lymphatic cell samples and n=8 Macrophage samples with or without anti-VEGFR3 treatment.

first: Carlotta

last: Tacconi

first: Silvia

last: D'Alessio

first: Federica

last: Ungaro

first: Silvio

last: Danese


title: Systemic approaches reveal anti-adipogenic signals at the onset of obesity–related inflammation in white adipose tissue

status: Public on Mar 18 2020

city: Lausanne

last: Gilardi

state: Vaud

address: Lausanne 1015

department: CIG - Center of Integrative Genomics

country: Switzerland

institute: University of Lausanne

type: Genome binding/occupancy profiling by high throughput sequencing

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Isolator: accurate and consistent analysis of isoform-level expression in RNA-Seq experiments

status: Public on Mar 17 2020

city: Raleigh

first: Xinxia

last: Peng

address: 1060 William Moore Drive

country: USA

institute: North Carolina State University

summary: While RNA-Seq has enabled great progress towards the goal of wide-scale isoform-level mRNA quantification, short reads have limitations when resolving complex or similar sets of isoforms. As a result, estimates of isoform abundance carry far more uncertainty than those made at the gene level. When confronted with this uncertainty, commonly used methods produce estimates that are unstable -small perturbations in the data often produce dramatically different results, confounding downstream analysis. We introduce a new method, Isolator, which analyzes all samples in an experiment in unison using a simple Bayesian hierarchical model. Combined with aggressive bias correction, it produces estimates that are simultaneously accurate and stable. In a comprehensive comparison of accuracy and stability, we show that this property is unique to Isolator. We further demonstrate that the approach of modeling an entire experiment enables new analyses, which we demonstrate by examining splicing monotonicity across several time points in the development of human cardiomyocyte cells.

overall_design: The same RNA sample was sequenced twice, once with 300nt paired-end reads on a Illumina MiSeq sequencer and again with 75nt paired-end reads using a Illumina GAIIx

first: Daniel

middle: C

last: Jones

first: Kavitha

middle: T

last: Kuppusamy

first: Nathan

middle: J

last: Palpant

first: Michael

middle: G

last: Katze

first: Charles

middle: E

last: Murry

first: Hannele

last: Ruohola-Baker

first: Walter

middle: L

last: Ruzzo


title: Trancriptome of entomopathogen fungi Beauveria bassiana growing in host hemocoel

city: Hangzhou

first: Shenghua

last: Ying

state: Zhejiang

address: Yu-hang-tang Road 688

country: China

institute: Zhejiang University

summary: B. bassiana regulates transcriptional adaptation to host hemocoel, which is a determinant to the biocontrol potential of fungal entomopathogens. The global transcriptome  related to fungal development in host was analyzed by using high throughput sequencing (RNA-Seq). Our transcriptional profiles revealed that majority of fungal genes are involved in fungal growth in host environmental, and are associated with various cellular processes.

overall_design: Total RNA was obtained from a mixed sample of B. bassiana hyphal bodies and host cells. Total RNA was analyzed by dual RNA-seq method. The data of fungal side were sorted by mapping the reads to fungal genome, were asembled into transcriptome.

first: Sheng-Hua

first: Ming-Guang

last: Feng


title: Hypoxia perturbs m6A-reader YTHDF2 to fuel cancer-promoting inflammation in hepatocellular carcinoma

city: Chicago

first: zhike

last: lu

state: IL

address: 5801 South Ellis Avenue

department: department of chemistry

institute: University of Chicago

summary: Dynamic N6-methyladenosine (m6A) modification was previously identified as a ubiquitous post-transcriptional regulation that affected mRNA homeostasis. However, the m6A-related epitranscriptomic alterations and functions remain elusive in human diseases such as cancer. Here we show that hypoxia regulates the ‘reader’ protein YTH domain family 2 (YTHDF2), to eventually stabilize the methylated oncogene mRNAs in inflammation-associated liver cancer. YTHDF2 silenced in human cancer cells or depleted in mouse hepatocytes evoked pro-inflammatory responses and accelerated tumor growth and metastatic progression. Under hypoxia, YTHDF2 processed the decay of m6A-containing interleukin 11 (IL11) and serpin family E member 2 (SERPINE2) mRNAs, which were responsible for the inflammation-mediated malignancy. Reciprocally, YTHDF2 transcription succumbed to hypoxia-inducible factor-2α (HIF-2α). Administration of a HIF-2α antagonist (PT2385) restored YTHDF2-programed epigenetic machinery and repressed liver cancer. Hence, our findings provide a new insight into the mechanism by which hypoxia adapts m6A-mRNA editing to promote cancer.

overall_design: m6A in liver cancer patient.tissues and SMMC7721 cell lines

first: Jun

last: Liu

first: Jiajie

last: Hou

first: Zhike

last: Lu

first: Chuan

last: He


title: CLL intraclonal fractions exhibit established and recently-acquired patterns of DNA methylation [GE]

status: Public on Mar 16 2020

city: Bronx

first: Boris

last: Bartholdy

state: NY

address: 1300 Morris Park Ave

department: Cell Biology

institute: Albert Einstein College of Medicine

summary: Intraclonal subpopulations of circulating chronic lymphocytic leukemia (CLL) cells with different proliferative histories and reciprocal surface expression of CXCR4 and CD5 have been observed in the peripheral blood of CLL patients and named proliferative (PF), intermediate (IF) and resting (RF) cellular fractions. Transcriptional differences between paired intraclonal fractions confirmed their proliferative experience and further supported a linear advancement from PF to RF in the peripheral blood. Marked expression differences in intraclonal fractions suggest potential pathological and therapeutic relevance of studying intraclonal CLL fractions as compared to bulk cells.

overall_design: Genome-wide RNA expression profiling of sorted, fractionated peripheral blood mononuclear cell (PBMC) samples from patients with CLL. For 21 patients, enough data was obtained to study the both RNA expression and DNA methylation using Illumina 450K beadarrays in 4 fractions. Patients had known differences in IGHV mutational status , as well as cellular birth rates, as determined by labeling with deuterated water ingested by the patients.

middle: A

first: Xiahoua

last: Wang

first: Xiao-Jie

last: Yan

first: Nicholas

last: Chiorazzi

first: Matthew

middle: D

last: Scharff

first: Sergio

last: Roa


title: Characteristic dissection of Xanthomonas oryzae pv. oryzae responsive microRNAs in rice

city: Beijing

first: yanfeng

last: jia

address: Beijing Beijing Chaoyang District Beichen West Road

institute: Institute of genetics and developmental biology, Chinese academy of science

type: Non-coding RNA profiling by high throughput sequencing


title: Transcriptome data of miR-483 overexpression in human pulmonary arterial endothelial cells

city: Xi'an

first: Jin

last: Zhang

state: Shaanxi

address: Yanta West Road No.76

institute: Xi'an Jiaotong University

summary: MicroRNA-483 (miR-483) regulate endothelial function through inhibition expression of connective tissue growth factor (CTGF). Endothelial dysfunction is involved in the pathogeneis of pulmonary arterial hypertension (PAH). We investigated the role of miR-483 overexpression on human pulmonary arterial endothelial cells (hPAECs) through comparing the transcriptome file of hPAECs transfected with miR-483 -3p and -5p mimic and with control mimic. Gene ontology analysis showed that several PAH-associated signaling pathways were regulated by miR-483, including transforming growth factor-β signaling, Wnt signaling and inflammatory response, cell adhesion, response to hypoxia, apoptotic processes, oxidative reduction processes and negative regulation of cell migration and proliferation.

overall_design: Transcriptome data of hPAECs transfected with an equimolar of miR-483-3p and -5p mimic or control mimic was generated by deep sequencing, in biological duplicate, using Illumia Hiseq platform.

first: Yangyang

first: Y

last: Shyy


title: Characteristic dissection of Xanthomonas oryzae pv. oryzae responsive microRNAs in rice [datatset 1]

summary: we emphatically monitored the responsive changes of genes targeted by  rice miRNAs miRNAs at 0, 8, 24 hours across Xoo strain PXO86 infection in its compatible rice variety IR24 and incompatible variety IRBB5 by degradome technology.These findings provide new insights into the complex roles of characteristic miRNAs  in rice-Xoo interactions.

overall_design: To recognize the post-transcriptional regulatory units caused by miRNAs during rice-Xoo interaction, two mixed degradome libraries, IR24-D(including IR24-0 h, IR24-8 h and IR24-24 h) and IRBB5-D(including IRBB5-0 h, IRBB5-8 h and IRBB5-24 h), were generated, which could provide the valuable experimental target genes validation through detecting the cleavage sites detection of miRNAs.

first: guanghuai

last: jiang

first: wenxue

last: zhai


title: Phosphate excess increases susceptibility to pathogen infection in rice

city: Bellaterra

first: Blanca

last: San Segundo

state: Barcelona

address: Edifici CRAG - Campus UAB

department: Plant Responses to Stress

country: Spain

institute: Center for Research in Agricultural Genomics (CRAG)

summary: Phosphorus (P) is an essential nutrient for plant growth and productivity. Due to soil fixation, however, phosphorus availability in soil is rarely sufficient to sustain high crop yields. Fertilizers are widely used to circumvent the limited bioavailability of phosphate (Pi) which led to a scenario of excessive soil P in agricultural soils. Whereas adaptive responses to Pi deficiency have been deeply studied, less is known about how plants adapt to Pi excess and how Pi excess might affect disease resistance. Here, we show that high Pi fertilization in rice plants, and subsequent Pi accumulation in leaves, enhances susceptibility to infection by Magnaporthe oryzae, the causal agent of the rice blast disease. Equally, MIR399f overexpression causes an increase in Pi content in rice leaves which results in enhanced susceptibility to M. oryzae. During pathogen infection, a weaker activation of defense-related genes occurs in rice plants accumulating Pi in leaves, a response that is in agreement with the phenotype of blast susceptibility observed in these plants. These data support that Pi, when in excess, compromises defense mechanisms in rice while demonstrating that miR399 functions as a negative regulator of rice immunity. The two signaling pathways, Pi signaling and defense signaling, must operate in a coordinated manner in controlling disease resistance. This information provides a basis to understand the molecular mechanisms involved in immunity in rice plants grown under a high Pi fertilization regime, an aspect that should be considered in management of the rice blast disease

sample_organism:
Oryza sativa
Pyricularia oryzae

platform_organism:
Oryza sativa
Pyricularia oryzae

overall_design: 12 samples in total: 1 wild-type (WT) and 2 miR399f overexpressing lines (L4, L20) with 2 treatments (Control, Infected), 2 biological replicates each. Samples are: C-WT, C-L4, C-L20 (Control);  I-WT, I-L4, I-L20 (Infected)

first: Lidia

last: Campos-Soriano

first: Mireia

last: Bundó

first: Marcel

last: Bach-Pages

first: Su-Feng

last: Chiang

first: Tzyy-Jen

last: Chiou


title: Defining the Secrebiome: the expressed secretome of the gut microbiome and its role in obese Mexican children

city: Cuernavaca

first: Fernanda

last: Cornejo

address: Av Universidad 2001

country: Mexico

institute: Instituto de Biotecnología UNAM

summary: high throughput sequencing of the metagenome of mexican children

overall_design: RNA seq from fecal samples of Mexican children

first: Luigui

last: Gallardo-Becerra

last: Cornejo-Granados

first: Rodrigo

last: García-López

first: Alejandra

last: Valdez-Lara

first: Shirley

last: Bikel

first: Samuel

last: Canizales-Quinteros

last: López-Contreras

first: Alfredo

last: Mendoza-Vargas

first: Henrik

last: Nielsen

first: Adrián

last: Ochoa-Leyva


title: Characteristic dissection of Xanthomonas oryzae pv. oryzae responsive microRNAs in rice [datatset 2]

first: yanfeng

last: jia

summary: we emphatically monitored the responsive changes of rice miRNAs at 0, 8, 24 hours across Xoo strain PXO86 infection in its compatible rice variety IR24 and incompatible variety IRBB5 by small RNA sequencing, and the genes targeted by miRNAs were also detected via degradome technology. These findings provide new insights into the complex roles of characteristic miRNAs and their targets in rice-Xoo interactions.

