title: Hazard Assessment of High-Nitrogen Compounds: Coupling Transcriptomics with Multi-Cellular Co-Culture Assays Provides Accurate Systemic Toxicity Screening [DNAN]

city: Vicksburg

first: Kurt

last: Gust

state: MS

address: 3909 Halls Ferry Rd.

department: Environmental Laboratory

institute: US Army ERDC

summary: Abstract - Current in vitro hazard assessment techniques lack the systems context necessary to holistically describe in vivo toxicity.  To remedy this shortcoming, we have employed the Integrated discrete Multiple Organ Co-Culture (IdMOC) system in conjunction with global-transcriptomic expression assessment to provide a systems context of interactive organ and toxicity pathway responses.  Specifically, IdMOC exposures containing human cells representative of five organ types (kidney, liver, lung, vascular endothelium and heart muscle) were compared to mono-culture exposures, to evaluate toxic effects in a well-studied legacy munition, 2,4,6-trinitrotoluene (TNT) compared to a structurally similar insensitive munition, 2,4-dinitroanisole (DNAN) having sparsely described toxicity.  DNAN toxicity, based on cell viability, was significantly lower than TNT for three cell lines: liver, vascular endothelium, and heart. Toxicity pathways enriched in transcriptional analysis of kidney cells exposed to TNT and DNAN through the IdMOC system reflected the literature-based in vivo mammalian toxicity of parent compounds and metabolites where multiple screening values matched chronic dosing levels within 1 order of magnitude.  Enriched pathways were primarily unique to each chemical where TNT exposures affected xenobiotic metabolism, oxidative stress, and cell cycle pathways in addition to pathways providing potential screening for hematotoxicity, renal toxicity and urinary cancer.  Ten pathway-level responses from IdMOC suggested that DNAN elicited toxicity representative of the primary metabolite, 2,4-dinitrophenol (2,4-DNP).  Relative to monoculture, IdMOC results provided a higher number and more robust enrichment of pathways involved in known in vivo toxicity mechanisms for TNT and a profile indicative of in vivo systemic toxicity of DNAN and metabolite 2,4-DNP.

overall_design: Human kidney proximal tubule epithelial cells (HK-2) derived from normal tissues (American Type Culture Collection, ATCC®, Manassas, VA) were exposed in mono-culture and co-culture to 2,4-dinitroanisole (DNAN).  Mono-cultures were conducted in standard 96 well plates whereas co-culutres were conducted in Integrated discrete Multiple Organ Co-Culture (IdMOC) 96 well plates where the kidney cells were co-exposed in a common media with liver (THLE-3), lung (NuLi-1), vascular endothelium (eloHAEC), and heart (AC10) cell, all from American Type Culture Collection (ATCC®, Manassas, VA).  The mono- and co-culture plates were  incubated on shakers at low speed for 24 hours while exposed to DNAN at 0 (1% DMSO carrier control), 100µM, and 1mM where all conditions included 4 replicates.  In summary, the experiment had a completely randomized design and included a 2 x 3 factorial treatment including 2 culture conditions (mono- and co-cultures) each combined with the 3 DNAN exposure levels (0, 100µM, and 1mM) all including x 4 replication for a total of 24 microarray samples.

first: Tony

last: Maurais

first: Keri

middle: B

last: Donohue

first: Anne

last: Mayo

first: Mitchell

last: Wilbanks

first: Natalie

last: Barker

first: Xin

last: Guan

first: Natàlia

last: Garcia-Reyero

first: Edward

last: Perkins

first: Christopher

last: Gellasch

first: Mary

middle: T

last: Brueggemeyer


title: Does APOBE3G expression affect the gene expression in T cells?

status: Public on Dec 01 2018

city: Würzburg

first: Claus

middle: Juergen

last: Scholz

address: Josef-Schneider-Str. 2

department: Core Unit SysMed

country: Germany

institute: University Hospital Würzburg

summary:
APOBEC3G in human CemSS T cells acts antivirally also against negative-strand RNA viruses as found in Vero cells (Fehrholz et al., 2012, J.Gen.Virol. 93, 565-575, DOI 10.1099/vir.0.038919-0).
This antiviral activity is not dependent on the deaminase activity of APOBEC3G, but may be mediated by induction of other antiviral mechanisms. Here we screened for antiviral genes induced by APOBEC3G.

