title: Single cell multi-omics analysis reveals novel roles for DNA methylation in sensory neuron injury responses

city: los angeles

first: Qin

last: An

state: CALIFORNIA

address: Room 6554 Gonda Building, UCLA

department: Department of Human Genetics

institute: ucla

type: Methylation profiling by high throughput sequencing

summary: We used single cell multi-omics method to simultaneously  profiled both DNA methylome and mRNA transcriptome from single DRG sensory neurons under either control or peripheral nerve injury condition.

overall_design: In this study, we performed sciatic nerve injury surgery on C57BL/6 and CAST/Ei crossing mice at different ages, and performed scMT-seq, μRNA-seq (low-input RNA-seq)  and μWGBS (low-input WGBS) on sensory neurons under intact and injured condition.  Bioinformatic analysis revealed novel role for DNA methylation in sensory neuron injury responses.

first: Youjin

last: Hu


title: RNA-sequencing of highly pure synovial tissue macrophages reveals two distinct osteoarthritis subgroups that indicate different disease mechanisms.

status: Public on Oct 24 2019

city: Newcastle

first: Catharien

last: Hilkens

state: Tyne and Wear

address: Framlington Place

department: Institute of Cellular Medicine

country: United Kingdom

institute: Newcastle University

type: Expression profiling by high throughput sequencing

summary: Osteoarthritis (OA) is a leading cause of disability globally. Despite an emerging role for synovial inflammation in OA pathogenesis, attempts to target inflammation therapeutically have had limited success. A better understanding of the cellular and molecular processes occurring in the OA synovium is needed to develop novel therapeutic strategies. Here, we contrasted mononuclear phagocytes and T cells in the synovial tissue of OA patients and inflammatory-arthritis (IA) patients. Compared to IA, OA synovial tissue contained fewer CD45+ leukocytes, consisting mostly of macrophages. Macrophages in OA synovial tissues displayed activated phenotypes shown by expression of proteins folate-receptor-2 and CD86. Macrophage phenotype, proliferation characteristics and transcriptome profile by RNA-sequencing distinguished two subtypes of patients within OA. One subgroup was more similar to IA - ‘inflammatory-like OA’ (iOA), and another non-inflammatory/mechanical, subgroup distinct from IA - ‘classical OA’ (cOA). Gene Ontology (GO) pathway analysis revealed that the iOA subgroup is characterised by a cell proliferation signature, whereas the cOA subgroup is defined by cartilage remodelling features. Furthermore, iOA synovial tissue contained higher proportions of macrophages, expressing higher levels of the proliferation marker Ki-67, as compared to cOA synovial tissue. The identification of these two distinct OA subtypes provides new insight into the heterogeneity of OA at the synovial tissue level, and suggests distinct cellular mechanisms in disease pathogenesis. Our findings could lead to the stratification of OA patients for suitable disease-modifying treatments, and the identification of novel therapeutic targets.

overall_design: RNA sequencing of 12 FACS purified macrophage samples isolated from synovial tisssue of arthritis patients

first: Matthew

middle: J

last: Wood

first: Adam

last: Leckenby

first: Gary

last: Reynolds

first: Rachel

last: Spiering

first: Arthur

middle: G

last: Pratt

first: Kenneth

middle: S

last: Rankin

first: Muzlifah

middle: A

last: Haniffa

first: John

middle: D

last: Isaacs

first: Simon

last: Milling


title: Transcriptomics analysis of gene expression in mouse lung after PM2.5 exposure

city: Beijing

first: Bao-Fa

last: Sun

address: Da-Tun Road

country: China

institute: Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)

summary: Total RNA was isolated from mouse lung harvested at different stages using TRIzol® Reagent (Ambion). mRNA was extracted with using Dynabeads® mRNA Purification Kit (Ambion) and subjected to TURBO™ DNase (Invitrogen) treatment at 37°C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA-Seq library construction. Libraries were directly constructed using the KAPA Stranded mRNA-Seq Kit (KAPA) and were sequenced using HiSeq2500 (Illumina) in paired-read mode, creating reads with a length of 125 bp.

first: Xiao

last: Han

first: Hanchen

last: Liu

first: Zezhong

last: Zhang

first: Yuigui

last: Yang

first: Wenjun

last: Ding


title: Single-cell RNA sequencing reveals regulatory mechanism for trophoblast cell-fate divergence in human peri-implantation embryo

first: Qin

last: An

country: USA

summary: We studied the transcriptomic dynamics underlying human per-implantation development of trophoblast cells.

overall_design: We obtained human peri-implantation embryos through blastocyst to early post -implantation stages using an in vitro coculture system, and profiled transcriptome of individual trophoblast cells collected from these embryos. By systematic analysis methods, we revealed the genetic networks regulating peri-implantation trophoblast development.

first: Bo

last: Lv


title: HT-Seq analysis of mouse lung after PM2.5 exposure

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

overall_design: Refer to individual Series


title: Whole blood transcriptome analysis in bipolar disorder reveals strong lithium effect

city: Los Angeles

first: Roel

last: Ophoff

state: CA

address: 695 Charles E. Young Drive South

department: Center for Neurobehavioral Genetics

institute: UCLA

summary:
BACKGROUND: Bipolar disorder (BD) is a highly heritable mood disorder with complex genetic architecture and poorly understood etiology. Previous transcriptomic BD studies have had inconsistent findings due to issues such as small sample sizes and difficulty in adequately accounting for confounders like medication use.

METHODS: We performed a differential expression analysis in a well-characterized BD case-control sample (Nsubjects = 480) by RNA sequencing of whole blood. We further performed co-expression network analysis, functional enrichment, and cell type decomposition, and integrated differentially expressed genes with genetic risk.

RESULTS: While we observed widespread differential gene expression patterns between affected and unaffected individuals, these effects were largely linked to lithium treatment at the time of blood draw (FDR < 0.05, Ngenes = 976) rather than BD diagnosis itself (FDR < 0.05, Ngenes = 6). These lithium-associated genes were enriched for cell signaling and immune response functional annotations, among others, and were associated with neutrophil cell-type proportions, which were elevated in lithium users. Neither genes with altered expression in cases nor in lithium users were enriched for BD, schizophrenia, and depression genetic risk based on information from genome-wide association studies, nor was gene expression associated with polygenic risk scores for BD.

CONCLUSIONS: These findings suggest that BD is associated with minimal changes in whole blood gene expression independent of medication use but emphasize the importance of accounting for medication use and cell type heterogeneity in psychiatric transcriptomic studies. The results of this study add to mounting evidence of lithium's cell signaling and immune-related mechanisms.

overall_design: Examination of RNA-sequencing profiles from peripheral whole blood of 240 bipolar disorder cases and 240 controls.

first: Catharine

middle: E

last: Krebs

first: Loes

middle: M

last: Loohuis


title: Rational targeting of cooperating layers of the epigenome yields enhanced therapeutic efficacy against AML

city: New York

first: Matt

last: Teater

state: NY

address: 445 E 69th St

institute: Weill Cornell Medical College

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Disruption of epigenetic regulation is a hallmark of Acute Myeloid Leukemia (AML), but therapeutic interventions are difficult by the interplay of epigenetic mechanisms controlling genomic elements. We hypothesized that concurrent targeting of aberrant promoter and enhancer epigenetic silencing improves efficacy against AML. To test this, we developed an ex vivo culturing system and treated 52 patient-derived AML with low-dose 5-Azacytidine and specific LSD1 inhibitors. Genetic analysis revealed that combination of 5-Azacytidine and LSD1 inhibition was most effective in TET2mut AML. Combination therapy further up-regulated expression of genes associated with both LSD1-bound enhancers and cytosine methylated promoters. Functional validation studies suggest that expression of these genes (e.g. GATA2, GFI1 and DLX2) contribute to drug efficacy. Mechanistically, combination therapy increased enhancer-promoter looping and chromatin-activating marks at the GATA2 locus. This gene induction effect was dampened by CRISPRi of the LSD1-bound enhancer in TET2mut AML. Concordant with TET2mut AML, knockdown of TET2 in human hematopoietic stem and progenitor cells induced loss of enhancer 5-hydroxymethylation and facilitated LSD1-mediated enhancer inactivation. Collectively, our platform revealed increased LSD1-mediated enhancer inactivation after TET2 deficiency that provided a basis for combinatorial epigenetic therapy to activate promoter-enhancer interactions.

overall_design: ERRBS, ChIPseq and RNAseq profiles in AML ex vivo cultures treated with 5-Azacitidine and LSD1 inhibitor

first: Cihangir

last: Duy

first: Ari

last: Melnick


title: Genetic Abnormalities in Large to Giant Congenital Nevi: Beyond NRAS mutations

city: Barcelona

first: Joan

middle: Anton

last: Puig-Butillé

state: Spain

address: Villarroel 170

department: Department of Biochemical and Molecular Genetics

country: Spain

institute: IDIBAPS-Hospital Clinic of Barcelona

summary: Large and giant congenital melanocytic nevi (CMN) are rare melanocytic lesions mostly caused by post-zygotic acquisition of NRAS alteration. However, large/giant CMN may exhibit phenotypic differences among distinct areas patients and in addition, patients differ in features such as presence of multiple CMN or Spilus-like lesions. Overall, 50 fresh-frozen biopsies corresponding to 37 phenotypically characterized areas of large/giant CMNs, 9 satellite lesions, 1 acquired nevus and 3 healthy skin biopsies were analyzed by a multigene panel and RNA sequencing (RNA-seq). Mutational screening showed mutations in 76.2% of large/giant CMN. NRAS mutation was found in 57.1% of cases, and mutations in other genes such as BRAF, KRAS, APC and MET were detected in 14.3% of patients. RNA-seq revealed the fusion transcript ZEB2-ALK and SOX5-RAF1 in large/giant CMN from two patients without point mutations. Both alterations were not detected in unaffected skin and were detected in different affected skin. These findings suggest that large/giant CMN may result from distinct molecular events in addition to NRAS mutations including point mutations and fusions transcripts.

overall_design: Molecular characterization of 50 fresh-frozen biopsies by RNA-seq method. The set of biopsies includes 37 distinct areas from 19 large/giant CMNs patients,  9 satellite lesions, one acquired nevi and 3 healthy skin biopsies.

first: Josep

last: Malvehy


title: Influence of endothelial Cx40 under atheroprone and atheroprotective flow

city: Geneva

first: Sylvain

last: LEMEILLE

address: 1 rue Michel-Servet

department: Department of Pathology and Immunology

country: Switzerland

institute: University of Geneva Medical School

summary: High laminar shear stress (HLSS), as observed in straight parts of arteries, assures a quiescent non-activated endothelium through the induction of the Krüppel-like transcription factors KLF2 and KLF4. Cx40-mediated gap junctional communication contributes to a healthy endothelium by propagating adenosine-evoked anti-inflammatory signals between endothelial cells. As the promoter of the Cx40 gene contains KLF consensus binding sites, we hypothesize that HLSS through the modulation of KLF4, may affect Cx40 expression in ECs, which may affect the quiescent non-activated state of the endothelium.

overall_design: Mouse ECs (bEnd.3) were exposed to static conditions, high LSS (HLSS; 20 dynes/cm2), or oscillatory SS (OSS; 5 dynes/cm2, 1Hz) for 48 hours using an Ibidi flow system. Knock-down of KLF4 or Cx40 was performed using siRNA.

first: Jean-Francois

last: Denis

first: Brenda

middle: R

last: Kwak


title: Exploring the impact of chonic hypoxia on the expression of DNA repair gene in Glioblastoma and Medulloblastoma cells.