overall_design: Examination of the responsive changes of rice miRNAs and their targets at 0, 8, 24 hours across Xoo strain PXO86 infection in its compatible rice variety IR24 and incompatible variety IRBB5 by small RNA sequencing and degradome technology

first: guanghuai

last: jiang

last: zhai


title: CLL intraclonal fractions exhibit established and recently-acquired patterns of DNA methylation

first: Boris

last: Bartholdy

type: Methylation profiling by genome tiling array


title: Genome-wide identification and characterization of long non-coding RNAs and mRNAs in goat tissues infected with PPRV

city: Karnal

first: Ravi Kumar

last: Gandham

state: Haryana

address: Makrampur

country: India

institute: ICAR-NBAGR

summary: We have used RNA-Seq to examine long non-coding RNAs (lncRNAs) and mRNAs from PPRV infected goat tissues (Lung, Spleen and Caecum). Our study reveals the prevalence of lncRNAs in goats, and has identified lncRNAs differentially expressed in different tissues of PPRV (Izatnagar94) infected goats, suggesting its important functions during virus infection.

overall_design: To assess lncRNAs and mRNAs expression in goats, we sequenced and analyzed lung, spleen and caecum tissues of control and  PPRV infected goats at 9 day post infection.

first: Aruna

last: Pandey

first: Amit

last: Ranjan Sahu

first: Sajad

last: Ahmad Wani

first: Raja

last: ishaq

first: Shikha

last: Saxena

first: Bina

last: Mishra

first: B

middle: P

first: A

middle: K

last: Tiwari

first: Ravi

last: Kumar Gandham


title: Identification of miRNAs enriched in Extracellular vesicles derived from serum samples of breast cancer patients

city: Curitiba

first: Patricia Midori

last: Murobushi Ozawa

state: PR

address: Av. Cel. Francisco H. dos Santos, 100

department: Genetics

country: Brazil

institute: Federal University of Parana

summary:
Purpose: In this study, we performed RNA-seq analysis as a screening strategy to identify EV-miRNAs derived from serum of well clinically annotated breast cancer (BC) patients from South of Brazil.
Methods: EVs from three groups of samples, healthy controls (CT), luminal A (LA), and triple negative (TNBC), were isolated from serum using a precipitation method and analyzed by RNA-seq (screening phase). Subsequently, four EV-miRNAs (miR-142-5p, miR-150-5p, miR-320a, and miR-4433b-5p) were selected to be quantified by RT-qPCR in individual samples (test phase).
Results: A panel composed of miR-142-5p, miR-320a, and miR-4433b-5p discriminated BC patients from CT with an AUC of 0.8387 (93.33% sensitivity, 68.75% specificity). In addition, the combination of miR-142-5p and miR-320a, presented an AUC of 0.941 (100% sensitivity, 93.80% specificity) in distinguishing LA patients from CT. Interestingly, decrease expression of miR-142-5p and miR-150-5p were significantly associated with more advanced tumor grades (grade III), while the decrease expression of miR-142-5p and miR-320a with larger tumor size.
Conclusion: These results provide insights into the potential application of EVs-miRNAs from serum as novel specific markers for early diagnosis of BC.

overall_design: MiRNAs derived from extracellular vesicles were isolated from serum samples of well clinically annotated breast cancer patients and control from South of Brazil

first: Evelyn

last: Vieira

first: Débora

middle: S

last: Lemos

first: Ingrid

last: Melo Souza

first: Silvio

middle: M

last: Zanata

first: Vânia

last: Pankievicz

first: Thalita

middle: R

last: Tuleski

first: Emanuel

last: Souza

first: Pryscilla

middle: F

last: Wowk

first: Cícero

middle: d

last: Urban

first: Flavia

last: Kuroda

first: Rubens

last: Lima

first: Rodrigo

last: Almeida

first: Daniela

last: Gradia

first: Iglenir

last: Cavalli

first: Luciane

first: Danielle

last: Malheiros

first: Enilze

last: Ribeiro


title: Mild, moderate and severe enterovirus 71 (EV71) isolates infection in human PBMCs

city: Singapore

first: Siti Naqiah

last: Amrun

address: 8A Biomedical Grove, Immunos

country: Singapore

institute: Singapore Immunology Network

summary: Hand, foot and mouth disease (HFMD), caused by enterovirus 71 (EV71), presents mild to severe disease, and sometimes fatal neurological and respiratory manifestations. However, reasons for the severe pathogenesis remain undefined. To investigate this, infection and viral kinetics of EV71 isolates from clinical disease (mild, moderate and severe) from Sarawak, Malaysia, were characterized in human rhabdomyosarcoma (RD), neuroblastoma (SH-SY5Y) and peripheral blood mononuclear cells (PBMCs). High resolution transcriptomics was used to decipher EV71-host interactions in PBMCs. Ingenuity analyses revealed similar pathways triggered by all EV71 isolates, although the extent of activation varied. Importantly, several pathways were found to be specific to the severe isolate, including triggering receptor expressed on myeloid cells 1 (TREM-1) signaling. Depletion of TREM-1 in EV71-infected PBMCs with peptide LP17 resulted in decreased levels of pro-inflammatory genes, and reduced viral loads for the moderate and severe isolates. Mechanistically, this is the first report describing the transcriptome profiles during EV71 infections in primary human cells, and the involvement of TREM-1 in the severe disease pathogenesis, thus providing new insights for future treatment targets.

overall_design: PBMCs from 4 donors were used. PBMCs were infected with three different viral isolates of EV71, and harvested at time points 0, 6, 12 and 24 hours post-infection. Mock-infected and heat-inactivated EV71 isolate were used as negative controls.

first: Siti

middle: N

first: Jeslin

last: Tan

first: Natasha

middle: Y

last: Rickett

first: Jonathan

last: Cox

first: Bernett

last: Lee

first: Michael

last: Griffiths

first: Tom

last: Solomon

first: David

last: Perera

first: Mong

middle: H

last: Ooi

first: Julian

last: Hiscox

first: Lisa

last: Ng


title: MKL1 deficiency results in a severe neutrophil motility defect due to impaired actin polymerization

city: Amsterdam

first: Evelien

last: Sprenkeler

address: Plesmanlaan 125

department: Department of Blood Cell Research

country: Netherlands

institute: Sanquin Research

summary: Megakaryoblastic leukemia 1 (MKL1) promotes the regulation of essential cell processes, including actin cytoskeletal dynamics by co-activating serum response factor. Recently, the first human case with MKL1 deficiency, leading to a novel primary immunodeficiency, was identified. We report a second family with two siblings with a homozygous frameshift mutation in MKL1. The index case deceased as an infant from progressive and severe pneumonia by Pseudomonas aeruginosa and poor wound healing. The younger sib was preemptively transplanted shortly after birth. The immunodeficiency was marked by a pronounced actin polymerization defect and a strongly reduced motility and chemotactic response by MKL1-deficient neutrophils. Apart from the lack of MKL1, subsequent proteomic and transcriptomic analyses of patient neutrophils revealed actin and several actin-related proteins to be downregulated, confirming a role for MKL1 as transcriptional co-regulator. Degranulation was enhanced upon suboptimal neutrophil activation, while production of reactive oxygen species was normal. Neutrophil adhesion was intact but without proper spreading. The latter could explain the observed failure in firm adherence and transendothelial migration under flow conditions. No apparent defect in phagocytosis and bacterial killing was found. Also monocyte-derived macrophages showed intact phagocytosis; lymphocyte counts and proliferative capacity were normal. Non-hematopoietic primary patient fibroblasts demonstrated defective differentiation into myofibroblasts but normal migration and filamentous actin (F-actin) content, most probably due to compensatory mechanisms of MKL2, which is not expressed in neutrophils. Our findings extend current insight into the severe immune dysfunction in MKL1 deficiency, with cytoskeletal dysfunction and defective extravasation of neutrophils as most prominent features.

overall_design: Transcriptome sequencing on human healthy control neutrophils and of MKL1-deficient neutrophils

first: Martin

last: de Boer

first: Iris

last: Kreft


title: Initiation of Parental Genome Reprogramming in Fertilized Oocyte by Splicing Kinase SRPK1-Catalyzed Protamine Phosphorylation

city: San Diego

first: Yajing

last: Hao

state: CA

address: George Palade Laboratories 9500 Gilman Drive, Room 217

department: Dept. of Cellular and Molecular Medicine

institute: University of California, San Diego

summary: We performed ATAC-seq in mouse sperms and fertilized eggs with wild-type or P1 mutation (phosphorylation sites by SRPK1) to capture early genome reprogramming events ~5 hours post insemination. Surprisingly, we detected broadly distributed ATAC-seq reads across the mouse genome to paternal and maternal gametes formed with wild-type and single mutant sperm, and in contrast, we saw individual peaks with zygotes formed with the double mutant sperm. After assigning to paternal and maternal genomes, we found that the reads assignable to paternal genome was decreased with single and double mutants, compare with wild-type. Furthermore, we found the paternal genome in eggs fertilized with the double mutant sperm essentially retained all sperm-specific ATAC-seq peaks, which were also overlapped with the published H3.3 ChIP-seq signals on wild-type sperm, mostly corresponding to TSSs. Strikingly, the ATAC-seq signals on the maternal genome from eggs fertilized with the double mutant P1 sperm were literally identical to those in MII oocyte. Based on these data, we draw two important conclusions: (i) dramatic chromatin remodeling takes place in a highly coordinated fashion in both paternal and maternal pronuclei before they merge, and (ii) SRPK1-catalyzed protamine phosphorylation initiates such synchronized genome reprogramming in both gametes.

overall_design: Mouse sperms were obtained from wild-type or knock-in male mice in the C57BL/6 background and MII oocytes were obtained from BALB/cJ female. Mouse fertilized eggs were harvested on 5 h after insemination. ATAC-seq was performed in these sperms and fertilized eggs.

first: Lan-Tao

last: Gou

first: Xiang-Dong

last: Fu


title: Microarray gene expression data from sorted lung epithelial cells during heterotypic immunity

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

summary:
Previous pneumococcal experience establishes lung-resident IL-17A-producing CD4+ memory TRM cells that accelerate neutrophil recruitment against heterotypic pneumococci. Herein, we unravel a novel crosstalk between CD4+ TRM cells and lung epithelial cells underlying this protective immunity.
Genome-wide expression analyses of lung epithelial cells in CD4+ cell sufficient and CD4+ cell deficient heterotypic immune murine lungs revealed a significant remodeling of the epithelial transcriptome of infected lungs due to infection history, ~80% of which was CD4+ cell-dependent.