overall_design: CemSS cells with and without APOBEC3G overexpression were compared.

first: Vishakha

last: Tiwarekar

middle: J

first: Jürgen

last: Schneider-Schaulies


title: Hazard Assessment of High-Nitrogen Compounds: Coupling Transcriptomics with Multi-Cellular Co-Culture Assays Provides Accurate Systemic Toxicity Screening [TNT]

middle: A

country: USA

summary: Abstract - Current in vitro hazard assessment techniques lack the systems context necessary to holistically describe in vivo toxicity.  To remedy this shortcoming, we have employed the Integrated discrete Multiple Organ Co-Culture (IdMOC) system in conjunction with global-transcriptomic expression assessment to provide a systems context of interactive organ and toxicity pathway responses.  Specifically, IdMOC exposures containing hµMan cells representative of five organ types (kidney, liver, lung, vascular endotheliµM and heart muscle) were compared to mono-culture exposures, to evaluate toxic effects in a well-studied legacy munition, 2,4,6-trinitrotoluene (TNT) compared to a structurally similar insensitive munition, 2,4-dinitroanisole (DNAN) having sparsely described toxicity.  DNAN toxicity, based on cell viability, was significantly lower than TNT for three cell lines: liver, vascular endotheliµM, and heart. Toxicity pathways enriched in transcriptional analysis of kidney cells exposed to TNT and DNAN through the IdMOC system reflected the literature-based in vivo mammalian toxicity of parent compounds and metabolites where multiple screening values matched chronic dosing levels within 1 order of magnitude.  Enriched pathways were primarily unique to each chemical where TNT exposures affected xenobiotic metabolism, oxidative stress, and cell cycle pathways in addition to pathways providing potential screening for hematotoxicity, renal toxicity and urinary cancer.  Ten pathway-level responses from IdMOC suggested that DNAN elicited toxicity representative of the primary metabolite, 2,4-dinitrophenol (2,4-DNP).  Relative to monoculture, IdMOC results provided a higher nµMber and more robust enrichment of pathways involved in known in vivo toxicity mechanisms for TNT and a profile indicative of in vivo systemic toxicity of DNAN and metabolite 2,4-DNP.

overall_design: HµMan kidney proximal tubule epithelial cells (HK-2) derived from normal tissues (American Type Culture Collection, ATCC®, Manassas, VA) were exposed in mono-culture and co-culture to 2,4,6-tinitrotoluene (TNT).  Mono-cultures were conducted in standard 96 well plates whereas co-culutres were conducted in Integrated discrete Multiple Organ Co-Culture (IdMOC) 96 well plates where the kidney cells were co-exposed in a common media with liver (THLE-3), lung (NuLi-1), vascular endotheliµM (eloHAEC), and heart (AC10) cell, all from American Type Culture Collection (ATCC®, Manassas, VA).  The mono- and co-culture plates were  incubated on shakers at low speed for 24 hours while exposed to TNT at 0 (1% DMSO carrier control), 10µM, and 100µM where all conditions included 4 replicates.  In sµMmary, the experiment had a completely randomized design and included a 2 x 3 factorial treatment including 2 culture conditions (mono- and co-cultures) each combined with the 3 TNT exposure levels (0, 10µM, and 100µM) all including x 4 replication.  The microarray of one control replicate within the TNT, co-culture exposure treatment was compromised and removed from the data analysis leaving a total of 23 microarray samples.

middle: H

middle: G

middle: S

middle: D


title: Gene based influence of PDGF/VEGF in colorectal cancer

summary: The aim of the study was to analyse the effects of PDGF and VEGF stimulation on tumor cell proliferation and metabolism for new therapeutic targets in colorectal cancer (CRC).

overall_design: We compared the effects of VEGF and PDGF treatment to vehicle substance in HT29 cell line after 24, 48 and 72 hours.