status: Public on Oct 23 2019

city: Liverpool

first: Sophie

last: Cowman

address: Crown Street

department: Institute of Integrative Biology

institute: University of Liverpool

summary: Hypoxia is known to impact DNA repair mechanisms. The primary aim of this study was to examine the impact of chronic (5 days) hypoxia on the expression of DNA repair genes in glioblastoma and medulloblastoma cell lines. The NanoString nCounter VantageTM RNA Panel for DNA Damage and Repair (LBL-10250-03) was utilised to analyse gene expression using total RNA extracted from cells.

overall_design: 4 glioblastoma and 2 medulloblastoma cell lines incubated in 21% 1% or 0.1% O2 for 5 days. Gene expression was compared to cells incubated at 21% (control). Experiments were performed in triplicate.

first: S

first: V

last: See


title: Dissecting CD248 role in tumor pericytes

city: taipei

first: shuwha

last: lin

state: taiwan

address: No.1 santer street taipei, taiwan

country: Taiwan

institute: medical technology

summary: We dissect CD248 gene function on tumor pericytes through RNA seq.

overall_design: Examination of CD248 null and hetero type pericytes expression profile.

first: ShuWha

last: Lin

first: Hsiang-Po

last: Huang

first: YihHsing

last: Yu

first: ChiaLun

last: Hong


title: Human cell line and subcutaneous tumor

city: Shanghai

first: Yuetong

last: Wang

address: 320 Yue Yang Road, Room 713

department: Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences

institute: Chinese Academy of Sciences

summary: To find different gene expression signature in OVCAR5 cells with PTPRR -WT expression or PTPRR-DA expression compared with control cells, we did RNA-seq analyses.To find different gene expression signature in xenagraft tumors generated from OVCAR5 cells with PTPRR -WT expression or PTPRR-DA expression compared with control cells, we did RNA-seq analyses.

overall_design: For cell ine RNA-seq, each sample was triplicated. For tumor RNA-seq, each sample was duplicated.

first: Wang

last: Yuetong

first: Weiwei

last: Liu

first: Yiqun

last: Zhang

first: Gaofeng

last: Fan


title: Cancer-associated missense mutations enhance the pluripotency reprogramming activity of OCT4 and SOX17

city: Guangzhou

first: YOGESH

last: SRIVASTAVA

state: Guangdong

address: 190 Kaiyuan Avenue

department: Biochemistry and Molecular Biology

institute: Guangzhou Institutes of Biomedicine and Health

summary: The functional consequences of cancer-associated missense mutations are unclear for majority of proteins, here we interrogated cancer mutation databases and identified recurrently mutated positions at structural contact interface of DNA-binding domains of SOX and POU family transcription factors. We used conversion of mouse embryonic fibroblasts (MEFs) to induced pluripotent stem cells (iPSCs) as a functional read out. In this study we identified several gain-of-function mutations that enhance cellular pluripotency reprogramming by SOX2 and OCT4. Wild type SOX17 does not support pluripotency reprogramming while recurrent missense mutation SOX17-V118M  converts SOX17 into a pluripotency inducer, viability of cancer cells and provides protein stability. Here, we conclude that mutational profile of SOX and OCT family factors in cancer association can give direction to design high-performance reprogramming factors.

overall_design: We analyzed the gene expression profiles of SOX17WT and SOX17-V118M mutant that is a recurrent mutation lies at contact interface of SOX/OCT heterodimer leading to a increased cooperativity binding in the presence of compressed motif “CATTGTATGCAAAT”  DNA element. Moreover, SOX17-V118M is an inducer to pluripotency and this mutation convert non reprogramming SOX17 to reprogramming SOX17 factor. Data in GEO is submitted by name SOX17-V118M, gene expression profile at day 9 somatic cell reprogramming  of SOX17WT and SOX17-V118M done by RNA-seq.

first: Yogesh

last: Srivastava

first: Vikas

last: Malik

first: Ralf

last: Jauch


title: PRMT1 regulates microRNA biogenesis through the methylation of the Large Drosha Complex

city: Milano

first: Francesco

last: Nicassio

address: Via Adamello 16

department: Center for genomic science

country: Italy

institute: Istituto Italiano di Tecnologia

type: Non-coding RNA profiling by high throughput sequencing

summary: MicroRNA (miRNA) biogenesis is a tightly controlled multi-step process operated in the nucleus by the activity of the Large Drosha Complex (LDC). We previously reported that the LDC is highly methylated. To investigate the extent of this post-translational modification, we extensively characterized the LDC methyl-proteome by combining heavy methyl SILAC metabolic labelling of cells with the affinity-enrichment of the complex, followed by high resolution mass spectrometry (MS) analysis. We found that arginine (R) methylation is the predominant modification, occurring on multiple sites of 13 of the 23 subunits of the complex. Interestingly, the depletion- or pharmacological inhibition- of PRMT1, the major protein R-methyltransferase in mammals, alters the LDC methylation state and this is linked to a global decrease of miRNA expression, due to the specific impairment of the pri-to-pre-miRNA processing step. Moreover, PRMT1 activity appears to be required for the binding of some LDC subunits to pri-miRNAs.  Overall, our study uncovers a previously uncharacterized role of R-methylation in the regulation of the LDC activity, thus effecting miRNA levels in mammalian cells

overall_design: MicroRNA expression analysis by deep-sequencing in HeLa cells upon PRMT1 knock-down

first: Valeria

last: Spadotto

last: Ghini

first: Toziana

last: Bonaldi


first: Qin

last: An

summary: Studying X-chromosome dosage compensation dynamics in human early embryos using single cell RNA sequencing

overall_design: Here, weuse single-cell RNA-seq to report the X:A ratio and timing of XCI in pre- and peri-implantation human embryos up to fourteen days in culture.

first: Kevin


title: CN133 hampers tumor growth in patient-derived pediatric ependymoma models

status: Public on Oct 22 2019

city: barcelona

first: roberta

last: antonelli

state: Cataluña

address: Passeig Vall d'Hebron 119-129 Collserola Building,, lab 207

institute: VHIR barcelona

summary: HDACs are known to play crucial roles in cancer by deacetylating histones and non-histone substrates, leading to altered expression of genes involved in several cellular processes such as cell cycle control, apoptosis, DNA-damage response, angiogenesis, and autophagy, among othersto caracterize  the transcriptomic changes induced by CN133 treatment on EPN cells, a microarray expression analysis of the EPP cell line treated with CN133 was performed

overall_design: Epp cell lines were treated for 5h with vehicle or CN133 at 1uM concentration. 3 samples were performed for each condictions

first: M

middle: F

last: Segura

first: R

last: Antonelli

first: C

last: Jimenez Jimenez


title: Lack of whey acidic protein (WAP) four-disulfide core domain protease inhibitor 2 (WFDC2) causes neonatal death from respiratory failure in mice

city: Yokohama

first: Shin-ichi

last: Tomizawa

state: Kanagawa

address: 3-9 Fukuura, Kanazawa-ku

department: School of Medicine

country: Japan

institute: Yokohama City University

summary: Respiratory failure is a life-threatening problem for pre-term and term infants, yet many causes remain unknown. Here, we present evidence that whey acidic protein (WAP) four-disulfide core domain protease inhibitor 2 (Wfdc2), a protease inhibitor previously unrecognized in respiratory disease, may be a causal factor in infant respiratory failure. Wfdc2 transcripts are detected in the embryonic lung and analysis of a Wfdc2-GFP knock-in mouse line shows that both basal and club cells, and type II alveolar epithelial cells (AECIIs), express Wfdc2 neonatally. Wfdc2-null-mutant mice display progressive atelectasis after birth with a lethal phenotype. Mutant lungs have multiple defects, including impaired cilia and the absence of mature club cells from the tracheobronchial airways, and malformed lamellar bodies in AECIIs. RNA sequencing shows significant activation of a pro-inflammatory pathway, but with low-quantity infiltration of mononuclear cells in the lung. These data demonstrate that Wfdc2 function is vitally important for lung aeration at birth and that gene deficiency likely causes failure of the lung mucosal barrier.

overall_design: RNA-seq was performed using Wfdc2 control (+/+) and knockout (GFP/GFP) mouse lung tissues. All experiments were done using duplicate animals.

first: Kuniko

last: Nakajima

first: Michio

last: Ono

first: Uroš

last: Radović

first: Selma

last: Dizdarević

first: Kazushige

last: Kuroha

first: Go

last: Nagamatsu

first: Ikue

last: Hoshi

first: Risa

last: Matsunaga

first: Takayuki

last: Shirakawa

first: Takeyuki

last: Kurosawa

first: Yasunari

last: Miyazaki

first: Masahide

last: Seki

first: Yutaka

last: Suzuki

first: Haruhiko

last: Koseki

first: Masataka

last: Nakamura

first: Toshio

last: Suda

first: Kazuyuki

last: Ohbo


title: m5C profiles in mouse lung after PM2.5 exposure

first: Bao-Fa

last: Sun

summary: Total RNA was isolated from mouse lung harvested at different stages using TRIzol® Reagent (Ambion). mRNA was extracted with using Dynabeads® mRNA Purification Kit (Ambion) and subjected to TURBO™ DNase (Invitrogen) treatment at 37°C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA-BisSeq library construction. Around 200 ng mRNA premixed with the in vitro transcribed Dhfr mRNA at a ratio of 300:1 (Dhfr mRNA serves as methylation conversion control) was fragmented to ~100-nt fragments for 1 min at 90°C in 10× RNA Fragmentation Reagent (Ambion), then stopped by 10× RNA stop solution (Ambion), and precipitated with 100% ethanol. The RNA pellet was resuspended in 100 µl bisulfite solution (pH 5.1), which is a 100:1 mixture of 40% sodium bisulfite (Sigma) and 600 µM hydroquinone (Sigma) and subjected to heat incubation at 75°C for 4.5 h. The reaction mixture was desalted by passing through Nanosep with 3K Omega 500/pk columns (PALL Corporation) with centrifugation. After washed with nuclease-free water and centrifuged for five times, the RNA was finally disolved in 75 μl nuclease-free water and then desulfonated by incubation with an equal volume of 1 M Tris-HCl (pH 9.0) at 75 °C for 1 h. After ethanol precipitation, the RNA was resuspended in 11 µl of RNase-free water and subjected to library construction. Reverse transcription was carried out with superscript II Reverse Transcriptase (Invitrogen) and ACT random hexamers. The following procedures were performed with the KAPA Stranded mRNA-Seq Kit (KAPA) according to the manufacturer’s instructions.Libraries were sequenced using HiSeq2500 (Illumina) in paired-read mode, creating reads with a length of 125 bp.

first: Xiao

last: Han

first: Hanchen

last: Liu

first: Zezhong

last: Zhang

first: Yuigui

last: Yang

first: Wenjun

last: Ding


title: Plasminogen activator inhibitor-2 regulates immune response in kidney injury and renal aging mpact of plasminogen activator inhibitor-2 in kidney injury and renal aging

city: Carl Neuberg strasse

first: Roland

last: Schmitt

state: academic

address: M06 ebene-4

country: Germany

institute: Hannover Medical School

summary:
The  plasminogen activator inhibitor-2 (PAI-2; encoded by the SerpinB2 gene) has been described in the context of macrophage activation and in cellular senescence. As both mechanisms are important in kidney disease we tested a possible role of PAI-2 in renal injury and repair.
Methods:Aging, ischemia/reperfusion injury and unilateral ureteral obstruction were performed on the mice. Bone marrow was transplantefrom SerpinB2-/- to wild-type littermates and vice versa. Primary tubular cells and macrophages from SerpinB2-/- and wildtype mice were used for functional studies and transcriptional profiling.
Results: PAI-2 expression was up-regulated in cultured senescent tubular cells and in kidneys of aged mice. In the lack of PAI-2 in SerpinB2-/- mice was associated with enhanced renal fibrosis and an inflammatory phenotype during aging and in kidney injury models. While acute injury was associated with fewer monocytes/macrophages in SerpinB2-/- kidneys the subsequent resolution of inflammation seen in wildtype kidneys was lacking in knockout mice.
Conclusion: PAI-2 regulates renal aging, tubular damage, and resolution of inflammation. PAI-2 is crucial for kidney repair in mice .