overall_design: To achieve a more comprehensive view of epithelial remodeling, and to identify the extent to which this event is CD4+ T cell-dependent, we performed transcriptomic analyses on sorted CD45-EpCAM+ cells from lungs of heterotypic immune or naïve mice treated with GK1.5 (Het GK1.5) or control IgG (Saline IgG or Het IgG). All mice had 7 hours of Sp3 pneumonia in these analyses. We aimed to determine whether prior experience with unrelated serotypes altered the epithelial transcriptome during pneumonia, and if this depended on CD4+ T cells.

first: Gregory

last: Wasserman

first: Anukul

middle: T

last: Shenoy

first: Joseph

last: Mizgerd


title: Molecular maps of the Lamin B1-associated genomic regions in oligodendrocyte lineage cells

city: New York

first: Patrizia

last: Casaccia

address: 85 St Nicholas Terrace

department: Neuroscience

institute: ASRC-CUNY

summary: This study addresses the mechanisms regulating the identity of oligodendrocyte progenitor cells (OPC) in physiological conditions and the pathological mechanisms leading to autosomal  adrenoleukodystrophy (ADLD), a disease caused by persistence of lamin B1 (LMNB1) expression in oligodendrocytes (OL).  Using mouse primary OPCs and a novel technique for the study of DNA-protein interaction, we identify the genomic regions showing dynamic interactions with LMNB1.  The transition from ESC to OPC revealed increased association of gene involved in pluripotency and neuronal function and decreased association of gene categories associated with the differentiation of OPC into OL (including genes regulating epigenetic modifiers, RNA processing and protein phosphorylation).  Since LMNB1 declines during the transition from OPC to OL, and its persistent expression has been linked to pathological conditions, such as ADLD, we further identified the molecular maps of genome-lamina reorganization in OPC differentiating into OL which continue to express LMNB1 (mOLLMNB1).  The transition from OPC to mOLLMNB1 revealed increased association to LMNB1 of genomic regions encoding for lipid metabolism and protein phosphorylation, and decreased association of genes negatively regulating differentiation. These data highlight the importance of LMNB1 in physiological conditions and identify mechanisms responsible for late onset ADLD.

overall_design: Quantifying laminB-DNA association through DamID high throughout sequencing

first: C

last: Yattah

first: M

last: Hernandez

first: D

last: Huang

first: W

last: Liao

first: B

last: Van Steensel

first: P


title: Meningeal lymphatic vasculature mediates cervical lymph node metastasis of brain tumors through VEGF-C/VEGFR3/eNOS signaling pathway

city: BeiJing

first: Yidong

last: Chen

address: Yiheyuan Road

institute: Peking University

summary: Purpose: The rediscovery of meningeal lymphatic vessels (MLVs) suggests a potential linkage between brain tumors and cervical lymph nodes (LNs). In this study, we investigated whether and how meningeal lymphatics regulate the metastasis of brain tumor cells. Experimental Design: We first examined the pattern of MLVs and LNs after tumor cells were injected into the cisterna magna (i.c.m.) or subdural space of mice. The meninges were isolated and analyzed by whole-mount immunofluorescence staining. LN metastasis was analyzed by detecting GFP+ tumor cells. Then we used inducible knock-out mice and AAV-VEGF-C delivery system to study the function of MLVs in mediating the metastasis of brain tumor cells. Finally, RNA-seq was used to determine the expression profiles of meningeal lymphatic endothelial cells (mLECs) in mice with or without tumors. The roles of the endothelial nitric oxide synthetase (eNOS) were evaluated both genetically and pharmacologically in vivo. Results: Meningeal lymphangiogenesis induced by GL261 and B16 tumors was correlated with dCLN swelling and metastasis. dCLN metastasis was suppressed in MLV-defective mice, while promoted in AAV-VEGF-C-treated mice. In addition, we found that VEGF-C/VEGFR3 signaling regulated both meningeal and tumor lymphangiogenesis. Tumor-associated mLECs have a distinct transcriptomic signature, which highly express eNOS. Furthermore, genetic or pharmacological inhibition of eNOS significantly suppressed meningeal lymphangiogenesis and dCLN metastasis. Conclusions: The meningeal lymphatic vasculature mediates the metastasis of brain tumors to cervical LNs, mainly through a VEGF-C/VEGFR3-eNOS signaling pathway, suggesting that MLV may be a potential therapeutic target for the extracranial metastasis of brain tumors.

overall_design: Here we sequenced meningeal lymphatic endothelial cells from control mice without tumor bearing, GL261 tumor bearing mice and B16 tumor bearing mice. 10 lymphatic endothelial cells were placed into the lysis buffer, n = 3 biological replicates per group. Marker genes were analyzed to be qualified, then differently expressed genes were screened.

first: Xueting

last: Hu

first: Qiuping

last: Deng

first: Lu

last: Ma

first: Fan

last: Zhou

first: Qingqing

last: Li

first: Yuhan

first: Yanan

first: Chen

last: Zhang

first: Weihai

last: Ning

first: Yan

last: Kong

first: Hui

last: Yang

first: Tubao

last: He

first: Yang

last: Cao

last: Ye

first: Yingqing

last: Huo

first: Aibin

first: Bing

last: Liu

first: Fuchou

last: Tang

first: Ralf

last: Adams

first: Yulong

first: Jincai

last: Luo


title: Control of Rice Tillering by RNA-directed DNA Methylation at Miniature Inverted-repeat Transposable Elements

city: Beiing

first: Yijun

last: Qi

address: NO.1 Qinghuayuan

department: School of Life Sciences

institute: Tsinghua University

summary: In rice, tillering is an important agricultural trait that affects plant architecture and grain yield. RNA-directed DNA methylation (RdDM), which establishes DNA methylation in all CG, CHG and CHH sequence contexts and maintains CHH methylation in plants, silences transposable elements (TEs) and regulates gene expression. Here we report that knockdown and knockout of OsNRPD1a and OsNRPD1b, genes encoding two orthologues of the largest subunit of OsPol IV holoenzyme that  transcribes 24-nucleotide (nt) siRNAs in RdDM, lead to a high-tillering phenotype, in addition to dwarfism and smaller panicles. In the shoot base of the osnrpd1a/b RNAi line, many genes are dysregulated, due to loss of 24-nt siRNAs and CHH methylation. Among these genes, OsMIR156d and OsMIR156j, which promote rice tillering, is derepressed when CHH methylation at Miniature Inverted-Repeat Transposable Elements (MITEs) in the promoters of OsMIR156d and OsMIR156j is lost. By contrast, D14, which suppresses rice tillering, is repressed when CHH methylation at a MITE in the 3’UTR of D14 is lost. Deletion of the MITE that is targeted by RdDM in D14 is sufficient to cause high-tillering. Our findings reveal control of rice tillering by RdDM at MITEs and provide the potential targets for agronomic trait enhancement by epigenome editing.

overall_design: We conducted small RNA sequencing, mRNA sequencing and whole-genome bisulfite sequencing  in three biological replicates using the shoot base of 4-week old seedlings of wild-type (WT, japonica) and the osnrpd1a/b RNAi lines.

first: Le

last: Xu

first: Kun

last: Yuan

first: Min

last: Chen

first: Jiayang


title: The Arabidopsis Protein CONSERVED ONLY IN THE GREEN LINEAGE20 is Required for Plastid 50S Ribosome Biogenesis

city: Planegg

first: Tatjana

last: Kleine

address: Großhaderner Straße 2

department: Biologie I, Botanik

country: Germany

institute: Ludwig-Maximilians-Universität München

summary: Biogenesis of plastid ribosomes is facilitated by auxiliary factors which process and modify ribosomal RNAs (rRNA) or are involved in ribosome assembly. In comparison to their bacterial and mitochondrial counterparts, the biogenesis of plastid ribosomes is less well understood and few auxiliary factors have been described so far. In this study, we report the functional characterization of CGL20 (CONSERVED ONLY IN THE GREEN LINEAGE20) in Arabidopsis thaliana (AtCGL20) a small, proline-rich protein which is targeted to mitochondria and chloroplasts. In Arabidopsis, CGL20 is encoded by segmentally duplicated genes of high similarity (AtCGL20A and AtCGL20B), and inactivation of both in the atcgl20ab mutant leads to a visible virescent phenotype, and growth arrest at low temperature. The chloroplast proteome, thylakoid complex abundance and pigment composition are significantly affected in atcgl20ab mutants, resulting in a combined proton gradient regulation (pgr) and chlororespiratory reduction (crr) phenotype. Loss of AtCGL20 alters plastid rRNA ratios, perturbs the formation of a hidden break in 23S rRNA and causes abnormal accumulation of 50S ribosomal subunits in the high-molecular-mass fraction of chloroplast stromal extracts. Moreover, AtCGL20A-eGFP fusion proteins comigrate with 50S ribosomal subunits in sucrose density gradients, even after RNase treatment of stromal extracts. Therefore, we propose that AtCGL20 participates in late stages of the biogenesis of 50S ribosomal subunits in plastids – a role which presumably evolved in the green lineage as a consequence of structural divergence of plastid ribosomes.

overall_design: Examination of differential gene expression in the Arabidopsis atcgl20ab mutant compared to the wild type Col-0


title: PHF19 mediated regulation of proliferation and invasiveness in prostate cancer

city: Barcelona

first: Enrique

last: Blanco

address: Dr. Aiguader 88

department: Gene Regulation, Stem Cells and Cancer

institute: Center for Genomic Regulation (CRG)

summary: The Polycomb-like protein PHF19/PCL3 associates with the Polycomb repressive complex 2 (PRC2) and mediates its recruitment to chromatin in embryonic stem cells, where it is essential for maintaining the repression of developmental genes. PHF19 is also overexpressed in many cancers. However, neither PHF19 targets in cancer cells nor potentially misregulated pathways involving PHF19 are known. Here, we investigate the role of PHF19 in prostate cancer cells. We find that PHF19 interacts with PRC2 and binds to PRC2 targets on chromatin. Direct PHF19 target genes are involved in proliferation, differentiation, angiogenesis, and extracellular matrix organization, among others. Depletion of PHF19 triggers an increase in MTF2/PCL2 recruitment to chromatin, along with a genome-wide gain in PRC2 occupancy and H3K27me3 deposition. Transcriptome analysis shows that loss of PHF19 promotes deregulation of key genes involved in growth, metastasis, and invasion, as well as of factors that stimulate formation of new blood vessels. Consistent with this, PHF19 silencing reduces cell proliferation rate and promotes invasive growth and angiogenesis. Taking together, our findings reveal a role for PHF19 in controlling the balance between cell proliferation and invasiveness in prostate cancer.

overall_design: ChIP-seq (15 samples) and RNA-seq (8 samples) of prostate cancer cells (DU145). CTR means shRNA Control, SH4 means knock-down of PHF19 long isoform and SH168 means knock-down of PHF19 short isoform. R2 means second replicate.

first: Cecilia

last: Ballare


title: CLL intraclonal fractions exhibit established and recently-acquired patterns of DNA methylation [ME]

first: Boris

last: Bartholdy

summary: Intraclonal subpopulations of circulating chronic lymphocytic leukemia (CLL) cells with different proliferative histories and reciprocal surface expression of CXCR4 and CD5 have been observed in the peripheral blood of CLL patients and named proliferative (PF), intermediate (IF) and resting (RF) cellular fractions. Here we found that these intraclonal circulating fractions share persistent DNA methylation signatures largely associated with the mutation status of the immunoglobulin heavy chain locus (IGHV) and their origins from distinct stages of differentiation of antigen-experienced B-cells. Increased leukemic birth rate (BR), however, showed a very limited impact on DNA methylation of circulating CLL fractions independent of IGHV mutation status. Additionally, DNA methylation heterogeneity increased as leukemic cells advanced from PF to RF in the peripheral blood. This frequently co-occurred with heterochromatin hypomethylation and hypermethylation of Polycomb-repressed regions in the PF, suggesting accumulation of longevity-associated epigenetic features in recently born cells.