first: Romana

last: Mönch

first: Ana

middle: M

last: Waaga-Gasser


title: Identification of candidate genes related to astringency in cucumber via RNA-seq based transcriptome profiling

city: Yangzhou

first: Xuewen

last: Xu

state: Jiangsu

address: 48 wenhui east road

country: China

institute: Yangzhou University

type: Expression profiling by high throughput sequencing

summary: Cucumber (Cucumis sativus L.) is one of the most important fruit vegetable crops and is widely grown worldwide (FAO STAT 2016, http://faostat3.fao.org). Astringency greatly affects the flavor quality of cucumber fruits and can be irritating due to the unpleasant oral sensation it causes. However, there are no available report addressing the molecular mechanisms driving the development of cucumber fruit astringency at the transcriptome level. A few relatively basic research efforts have been carried out in our previous studies. In this study, genome-wide analysis of gene expression in the highly astringent cucumber inbred line ‘YB’ was performed using RNA-seq. The aims of this research were to identify the genes responsible for fruit astringency development and to provide new insights into the mechanism underlying the synthesis of astringent compounds in cucumber fruits.

overall_design: Peel and flesh of  the cucumber inbred line ‘YB’ at 3, 6 and 9 days after slef-pollination were dissected separately for RNA-seq analysis.

first: Xuehao

last: Chen


title: The transcriptomes of suicide completers and deceased controls.

summary: Neurobiological causes of suicide are largely unknown. Volumes and dysfunction of brain regions amygdala, hippocampus, prefrontal cortex and thalamus were reported to play a role in suicidal intention.

overall_design: Expression profiles were generated from amygdala, hippocampus, prefrontal cortex and thalamus from nine suicide completers and six control individuals.

first: Aurel

last: Popa-Wagner


title: Expression profile of Ras, MEK and ERK inhibited 16HBE bronchial epithelial cells

city: New York

first: Jeffrey

last: Zhao

state: NY

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

summary: To identify Ras, MEK and ERK target genes which regulate tight junction formation in 16HBE bronchial epithelial cells

overall_design: 16HBE cells were stably infected with pQCXIP retroviral vector, or pQCXIP expressing dominant negative Ras (DN Ras). pQCXIP cells were treated with DMSO (control), 500nM GSK1120212 (MEK inhibitor) or 1uM SCH772984 (ERK inhibitor) for 4 days, then total RNA was extracted. 4 samples were harvested per experiment: pQCXIP/DMSO, pQCXIP/MEKi, pQCXIP/ERKi, pQCXIP.DN Ras. This was repeated in 3 independent experiments. Gene expression was compared to the pQCXIP/DMSO control.

first: Joanne

last: Durgan

first: Guangbo

last: Tao

first: Matthew

last: Walters

first: Oliver

last: Florey

first: Anja

last: Schmidt

first: Vanessa

last: Arbelaez

first: Neal

last: Rosen

first: Ronald

last: Crystal

first: Alan

last: Hall


title: Overexpression of AtCAMTA5 enhances drought tolerance in Arabidopsis.

city: lucknow

first: poonam

last: pant

state: utter pradesh

address: Rana Pratap Marg

department: plant molecular biology

country: India

institute: NBRI

summary:
The Overexpression of AtCAMTA5 leads to higher plant weight and seed weight as compare to Col-0. Under drought condition overexpression lines had reduce water loss,high water use efficiency decline in photosynthesis contributes to 95% survivability wherase Col-0 and camta5 showed enhance sensitivity.Microarray analysis revealed that AtCAMTA5 regulates genes enriched with CAMTA recognition motif like ANAC19, SPL16, aminotransferase, chitinase, MAPK7, SnRK2.2, E3-ligase, RUBISCO, PSI and PSII, etc which were involved in stress response, development, protein modification and photosynthesis.
We used affymatrix expression analysis to validate role of CAMTA5 under drought stress along with physiological and biochemical assay.

overall_design: The total RNA of Col-0, camta5-a and Overexpresion (OX-5) lines were isolated under water and  14 days drought condition.The ATH1 gene chip was used for expression analysis.