overall_design: PMA treated wildtype and SerpinB2 -/- primary tubular cells

first: Payel

last: Sen


title: Syngeneic, in contrast to allogeneic, mesenchymal stem cells have superior therapeutic potential following spinal cord injury

city: Stockholm

first: Mikael

last: Svensson

state: Stockholm

address: Solnavägen 30

department: Clinical neuroscience

country: Sweden

institute: Karolinska Institutet

summary: We evaluated the importance of histocompatibility of transplanted MSCs in terms of therapeutic potential. Mouse syngeneic MSCs or allogeneic MSCs were transplanted following SCI in mouse. In this study we found that syngeneic, but not allogeneic, MSCs alternatively activated macrophages resulting in a down-regulation of pro-inflammation. Syngeneic MSCs also had a general suppressive effect on the immune response as compared to allogeneic MSCs. Additionally, syngeneic, but not allogeneic, MSCs significantly enhanced the recovery of hind limb function. In this study we show that the histocompatibility of transplanted MSCs is of importance for their therapeutic potential.

overall_design: Transplantation of mesenchymal stem cells into spinal cord injury.

first: Ramil

last: Hakim

first: Ruxandra

last: Covacu

first: Arvid

last: Frostell

first: Sreenivasa

last: Sankavaram

first: Lou

last: Brundin


title: Transcriptome-wide analysis of wounded region gene expression using detached first-pair rosette leaves before culture (time 0) and 2 day after culture (DAC) from 12-day-old Col-0 seedlings

first: Lin

last: XU

address: 300 Fenglin Road

department: Chinese Academy of Sciences

institute: Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences

summary: To reveal the molecular mechanism during de novo root regeneration from Arabidopsis leaf explants cultured on B5 medium without exogenous hormones, we carried out an RNA-seq experiment using detached leaf explants with partial petiole before culture (i.e. time 0) and 2 d after culturing (DAC) from12-d-old Col-0 seedlings.  Gene expression of the wounded region (including the partial petiole and some surrounding tissues), which comprises regeneration-competent cells, was analyzed.

overall_design: Arabidopsis thaliana Col-0 seeds were grown on 1/2 MS medium with sucrose at 22 °C under a 16-h light/8-h dark photoperiod. Detached leaf explants with partial petiole from 12-day-old seedlings were cultured on B5 medium with sucrose at 22 °C under dark conditions for 0 (time 0) or 2 days (2 DAC). The wounded region (including the partial petiole and some surrounding tissues), which comprises regeneration-competent cells, was separated and collected for RNA extraction.

first: Yuyun

first: Jie

last: Yu

last: Xu


title: Transcriptome gene expression analysis of root tip, leaf tip, shoot tip, root (without root tip) and leaf (without leaf tip) from Ceratopteris richardii sporophytes

summary: To study genes specially expressed in  root tip, leaf tip, shoot tip, root (without root tip) and leaf (without leaf tip)  of Ceratopteris richardii,  we carried out an RNA-seq to analyze gene expression levels from these five tissues.

overall_design: Ceratopteris richardii (wild type RNWT1) spores were cultured on 1/2MS medium at 26 °C under a 16-h-light/8-h-dark photoperiod in a growth chamber. The root, leaf, root tip, leaf tip and shoot tip tissue were separated  from 50 days sporophyte seedlings and frozen in liquid nitrogen for RNA extration. Library construction and deep sequencing were carried out using the Illumina HiSeq 3000 platform following the manufacturer's instructions by Genergy Biotechnology (Shanghai, China).


title: Non-floral Cascade RNA-seq

city: Corvallis

first: John

last: Henning

state: OR

address: 3450 SW Campus Way

institute: USDA-ARS

summary: This is an RNA-seq study looking at different non-floral hop tissue (stems, meristems and leaves) in the cultivar 'Cascade'

overall_design: Tissue-specific RNA-seq studies in hop cultivar Cascade. There are two sample replicates for each tissue, including leaf, meristem, and stem.

first: Lillian

last: Padgitt-Cobb

first: David

last: Hendrix


title: Gene Expression Analysis of HUVEC Seeded rBEL Contructs at Low and High Phases of Glucose Consumption

city: Rochester

first: Asha

last: Nair

address: 200 1ST ST SW

institute: Mayo Clinic

summary: This study was designed to measure global changes in gene expression in reendothelialized bioengineered liver contructs (rBELs) between early (low glucose consumption) and late (high glucose consumption) stages of perfusion bioreactor culture.

overall_design: This study included rBELs in low (n=2) and high (n=6) glucose consumption phases. HUVECs (n=1) and human liver sinusoidal endothelial cells (HLSECs) (n=1) were included as controls.

first: Mohammed

last: Shaheen

first: DongJin

last: Joo

first: Jeffrey

last: Ross

first: Brett

last: Anderson

first: Harvey

last: Chen

first: Robert

middle: C

last: Huebert

first: Yi

last: Li

first: Bruce

last: Amiot

first: Anne

last: Young

first: Viviana

last: Zlochiver

first: Erek

last: Nelson

first: Taofic

last: Mounajjed

first: Allan

middle: B

last: Dietz

first: Gregory

last: Michalak

first: Benjamin

last: Steiner

first: Dominique

last: Davidow

first: Christopher

last: Paradise

first: Andre

last: van Wijnen

first: Vijay

middle: H

last: Shah

first: Mengfei

last: Liu

first: Scott

middle: L

last: Nyberg


title: Transcriptome response of Pseudomonas aeruginosa PA14 to antimicrobial peptides

first: Thilo

last: Kohler

address: 1, rue Michel Servet

department: Microbiology and Molecular Medicine

institute: University of Geneva

summary: We analyzed the transcriptome of P. aeruginosa grown for 16h in the presence or absence of 0.25 x MIC of polymyxinB, G3KL or T7

overall_design: Comparative transcriptome in triplicate samples

first: T

last: Köhler

first: Fatma

last: Jeddou


title: Synthetic lethal screen reveals selective vulnerability of ATRX-mutant cancers to WEE1 inhibition

first: Xiaoyue

last: Wang

address: 5 Dongdansantiao, Dongcheng District

institute: Chinese Academy of Medical Sciences

summary: we performed a genome-wide synthetic lethal screen, using CRISPR-Cas9 genome editing, to identify potential therapeutic targets specific for ATRX-mutated cancers. In isogenic hepatocellular carcinoma (HCC) cell lines engineered for ATRX loss, we identified 58 genes, including the checkpoint kinase WEE1, uniquely required for the cell growth of ATRX null cells. Treatment with the WEE1 inhibitor AZD1775 robustly inhibited the growth of several ATRX-deficient HCC cell lines in vitro, as well as xenografts in vivo. The increased sensitivity to the WEE1 inhibitor was caused by accumulated DNA damage induced apoptosis. AZD1775 also selectively inhibited the proliferation of patient-derived primary cell lines from gliomas with naturally occurring ATRX mutations, indicating that the synthetic lethal relationship between WEE1 and ATRX could be exploited in a broader spectrum of human tumors. As WEE1 inhibitors have been investigated in several phase II clinical trials, our discovery provides the basis for an easily clinically testable therapeutic strategy specific for cancers deficient in ATRX.

overall_design: Genome-scale CRISPR-Cas9 knockout screen were applied in Wild Type cells and ATRX(-/-) cells to identify ATRX synthetic lethal genes

first: Junbo

last: Liang

first: Hong

last: Zhao

first: Bill

last: Diplas

first: Song

first: Jianmei

first: Dingding

first: Yan

last: Lu

first: Qing

last: Zhu

first: Jiayu

last: Wu

first: Wenjia

first: Hai

last: Yan

first: Yi-Xin

last: Zeng

first: Yuchen

last: Jiao


title: BRIN-BD11 pancreatic beta cell mRNA profile upon treatment with Class1 HDAC inhibitor MS-275

city: Hyderabad

first: PRASENJIT

last: MITRA

state: Telangana

address: University of Hyderabad Campus, Gachibowli

country: India

institute: Dr.Reddy’s Institute of Life Sciences

summary:
Methods: We performed mRNA sequence analysis by deep sequencing, in triplicate, using Illumina HiSeq to assess the impact of Class1 HDAC inhibitor MS-275 in regulating gene expression in BRIN-BD11 pancreatic beta cells. The transcriptome libraries were constructed using the NEB adapters and were sequenced on at 150 nucleotide read length using the paired-end chemistry. The raw reads were subjected to Adapter and low quality reads removal by Trimmomatic -0.36v. The sequence reads that passed quality filters was mapped to the Rattus_norvegicus Rnor_6.0 using STAR , counted using feature count module of sub reads package and was normalized in DESeq2-3. Differentially expressed genes were selected based on log2-ratio change with p-value <0.05 (Student‘s t test, unpaired). Hierarchical clustering was performed with the programs Cluster (uncentered correlation; average linkage clustering) and Treeview.
Results: We mapped 136,002,940 (136 million reads) reads per sample to rat genome (Rnor_6.0) and observed 97% alignment to the reference rat genome. We found that 1858 genes were up regulated and 624 genes got down regulated on MS-275 treatment (log fold change ≥±2 p value < 0.05).
Inference: Gene ontology reveals that the upregulated pathways upon MS-275 treatment include endocytosis, cAMP signaling, insulin secretion, Wnt signaling PI3K-Akt signaling and thermogenesis while the downregulated genes include histone modification, chromosome organization and cell cycle regulation. The study represents first detailed mRNA profiling of BRIN-BD11 pancreatic beta cell in context of modulation of expression upon treatment with Class1 HDAC inhibitor MS-275.

overall_design: Effect of Class1 HDAC inhibitor MS-275 on BRIN-BD11 pancreatic beta cell transcriptome

first: Prasenjit

last: Mitra

first: Shilpak

last: Bele

first: Naresh

middle: V

last: Mutha

first: Madhumohan

last: Katika


title: Global characterization of myeloid cells in murine lung cancer models by single-cell seqencing

city: La Jolla

first: Judith

middle: Anne

last: Varner

address: Center for Novel Therapeutics 9310 Athena Circle 9310 Athena Circle

department: Pathology

institute: University of California, San Diego

summary: We characterized myeloid cell populations in murine lung cancer models by single-cell sequencing. These data were in line with our previous findings about myeloid cell subsets in tumor microenvironment.

overall_design: The gene expression profiles of 3501 cells from murine LLC lung cancer models was generated by BD Rhapsody Single-Cell Analysis System and Illumina NextSeq.

first: Hideyuki

last: Takahashi


title: hCMEC/D3 cell line with single atorvastatin,single dexamethasone or low-dexamenthasone and atorvastatin treatment  after hematoma injuried

city: Tianjin

first: Yueshan

last: Fan

address: 154 Anshan Road, Tianjin, China

institute: Tianjin Medical University General Hospital

summary: Some studies have revealed that treating chronic subdural hematoma (CSDH) with drugs is effective; however, the specific mechanism of this process has been seldom discussed. Herein, we sought to identify the potential underlying mechanism of atorvastatin and low-dose dexamethasone for CSDH treatment. We sequenced the hCMEC/D3 cell lines treated with single statin, dexamethasone and low dose dexamethasone after hematoma injuried and statin to find out the key point.