overall_design: Genome-wide DNA methylation profiling of sorted, fractionated peripheral blood mononuclear cell (PBMC) samples from patients with CLL. For 21 patients, enough data was obtained to study the DNA methylation using Illumina 450K beadarrays in 4 fractions, and matching RNA expression. Patients had known differences in IGHV mutational status , as well as cellular birth rates, as determined by labeling with deuterated water ingested by the patients.

first: Xiahoua

last: Wang

first: Xiao-Jie

last: Yan

first: Nicholas

last: Chiorazzi

first: Matthew

last: Scharff

first: Sergio

last: Roa


title: Systematic characterization of epigenetic modifying enzymes identifies KDM3B as a key regulator in castration resistant prostate cancer

city: Vancouver

first: Nathan

middle: Allan

last: Lack

state: British Columbia

address: 2660 Oak Street

department: Vancouver Prostate Centre

country: Canada

institute: University of British Columbia

summary: Androgen deprivation therapy (ADT) is the standard care for prostate cancer patients who fail surgery and radiotherapy. While initially effective, the cancer almost always recurs into a more aggressive Castration Resistant Prostate Cancer (CRPC). Despite the existing evidence on the role of epigenetic modifiers in CRPC, only a handful of enzymes have been tested. In this study, we conducted a systematic shRNA library screen, focusing of epigenetic modifiers linked to stem-cell reprogramming, in LNCaP-abl cells, a model of CRPC. Amongst the shRNA hits, KDM3B, a histone H3K9 demethylase, was identified to have the most significant anti-proliferative effect on LNCaP-abl cells. KDM3B CRISPR/Cas9 knockout phenocopied the shRNA treatment, proving the observed phenotype was not due to shRNA off-target effects. Interestingly, this decrease in proliferation was remarkably specific to androgen-independent cells. Additionally, genetic rescue experiment showed that only enzymatically active KDM3B recovers the phenotype. No alterations in the cell cycle distribution or expression of AR downstream effectors were observed, but RNASeq revealed subtle changes in the genes expression profile for cells treated with KDM3A shRNA, including in metabolome-related enzymes such as ARG2, RDH11. However, metabolomic analysis in KDM3B knockout cells showed little change overall compared to untreated cells. Interestingly, we observed a decrease in the availability of amino acids in the absence of KDM3B which requires further investigation. Overall, our studies are the first ones to show the specificity of KDM3B in CRPC.

overall_design: Comparison of global gene expression from control shRNA or KDM3B shRNA treated LNCaP-abl cells (at t=0 and t=7 days post-selection) and LNCaP cells (at t=7 days post-selection)

first: Hilal

last: Sarac


title: Loss of non-CpG methylation in inhibitory neurons impairs neural function through a mechanism that partially overlaps with Rett syndrome

city: Houston

first: Laura

last: Lavery

state: TX

address: 1250 Moursund St., Suite 1350

department: Molecular and Human Genetics

institute: Baylor College of Medicine

summary: Whole striatum were dissected from wild-type, as well as in mice where Dnmt3a or MeCP2 was conditional deleted in inhibitory neurons. Inhibitory neuronal nuclei were also conditionally tagged with GFP in all mice. Tissues were snap-frozen in liquid nitrogen until further analysis. Inhibitory neurons were sorted from whole striatum using anti-GFP-488 and anti-NeuN-647 signals and snap frozen until further analysis. Total nuclear RNA was purified from each sample using the Single Cell RNA Purification Kit from Norgen Biotek according to manufactures instructions and stored at -80C until library preparation at the Genomic and RNA Profiling Core at Baylor College of Medicine. NuGEN Ovation RNA-Seq v2 & Rubicon ThruPlex DNA-Seq kits were utilized for library preparation. A paired-end 100 cycle run was used to sequence the flowcell on a HiSeq 2500 Sequencing System.

overall_design: Examination of gene expression in Dnmt3a-null and MeCP2-null inhibitory neurons versus wild-type inhibitory neurons from control littermates.

first: Ying-Wooi

last: Wan

first: Huda

last: Zoghbi


city: La Jolla

first: Joseph

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

type: Methylation profiling by high throughput sequencing

summary: Whole striatum were dissected from wild-type, as well as in mice where Dnmt3a or MeCP2 was conditional deleted in inhibitory neurons. Inhibitory neuronal nuclei were also conditionally tagged with GFP in all mice. Tissues were snap-frozen in liquid nitrogen until further analysis. Inhibitory neurons were sorted from whole striatum using anti-GFP-488 and anti-NeuN-647 signals and snap frozen until further analysis. Total DNA was purified from each sample using the DNeasy Blood & Tissue Kit from Qiagen according to manufactures instructions and stored at -20C until library preparation. DNA methylome libraries were generated using a modified snmC-seq method adapted for bulk DNA samples. Paired-end 150 cycle runs was used to sequence the libraries on a Illumina HiSeq 4000 Sequencing System.

overall_design: Examination of DNA methylome in Dnmt3a-null and MeCP2-null inhibitory neurons versus wild-type inhibitory neurons.

first: Chongyuan

last: Luo

first: Rosa

last: Castanon

last: Nery


title: Affymetrix SNP6.0 array data for isogenic melanoma cell lines

city: Wien

first: David

last: Schörghofer

address: Währingerstraße 10

department: Department for Pathobiochemistry and Genetics

country: Austria

institute: Medical University of Vienna

summary: Here we report on the DNA profile of the isogenic melanoma cell lines MCM1, MCM1G, MCM1D and MCM1DLN. MCM1 cells are melanoma cells generated from a nodular melanoma stage T2a, N0 of a 61 year old male patient (see GSE35991). Two subclones were derived from MCM1 termed MCM1G and MCM1D. When transplanted into SCID mice, MCM1, MCM1G and MCM1D formed tumors at the injection site. However, only MCM1D metastasized to lymph nodes. Subsequently, MCM1D cells were isolated from the lymph nodes of SCID mice and termed MCM1DLN. Upon reimplantation into SCID mice, MCM1DLN cells showed a stable metastatic phenotype. Interestingly, MCM1D and MCM1DLN tumors showed reduced NLGN4X expression on the mRNA and protein level, suggesting a role in melanoma progression.

overall_design: Affymetrix SNP arrays were performed according to the manufacturer`s instructions. DNA was extracted from the melanoma cell line MCM1 and its derived subclones MCM1G, MCM1D and MCM1DLN.

first: Mario

last: Mikula


title: Copanlisib modulates HAIR-M transcriptome

city: Bellinzona

first: Francesco

last: Bertoni

state: Ticino

address: Via V. Vela 6

department: Lymphoma & Genomics Research Program

institute: IOR

summary: Exposure to copanlisib in an MZL cell line heavily affected the lymphoma cell transcriptome, downregulating the MYC transcriptional program, alongside NFkB signaling, mTOR signaling, glycolysis, genes that are essential for cancer cells and also molecules important for immune escape (CD274, PDCD1, CSF1, TIMP1), suggesting the exploration of combinations including copanlisib and immune-checkpoint modulators.

overall_design: To assess the effects of copanlisib on the transcriptome, we exposed the MZL cell line HAIR-M to DMSO or copanlisib (5nM, for 4, 8 and 12 h) in triplicates.

first: Luciano

last: Cascione


title: Characterisation of the outflow tract banded heart utilising RNA sequencing to direct functional analysis

city: Nottingham

first: Chrysostomos

last: Perdios

state: Nottinghamshire

address: Queen's Medical Centre, Derby Road

department: Medical School

country: United Kingdom

institute: The University of Nottingham

summary:
Heart development is known to be influenced by haemodynamics, however the effects of abnormal load on gene expression are not clearly defined. To determine the hearts transcriptional response to stress, a model of haemodynamic alteration, outflow tract (OFT) banding, was employed in the chick embryo at HH21. Stereological and expression analysis were performed at HH29, with targeted expression studies at HH35. We defined a phenotype of left sided heart dilation and performed RNA sequencing on OFT-banded hearts compared to Sham controls.
Globin transcripts were depleted in the RNA during library preparation, and 28 differentially expressed genes were identified. Expression appeared to represent a mechanism of cardioprotection with calcium sequestering, metabolic and developmental genes highlighted. Significant reductions in apoptosis were also seen. We have presented a model of left sided dilation in OFT-banded hearts and found differential expression of genes that may be associated with stress and maintaining cardiac output.

overall_design: mRNA profiles of HH29 chick heart in 3 OFT-banded samples and 3 Sham samples were generated by DEEP Sequencing using the Illumina NextSeq500 platform

last: Parnall

first: Chysostomos


title: 10x and C1 CAF sequencing

city: West Lafayette

first: Nadia

middle: Marie

last: Atallah

state: IN

address: 201 S. University St

department: Center for Cancer Research

institute: Purdue University

summary: Single-cell mRNA sequencing (scRNA-seq) study was conducted to to probe heterogeneity of human prostate CAF cells.

overall_design: CAF cells were cultured and sorted using FACs

first: Renee

last: Vickman

first: Simon

last: Hayward

first: Omar

last: Franco

first: Timothy

last: Ratliff


title: Knockdown of NLGN4X in melanoma cells

status: Public on Mar 15 2020

summary: NLGN4X is a postsynaptic cell adhesion molecule that is important for synaptic function and has recently been implicated to play a role in various neuronal disorders. We detected high NLGN4X expression in non-metastatic melanoma cell lines and low NLGN4X expression in metastatic melanoma cells by Western blot and real time PCR analysis. Here, we used whole genome mRNA profiling to  investigate the consequences of NLGN4X loss for melanoma progression. Therfore, we determined gene expression changes after NLGN4X knockdown and identified HIF1 pathway up-regulation in two non-metastatic melanoma cell lines.

overall_design: We transfected MCM1G and WM793B melanoma cell lines with either control non-targeting siRNA or NLGN4X siRNA for 24h (3 biological replicates per treatment and cell line). RNA was isolated 24h after knockdown, followed by hybridization on Affymetrix microarrays.


title: single-cell transcriptional profiling of the murine habenular complex

first: Michael

last: Wallace

address: 220 Longwood Ave

department: Neurobiology

institute: Harvard Medical School

summary: The lateral habenula (LHb) is an epithalamic brain structure critical for processing and adapting to negative action outcomes. However, despite the importance of LHb to behavior and the clear anatomical and molecular diversity of LHb neurons, the neuron types of the habenula remain unknown. Here, we use high-throughput single-cell transcriptional profiling, monosynaptic retrograde tracing, and multiplexed FISH to characterize the cells of the mouse habenula. We find five subtypes of neurons in the medial habenula (MHb) that are organized into anatomical subregions. In the LHb, we describe four neuronal subtypes and show that they differentially target dopaminergic and GABAergic cells in the ventral tegmental area (VTA). These data provide a valuable resource for future study of habenular function and dysfunction and demonstrate neuronal subtype specificity in the LHb-VTA circuit.