first: Samir

middle: V

last: Sawant

first: Neha

last: Pandey

first: Poonam

last: Pant


title: Acc1 determines memory potential of individual CD4+ T cells by regulating de novo fatty acid biosynthesis [RT-PCR]

status: Public on Nov 30 2018

city: Chiba-city

first: Yusuke

last: ENDO

state: Chiba

address: 1-8-1 Inohana, Chuo-ku

department: Immunology

country: Japan

institute: Chiba University

summary: Immunological memory is central to adaptive immunity and protection from disease. Changing metabolic demands as antigen-specific T cells transition from effector to memory have been well documented, but the cell-specific pathways and molecules that govern this transition are poorly defined. ACC1 is a rate-limiting enzym in fatty acid biosynthesis. We show that genetic deletion of ACC1 enhanced the formation of CD4+ T cell memory, and that inhibition of ACC1 function enhanced memory T cell formation during parasite infection in mice. ACC1-deficient effector Th cells had similar metabolic signatures to wild-type memory Th cells, and Acaca expression was inversely correlated with a memory gene signature in individual cells. Single cell analysis allowed us to identify a memory precursor-enriched population (CCR7hiCD137lo) present during early differentiation of effector CD4+ T cells. Thus, fatty acid metabolism directs cell fate determination during the generation of memory CD4+ T cells.

overall_design: Phenotypic characterization of memory precursor population of CD4+ T cells

last: Endo

first: Atsushi

last: Onodera

first: Kazushige

last: Obata-Ninomiya

first: Ryo

last: Koyama-Nasu

first: Hikari

middle: K

last: Asou

first: Toshihiro

last: Ito

first: Takeshi

last: Yamamoto

first: Toshio

last: Kanno

first: Takahiro

last: Nakajima

first: Kenji

last: Ishiwata

first: Hirotaka

last: Kanuka

first: Damon

last: Tumes

first: Toshinori

last: Nakayama


title: Hazard Assessment of High-Nitrogen Compounds: Coupling Transcriptomics with Multi-Cellular Co-Culture Assays Provides Accurate Systemic Toxicity Screening

first: Kurt

last: Gust

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

overall_design: Refer to individual Series


title: The role of oxygen in regulating microRNAs that control the placental renin-angiotensin system

city: Newcastle

first: Kirsty

last: Pringle

state: NSW

address: 1 Kookaburra Circuit

department: HMRI

country: Australia

institute: University of Newcastle

summary:
The human placental renin-angiotensin system (RAS) genes encoding for prorenin (REN), angiotensinogen (AGT), prorenin receptor (ATP6AP2) and angiotensin II type I (AGTR1) receptor are upregulated in early gestation and affect placental development. At this time, the placental oxygen tension is at its lowest (1-3%). Some miRNAs predicted to target the RAS are downregulated in early gestation. Our hypothesis is that the low oxygen tension in early pregnancy suppresses expression of miRNAs that target the placental RAS; thus expression of these RAS genes are upregulated.
Ten miRNAs predicted to target RAS mRNAs were downregulated in response to 1% vs. 20% oxygen, and six miRNAs were decreased in cells cultured in 1% vs. 5% oxygen.

overall_design: HTR-8/SVneo cells, a human extravillous trophoblast cell line, were cultured in 1%, 5% and 20% oxygen tensions (to reflect the oxygen tensions of the chorionic plate, decidua and standard culture conditions respectively) for 48 h (n=3 in triplicate). Any differences in expression of miRNAs between these groups were determined. Affymetrix miRNA microarray analysis was conducted, which detected up to 2006 miRNAs. Statistically different levels of expression were determined. MiRNAs predicted to target the placental RAS were identified using a variety of databases (mirbase.org, mirdb.org, targetscan.org, and targetexplorer.ingenuity.com). Differences in miRNA expression measured on the microarray were confirmed for some miRNAs by RT-PCR (qPCR, n=3 in triplicate for all groups).