overall_design: sham group, hematoma stimulation group, single atorvastatin treatment group, single dexamethasone treatment, and combination treatment group.

first: Dong

last: Wang

first: Bo


title: Enrichment of ovine gonadotropes via adenovirus gene targeting enhances assessment of transcriptional changes in response to estradiol-17β.

city: Fort Collins

first: Colin

last: Clay

state: CO

address: 1683 Campus Delivery Mail

department: Biomedical Sciences

institute: Colorado State University

summary:
The goals of this study is to enrich the population of ovine gonadotropes via adenovirus-mediated targeting and flow cytometry to compare NGS-derived transcriptome profiling (RNA-seq) of a gonadotrope-enriched cell population to the combined transcriptome of all anterior pituitary cells  and apply enrichment method to query the transcriptome of sorted ovine pituitary cells in response to treatment with 10 nM estradiol (E2) for six hours.
Methods: mRNA profiles of sheep anterior pituitary cells were generated by deep sequencing, in sextuplicates, using Illumina HiSeq. The sequence reads that passed quality filters were analyzed at the transcript level with GSNAP, followed by featureCounts and then followed by edgeR. qRT–PCR validation was performed using SYBR Green assays.
Results: About 124 million sequence reads per sample were mapped to the sheep genome (Oar v.3.1) which identified 17,082 transcripts in the pituitaries. RNA-seq data confirmed overrepresentation of genes known to be expressed in pituitary in sorted samples; 11 of genes (5 gonadotrope-specific and 6 non gonadotrope-specific) were validated with qRT–PCR. RNA-seq data had a linear relationship with qRT–PCR. Approximately 7.2% of the transcripts showed differential expression between the sorted (gonadotropes) and unsorted (all anterior pituitary cells) pituitary cells, with a fold change ≥3 and FDR <0.05. Hierarchical clustering of differentially expressed genes uncovered several as yet uncharacterized genes that may contribute to gonadotrope function. 232 genes were detected as upregulated in the sorted GFP-positive cells treated with E2 (gonadotropes) and 31 were downregulated following E2 treatment with a fold change ≥1.5 and FDR <0.1.
Conclusions: Our study represents the first detailed analysis of the gonadotrope transcriptome, with 6 biologic replicates, generated by RNA-seq technology. The data analysis workflows reported here should provide a framework for comparative investigations of gonadotrope expression profiles. This method was applied to determine differentially expressed genes in the sorted population of pituitary cells (gonadotropes) in response to 10 nM E2.

overall_design: Pituitary mRNA profiles from primary ovine cultures infected with virus specifically labeling gonadotropes (cont-sorted), sorted cells treated with E2 (e2-sorted), unsorted (anterior pituitary cells) (cont-unsorted) and unsorted treated with E2 (e2-unsorted) were generated by deep sequencing, in sextuplicates, using Illumina HiSeq.

first: Dilyara

last: Murtazina

first: Jeremy

last: Cantlon

first: Hamidreza

last: Chitsaz

first: Ali

last: Boroojeny

first: Akash

last: Shrestha

first: Kenneth

last: Jones


title: RNA-Seq analysis of cSCC cells followed by siRNA-induced gene knockdown of C1s.

city: Turku

first: Liisa

last: Nissinen

address: Medisiina D, 5th floor; Kiinamyllynkatu 10

department: Dermatology

country: Finland

institute: University of Turku

summary: Keratinocyte-derived cutaneous squamous cell carcinoma (cSCC) is the most common metastatic skin cancer, and its incidence is increasing globally. Chronic inflammation has been recognized as a risk factor for cSCC and inflammation is a typical feature in the progression of premalignant actinic keratosis lesions to invasive and metastatic cSCC. The complement system is an important part of innate immunity, and activation of complement is detected in the microenvironment of tumors and has been considered a host defense mechanism against cancer cells. The complement cascade can be activated via three distinct pathways, namely the classic, lectin, or alternative pathways, which all lead to activation of lytic pathway and formation of the membrane attack complex, a pore-like structure on the target cell membrane resulting in the lysis of the target cell. The classical pathway of complement is typically activated by binding of C1 complex to antibodies bound to their target antigens. The C1 complex consists of six subcomponents of C1q, each with a collagenous triple helix of subunits C1qA, C1qB, and C1qC chains and two copies of serine proteases C1r and C1s subunits each. Whole transcriptome analysis of cSCC cells (n=8) and normal human epidermal keratinocytes (NHEKs, n=4) and oligonucleotide array-based expression analysis of cSCC cells (n=8) and normal human epidermal keratinocytes (NHEKs, n=5) revealed overexpression of C1s in cSCC cells (GSE66412 and GSE66368, respectively). Inthis respect, we have wanted to futher study the RNA expression profile of C1s knockdown cSCC cells.

overall_design: Total RNAs from negative control siRNA and C1s siRNA-treated cSCC cell lines (n=3) were extracted. The samples were sequenced using Illumina sequencing.

first: Kristina

last: Viiklepp

first: Pilvi

last: Riihilä

first: Veli-Matti

last: Kähäri


title: miR200 family target gene identification in Neuro2A cells

city: Freiburg

first: Tanja

last: Vogel

address: Albertstr. 17

department: Institute for Anatomy and Cell Biology

institute: University of Freiburg

summary: Rett syndrome is a complex neurodevelopmental disorder that is mainly caused by mutations in MECP2. However, mutations in FOXG1 cause a less frequent non-congenital form called atypical Rett syndrome. FOXG1 is a key transcription factor implicated in forebrain development, where it maintains the balance between progenitor proliferation and neuronal differentiation. Using quantitative proteomics and genome-wide small RNA sequencing, we identified that FOXG1 interacts with the ATP-dependent RNA helicase, DDX5/p68 and controls the biogenesis of miRNAs. Both, FOXG1 and DDX5 bind to the miR200b/a/429 primary transcript and associate with the microprocessor complex, whereby DDX5 recruits FOXG1 to DROSHA. In vivo and in vitro experiments show that both FOXG1 and DDX5 are necessary for effective maturation of miR200b/a/429. RNAseq analyses of Foxg1-heterozygote hippocampi and miR200b/a/429 overexpressing Neuro-2a cells revealed that the cAMP-dependent protein kinase type II-beta regulatory subunit (PRKAR2B) is a target of miR200 in neural cells. Since it is known that PRKAR2B inhibits postsynaptic functions by attenuating protein kinase A (PKA) activity, increased PRKAR2B levels may contribute to neuronal dysfunctions in FOXG1 Rett syndrome.

overall_design: miR200 family members were overexpressed in Neuro2A cells to identify target genes for miR200 family members. As a control a sponge for miR200 family members was transfected in Neuro2A cells. 2 replicates of miR200 family overexpression were compared to 3 replicates of sponge transfected samples. miR200 overexpression was verified by RT-qPCR

first: Stefan

last: Weise

first: Ganeshkumar

last: Arumugam

first: Pavankumar

last: Videm

first: Rolf

last: Backofen

first: Andre

last: Fischer

first: Farahnaz

last: Sananbenesi


title: Characterization of eQTLs associated with androstenone by RNA sequencing in porcine testis (RNASeq Database)

city: Kongens Lyngby

first: Haja

middle: N

last: Kadarmideen

address: Richard Petersens Plads, Building 324

department: Department of Applied Mathematics and Computer Science

country: Denmark

institute: Technical University of Denmark

summary: Boar taint is an offensive odour and flavour from developed in a proportion of non-castrated male pigs (boars). Surgical castration is an effective solution but is under debate due to animal welfare concerns. Gene-based selection for low boar taint has been proposed as concentrations of the main compounds responsible for boar taint (androstenone and skatole [AS]) exhibit heritability but candidate biomarkers are lacking. The aims of this study were to identify expression quantitative trait loci (eQTLs) associated with AS in order to aid development of candidate biomarkers and to generate insights into biological pathways.

overall_design: A total of 48 Danish crossbred Duroc X Landrace/Yorkshire male pigs with divergent androstenone and skatole concentrations were subjected to genotyping of loin muscle. Of these, a total of 32 pigs were subjected to RNA-sequencing of the testis. A group of pigs received a chicory-additive three days before slaughter. Expression quantitative traits (eQTLs) associated with AS were revealed by the Matrix eQTL software. The genes and SNP markers associated with the eQTLs were discussed as candidate biomarkers.

first: Markus

last: Drag

first: Lisette

last: Kogelman

first: Hanne

last: Maribo

first: Lene

last: Meinert

first: Preben

last: Thomsen


title: Mechanistic Evaluation of Daphnia magna’s Behavioral and Life History Responses to Photoperiod [Experiment 1]

city: Vicksburg

first: Kurt

last: Gust

state: MS

address: 3909 Halls Ferry Rd.

department: Environmental Laboratory

institute: US Army ERDC

summary: Across evolutionary time, nearly all animal species have harnessed photoperiod to initiate processes that ultimately influence seasonal behavior and life history traits.  In the freshwater cladoceran Daphnia magna, the effect of photoperiod on various life history traits has generally been investigated in conjunction with additional environmental stimuli.  In the present study, we sought to untangling responses directly attributable to photoperiod in D. magna and identify the molecular processes underlying resultant behavioral and life history responses using functional analysis of global transcriptomic expression.  D. magna were exposed to five different photoperiods immediately post-hatch for 21d where a standard long-day photoperiod of 16 hours light and 8 hours dark (16L:8D) served as the control relative to 4L:20D, 8L:16D, 12L:12L, and 20L:4D photoperiods.  Entrainment to short-day photo-periods (4L:20D, 8L:16D, and 12L:12L) resulted in significantly increased light-avoidance behaviors relative to the control photoperiod where young Daphnia (7d old) displayed the most pronounced avoidance responses.  Correspondingly, functional transcriptomics identified differential transcriptional expression of genes involved in glutamate signaling, which is critical in arthropod light-avoidance responses, as well as period circadian protein and proteins coding F-box/LRR-repeat domains, all of which contribute to establishing circadian rhythms in arthropods.  Short-day photoperiods also induced increased metabolic rates which corresponded with broad-scale changes in transcriptional expression across multiple systems-level energy metabolism pathways.  The most striking observation was increased male production across short-day photoperiods (4L:20D, 8L:16D, and 12L:12D).  Transcriptional expression consistent with multiple putative mechanisms of male production were observed including expression suggestive of increased glutamate signaling; a response observed to induce male production in D. pulex via photo-period sensitive mechanisms.  Overall, the results demonstrate the importance of photoperiod on behavior and life history trajectories in D. magna where we have now established multiple putative mechanistic pathways underlying several critical responses.