overall_design:
Single cell RNA sequencing of live dissociated cells (unsorted) from mouse brain tissue containing the habenula using the inDrops v3 platform.
Please note that two libraries were pooled for sequencing (represented as one sample records) and demultiplexed using library barcodes (as detailed in the README file).

first: Bernardo

last: Sabatini


title: GPD1 enhances the anti-cancer effects of metformin by synergistically increasing total cellular glycerol-3-phosphate

city: Guangzhou

first: Yifeng

state: Guangdong

address: 58 Zhongshan 2nd Road

department: Institute of Respiratory Diseases of Sun Yat-sen University

institute: The First Affiliated Hospital of Sun Yat-sen University

summary: GPD1 overexpression enhances the anti-cancer effect of metformin through synergistic inhibition of mitochondrial function, thereby providing new insight into metformin-mediated cancer therapy.

overall_design: To further explore the potential molecular mechanisms of how GPD1 affects cancer cell growth with or without metformin, we upregulated GPD1 expression in A549 and786-O cells which showed relatively low GPD1 expression, and then performed the RNA-seq in A549-NC, A549-GPD1, 786-O-NC and 786-O-GPD1 cells, with or without metformin treatment.

first: Jianjiang

last: Xie

first: Weide

last: Zhong


title: Expression data from human submandibular gland cell lines

status: Public on Mar 14 2020

city: Tokushima

first: noriko

last: mizusawa

address: 3-18-15 Kuramoto-cho

department: Department of Medical Pharmacology

country: Japan

institute: The University of Tokushima Graduate School, Institute of Health Biosciences

summary: The immortalized normal human salivary gland ductal cells (NS-SV-DC) and acinar cells (NS-SV-AC) had characteristic morphologic differences, and useful for organizing knowledge of bio-functional mechanisms of human salivary gland.

overall_design: Comprehensive characterization of molecular lebels to clarify the differences between NS-SV-AC and NS-SV-DC cells.

first: Noriko

last: Mizusawa

first: Hideaki

last: Horikawa

first: Katsuhiko

last: Yoshimoto


title: Differential Gene expression of furin knockout (KO) DLD1, HCA7 and HT29 colorectal cancer cells

city: Leuven

first: Zongsheng

last: He

address: Herestraat 49

country: Belgium

institute: KU Leuven

summary: We created furin KO cells in three colorectal cancer cell lines (DLD1, HCA7 and HT29) using CRISPR-Cas9 genome editing. And then we performed RNA-Seq analysis in furin KO colorectal cancer cells to identify potential effect of furin on gene expression patterns in DLD1, HCA7 and HT29 cells.

overall_design: mRNA profiles of DLD1 cells (WT or furin KO), HCA7 cells (WT or furin KO) and HT29 cells (WT or furin KO) using RNA-Seq.


title: RNA-sequencing of Imiquimod-induced rat dorsal root ganglion (DRG) tissues treated with or without epidural lidocaine injection

city: Shanghai

first: Qianqian

last: YIN

address: Chongqing South Road

department: Institute of Immunology

institute: Shanghai Jiao Tong University School of Medicine

summary: We use dorsal root ganglion tissues of WT SD rats, or imiquimod(IMQ)-induced psoraisis-like rat model treated with or without epidural injection of 1% lidocaine. We isolated total RNA for RNA-sequencing.

overall_design: We manipulate imiquimod (IMQ) on rat back skin for consecutive 6 days. Epidural injection of 1% lidocaine are conducted from day 3 of IMQ induction for continuous 4 days. Rat DRG tissues were collected on day 7 after sacrificing rats.

last: Yin


title: Transcriptomic analysis of porcine peripheral blood reveals differentially expressed genes from the cytokine-cytokine receptor interaction pathway related to health status

city: Edmonton

first: Graham

last: Plastow

institute: University of Alberta

summary: RNA-Seq has been an effective method for exploring pathology-associated transcriptional changes in peripheral blood. The main goal of this study is to explore the expression changes of transcripts in the peripheral blood of sick pigs which may be infected with multiple pathogens on farms. We aim to find a subset of marker genes which may be useful candidate genes in the evaluation and prediction of health status in pigs under commercial production conditions.

overall_design: Peripheral blood transcriptome architecture in 64 Duroc sired commercial pigs, including 18 healthy animals at entry to a growing facility (set as a control) and 23 pairs of samples from healthy and sick pen mates, was generated using RNA-Seq technology. Differentially expressed genes specific to the sick animals were identified. Functional enrichment analysis for those genes revealed that the over-represented gene ontology terms for the biological processes category were exclusively immune activity related. The cytokine-cytokine receptor interaction pathway was significantly enriched. Nine functional genes from this pathway encoding members (as well as their receptors) of the interleukins, chemokines, tumor necrosis factors, colony stimulating factors, activins and interferons exhibited significant transcriptional alteration in sick animals. We suggested that these cytokines genes are directly involved in peripheral regulation of immune responses in the pig. They might be valuable diagnostic markers for the differential diagnosis of infection in pig.

first: Manhong

last: Ye

first: Hua

last: Bao

first: Yan

last: Meng

first: Le

last: Guan

first: Paul

last: Stothard


title: Altered lncRNAs transcriptomic profiles in atherosclerosis-induced ischemic stroke

status: Public on Mar 13 2020

city: Nanjing

first: Jiayang

last: Wu

address: No. 24 Tongjia Lane, Gulou District

institute: China Pharmaceutical University

summary:
Long non-coding RNAs (lncRNAs) can not only regulate gene transcription and translation, but also participate in the development of central nervous system diseases as epigenetic modification factors. However, their functional significance in atherosclerosis-induced ischemic stroke (AIIS) is unclear. The study aimed to screen out differentially expressed lncRNAs (delncRNAs), and to elucidate their potential regulatory mechanisms in the pathophysiology of AIIS.
We screened out 10 patients with AIIS and recruited 10 healthy volunteers. We used microarray to detect the whole blood RNA of subjects, and explored the biological functions of delncRNAs by GO and KEGG analysis. After further analyzing the delncRNAs of THP-1 stimulated by ox-LDL, selective lncRNAs were screened. Through co-expression analysis, a corresponding lncRNA-mRNA interaction network was constructed. We yielded 180 delncRNAs (44 up-regulated and 136 down-regulated) and 218 demRNAs (45 up-regulated and 173 down-regulated). Lnc-SCARNA8 and lnc-SNRPN-2 are the highest elevated and decreased lncRNA in AIIS, respectively. The delncRNAs may play a significant role in ubiquitination-mediated protein degradation signaling pathways. In THP-1 cells models, the expression levels of lnc-SLC22A16-3, lnc-MTRNR2L1-10 and lnc-ACAT1-4 were consistent to the microarray results. According to lncRNA-mRNA network, the expression of vacuolar protein sorting 13 homolog B (VPS13B) and biliverdin reductase B (BLVRB) were significantly regulated. This study identified selective delncRNAs through microarray detection and validated by in vitro cell experiment. Our findings suggest that the ubiquitinated proteasome pathway, VPS13B and BLVRB may play a fundamental role in the pathological process of AIIS.

overall_design: Based on the clinicopathological features and clinical images, we screened out 10 patients with AIIS and recruited 10 healthy volunteers. We used microarray to detect the whole blood RNA of subjects, and explored the biological functions of delncRNAs by GO and KEGG analysis. After further analyzing the delncRNAs of THP-1 stimulated by ox-LDL, selective lncRNAs were screened. Through co-expression analysis, a corresponding lncRNA-mRNA interaction network was constructed.

first: Wenchen

last: Ruan

first: Jingjing

last: Su

first: Yongcheng

last: Jiang

first: Tao

last: Pang

first: Jingwei

last: Li


title: RNA-sequencing of Imiquimod-induced rat skin treated with or without epidural lidocaine injection

summary: We use back skin of WT SD rats, or imiquimod(IMQ)-induced psoraisis-like rat model treated with or without epidural injection of 1% lidocaine. We isolate total RNA for RNA-sequencing.

overall_design: We manipulate imiquimod(IMQ) on rat back skin for consecutive 6 days. Epidural injection of 1% lidocaine are conducted from day 3 of IMQ induction for continuous 4 days. Rat back skin are collected on day 7 after sacrificing rats.


title: Modifications induced by HIV-1 Tat protein in cellular splicing mechanisms

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

summary: Intracellular Tat101 deregulated the expression of spliceosome core components, such as SF3B2, SF3A1, SFPQ, PCBP1, SYNCRIP, YBX1 and HSP8A/HSP7C, and thus likely the splicing pathway. Viral splicing experiments showed that Tat101 favored the expression of viral unspliced RNA, which are used at the late steps of the viral cycle, rather than spliced RNAs allowing the progression of HIV-1 replication.

overall_design:
CD4+ T cell line stably transfected with TetOff and pTRE2hyg-Tat72 vectors (Tat72 is the first exon of HIV-1 Tat protein regulator)
CD4+ T cell line stably transfected with TetOff and pTRE2hyg-Tat101 vectors (Tat101 contains the first and second exons of HIV-1 Tat protein regulator)
CD4+ T cell line stably transfected with TetOff and pTRE2hyg-Tat101C22G vectors (Tat101 contains the first and second exons of HIV-1 Tat protein regulator with the change C22G)

first: María

last: López Huertas

first: Sara

last: Rodríguez-Mora

first: Elena

last: Mateos

first: Guillermo

last: López-Campos

first: José

last: Alcamí

first: Mayte

last: Coiras


title: CK1 Delta Is an mRNA Cap-Associated Protein That Drives Translation Initiation and Tumor Growth

city: New York

first: Prabhjot

middle: Singh

last: Mundi

address: 1130 St. Nicholas Avenue

department: Medicine; Systems Biology

institute: COLUMBIA UNIVERSITY HEALTH SCIENCES

summary: We perform expression analysis on lymphoma cell lines Z-138 and OCI-Ly10 treated with a novel Casein Kinase 1 delta inhibitor SR-3029

overall_design: Gene expression profiles pre- and post-treatment with SR-3029 in two Non-Hodgkin lymphoma cell lines

first: Changchun

last: Deng


title: Pervasive functional translation of noncanonical open reading frames

city: Dallas

first: Jin

last: Chen

address: 5323 Harry Hines Blvd

institute: UT Southwestern Medical Center

summary: Ribosome profiling has revealed pervasive but largely uncharacterized translation outside of canonical coding sequences (CDSs). Here, we exploit a systematic CRISPR-based screening strategy to identify hundreds of non-canonical CDSs that are essential for cellular growth and whose disruption elicit specific, robust transcriptomic and phenotypic changes in human cells. Functional characterization of the encoded microproteins reveals distinct cellular localizations, specific protein binding partners, and hundreds that are presented by the HLA system. Interestingly, we find multiple microproteins encoded in upstream open reading frames, which form stable complexes with the main, canonical protein encoded on the same mRNA, thus revealing the diverse use of functional bicistronic operons in mammals. Together, our results point to a family of functional human microproteins that play critical and diverse cellular roles.

overall_design: Paired RNA-seq and ribosome profiling sequencing data for human induced pluripotent stem cells (iPSCs) and iPSC-derived cardiomyocytes,  either with or without the translational inhibitor harringtonine. Three replicates are availble for the no drug treatment samples.