first: Anya

middle: L

last: Arthurs

first: Eugenie

middle: R

last: Lumbers

first: Sarah

last: Delforce

first: Andrea

last: Mathe

first: Brian

last: Morris


title: Expression data of RPTEC cells treated with/without HGF, aMD5-PEG11 and aMD5-BMH

city: Kanazawa

first: Kunio

last: Matsumoto

address: Kakuma

institute: Kanaawa University

summary: We synthesized HGF mimic Met-agonist, which is a kind of Met high-affinity dimeric peptide that can activate the Met through dimerization of Met, and induce cell growth, migration, and branching morphogenesis in a similar manner to HGF. Here we detected the gene expression profile induced by HGF and artificial Met-agonist (aMD5-PEG11 and aMD5-BMH). HGF and aMD5-PEG11 show similar induction of gene expression pattern, including multicellular organismal development, multicellular organismal process and anatomical structure development.

overall_design: RPTEC cells were cultured in Cellmatrix type I-A collagen at 3D condition, and treated with/without 1.2nM HGF, 120nM aMD5-PEG11 and 120nM aMD5-BMH for 8 hr. Total RNA was extracted and RNA samples (n=2 for each groups) were subjected to microarray analysis.

first: Wenyu

last: Miao

first: Katsuya

last: Sakai


title: NEMO is distinct from IKK2 by regulating non-canonical pathway in the experimental nephrotoxic serum nephritis mouse model

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

summary: Experimental nephrotoxic serum nephritis (NTN) is a model for T-cell mediated human rapid progressive glomerulonephritis. T-cell receptor (TCR) stimulation leads to intracellular signaling events ultimately causing activation of transcription factors, such as NF-κB. Using CD4creIKK2fl/fl (CD4xIKK2Δ) and CD4creNEMOfl/fl (CD4xNEMOΔ) and CD4cre mice our results demonstrated that NTN was not attenuated in CD4xIKK2Δ, CD4xNEMOΔ when compared with CD4cre mice as showing no significant kidney functional difference with respect to BUN and proteinuria data as well as histological damage. Although the percentage of CD4+ T cells infiltrating kidneys was not significantly changed between the examined groups on day 10, further analysis showed significantly reduced Tregs and significant increase in Th1 and Th17 cells in CD4xIKK2Δ and CD4xNEMOΔ mice. The expression of renal cytokines and chemokines, IL-1β, CCL2 and CCL20, was significantly changed in CD4xIKK2Δ and CD4xNEMOΔ mice when compared with nephritic CD4cre animals. The microarray data confirmed the increased expression of Th17 related cytokines in splenetic CD4+ T cells. More importantly, our array data also demonstrated the interrupted canonical pathway in nephritic CD4xNEMOΔ mice, which highlighted the possible different downstream pathway when IKK2 or NEMO is specifically deleted in lymphocytes. By combining microarray gene expression and bioinformatics analyses our data have identified genes involved in T cell proliferation and differentiation that were differentially expressed between IKK2 and NEMO deficient CD4+ T cells. We propose that better understanding the role of IKK2 and NEMO in T cell regulation will help to recognize the role of IKK2 and NEMO kinase inhibitors in the clinical application in patients with glomerulonephritis.

overall_design: expression profiles of CD4 T cell isolated from IKK2 and Nemo knock out mice under inflammation (experimental nephrotoxic serum nephritis (NTN)) compared to expression leves in wilde type mice

first: F

last: Thaiss

first: R

first: L

last: Guo


title: Acc1 determines memory potential of individual CD4+ T cells by regulating de novo fatty acid biosynthesis [RNA-seq]

first: Yusuke

last: ENDO

overall_design: Phenotypic characterization of CCR7hiCD137lo and CCR7loCD137hi CD4+ T cell populations.