overall_design: The experimental approach was to investigate the effects of photoperiod on key life history traits, metabolic rates, photo-taxis responses and global transcriptomic expression in D. magna to characterize foundational responses to light.  Separate groups of D. magna were simultaneously exposed to five different photoperiods representing varying seasonal day lengths; this included a comparative control of 16 hours light and 8 hours dark (16L:8D) that is the standard for acute (USEPA 1996a; USEPA 2002; OECD No. 202(2004)) and chronic (USEPA 1996b; ASTM E1193-97(2012) , OECD No. 211 (2012)) ecotoxicological methods and an array of alternative photoperiods including extreme short days (4L:20D), short days (8L:16D), equinox (12L:12L), and extreme long days (20L:4D).  Since changes in life history strategy are likely to involve changes in energy utilization (Ananthasubramaniam et al 2015), overall metabolic rate was also investigated. Provided the inherently variable nature of life history and behavioral responses to stimuli, we repeated the photoperiod exposures in two temporally separated experiments on 17 October 2014 and 11 March 2015, hereafter referred to as Experiment 1 and Experiment 2, to assess the reproducibility of all measures and endpoints from one experiment to the next, and assessed if the two data sets could be combined for examination as one large dataset. In summary, 2 duplicate photoperiod experiments were conducted where each included 5 photoperiods x 3 exposure replicates.  The present GEO dataset represents Experiment 1.   In addition to life history endpoints, basic behavioral responses to photo-period were of interest; thus, instantaneous response to light as a stimulus where photo-taxis (“light oriented reactive swimming” Fraenkel et al 1961) was investigated in real-time light/dark preference assays and time series light acclimation assays.  Lastly, an investigation of global-transcript expression was conducted to identify the genes and genetic pathways that were responsive to the five different, static photoperiod lengths and to establish potential relationships between affected genes/pathways and any observed changes in life history traits, metabolic rate and behavioral responses.

first: Alan

middle: J

last: Kennedy

first: Jennifer

last: Laird

first: Mitchell

last: Wilbanks

first: Xin

last: Guan

first: Nicolas

last: Melby

first: Lyle

last: Burgoon

first: Michael

last: Kjelland

first: Todd

last: Swannack


title: Cell-Cell communication between skin keratinocytes and fibroblasts is non-redundantly coded through inflammatory cytokines

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

institute: University of Lübeck

summary: Cell-cell communication between keratinocytes and fibroblasts is essential for skin homeostasis, regulation and regeneration. How extracellular cytokine signaling, intra-cellular protein signaling and transcriptional regulation initiate and maintain this communication is still largely unknown. Here, we study in vitro the secretome and transcriptome dynamics that establish double paracrine cell-cell communication between primary human keratinocytes and fibroblasts. We find that keratinocyte-derived interleukin 1α initiates the cell communication, eliciting a constitutive NF-κB-mediated inflammation response in the fibroblasts. Their resulting transcriptome response over at least 12 hours induces a fibroblast secretome capable of enhancing keratinocyte migration.  Applying partial least square regression to secretome perturbation experiments using recombinant proteins or antibodies demonstrates the synergistic interaction of early and late secreted inflammatory CC and CXC chemokines as well as IL6, whose relative composition directly controls keratinocyte migration. Conversely, inhibiting individual cytokines during cell-communication abrogates the keratinocyte phenotype. Hence, only the simultaneous activity of multiple inflammatory cytokines together with prolonged inflammatory response in the fibroblasts lead to increased keratinocyte migration after double paracrine cell communication, putatively serving as safeguard mechanisms for proper skin regeneration.

overall_design: The isolation time points for keratinocyte conditioned medium-treated human dermal fibroblasts  were recorded at t=[1,2,3,4,6,8,10,12,24] hours after stimulation.  Unstimulated control time points were taken at  t=[0,2,4,8,12,24] hours.

first: Melanie.

last: Boerries

first: Juliana

last: Minardi-Nascimento

first: Silke

last: Kowar


title: Differential DNA methylation following developmental exposure to triclosan (TCS) in 7dpf zebrafish larvae

city: Namur

first: Elodie

last: Falisse

address: rue de Bruxelles 61

department: Biology

country: Belgium

institute: University of Namur

summary: There is increasing evidences that toxicant exposure can alter methylation profiles, particularly during embryogenesis when DNA methylation patterns are established. In order to investigate the effects of TCS on DNA methylation and its consequences on gene expression during embryogenesis, we exposed zebrafish eggs during 7 days post fertilisation (dpf) to 50 and 100 µg/L of TCS. Although, global DNA methylation was not affected by TCS exposure, a total of 171 differentially methylated fragments (DMFs) between conditions were identified. The majority of the DMFs were found between the two exposed groups, reflecting distinct triggered responses. Gene ontology analysis revealed that pathways involved in TGF-beta signaling were enriched in larvae exposed to 50 µg/L, while de novo pyrimidine biosynthesis functions were overrepresented in fish exposed to 100 µg/L of TCS. In parallel, gene expression analysis revealed a positive correlation between DNA methylation patterns and gene expression levels for introns, together with significant alterations of the transcription of genes involved in nervous system development, transcriptional factors and histone methyltransferase. Overall our work provides evidence that TCS impacts DNA methylation during zebrafish early embryogenesis and brings clues about the toxicity mechanisms of TCS during this critical period of development.

overall_design: Collected eggs were distributed individually in 24-well microplates, each well containing 2 mL of test solutions. 6 plates were used per conditions (control, exposed to 50 µg/L and exposed to 100 µg/L of TCS)  for RRBS analysis. At the end of the 7 days of exposition, 6 pools of 24 larvae were sampled and only 4 were used for RRBS librairies.

first: Falisse

last: Elodie

first: Peter

last: Stockwell

first: Ian

last: Morison

first: Aniruddha

last: Chatterjee

first: Frédéric

last: Silvestre


title: Mechanistic Evaluation of Daphnia magna’s Behavioral and Life History Responses to Photoperiod [Experiment 2]

first: Kurt

last: Gust

overall_design: The experimental approach was to investigate the effects of photoperiod on key life history traits, metabolic rates, photo-taxis responses and global transcriptomic expression in D. magna to characterize foundational responses to light.  Separate groups of D. magna were simultaneously exposed to five different photoperiods representing varying seasonal day lengths; this included a comparative control of 16 hours light and 8 hours dark (16L:8D) that is the standard for acute (USEPA 1996a; USEPA 2002; OECD No. 202(2004)) and chronic (USEPA 1996b; ASTM E1193-97(2012) , OECD No. 211 (2012)) ecotoxicological methods and an array of alternative photoperiods including extreme short days (4L:20D), short days (8L:16D), equinox (12L:12L), and extreme long days (20L:4D).  Since changes in life history strategy are likely to involve changes in energy utilization (Ananthasubramaniam et al 2015), overall metabolic rate was also investigated. Provided the inherently variable nature of life history and behavioral responses to stimuli, we repeated the photoperiod exposures in two temporally separated experiments on 17 October 2014 and 11 March 2015, hereafter referred to as Experiment 1 and Experiment 2, to assess the reproducibility of all measures and endpoints from one experiment to the next, and assessed if the two data sets could be combined for examination as one large dataset. In summary, 2 duplicate photoperiod experiments were conducted where each included 5 photoperiods x 3 exposure replicates.  The present GEO dataset represents Experiment 2.   In addition to life history endpoints, basic behavioral responses to photo-period were of interest; thus, instantaneous response to light as a stimulus where photo-taxis (“light oriented reactive swimming” Fraenkel et al 1961) was investigated in real-time light/dark preference assays and time series light acclimation assays.  Lastly, an investigation of global-transcript expression was conducted to identify the genes and genetic pathways that were responsive to the five different, static photoperiod lengths and to establish potential relationships between affected genes/pathways and any observed changes in life history traits, metabolic rate and behavioral responses.

first: Alan

last: Kennedy

first: Jennifer

middle: G

last: Laird


title: Comprehensive Profiling of Rheumatoid Arthritis Antibody Repertoire

status: Public on Oct 21 2019

city: Madison

first: Ken

last: Lo

state: WI

address: 6014 Sandstone Drive

institute: NimbleTherapeutics

summary: 8 controls and 26 RA samples were profiled using NimbleTherapeutics high density peptide array.  Array consists of >4.6M peptides, includes citrullination and homocitrullination against the entire human proteome represented as overlapping 16mer peptides.

overall_design: retrospective disease vs. control

first: Lo

last: Ken


title: Transcriptomic and Single Cell Analysis of the Murine Parotid Gland

city: Buffalo

first: Rose-Anne

last: Romano

state: New York

address: 3435 Main Street

department: Department of Oral Biology

institute: State University of New York at Buffalo

summary: By combining bulk RNA-seq and scRNA-seq approaches we have generated a comprehensive transcriptomic map of the murine parotid gland at different stages of maturation.

overall_design: 10x scRNA-Seq of murine parotid gland postnatal day 18 mice.

first: Akinsola

last: Oyelakin

first: Eun-Ah

last: Song

first: Sangwon

last: Min

first: Jonathan

last: Bard

first: Julien

last: Kann

first: Erich

last: Horeth

first: Kirsten

last: Smalley

first: Jill

last: Kramer

first: Satrajit

last: Sinha


title: Expression data from 12 and 52 weeks old Rar-alpha WT and KO male mice

city: Paris

first: Franck

last: Letourneur

address: 22 rue mechain

country: France

institute: INSERM

summary: Primary aldosteronism (PA) is the most frequent form of secondary arterial hypertension. Mutations in different genes increase aldosterone production in PA, but additional mechanisms may contribute to increased cell proliferation and aldosterone producing adenoma (APA) development. We performed transcriptome analysis in APA and identified retinoic acid receptor alpha (RARα) signaling as a central molecular network involved in nodule formation. To understand how RARα modulates adrenal structure and function, we explored the adrenal phenotype of male and female Rarα knockout mice. Inactivation of Rarα in mice led to major structural disorganization of the adrenal cortex in both sexes, with increased adrenal cortex size in female mice and increased cell proliferation in males. Abnormalities of vessel architecture and extracellular matrix were due to decreased Vegfa expression and modifications in extracellular matrix components. On the molecular level, Rarα inactivation leads to inhibition of non-canonical Wnt signaling, without affecting the canonical Wnt pathway nor PKA signaling. Our study suggests that Rarα contributes to the maintenance of normal adrenal cortex structure and cell proliferation, by modulating Wnt signaling. Dysregulation of this interaction may contribute to abnormal cell proliferation, creating a propitious environment for the emergence of specific driver mutations in PA.

overall_design: Because Rar-alpha is a transcription factor, we performed transcriptome analysis to better understand the underlying molecular changes due to Rar-alpha invalidation and correlate them to the observed phenotype.   Adrenal glands from 12 and 52 weeks old WT and Rar-alpha KO male mice were used. RNA was extracted from four adrenals per group and hybridized on Affymetrix microarray.

first: Rami

last: El Zein

first: Maria-Christina

last: Zennaro

first: Sheerazed

last: Boulkroun


title: Elucidating the molecular determinants of Aβ aggregation with deep mutational scanning

city: Seattle

first: Douglas

last: Fowler

state: WA

address: William H. Foege Hall, 3720 15th Ave NE

department: Genome Sciences

institute: University of Washington

summary: Despite the importance of Aβ aggregation in Alzheimer’s disease etiology, our understanding of the sequence determinants of aggregation is sparse and largely derived from in vitro studies. For example, in vitro proline and alanine scanning mutagenesis of Aβ40 proposed core regions important for aggregation. However, we lack even this limited mutagenesis data for the more disease-relevant Aβ42. Thus, to better understand the molecular determinants of Aβ42 aggregation in a cell-based system, we combined a yeast DHFR aggregation assay with deep mutational scanning.  We measured the effect of 791 of the 798 possible single amino acid substitutions on the aggregation propensity of Aβ42. We found that ~75% of substitutions, largely to hydrophobic residues, maintained or increased aggregation. We identified 11 positions at which substitutions, particularly to hydrophilic and charged amino acids, disrupted Aβ aggregation. These critical positions were similar but not identical to critical positions identified in previous Aβ mutagenesis studies. Finally, we analyzed our large-scale mutagenesis data in the context of different Aβ aggregate structural models, finding that the mutagenesis data agreed best with models derived from fibrils seeded using brain-derived Aβ aggregates.