first: Andreas-David

last: Brunner

first: James

middle: Z

last: Cogan

last: Nuñez

first: Alexander

last: Fields

first: Britt

last: Adamson

first: Matthias

last: Mann

first: Manuel

last: Leonetti

first: Jonathan

last: Weissman


title: mRNA sequencing of mouse and human heart tissue

city: Durham

first: Li

last: Wang

address: 111 T.W. Alexander Dr

institute: NIH

summary: We deposit the data of single-cell and bulk-cell rna-seq of normal mouse heart. In addition, we conducted bulk rna-seq in human sample and found that many of the heart remodelling-associated genes we discovered show conserved expression pattern in human hypertrophy and heart failure stage.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Single-cell RNA-seq of cells from left ventricle of mouse heart. Bulk cardiomyocyte rna-seq of mouse and rna-seq of human tissue were also conducted.

first: Peng

last: Yu

first: Zongna

last: Ren

first: Zheng

last: Li

first: Hanshi

last: Xu


title: Common regulatory targets of NFIA, NFIX and NFIB during postnatal cerebellar development

status: Public on Mar 12 2020

city: St Lucia

first: Mikael

last: Boden

state: Queensland

address: Cooper Rd

department: School of Chemistry and Molecular Biosciences

country: Australia

institute: The University of Queensland

summary: Transcriptional regulation plays a central role in controlling neural stem and progenitor cell proliferation and differentiation during neurogenesis. For instance, transcription factors from the nuclear factor I (NFI) family have been shown to co-ordinate neural stem and progenitor cell differentiation within multiple regions of the embryonic nervous system, including the neocortex, hippocampus, spinal cord and cerebellum. Knockout of individual Nfi genes culminates in similar phenotypes, suggestive of common target genes for these transcription factors. However, whether or not the NFI family regulates common suites of genes remains poorly defined. Here, we use granule neuron precursors (GNPs) of the postnatal murine cerebellum as a model system to analyse regulatory targets of three members of the NFI family: NFIA, NFIB and NFIX. By integrating transcriptomic profiling (RNA-seq) of Nfia- and Nfix-deficient GNPs with epigenomic profiling (ChIP-seq against NFIA, NFIB and NFIX, and DNase I hypersensitivity assays), we reveal that these transcription factors share a large set of potential transcriptional targets, suggestive of complementary roles for these NFI family members in promoting neural development.

overall_design: Genome-wide ChIP-seq analysis of the binding of NfiX (Sigma Aldrich, SAB1401263), NfiA (Abcam, ab41851) and NfiB (Sigma HPA003956) on the genome in granule neuron progenitor cells isolated from the cerebellum of postnatal day 7 CD1 mice.

last: Brown

first: Matthew

last: Scott


title: mRNA microarray analysis of  murine CTL EVs separated by ion exchange method [mRNA]

city: Tsu

first: Naohiro

last: Seo

state: Mie

address: 2-174 Edobashi

department: Immuno-Gene Therpy

institute: Mie University Graduate School of Medicine

summary:
EVs in culture supernatant can be concentrated with removing exsomeres and 97% free proteins by MWCO 750 kDa UF.
DEAE chromatography can be divided into bioactive EXO and other EVs as nucleic acid (DNA) cargo in UF-concentrated EVs.

overall_design: Recently, instead of ultracentrifugation, development of new preparation protocol is demanded for research of reliable bioactivity and drug discovery of extracellular vesicles (EVs). In this study, we propose a novel method for large scale preparation of high-performance extracellular vesicles focusing on membrane negative charge. Murine cytotoxic T lymphocyte (CTL) EVs in supernatant are concentrated more than 20 times at over 97% purity without leaking by 750 kDa MWCO ultrafiltration, replaced with PBS, and subjected to ion exchange DEAE column chromatography.


title: Global studies of repeat RNAs on heterochromatin regions in Drosophila S2 cells

city: San Diego

first: Yajing

last: Hao

address: George Palade Laboratories 9500 Gilman Drive, Room 217

department: Dept. of Cellular and Molecular Medicine

institute: University of California, San Diego

summary: Heterochromatin formation and maintenance, key for epigenetic inheritance of cells and organisms, have two major unsolved problems: One is the unclear source and action mode of repeat-derived RNAs in the process and the second is distinct machineries employed by different organisms, as the siRNA and piRNA pathways respectively used in fission yeast and Drosophila germline both require RNA amplification, but such mechanism does not seem to exist in somatic cells of flies and mammals. We attack these problems by defining the origins of repeat-derived RNAs and their specific chromatin registers in Drosophila S2 cells that lack active piRNA. We demonstrate that Dicer-2 is responsible for processing diverse repeat-derived RNAs, particularly those transcribed from active Gypsy elements, which act in cis and trans to maintain pericentromeric heterochromatin. These findings suggest that somatic cells trade genome vulnerability for stable genetic inheritance while germ cells use RNA amplification to abate such trade-off.

overall_design: Examination of H3K9me3, H3K27me3 and H3K4me3 three different histone modifications in S2 cells in four different conditions.

first: Runsheng

last: Chen

first: Xiang-Dong

last: Fu

first: Shunmin

last: He


title: Single-cell RNA-seq of B cell polustion in breast cancer patients

first: Jian-You

last: Liao

address: 107# Yanjiang West Road

department: Sun Yat-Sen Memorial Hospital

institute: Sun Yat-Sen University

summary: Re-education of immune cells in tumor microenvironment is required for optimal treatment outcome. The prevailing notion is that B cells, a major immune cell type in tumors, are immunosuppressive and pro-tumoral. However, why B cells inhibit tumor progression in certain contexts remains unexplained. By single cell dissection of B cell heterogeneity in longitudinal samples of breast cancer patients before and after neoadjuvant chemotherapy, we revealed a distinct subset of B cells emerges after chemotherapy, which is predictive for therapeutic efficacy and prognosis in multiple patient cohorts. Using three immunocompetent mouse models, our in vivo experiments faithfully recapitulated the subset switch of human tumor-infiltrating B cells during chemotherapy. Employing B-specific deletion and adoptive transfer experiment, we showed that ICOSL in this B cell subset boosts anti-tumor immunity by enhancing the ratio of effector and regulatory T cells. The signature of ICOSL+ B cell subset is imprinted by complement-CR2 signaling, which is triggered by chemotherapy-induced immunogenic tumor cell death. Moreover, by screening the cell line encyclopedia, we identified CD55, a complement inhibitory protein, determines the dual roles of B cells in the response of various malignancies to chemotherapy. Collectively, our study demonstrates a critical role of B cell subset switch in chemotherapy response and have implications for designing novel therapeutic approaches.

overall_design: Two experimental conditions: before and after neoadjuvant chemotherapy (NAC)

first: Yiwen

last: Lu

first: Qiyi

last: Zhao

first: Erwei

last: Song

first: Qidong

last: Xia

first: Jiaqian

first: Boxuan

last: Zhou

first: Yingying

last: Ye

first: Can

last: Di

first: Shubin

first: Junchao

last: Cai

first: Shicheng

last: Su


title: Single-cell sequencing reveal  transformation of neural stem cells into tumor-promoting cells mediated by extracellular vesicles derived from glioblastoma

city: Beijing

first: Jian

last: Wang

address: 28 Fuxing

department: neurosurgery

institute: Chinese People's Liberation Army of China(PLA) General Hospital

summary: We use transcriptome single-cell sequencing to clarify the transformation of neural stem cell into tumor-promoting cells induced by glioblastoma extracellular vesicles. We found several key genes and re-direction of signaling pathway may be involved in the transformation

overall_design: Three samples were examined, containing one positive and one negative control.

first: Jialin

last: Liu

first: Guochen

last: Sun

first: Ling

first: Xinguang

last: Yu

first: Anhua

last: Wu


title: Tristetraprolin specifically binds to intron regions and regulates alternative splicing of immune response genes in HeLa cells

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

summary: Tristetraprolin (TTP) regulates inflammatory and immune responses by destabilizing target mRNAs via binding to their 3’-UTR AREs. However, we first found that TTP can regulate gene expression and alternative splicing of inflammatory and immune responses genes in the absence of stimulation. In order to find the regulatory mechanisms, we performed iRIP-seq experiments in HeLa cells. iRIP-seq study revealed that TTP binding sites are enriched in the CDS and intronic RNA regions. We also found that the TTP-targets genes were enriched in positive regulation of I-kappaB kinase/NF-kappaB cascade and positive regulation of NF-kappaB transcription factor activity pathway, such as STAT4, EGR3, RELB, TRIM22, RNF25, and TRAF1. Furthermore, we found that alternative splicing of the innate immune response genes were globally regulated by TTP in HeLa cells. Genome-wide mapping of TTP-RNA interactions now reveal that dominant TTP binding near a competing constitutive splice site, whereas prevalent binding close to an alternative site often causes intron retention. This positional effect was further demonstrated by disrupting a TTP-binding site on minigene constructs and detecting their AS events. These findings suggest a mechanism for TTP to modulate splice site competition to produce opposite functional consequences in HeLa cells.

overall_design: RIP-seq analysis of TTP IP versus input in Hela cells

first: Yafang

last: Tu


title: Differentially expressed genes following PARK2 depletion in  Esophageal Squamous Cell Cancer Cell Line

city: xinxiang

first: xiaofeng

last: zhou

address: No. 601 Jinsui Avenue

institute: xinxiang medical university

summary:
We konckout PARK2 in Esophageal Squamous Cell Cancer Cell Line EC9706 and then detected differentially expressed genes
We konckout PARK2 in Esophageal Squamous Cell Cancer Cell Line EC9706 and then detected differentially expressed genes

overall_design: The experiment involves 3 replicates of a wildtype cell line (WT - Samples 1-3), and 3 replicates of the same cell line within which a single gene was knocked out(KO6-KO8-KO13)

first: X

last: Li


title: Dissecting cellular crosstalk by sequencing physically interacting cells

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

summary: Crosstalk between neighboring cells underlines many biological processes, such as cell activation, differentiation and signaling. Current single-cell genomic technologies lack information of cell-cell interactions, as each cell is profiled separately following tissue dissociation. Here we present Physically Interacting Cells sequencing (PIC-seq), which combines fluorescently activated cell sorting of physically interacting cells along with massively parallel single-cell RNA-sequencing and computational modeling to systematically map in situ cellular interactions and characterize their molecular crosstalk. Focusing on interactions between T cells and dendritic cells (DC) in vitro and in vivo, we map T-DC interaction preferences, and discover regulatory T cells as the major T cell subtype interacting with DC. Analysis of T-DC pairs characterized interaction-specific transcription, including upregulation of a costimulatory program in rare interactions between pathogen-presenting DC and T cells. In summary, PIC-seq provides a new technology to profile cell-cell interactions and characterize interaction-specific pathways and target genes at high resolution.

overall_design: Transcriptional profiling of thousands of single cells and doublets (PIC) from both in vivo and in vitro assays of interacting T and dendritic cells.

first: Amos

last: Tanay

first: Amir

last: Giladi

first: Merav

last: Cohen


title: Synchrony and asynchrony between an epigenetic clock and developmental timing [450K array]

city: Los Angeles

first: Steve

last: Horvath

address: 695 Charles E. Young Drive South, Box 708822

department: Human Genetics

country: USA

institute: University of California, Los Angeles

summary:
Genome wide DNA methylation profiling of human fetal retina samples. The Illumina Infinium DNA methylation Beadchip was used to obtain DNA methylation profiles in human fetal retina samples that were cultured in different ways.
To better undrestand the relationship between developmental stage and epigenetic age (measured by the Horvath clock based on 353 CpGs as detailed in pubmed identifier: 24138928), we analyzed the highly regular sequence of developmental stage in the human neural retina. Findings: epigenetic age of fetal retina is highly correlated with chronological age. We find that epigenetic aging progresses normally in vitro. The correlation is retained in stem cell derived organoids but is accelerated in individuals with Down syndrome.