last: Endo

first: Atsushi

last: Onodera

first: Kazushige

last: Obata-Ninomiya

first: Ryo

last: Koyama-Nasu

first: Hikari

last: Asou

first: Toshihiro

last: Ito

first: Takeshi

last: Yamamoto

first: Toshio

last: Kanno

first: Takahiro

last: Nakajima

first: Kenji

last: Ishiwata

first: Hirotaka


title: Transcriptome and proteome of fish-pathogenic Streptococcus agalactiae are modulated by temperature change

city: Belo Horizonte

first: Henrique

middle: César Pereira

last: Figueiredo

state: Minas Gerais

address: Av. Antônio Carlos 6627, Caixa Postal 567, Pampulha

country: Brazil

institute: AQUACEN - National Reference Laboratory for Aquatic Animal Diseases

summary: Streptococcus agalactiae is one of the most important pathogens associated with outbreaks of streptococcis in Nile tilapia farms around the world. High water temperature (above 27°C) have been described as factor predisposing for disease in fish. On the other hand, at low temperature (below 25°C) fish mortalities are no usually observed in farms. The temperature variation can modulate the expression of genes and proteins involved with metabolism, adaptation and bacterial pathogenicity, increasing or decreasing the host susceptibility to infection. The aim of this study was to evaluate the transcriptome and proteome of fish-pathogenic S. agalactiae strain (SA53) submitted to in vitro growth under different temperatures using microarray and label-free shotgun LC-HDMSE approach, and to compare the expression trends of proteins shared among GBS strains from different hosts (SA53 and NEM316). Biological triplicates of isolates were cultured in BHIT broth at 22°C or 32°C for RNA and protein isolation and submitted to transcriptomic and proteomic analysis. Total of 1730 transcripts were identified in SA53, being 107 genes differentially expressed among the temperature evaluated. A higher number of genes related with metabolism were detected as up-regulated proteins at 32°C, mainly PTS system and ABC transport system. In proteome analysis, 1046 proteins were identified in SA53 strain, being 81 proteins differentially regulated at 22 and 32ºC. Proteins involved in Defense mechanisms (V), Lipid transport and metabolism (I), and Nucleotide transport and metabolism (F) were up-regulated at 32ºC. A higher number of interactions was observed in the category F. The induction of genes/proteins involved in virulence were detected in both temperatures evaluated. A low correlation between transcriptome and proteome datasets was observed. And there is a distinct adaptation between fish and human GBS strains at the proteome level. Our study showed that the transcriptome and proteome of fish-adapted GBS strain are modulated by temperature, especially regulating the differential expression of genes/proteins involved with metabolism, adaptation and virulence, and revealing a host specificity at proteome regulation for human and fish hosts

overall_design: The S. agalactiae SA53 (ST-260) isolated from diseased fish was used in this study. Triplicate culture of this strain on BHI broth were incubated at 32 ºC or 22 ºC and harvested at the mid-exponential phase of bacterial growth (OD600 = 0.2) for RNA extraction.

first: H

middle: P

first: G

middle: C

last: Tavares

first: A

last: Carvalho

last: Pereira

first: C

last: Rezende

last: Leal


title: Microarray-based Gene Expression Analysis of Melanoma Cell Lines

city: Fort Worth

first: Yu-Chieh

last: Wang

state: TX

address: 3500 Camp Bowie Blvd

department: Pharmaceutical Sciences

institute: University of North Texas Health Science Center

summary: Analysis of the functional significance of peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine amidase in human melanoma cells. The hypothesis tested in the present study was that this glycosidase may be involved in melanoma development.

overall_design: Short hairpin RNAs were used to knockdown the expression of peptide-N(4)-(N-acetyl-beta-glucosaminyl)-asparagine amidase in human melanoma cells. The total RNA sample were isolated from the cell samples and prepared for global gene expression profiling using HT-12v4 Human Gene Expression Bead Chips and a HiScan array scanning system. The study included 12 experimental conditions. Each experimental condition had two biological replicates, for a total of 24 samples in the analysis. Samples with non-targeting shRNA (NT-shRNA) served as controls.

first: Victor

last: Lin

first: Ashwini

last: Zolekar


title: RNA expression profiling in cardiomyocytes

city: NANJING

first: MIN

last: HUANG

state: JIANGSU

address: 300 GUANGZHOU ROAD

department: Geriatrics

institute: The First Hospital Affiliated to Nanjing Medical University

summary: Using the highly sensitive RNA array, we assessed the effect of 11β-HSD1 and BVT.2733 on modulating RNAs expression in the neonatal rat ventricular cardiomyocytes.