overall_design: Examination of Aβ mutations in 3 replicates

first: Vanessa

last: Hasle


title: Ebola virus (EBOV) infection of ARPE-19 cells: small RNA transcriptome

city: Adelaide

first: Justine

last: Smith

address: Bedford Park

country: Australia

institute: Flinders University

summary: We used small RNA sequencing (RNA-Seq) to identify miRNA expression in EBOV-infected human RPE cells, and conducted in silico analyses to identify biological targets of, and molecular interactions with, these miRNAs.

overall_design: Small RNA transcriptomic profiles of ARPE-19 cells 24 hours following infection with EBOV or mock-infection


title: Next Generation Sequencing and m6A sequencing Facilitates Quantitative Analysis of Wild Type and genetic FTO knockdown ccRCC cells Transcriptomes

city: Stanford

first: Yiren

last: Xiao

state: CA

address: 1291 WELCH ROAD

institute: Stanford	University

summary:
Purpose:  FTO is an N6-methyladenosine (m6A) RNA demethylase. The goals of this study are to to identify functional mRNA targets of FTO m6A demethylase activity in VHL deficient ccRCC cells. We performed transcriptome wide m6A sequencing and RNA sequencing analysis of two independent FTO deficient and wild type ccRCC cell lines.
Methods: We performed transcriptome wide m6A sequencing and RNA sequencing analysis of two independent FTO deficient (shFTO#2 and shFTO#5) and wild type ccRCC cell lines.
Results:  Analysis using exomePeak identified a total of 20,168 m6A peaks that are different between the shFTO cells and the control cells. A total of 2,680 and 4,049 m6A peaks showed a significant increase and decrease (p < 0.05), respectively, in abundance (normalized to input), in shFTO cells relative to Ctrl_cells, and they were thus termed hyper- and hypo-methylated m6A peaks, respectively. Through integrative analysis of the RNA-seq data, we identified 459 hypermethylated m6A peaks the RNA transcripts of which were significantly (p < 0.05) downregulated (255; Hyper-down) or upregulated (204; Hyper-up) in shFTO cells relative to Ctrl cells (Figure XB).
Conclusions: Our study represents the first detailed analysis of FTO driving transcriptomes, with biologic replicates, generated by RNA-seq technology and m6A sequencing. Our results confirmed the functional role of FTO in mRNA demethylase and identify the targets of FTO. We conclude that FTO plays important role in mRNA destiny determination by m6A demethylase activity.

overall_design: m6A-specific antibodies are used to immunoprecipitate RNA. RNA is reverse-transcribed to cDNA and deep sequenced. In paralal mRNA of UMRC2 cell transfected with shSCM, shFTO#1 and shFTO#2 were generated by deep sequencing.

first: Subarna

first: Erinn

last: Rankin


title: Transcriptome analysis suggests a compensatory role of the cofactors coenzyme A and NAD+ in medium-chain acyl-CoA dehydrogenase knockout mice

city: Groningen

first: Sarah

last: Stolle

address: Antonius Deusinglaan 1

country: Netherlands

institute: University of Groningen

summary: During fasting, mitochondrial fatty-acid β-oxidation (mFAO) is essential for the generation of glucose by the liver. Children with a loss-of-function deficiency in the mFAO enzyme medium-chain acyl-Coenzyme A dehydrogenase (MCAD) are at serious risk of life-threatening low blood glucose levels during fasting in combination with intercurrent disease. However, a subset of these children remains asymptomatic throughout life. In MCAD-deficient (MCAD-KO) mice, glucose levels are similar to those of wild-type (WT) mice, even during fasting. We investigated if metabolic adaptations in the liver may underlie the robustness of this KO mouse. WT and KO mice were given a high- or low-fat diet and subsequently fasted. We analyzed histology, mitochondrial function, targeted mitochondrial proteomics, and transcriptome in liver tissue. Loss of MCAD led to a decreased capacity to oxidize octanoyl-CoA. This was not compensated for by altered protein levels of the short- and long-chain isoenzymes SCAD and LCAD. In the transcriptome, we identified subtle adaptations in the expression of genes encoding enzymes catalyzing CoA- and NAD(P)(H)-involving reactions and of genes involved in detoxification mechanisms. We discuss how these processes may contribute to robustness in MCAD-KO mice and potentially also in asymptomatic human subjects with a complete loss of  MCAD activity.

overall_design: Acadm-knockout and wild-type C57BL/6J mice were kept on a low-fat control diet or a high-fat semisynthetic diet for 6 weeks and subsequently fasted for 16 hours ) or kept on the diet for these 16 hours.

first: Anne-Claire

last: Martines

first: Albert

last: Gerding

first: Marcel

last: Vieira-Lara

first: Justina

last: Wolters

first: Angelika

last: Jurdzinski

first: Laura

last: Bongiovanni

first: Alain

last: de Bruin

first: Pieter

last: van der Vlies

first: Gerben

last: van der Vries

first: Vencent

middle: W

last: Bloks

first: Terry

last: Derks

first: Dirk-Jan

last: Reingoud

first: Barbara

last: Bakker


title: Transcriptome of Acinetobacter oleivorans DR1 in 0.1 % NaAc_MSB media

city: Seoul

first: Chulwoo

last: Park

address: Anam

country: South Korea

institute: Korea univ.

summary: We report the trascriptomic information of wild type (WT) and aceA mutant during the growth on 0.1 % NaAc added MSB media

overall_design: Examination of one WT and one aceA mutant strain samples

first: Woojun


title: Dynamics of Trophoblast Differentiation in Peri-implantation Stage Human Embryos

city: Gainesville

first: Zongliang

last: Jiang

state: FL

address: 2033 Mowry Rd

department: Animal Sciences

institute: University of Florida

summary: Single cell RNA sequencing of cells from cultured human blastocysts has enabled us to define the transcriptomic landscape of placental trophoblast (TB) that surrounds the epiblast and associated embryonic tissues during the enigmatic day (D) 8 to D12 peri-implantation period before the villous placenta forms. We analyzed the transcriptomes of three early placental cell types, cytoTB (CTB), syncytioTB (STB) and migratoryTB (MTB) picked manually from cultured embryos dissociated with trypsin and were able to follow sub-lineages that emerged from proliferating CTB at the periphery of the conceptus. A unique form of CTB with some features of STB was detectable at D8, while mature STB was at its zenith at D10. A form of MTB with a mixed MTB/CTB phenotype arose around D10. By D12, STB generation was in decline, CTB had entered a new phase of proliferation, and mature MTB cells had begun to move from the main body of the conceptus. Notably, the MTB transcriptome at D12 indicated enrichment of transcripts associated with interferon signaling, migration and invasion, and upregulation of HLA-C, HLA-E, and HLA-G. The STB, which is distinct from the STB of later villous STB, had a phenotype consistent with intense protein export and placental hormone production, as well as migration and invasion. The studies show that TB associated with human embryos is in rapid developmental flux during peri-implantation period when it must invade, signal robustly to the mother to ensure that the pregnancy continues, and make first contact with the maternal immune system.

overall_design: Single Cell RNA sequencing of early trophoblast revealed the mystery of human implantation, highlighting the critical role of interferon signaling. In original datasets, S, L and EVT represent CTB, STB and MTB trophoblasts sub-lineages, respectively.

first: Ye

last: Yuan


title: small RNA-mediated regulation during Zea mays (maize) Somatic Embryogenesis [RNA-Seq]

city: MEXICO CITY

first: TZVETANKA

middle: DIMITROVA

last: DINKOVA

state: DISTRITO FEDERAL

address: CIRCUITO EXTERIOR, CIUDAD UNIVERSITARIA DELEGACION COYOACAN

department: BIOCHEMESTRY

country: Mexico

institute: UNIVERSIDAD NACIONAL AUTONOMA DE MEXICO, FACULTAD DE QUIMICA

summary: We report the role of sRNAs populations during the induction of callus tissues from VS-535 maize embryos displaying contrasting in vitro embryogenic potential; characterized through Next-generation sequencing (NGS). We conclude that the Embryogenic Response during Maize Somatic Embryogenesis induction is closely related to sRNAs regulation and depends on the developmental stage of the explant.

overall_design: Six RNA-seq samples were analyzed: Immature Embryo 15 Days After pollination (DAP; IE15); Immature Embryo 23 DAP ( IE23); Mature Embryo (ME); Calli obtained from IE15 at one month of subculture (C15); Calli obtained from IE23 at one month of subculture (C23); and Calli obtained from ME at one month of subculture (CM). Data generated by deep sequencing, in duplicate, using Illumina Hiseq2000 in paired end format

first: Vasti

middle: T

last: Juárez-González

first: Brenda

middle: A

last: López-Ruiz

first: Patricia

last: Baldrich

first: Blake

last: Meyers

first: Tzvetanka

last: Dinkova


title: small RNA-mediated regulation during Zea mays (maize) Somatic Embryogenesis [smRNA-Seq]

overall_design: Six sRNAs samples were analyzed: Immature Embryo 15 Days After pollination (DAP; IE15); Immature Embryo 23 DAP ( IE23); Mature Embryo (ME); Calli obtained from IE15 at one month of subculture (C15); Calli obtained from IE23 at one month of subculture (C23); and Calli obtained from ME at one month of subculture (CM). Data generated by deep sequencing, in duplicate, using Illumina NextSeq-2000  in single end format

middle: D


title: small RNA-mediated regulation during Zea mays (maize) Somatic Embryogenesis

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

overall_design: Refer to individual Series


title: Escherichia coli DH5alpha Transcriptome Sequencing  under Wi-Fi radiofrequency radiation

city: beirut

first: Ilham

middle: Hassan

last: Salman

address: Hadath

country: Lebanon

institute: Lebanese university

summary:
Purpose:  In this study, Escherichia coli DH5alpha whole transcriptome sequencing was performed in order to compare the different gene expression profiles between control and  exposed  to Wi-Fi radiofrequency radiations.
Methods:Escherichia coli DH5alpha were exposed to Wi-Fi radiations. Total RNA samples( control and exposed ) were extracted by bacteria protect-Rneasy kit,treated with DNAase and subjected to sequnecing using an Illumina-NovaSeq 6000 platform. Library preparation and sequencing were performed by Macrogen (south korea).Trimmed reads are mapped to reference genome with Bowtie. HTseq was used for expression profiling. Expression profile was calculated for each sample and gene as read count.

overall_design: 6 samples at mid log phase including control and Wi-Fi exposed E.coli DH5α for 5 hours, in triplicate, were analyzed using Illumina NovSeq6000 plateform

last: Said-Salman

first: Ftaima

last: Jebaii


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type Mice and Toll-like Receptor 4 Intestianl Epithelial Conditional Knockout Mice Ileal Transcriptomes

status: Public on Oct 20 2019

city: Baltimore

first: David

middle: J.

last: Hackam

state: MD

address: Room 7323, 1800 Orleans Street

department: Surgery

country: USA

institute: The Johns Hopkins University

summary: Toll-like receptor 4 (TLR4), the receptor of gram-negative bacterial endotoxin, is present on the intestinal epithelium and plays pivotal roles in intestinal epithelial differentiation and host defense. To better understand TLR4 on the intestinal epithelium, the ileum samples from wild type mice and mice lacking TLR4 in the intestinal epithelium (TLR4ΔIEC) were subjected to RNA-seq analysis to interrogate the transcriptome. We mapped about 20 million sequence reads per sample to the mouse genome and identified 86477 genes in the ileum of wild type and TLR4ΔIEC mice. 455 genes were differentially expressed between wild type and TLR4ΔIEC mice and 1037 genes were absent either from wild type or TLR4ΔIEC mice with G-factor value 0.015 and Δ cutoff value 0.54. Pathway analysis via IPA indicated some impacted canonical KEGG pathways such as DNA replication, PPAR signaling, Toll-like receptor signaling, cytokine-cytokine interaction, adherens junction, Jak-STAT signaling, and tight junction.