overall_design: We analyzed the DNA methylation patterns from the same developmental ages as the RNAseq study to evaluate DNA methylation patterns. In order to test whether the epigenetic clock continues to progress when isolated from the rest of the organism, epigenetic clock analyses were performed on explant cultures of fetal retinas from various stages of development. Explants were maintained for 3 to 6 weeks and the rate of development and the epigenetic clock was evaluated DNA methylation and RNA seq. For additional in vitro studies, we cultured retinas and showed that they progressed at approximately normal rates with respect to epigenetic age. To further test whether the aging clock is an independent property of the tissue,we asked if cells that develop completely in vitro would also follow the epigenetic clock, such as stem cell-derived retinal organoids. We derived retinal organoids from stem cells using the established protocols.

first: Thomas

middle: A

last: Reh

first: Akina

last: Hoshino


title: Synchrony and asynchrony between an epigenetic clock and developmental timing [EPIC array]


title: Identification of auxin and cytokinin cross-talk components involved in lateral root initiation

city: Amiens

first: Jerome

last: Duclercq

address: 33 rue St Leu

institute: UPJV

type: Expression profiling by genome tiling array

summary:
Genome wide transcriptome profiling of pericycle cells from roots exposed to auxin, cytokinin and both hormones simultaneously.
Lateral root organogenesis in Arabidopsis is governed by a complex network of hormonal regulations. Plant hormones auxin and cytokinin were demonstrated to be the key regulators of this lateral root organogenesis and their mode of interaction is antagonistic. The aim of the project is to understand the role of the auxin - cytokinin signalling pathways in lateral root organogenesis.

overall_design:
12 samples (4 conditions with 3 replicates for each). J0121 seedlings were growing on MS. These 5 day-old seedlings were used for different treatments: 1µM NAA 3h (NAA); 10µM BAP 3h (BAP); 1µM NAA + 10µM BAP 3h (NB).  After cell sorting the RNA were extracted from pericycle cell sorted using the RNeasy Plant Mini Kit (Qiagen). A DNase treatment with the RNase-free DNase Set (Qiagen) was carried out for 15 min at 25°C. Total RNA concentration was determined using a Nanodrop ND-1000 spectrophotometer. All RNA samples were rejected if they did not reach a minimum concentration of 100 ng μl−1, a 260 nm/280 nm ratio between 1.8 and 2.0 and a RNA integrity number superior to 7.5, measured with an Agilent 2100 Bioanalyzer (Agilent, USA). Arabidopsis Tiling 1.0R arrays (Affymetrix) were hybridized at the VIB Nucleomics Core (www.nucleomics.be) according to the manufacturer’s instructions. Data were normalized from CEL files using the robust multiarray average (RMA) algorithm (Irizarry et al., 2003). The probe annotation was obtained from athtiling1.0rcdf (Naouar et al., 2009). Differential expression analysis was determined using the eBayes function from the limma package in R (Smyth, 2004). P values were calculated and then transformed into false-discovery rates (FDR), or Q values according to the method described by Storey and Tibshirani (2003), as implemented in the R package qvalue.
Please note that the Data.xlsx contains the result from differential expression analysis (and the full set of normalized data for each individual sample is not available).

first: Eva

last: Benkova


title: Altered mRNA splicing by mutant p53 activates oncogenic RAS in pancreatic cancer

first: Xiaoli

last: Mi

address: 1275 York Ave

department: Human Oncology and Pathogenesis Program

institute: Memorial Sloan Kettering Cancer Center

summary: Integrating transcriptomic analyses of both clinical PDAC and PDAC models, we identified that the most common neomorphic TP53 mutation (p53R175H) rewires RNA splicing promoting transcriptome-wide retention of cassette exons bearing cytosine(C)-rich sequences.

overall_design: Examination of splicing changes attributed to p53R175H in  patient derived organoids (HT42), murine pancreatic cancer cell line (KPC), murine pancreatic intraepithelial neoplasia (PanIN).

first: Luisa

last: Escobar-Hoyos

first: Alex

last: Penson

first: Robert

last: Bradley

first: Omar

last: Abdel-Wahab

first: Steven

middle: D

last: Leach


title: Immunoresolving lipid mediators support effective skeletal muscle repair

city: Ann Arbor

first: Jacqueline

last: Larouche

state: MI

address: 2800 Plymouth Rd, Building 20 Room 316WB

department: Biomedical Engineering

institute: University of Michigan

summary: Specialized pro-resolving mediators (SPMs) function to limit inflammation and actively stimulate

overall_design: RNA profiles of muscle stem cells FACS enriched from adult mice 3 days post barium chloride injury treated with RvD1 or delivery vehicle.

first: James

last: Markworth

first: Lemuel

last: Brown

first: Eunice

last: Lim

first: Carolyn

last: Floyd

first: Jesus

last: Castor-Macias

first: Peter

last: Macpherson

first: Carol

last: Davis

first: Carlos

last: Aguilar

first: Krishna

last: Rao Maddipati

first: Susan

middle: V

last: Brooks


title: mRNA expression of spinal dorsal horn in oxaliplatin-treated rats

status: Public on Mar 11 2020

city: guangzhou

first: xiangcai

last: ruan

state: guangdong

address: 602 Renminbei Rd.

country: China

institute: Guangzhou First People's Hospital

summary: Oxaliplatin-induced neuropathic pain is a common dose-limiting side effect of cancer treatment but the underlying mechanisms are largely unknown. The neuropathic pain model was established by oxaliplatin intraperitoneal administration for five consecutive days. In the present study, we performed whole genome expression microarray analysis by using spinal dorsal horn from oxaliplatin-treated and vehicle-treated rats on day 10.

overall_design: 2 oxallipaltin-treated samples and 2 vehicle-treated samples

first: Jie

last: Deng

first: Huan-Huan

last: Ding

first: Jia-Li

last: Long

first: Su-Yan

last: Lin

first: Meng

last: Liu

first: Xue-Qin

last: Zhang

first: Wen-Jun

last: Xin

first: Xiangcai

last: Ruan


title: Hypoplastic Left Heart Syndrome Single Cell RNA Sequencing

city: Palo Alto

first: Sharon

last: Paige

address: 265 Campus Drive

institute: Stanford University

summary: Single cell transcriptome analysis was performed on one Hypoplastic Left Heart Synrome (HLHS) cell line and one control cell line.

overall_design: To compare the transcriptomic profiles of control versus disease state, induced pluripotent stem cells (iPSCs) isolated from one HLHS patient (146-001) and one control (WTC) underwent cardiac directed differentiation. 10X Genomics Chromium single cell isolation (3' reagent Kit, version 3) and RNA sequencing was performed on Day 30 WTC and 146-001 iPSC-derived cardiomyoctes.

middle: L

first: Sean

last: Wu


title: TAK-418-418, a LSD1 inhibitor, can rescue the genome wide chromatin abnormality in hippocapmus tissue in KMT2D+/bGeo mice  after 2 week treatment [ChIP-seq]

city: Ellicott city

first: Li

state: Maryland

address: 733N Broadway

department: Department of Human Genetics

institute: The Johns Hopkins University

summary: KMT2D+/bGeoation in KMT2D, a histone-lysine N-methyl transferase, is responsible for majority of Kabuki syndrome in human. A mouse model of Kabuki syndrome with heterzygous KMT2D+/bGeoation of KMT2D, KMT2D+/bGeo was created to understand the disease mechanism and for drug discovery. TAK-418-418, a lysine-specific histone demethylase (LSD1) inhibitor, was tested on these mice for therapeutic treatment of the disease. Rescue of genome wide chromatin abnormality, which has been reported in KMT2D+/bGeo mice, was evaluated by high throughput next generation sequencing following chromatin immunoprecipitation of H3K4me1 and H3K4me3.

overall_design: Wild type mice and KMT2D+/bGeo mice were treated with either TAK-418-418 (3-4 per group) or vehicle control (3-4 per group) starting at age of 2-week  old. Hippacampi were harvested at the end of 2-week treatment. Global chromatin changes were investigated by high throughput CHIPSEQ of H3K4me1 and H3K4me3.

first: Hans

last: Bjornsson


title: TAK-418-418, a LSD1 inhibitor, can rescue the genome wide chromatin abnormality in hippocapmus tissue in KMT2D+/bGeo mice  after 2 week treatment [RNA-seq]

summary: Mutation in KMT2D, a histone-lysine N-methyl transferase, is responsible for majority of Kabuki syndrome in human. A mouse model of Kabuki syndrome with heterzygous mutation of KMT2D, KMT2D+/bGeo was created to understand the disease mechanism and for drug discovery. TAK-418-418, a lysine-specific histone demethylase (LSD1) inhibitor, was tested on these mice for therapeutic treatment of the disease. Differences between expression levels among different experimental conditions was evaluated by high throughput RNA sequencing (RNA-Seq).


title: Large-scale RNAi screening uncovers new therapeutic targets in the human parasite Schistosoma mansoni

first: James

middle: Joseph

last: Collins

state: Texas

address: 6001 Forest Park Rd

department: Pharmacology

institute: University of Texas Southwestern Medical Center

summary: stk25 and tao genes came out of an RNAi screen in the parasitic flatworm Schistosoma mansoni, and these genes shared a similar knockdown phenotype. To test for a functional relationship, we compared transcriptomes of early knockdown worms for each gene, compared to mock controls.

overall_design: Adult male parasites were treated with either control dsRNA or gene-targeting dsRNA (stk25 or tao) then subjected to RNAseq at earliest phenotype onset (d9 for stk25 and mock control, d6 for tao and mock control)

first: Jipeng

last: Wang

last: Paz

middle: J


title: TAK-418-418, a LSD1 inhibitor, can rescue the genome wide chromatin abnormality in hippocapmus tissue in KMT2D+/bGeo mice  after 2 week treatment