overall_design: Total RNA was isolated from the ileum of 3 wild type mice and 3 TLR4ΔIEC mice, and a barcode was added to the sample from each individual mouse during the whole transcriptome library preparation. The pooled samples from 3 wild type mice (barcodes BC01, BC02 and BC03) and from 3 TLR4ΔIEC mice (barcodes BC07, BC08 and BC09) were subjected to RNA sequencing, respectively.


title: Mechanistic Evaluation of Daphnia magna’s Behavioral and Life History Responses to Photoperiod

first: Kurt

last: Gust


title: RNA-seq data of soybean GFP-GmSRKP1.

city: Nanjing

first: Jie

last: Huang

state: Jiangsu

address: NO.1 Weigang

department: Plant Pathology

country: China

institute: Nanjing Agricultural University

summary: One fascinating aspect of plant pathogen co-evolution is that pathogens use effectors to alter a broad range of host responses. RNA splicing functions in many physiological processes including plant immunity. However, how plant pathogens manipulate host RNA splicing process remains unknown. Here we demonstrate that PsAvr3c, an avirulence effector from oomycete pathogen Phytophthora sojae, physically binds to and stabilizes soybean (Glycine max) serine/arginine/lysine rich proteins GmSRKPs in vivo. SRKP, novel proteins associating with spliceosome components, are plant susceptibility factors against Phytophthora. Furthermore, RNA-seq data uncovers that differential splicing over one thousand soybean mRNA transcripts, including defense related genes, are significantly changed in GmSRKP1 over-expressing lines. Representative splicing events are verified in either infection assay or soybean transient expression assay. Our results demonstrate that plant pathogen utilize effector to reprogram host RNA splicing, uncovering a new strategy evolved by pathogens to defeat host immune system

overall_design: Two independent soybean GFP-GmSRKP1 over-expression lines and one GFP control sample

first: Suomeng

last: Dong


title: Transcriptional profile Lactobacillus plantarum WCFS1 : Oleuropein treated cells

city: Madrid

first: Felix

last: Lopez de Felipe

address: Jose Antonio Novais

country: Spain

institute: ICTAN-CSIC

summary: Whole genome transcriptional profiling was used to characterize the response of Lactobacillus plantarum WCFS1 human isolate during challenge with oleuropein. Twelve independent experiments were performed and mixed at random in groups of four for total of three RNA samples. The transcriptional profile shows that Lactobacillus plantarum WCFS1 adapts its metabolic capacity to acquire certain carbohydrates and repress the expression of genes involved in fatty acid biosyntheis. The transcriptomic datasets also revealed the downregulation of genes related to the biosynthesis of capsular polysaccharides and genes coding for ABC-type transporters. In addition, induction of oligopeptide permeases is also part of the response of Lactobacillus plantarum WCFS1 to oleuropein.

overall_design: Biological triplicates: untreated cells: Control vs. Oleuropein treated cells: Experimental

first: Inés

last: Reverón

first: Laura

last: Plaza

first: Blanca

last: de las Rivas

first: Rosario

last: Muñoz

first: Félix

last: López de Felipe


title: Profiling gene expression changes in ovarian cancer cells seeded on 3D organotypic culture of omentum

status: Public on Oct 18 2019

city: Bloomington

first: Anirban

middle: K

last: Mitra

state: IN

address: 915 E 3rd St

institute: Indiana University School of Medicine - Bloomington

summary: Ovarian cancer is the deadliest gynecologic malignancy and the fifth leading cause for cancer related deaths among women in USA. Most patients have metastatic disease at the time of diagnosis and this causes the poor prognosis. Regulation of early steps of metastatic colonization - the rate limiting step of metastasis - is poorly understood. Using an organotypic 3D culture model of the omentum, we have mimicked the early stages of metastatic colonization in vitro. Using this, we have profiled the mRNA expression changes occurring in high grade serous ovarian cancer cell line Kuramochi, OVCAR4 and OVCAR8 when they are seeded on the 3D omentum culture compared to controls seeded on normal culture dishes. The ovarian cancer cells were separated by FACS after 2 days of culture and their RNA was isolated and RNA-seq was performed. Library preparation and next generation RNA sequencing was carried out at the Center for Genomics and Bioinformatics core facility, Indiana University, Bloomington. The library preparation was done using TruSeq Stranded mRNA HT Sample Prep kit (Illumina cat#RS-122-2103) according to the manufacturer’s protocol and 8-neucleotide barcodes were added for multiplexing. The barcoded libraries were cleaned by bead cut with AMPure XP beads (Beckman Coulter, cat#A63882), verified using Qubit3 fluorometer (ThermoFisher Scientific) and 2200 TapeStation bioanalyzer (Agilent Technologies), and then pooled. The pool was sequenced on NextSeq 500 (Illumina) with NextSeq75 High Output v2 kit (Illumina cat#FC-404-2005).

overall_design: Kuramochi, OVCAR4 and OVCAR8 cells seeded on the 3D omentum culture or on plastic culture dishes (n=3/cell line) were used for sequencing. The library preparation was done using TruSeq Stranded mRNA HT Sample Prep kit (Illumina cat#RS-122-2103) according to the manufacturer’s protocol and 8-neucleotide barcodes were added for multiplexing. The barcoded libraries were cleaned by bead cut with AMPure XP beads (Beckman Coulter, cat#A63882), verified using Qubit3 fluorometer (ThermoFisher Scientific) and 2200 TapeStation bioanalyzer (Agilent Technologies), and then pooled. The pool was sequenced on NextSeq 500 (Illumina) with NextSeq75 High Output v2 kit (Illumina cat#FC-404-2005). Reads were adapter trimmed and quality filtered using Trimmomatic ver. 0.33, with the cutoff threshold for average base quality score set at 20 over a sliding window of 3 bases. Reads shorter than 20 bases post-trimming were excluded. Cleaned reads mapped to human genome GRCh38 with gencode v25 annotation using Tophat2 ver 2.1.0. Significantly differentially expressed genes at 5% FDR with at least 2 fold change were called using DESeq2 ver. 1.12.3.

first: Sumegha

first: Ram

last: Podicheti


title: Circular RNA expression signature of low-glucose-treated MIA PaCa-2 cells

city: Guangzhou

first: Shineng

last: Zhang

state: Guangdong

address: No.107 Yanjiang West Road

institute: Sun Yat-sen Memorial Hospital, Sun Yat-sen University

summary: Glucose metabolism makes contributions to the development of pancreatic ductal adenocarcinoma (PDAC). Meanwhile, circular RNAs, a subset of noncoding RNAs, plays an important role in glucose metabolism and cancer progression. Analysis of low-glucose-treated and normal-glucose-treated MIA PaCa-2 cells from 6 samples (3 samples each group) was conducted. Results indicate insight into molecular signature of the pathogenesis of PDAC in abberant glucose metabolism.

overall_design: High throughput sequencing analysis was conducted to identify the differentially expressed circular RNAs between low-glucose-treated and normal-glucose-treated MIA PaCa-2 cells from 6 samples.

first: Y

last: Li

first: F

first: S


title: Profiling gene expression changes in primary ovarian tumors compared to matched normal fallopian tubes

summary: Ovarian cancer is the deadliest gynecologic malignancy and the fifth leading cause for cancer related deaths among women in USA. For a comprehensive understanding of the gene expression changes accompanying ovarian carcinogenesis, we isolated RNA from 8 pairs of matched FT and primary tumors from OC patients and sequenced them. Library preparation and next generation RNA sequencing was carried out at the Center for Genomics and Bioinformatics core facility, Indiana University, Bloomington. The library preparation was done using TruSeq Stranded mRNA HT Sample Prep kit (Illumina cat#RS-122-2103) according to the manufacturer’s protocol and 8-neucleotide barcodes were added for multiplexing. The barcoded libraries were cleaned by bead cut with AMPure XP beads (Beckman Coulter, cat#A63882), verified using Qubit3 fluorometer (ThermoFisher Scientific) and 2200 TapeStation bioanalyzer (Agilent Technologies), and then pooled. The pool was sequenced on NextSeq 500 (Illumina) with NextSeq75 High Output v2 kit (Illumina cat#FC-404-2005).

overall_design: 8 pairs of matched primary ovarian tumors and fallopian tubes from ovarian cancer patients were used for sequencing. The library preparation was done using TruSeq Stranded mRNA HT Sample Prep kit (Illumina cat#RS-122-2103) according to the manufacturer’s protocol and 8-neucleotide barcodes were added for multiplexing. The barcoded libraries were cleaned by bead cut with AMPure XP beads (Beckman Coulter, cat#A63882), verified using Qubit3 fluorometer (ThermoFisher Scientific) and 2200 TapeStation bioanalyzer (Agilent Technologies), and then pooled. The pool was sequenced on NextSeq 500 (Illumina) with NextSeq75 High Output v2 kit (Illumina cat#FC-404-2005). Reads were adapter trimmed and quality filtered using Trimmomatic ver. 0.33, with the cutoff threshold for average base quality score set at 20 over a sliding window of 3 bases. Reads shorter than 20 bases post-trimming were excluded. Cleaned reads mapped to human genome GRCh38 with gencode v25 annotation using Tophat2 ver 2.1.0. Significantly differentially expressed genes at 5% FDR with at least 2 fold change were called using DESeq2 ver. 1.12.3.


title: Comparison of microbial communities with different carbon source types

status: Public on Oct 19 2019

city: muang

first: Dome

last: Adoonsook

state: ChiangMai

address: Suthep

country: Thailand

institute: Dome

summary: We reported the microbial communities in the biofilm anoxic-oxic-MBR system operated with different carbon source types.

overall_design: Examination of 3 different carbon source types.

first: A

last: Dome

first: W

last: Aunnop


title: Changes in autumn leaf senescence and coloration in Ginkgo biloba

city: Yangzhou

first: Li

last: Wang

address: Wenhui east road no. 48

institute: Yangzhou University

summary: We sequenced mRNA from Ginkgo biloba leaves grown at different developmental stages using the Illumina HiSeq4000 platform to generate the transcriptome dynamics that may serve as a gene expression profile blueprint for different response patterns during autumn leaf senescence and coloration. These results contribute to the elucidation of the molecular mechanisms involved in the leaf coloration and senescence in G. biloba as well as to the identification of candidate genes involved in this process.

overall_design: Transcriptome sequencing in G. biloba leaves grown at different developmental stages during leaf senescence and coloration

first: Lu


title: Identification of somatic memory genes during bovine nuclear reprogramming by transcriptome sequencing

city: Yangling

first: Chuan

last: Zhou

state: Shaanxi

address: 3 Taicheng Road

department: College of Veterinary Medicine

institute: Northwest A&F University

summary: We hypothesized aberrant transcriptional silence was existed in bovine clone reprogramming as well as abnormal transcriptional activation and the result of RNA-seq confirmed this hypothesis. On the one hand, SCNT (somatic cell nuclear transfer) embryos exhibited excessive RNA processing and translation while these two biological processes were deficient in human and mouse; on the other hand, SCNT embryos exhibited the transcriptional defects of reproduction-related genes. These results proved the existences of active- and silent-memory genes which inherited from donor cells in bovine early SCNT embryos. Then, H3K4me3-specific demethylase 5B (KDM5B) mRNAs were injected into cloned embryos to erase active or silent memory respectively. KDM5B overexpression not only reduced the transcription level of active-memory genes but also promoted the expression of silent-memory genes, especially rescued multiple development-related genes.