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

overall_design: Refer to individual Series


title: RNA-seqencing of Jojoba seed tissues, seed developmental stages, and other tissues

city: Denton

first: Drew

last: Sturtevant

state: TEXAS

address: 155 Union Circle #305220

department: BioDiscovery Institute

institute: University of North Texas

summary: Seeds of the desert shrub, jojoba (Simmondsia chinensis) are an abundant, renewable source of liquid wax-esters, which are valued additives in cosmetic products and industrial lubricants. Jojoba is relegated to its own taxonomic family, and there is little genetic information available to elucidate its phylogeny. Here we report the high-quality, 887 Mb, genome of jojoba assembled into 26 chromosomes with 23,490 protein-coding genes. The jojoba genome has only the whole-genome triplication (γ) shared among eudicots, and no recent duplications. These genomic resources coupled with extensive transcriptome, proteome and lipidome data helped to define heterogeneous pathways and machinery for lipid synthesis and storage, provided missing evolutionary history information for this taxonomically-segregated dioecious plant species, and will support efforts to improve the agronomic properties of jojoba

overall_design: RNA-sequencing of Jojoba developing seed cotyledons (n = 5), embryonic axis (n=5), seed coat (n=5), and whole developing seeds (n=5); Developmental seed time course, early stage (n=6), mid stage (n=6), late stage (n=6), and dry seed (n=6); Individual tissues for genome annotation woody stem (n=1), senescing leaf (n=1), male flowers (n=1), female flowers (n=1), developing capsule (n=1), 5 day old germinating roots (n=1), 14 day old seedling shoots (n=1), 14 day old seedling roots (n=1)

first: Kent

last: Chapman


title: Allyl isothiocyanate (AITC) trigged morphological, sensing process and transcription profiling alternation in Fusarium solani

first: Yingbin

last: Li

address: No.2 Yuanmingyuan West Road, Haidian District

department: plant protection college

institute: China Agricultural University

summary: Allyl isothiocyanate (AITC) is a natural product used as a food additive. Due to its strong volatility and broad biological activity, AITC is being considered as a bio-fumigant to control soil-borne fungal diseases in agriculture, creating an urgent need for evaluation of the antifungal activity of AITC. Here, AITC-trigged growth inhibition, sensing, and related molecular mechanisms were analyzed in Fusarium solani by employing morphological, genetic, and transcriptional profiling analysis. The results indicated that AITC causes rapid inhibition of F. solani after 5 min, hyphal deformity, and electrolyte leakage. A yeast-like vacuolar transient receptor potential channel regulator (FsYvc1, a STRPC family member) was identified in F. solani that is play a switch role for sensing AITC. Genetic evidence suggests the gene FsYvc1 involved in growth, development, and pathogenicity. Loss of FsYvc1 resulted in hypersensitivity of F. solani to AITC and high levels of reactive oxygen species with weak responses to CaCl2, NaCl, KCl, SDS, and Congo red as well as triadimefon, triadimenol, chlorothalonil, and azoxystrobin. Transcription profiling and qRT-PCR showed that three transcripts were up-regulated in the wild type (WT) but down-regulated in the FsYvc1 mutants (∆FsYvc1), which were involved in TRP ion channel expression, biosynthetic process, and oxidoreductase activity. Three transcripts down-regulated in WT but up-regulated in the ∆FsYvc1 were involved in metabolic process, proper enzyme folding (GrpB protein), and the response to abiotic stress (WD40 repeat). This study provides novel insights into the toxicity mechanisms of AITC. Considering the key role of FsYvc1, it could act as a new molecular target for future fungicide development.

overall_design: Total RNA from the 12 samples, including WT (F. solani) and ∆FsYvc1-17 that were treated and untreated with or without AITC at 4.8 μg/mL for 3 hours, with three biological replicates.

first: Laixin

last: Luo


title: ChIP of H4K16ac

city: West Haven

first: Matthew

last: Simon

state: CT

address: 600 West Campus Dr. MIC312

department: Molecular Biophysics & Biochemistry

institute: Yale University Chemical Biology Instiute

summary: Understanding the targeting and spreading patterns of lncRNAs on chromatin requires a technique that can detect both high intensity binding sites and reveal genome-wide spreading patterns with high confidence. We developed an improved hybridization capture protocol to determine lncRNA localization using biotinylated LNA-containing oligonucleotides that hybridize to the target RNA and enhance capture specificity by including a protecting oligonucleotide that competitively displaces contaminating species, leading to highly specific RNA capture. This approach revealed the spreading pattern of roX2, a lncRNA involved in dosage compensation in D. melanogaster, how this pattern relates to chromatin features, and how spreading of roX2 changes upon cellular stress.  Upon heat shock, roX2 displays reduced spreading on X chromosome and surprising relocalization to sites on autosomes, revealing how this improved hybridization capture approach can reveal previously uncharacterized changes in the targeting and spreading of a lncRNAs on chromatin.

overall_design: Experiment contain 2 replicates of control, heat shock and heat shock + recovery samples from S2 cells.

first: Martin

last: Machyna

first: Lea

last: Kiefer


title: TWIST1 direct targets during embryonic stem cell differentiation [RNA-seq]

city: WESTMEAD

first: PIERRE

last: OSTEIL

state: NSW

address: 214 Hawkesbury Road

department: Embryology

institute: CMRI

summary: To understand the mechanism underlying the transcriptional regulation by TWIST1-dimers, we analysed dimer-expressing embryoid bodies by RNA-seq.

overall_design: We constructed dimers of TWIST1 and selected E-proteins partners: TWIST1-TWIST1 (TT), TWIST1-TCF3 (T3), TWIST1-TCF4 (T4) and TWIST1-TCF12 (T12), and also TWIST1 monomer (T0) for comparison. The coding sequences were stably integrated into the genome of A2LoxCre ESCs, downstream of a doxycycline inducible promotor (Iacovino et al., 2014). ESC lines were differentiated for three days subjected for transcriptome analysis. Protein expression were induced 16 hours before sample collection.

first: Xiaochen

last: Fan

first: Pierre

last: Osteil

first: Ashley

last: Waardenberg


title: Identification of important genetic resources of tea oil accumulation and quality formation in Camellia oleifera based on gene expression

city: Changsha

last: Jiang

state: Hunan

address: 88 Shaoshan Road

institute: Central South University of Forestry and Technology

summary: To identify the important genetic resources of tea oil accumulation and quality formation in Camellia oleifera, an important woody edible oil tree native to Southern China, we have designed and customized an expression profile chip of C. oleifera with 8×60 K on the basis of transcriptome sequencing of multiple tissue samples including kernels, roots, and leaves from multiple varieties. we used the mcroarrays to determine the gene expressions in kernel development of C. oleifera elite varieties'Huashuo' , 'Huaxin' , 'Huajin' and 'Jujian' respectively. Microarray results indicated a total of 10710 gene probes showed stable differential expression in the comparation of August vs June and 9987 in the comparation of October vs August. PATHWAY enrichment results of DEGs indicated that the oil synthesis and accumulation occured in the whole kernel development of C. oleifera, but were mainly concentrated from the  nutrition high-speed synthesis period to the seed mature period, which was consistent with the variation trend of oil content and fatty acide composition in C. oleifera kernel development.

overall_design: In this study, twenty-four samples from three kernel developing stages of four C. oleifera elite varieties 'Huashuo' , 'Huaxin' , 'Huajin' and 'Jujian' were hybridized with the microarray of C. oleifera gene expression profile chip customized in Agilent respectively. The slected three kernel developing stages include the fruit swelling period (samples at June 30th), the nutrition high-speed synthesis period (samples at August 30th) and the seed mature period (samples at October 25th). biological repeat hybridization once for each period.

first: Xiao

last: Tan


title: The X-linked trichothiodystrophy-causing gene RNF113A links the spliceosome to cell survival upon DNA damage

city: Liège

first: Alice

last: Mayer

address: GIGA, CHU, Sart-Tilman

institute: University of Liège

summary: We report a global impact of the depletion of RNF113A on splicing, especially in cells treated with cisplatin.

overall_design: RNA sequencing was performed on control and RNF113A-depleted A549 cells treated or not with Cisplatin. Three biological replicates were prepared for each condition.

first: Alain

last: Chariot

first: Kateryna

last: Shostak

first: Benoit

last: Charloteaux


title: Histone Modifications and Chromatin Accessibility in Endothelial Cells under Shear Stress

city: La Jolla

first: John

last: Shyy

state: California

address: 9500 Gilman Dr., BRF2 Rm 1217 Bay LL

department: Medicine

institute: University of California, San Diego


title: thCHART of roX2 lncRNA [RNA]

summary: Specificity of target RNA recovery by thCHART was compared to CHART and other strategies.

overall_design: Target RNA is enriched from formaldehyde chromatin extract using biotinylated antisense oligonucleotide. Our new oligonucleotide strategy includes incorporating LNA nucleotides and toehold design to increase specificity and affinity of hybridization. RNA complexes are rinsed under stringent conditions and eluted using elution oligonucleotide.


title: Histone Modifications and Chromatin Accessibility in Endothelial Cells under Shear Stress (ChIP-seq)

summary: This data set reveals the changes of histone modifications and chromatin accessibility in human umbilical vein endothelial cells (HUVECs) under atheroprotective pulsatile shear (PS), atheroprone oscillatory shear (OS), or with KLF4 overexpression. Using ChIP-Seq, we defined the H3K27ac and H3K4me1 enrichment under PS and OS conditions. Using ATAC-seq, we identified the chromatin accessibility under KLF4 overexpression.

overall_design: PS or OS was applied to endothelial cells (ECs) with a shear stress of 12 ± 5 dyn/cm2 or 1 ± 4 dyn/cm2 for 16 hr. The histone marks were assayed by ChIP-seq.

first: Ming

last: He

first: Tse-Shun

last: Huang

first: Shuai

first: Hsiao-Chin

last: Hong

first: Zhen

last: Chen

first: Marcy

last: Martin

first: Hsi-Yuan

first: Jian

last: Kang

first: Hsien-Da

first: Shu

last: Chien


title: TT-TimeLaps-seq of S2 cells response to heat shock

first: Matthew

last: Simon

summary: Comparing gene expression between heat shock-treated and untreated S2 cells.

overall_design: RNA isolated from s4U fed cells was enriched with MTS-biotin pulldown, subjected to oxidative-nucleophilic-aromatic-substitution chemistry and sequenced.

first: Martin

last: Machyna

first: Lea

last: Kiefer


title: NFYB-1 regulates mitochondrial function and longevity via lysosomal prosaposin

city: Koln

first: Jorge

last: Boucas

address: Joseph-Stelzmann-Str. 9b

department: Bioinformatics

institute: Max Planck Institute for Biology of Ageing

summary: Mitochondrial activity is critical for cellular vitality and organismal longevity, yet underlying regulatory mechanisms spanning these different levels of organization remain elusive. From RNAi screens for mitochondrial biogenesis, we discovered NFYB-1, a subunit of the NF-Y transcriptional complex, as an ancestral regulator of mitochondrial function. NFYB-1 loss leads to reduced mitochondrial gene expression and oxygen consumption, mitochondrial fragmentation, disruption of mitochondrial stress pathways, and abolition of organismal longevity triggered by mitochondrial impairment. Multi-omics analysis reveals that NFYB-1 is a potent repressor of the ER stress response, as well as lysosomal prosaposin. Surprisingly, limiting prosaposin expression alters ceramide and cardiolipin pools, restores mitochondrial fusion, gene expression and longevity. Thus, the NFYB-1/prosaposin axis coordinates lysosomal to mitochondrial communication to enhance cellular mitochondrial function and organismal health.

overall_design: Trancsriptome of C. elegans wild type (N2), nfyb-1, isp-1 and isp-1;nfyb-1 (Day 1 adults) under ad libitum bacteria conditions

first: Rebecca

last: George Tharyan

first: Adam

last: Antebi


title: Expression data of keratinocytes from condyloma acuminata and skin tissues

first: chao

middle: zhi

last: gu

address: Liberation Road No. 1095

department: Department of Dermatology, Tongji Hospital

institute: Huazhong University of Science and Technology

summary: To explore the biological changes of keratinocytes in condyloma acuminata (CA) warts, we performed mRNA and lncRNA expression profiling of keratinocytes from normal skins and warts of condyloma acuminata patients to compare the gene expression.

overall_design: Tissue specimens of keratinocytes from three normal donors’ foreskins and five CA warts located at the skin of the patients’ penis were collected. All the patients were selected by HPV DNA detection with type 6 or 11 positive while other HPV subtypes negative.Microarray data was further performed for bioinformatics analysis.

first: Zhichao

last: Gu

first: Huafeng

last: Zhang

first: Yuchun

last: Cao