overall_design: RNA-Seq profiles from pools of IVF eight-cell embryo (3 replicates), SCNT eight-cell embryo with (3 replicates) or without (3 replicates) KDM5B overexpression were generated using Illumina HiSeq 4000.RNA-Seq profiles from pools of bovine fetal fibroblast (BFF) (3 replicates) were generated using BGIseq-500.

first: Zhang

last: Yong

first: Zhou

last: Chuan

first: Liu

last: Xin

last: Jingcheng


title: N6-methyladenosine is a molecular signature for discrimination of self and non-self RNA by cytoplasmic RNA sensor RIG-I

city: CHICAGO

first: Zijie

state: IL

department: Chemistry

institute: University of Chicago

summary: Internal N6-methyladenosine (m6A) modification of RNA is one of the most common and abundant modifications in eukaryotic cells as well as in viruses. However, the biological role(s) of RNA m6A in virus-host interaction remains elusive. Using human metapneumovirus (hMPV), a medically important non-segmented negative-sense RNA virus as a model, we demonstrate that m6A serves as a molecular marker for innate immune discrimination self and nonself RNAs. We show that hMPV RNAs are m6A methylated and that viral m6A methylation promotes hMPV replication and gene expression. HMPV infection leads to differential expression of interferon-related genes involved in innate immune signaling pathways. Inactivating these m6A sites with synonymous mutations resulted in m6A deficient recombinant hMPVs that induced significantly higher expression of type I interferon that restricted viral replication. Notably, the induction of type I interferons by m6A-deficient rhMPVs and virion RNA was dependent on the cytoplasmic RNA sensor RIG-I, not MDA5. Mechanistically, m6A-deficient virion RNA induces higher expression of RIG-I, enhances its binding affinity to RIG-I, and facilitates the conformational change of RIG-I, leading to enhanced induction of type I IFN expression. The replication of m6A-deficient rhMPVs was attenuated in wild type A459 cells but was restored in cells knocked out for RIG-I and MAVS. Furthermore, m6A-deficient rhMPVs triggered higher type I interferon in vivo and were significantly attenuated in the lower respiratory tract yet retained high immunogenicity in cotton rats. Collectively, our results highlight that (i) virus acquires m6A in their RNAs as a means of mimicking cellular RNA to avoid the detection by innate immunity; and (ii) viral m6A RNA can serve as a novel target to attenuate hMPV for vaccine purposes.

overall_design: HMPV virions were purified from supernatants of hMPV-infected Hela and A549 cell lines. Virus derived mRNA as well as host mRNA were purified from total RNA, which were extracted from hMPV infected cells.

first: Mijia

last: Lu

first: Jianrong


title: Glycosyltransferase-like RSE1 negatively regulates leaf senescence by modulating salicylic acid signaling in Arabidopsis

city: DAEGU

first: JAE

middle: HO

last: LEE

address: 333, Techno jungang-daero, Hyeonpung-myeon, Dalseong-gun

department: NewBiology

institute: DGIST

summary: Leaf senescence is a developmental process designed for nutrient recycling and relocation to maximize growth competence and reproductive capacity of plants.  Thus, plants integrate developmental and environmental signals to precisely control senescence.  However, it remains largely elusive as to how plants coordinate genetic, epigenetic, and metabolic pathways for the regulation of senescence.  To genetically dissect the complex regulatory mechanism underlying leaf senescence, we identified an early leaf senescence mutant, rse1.  RSE1 encodes a putative glycosyltranferase.  Loss-of-function mutations in RSE1 resulted in precocious leaf yellowing and up-regulation of senescence maker genes, indicating enhanced leaf senescence.  Transcriptome analysis revealed that salicylic acid (SA) and defense signaling cascades were activated in rse1 prior to the onset of leaf senescence.  In agreement with the phenotypes, we found that SA accumulation was significantly increased in rse1.  We also discovered that the rse1 phenotypes are dependent on SA-INDUCTION DEFICIENT 2 (SID2), indicating a role of SA in accelerated leaf senescence in rse1.  Furthermore, RSE1 protein was localized to the cell walls, and rse1 displayed increased glucose contents in the cell walls, implying a possible link between the cell walls and RSE1 function. Together, we show that RSE1 negatively modulate leaf senescence through an SID2-dependent SA signaling pathway.

overall_design: Transcriptome analysis was performed in Ler and rse1-1 via high-throughput mRNA sequencing

first: Seulbee

last: Lee

first: Myung-Hee

last: Kim

first: Jae-Ho

first: Jieun

last: Jeon

first: June

middle: M

last: Kwak

first: Yun-Ju


title: Profiling gene expression changes in primary ovarian tumors compared to matched metastasis

first: Anirban

last: Mitra

summary: Ovarian cancer is the deadliest gynecologic malignancy and the fifth leading cause for cancer related deaths among women in USA. Most patients have metastatic disease at the time of diagnosis and this causes the poor prognosis. For a comprehensive understanding of the gene expression changes accompanying ovarian cancer metastasis, we isolated RNA from 11 pairs of matched primary tumors and metastasis from OC patients and sequenced them. Library preparation and next generation RNA sequencing was carried out at the Center for Genomics and Bioinformatics core facility, Indiana University, Bloomington. The library preparation was done using TruSeq Stranded mRNA HT Sample Prep kit (Illumina cat#RS-122-2103) according to the manufacturer’s protocol and 8-neucleotide barcodes were added for multiplexing. The barcoded libraries were cleaned by bead cut with AMPure XP beads (Beckman Coulter, cat#A63882), verified using Qubit3 fluorometer (ThermoFisher Scientific) and 2200 TapeStation bioanalyzer (Agilent Technologies), and then pooled. The pool was sequenced on NextSeq 500 (Illumina) with NextSeq75 High Output v2 kit (Illumina cat#FC-404-2005).

overall_design: 11 pairs of matched primary ovarian tumors and metastasis from ovarian cancer patients were used for sequencing. The library preparation was done using TruSeq Stranded mRNA HT Sample Prep kit (Illumina cat#RS-122-2103) according to the manufacturer’s protocol and 8-neucleotide barcodes were added for multiplexing. The barcoded libraries were cleaned by bead cut with AMPure XP beads (Beckman Coulter, cat#A63882), verified using Qubit3 fluorometer (ThermoFisher Scientific) and 2200 TapeStation bioanalyzer (Agilent Technologies), and then pooled. The pool was sequenced on NextSeq 500 (Illumina) with NextSeq75 High Output v2 kit (Illumina cat#FC-404-2005). Reads were adapter trimmed and quality filtered using Trimmomatic ver. 0.33, with the cutoff threshold for average base quality score set at 20 over a sliding window of 3 bases. Reads shorter than 20 bases post-trimming were excluded. Cleaned reads mapped to human genome GRCh38 with gencode v25 annotation using Tophat2 ver 2.1.0. Significantly differentially expressed genes at 5% FDR with at least 2 fold change were called using DESeq2 ver. 1.12.3.

first: Sumegha

first: Ram

last: Podicheti


title: Identification of differentially-expressed circular RNAs after human bone marrow-mesenchymal stromal cells (hMSCs) detachment

city: Davos Platz

first: Martin

last: Stoddart

address: Clavadelerstrasse 8

country: Switzerland

institute: AO Research Institute Davos

summary: The aim of this study was to identify non-coding RNA that were rapidly differentially expressed after loss of anchorage in human bone marrow-mesenchymal stromal cells (MSCs).

overall_design: Human MSCs cultures in monolayer were either lysed directly with TRIreagent (day_0_2D) or trypsinized and samples collected within 30 minutes from detachment (day_0_3D).

first: Elena

last: Della Bella


title: Downregulation of miR-194-5p induces paclitaxel resistance in ovarian cancer cells by altering MDM2 expression.

city: Suita

first: Kenjiro

last: Sawada

state: Osaka

address: Yamadaoka 2-15

department: Obstetrics and Gynecology

country: Japan

institute: Osaka University Faculty of Medicine

summary: Paclitaxel is a first-line drug for treating epithelial ovarian cancer (EOC). However, prognosis for patients with advanced stage cancer remains poor due to primary or acquired drug resistance. Therefore, overcoming chemoresistance is one of the greatest challenges in treating EOC. In this study, we identified microRNAs (miRNA) that regulate paclitaxel resistance and tested their potential utility as therapeutic targets. Paclitaxel-resistant cell lines were established using two EOC cell lines: SKVO3ip1 and HeyA8. miRNA PCR arrays showed that miR-194-5p was downregulated in paclitaxel-resistant cells. Forced expression of miR-194-5p resensitized resistant cells to paclitaxel. Conversely, miR-194-5p inhibition induced paclitaxel resistance in parental cells. In silico analysis and luciferase reporter assay revealed that MDM2 is a direct target of miR-194-5p. MDM2 was upregulated in paclitaxel resistant cells compared with parental cells. MDM2 inhibition also resensitized resistant cells to paclitaxel and forced MDM2 induced paclitaxel resistance in parental cells. miR-194-5p induced p21 upregulation and G1 phase arrest in resistant cells by downregulating MDM2. Furthermore, a public database showed that high MDM2 expression was associated with a shorter progression-free survival in EOC patients treated with paclitaxel. Collectively, our results show that restoring miR-194-5p expression resensitizes EOCs to paclitaxel, and this may be exploited as a therapeutic option.

overall_design: We established paclitaxel resistant high grade serous ovarian cancer cell lines (SKOV3ip1-TR and HeyA8-TR) from 2 parental cell lines (SKOV3ip1 and HeyA8),. Then miRNA expression profiles were assessed in these 4 ovarian cancer cell lines by TaqMan miRNA arrays. Relative expression of miRNAs in paclitaxel resistant sublines were calculated when compared with parental cell lines.

first: Koji

last: Nakamura


title: Identification of differentially-expressed miRNAs after human bone marrow-mesenchymal stromal cells (hMSCs) detachment


title: Identification of differentially-expressed piRNAs after human bone marrow-mesenchymal stromal cells (hMSCs) detachment


title: Muscle transcriptional profiles of chickens from slow and fast growing lines with different degree of WS and WB myopathies

city: Nouzilly

first: Eva

last: Pampouille

address: UMR BOA

institute: INRA

summary: Broiler industry is facing an increasing prevalence of breast myopathies such as white striping (WS) and wooden breast (WB), whose precise etiology remains poorly understood. In order to progress in the understanding of the structural changes and the molecular pathways involved in these myopathies, and identify biomarkers, a transcriptomic analysis using an 8×60K Agilent chicken microarray was performed. The study used pectoralis major muscles from three groups: slow-growing animals (n=8), fast-growing animals visually free from defects (n=8) or severely affected by both WS and WB (n=8). In addition, a weighted correlation network analysis was performed to investigate the relationship between modules of co-expressed genes and histological traits.

overall_design: Gene expression was measured in pectoralis major muscles from three groups: slow-growing animals, visually free from defects (SG, n=8) and fast-growing animals visually free from defects (FG-C, n=8) or severely affected by both WS and WB defects (FG-WSWB, n=8), at 42 days of age.

first: Christelle

last: Hennequet-Antier

first: Christophe

last: Praud

first: Amélie

last: Juanchich

first: Aurélien

last: Brionne

first: Estelle

last: Godet

first: Thierry

last: Bordeau

first: Maxime

last: Banville

first: Elisabeth

last: LeBihan-Duval

first: Cécile

last: Berri


title: Cell detachment rapidly induces changes in non-coding RNA expression in human mesenchymal stromal cells

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

overall_design: Refer to individual Series