overall_design: In this study, samples from neonatal rat ventricular cardiomyocytes transfected either with the expression vector for 11β-HSD1 or co-treated with overexpression 11β-HSD1 vector and 11β-HSD1 inhibitor BVT.2733, or transfected with corresponding empty vector were used to acquire the RNA expression profiling thus to elucidate the possible molecular mechanism underlying the effect of 11β-HSD1 on hypertrophy.

first: Min

last: Huang

first: Yunlu

last: Sheng


title: Knockdown of DKK3 decreases malignant property in  head and neck squamous cell carcinoma-derived HSC-3 cells.

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

institute: Toray Industries,Inc.

summary:
We hypothesized that DKK3 may exert oncogenic function supecifically in head and neck squamous cell carcinoma (HNSCC).
DKK3 knockdown in HNSCC cell resulted in decreased cellular proliferation, migration, invasion and in vivo tumor growth.

overall_design: Single analysis for each condition (HSC-3 parental cell, HSC-3 shRNA (scramble) and HSC-3 shDKK3 (lentvirus-mediated shRNA targeting to DKK3)

first: Naoki

last: Katase


title: Gene expression profiling of resistance genes to salt stress in roots of peanut (Arachis hypogaea L.)

city: Qingdao

last: Chen

address: wannianquan road

institute: Shandong Peanut Research Institute

summary:
Investigation of  resistance genes from 36,158 peanut ESTs after salt stress treatment, compared with untreated peanut.
Yield some useful insights into salt-mediated signal transduction pathways in peanut.

overall_design: A nine chip study using total RNA recovered from three separate untreated peanut roots, three separate 3h salt-treated peanut roots and  three separate 48h salt-treated peanut roots.  Each chip measures the expression level of 36,158 ESTs.

first: Shanlin

last: Yu


title: Gene expression profile of Epiblast stem cells

city: Bunkyo-ku

first: Shin

last: Kobahashi

state: Tokyo

address: 1-5-45 Yushima

department: Department of Epigenetics

institute: Tokyo Medical & Dental University, Medical Research Institute

summary: To characterize the EpiSCs (Epiblast stem cells) we established in our lab, we have employed whole genome microarray expression profiling as a platform to distinguish the EpiSCs (primed state) from ES cells (naïve state).

overall_design: Gene expression of the EpiSCs established in our laboratory was examined using microarray, confirming our EpiSCs have identical characteristics  to the previous reported  EpiSCs (Sumi T et al, PLoS One. 2013 May 14;8(5):e63378.,; Brons IG et al. Nature. 2007 Jul 12;448(7150):191-5.; Tesar PJ, Nature. 2007 Jul 12;448(7150):196-9.)

first: Saori

last: Takahashi

last: Kobayashi


title: Gene expression in developing ears of ra3;tpp4 maize mutants compared to wild-type

status: Public on Nov 29 2018

city: Cold Spring Harbor

first: Hannes

last: Claeys

state: New York

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

summary: We performed mRNA-seq on developing ears (2-3 mm length) of ra3;tpp4 maize mutants compared to segregating wild-types.

overall_design: Standard mRNA-seq libraries were made from total RNA extracted from developing ears, in three biological replicates, and sequenced on the Illumina NextSeq platform, PE150.

first: David

last: Jackson


title: Dissecting the Variations of Transcriptome in Grape Berries Grown under Double Cropping System

city: Beijing

first: Jun

state: Beijing

address: No. 17 Tsinghua East Road, Beijing, 100083, China.

department: College of Food Science and Nutritional Engineering

institute: China Agricultural University

summary: A double cropping system has been commercially adopted in subtropical regions in southern China, where there is abundant sunshine and heat resources. In this viticulture system, the first growing season normally starts as a summer cropping cycle; then, the vine is pruned and forced by hydrogen cyanamide, resulting in a second crop in January of the next year. Due to climate differences between the two growing seasons,the transcriptome varies greatly between summer- and winter- grape berries. In this study, we conducted RNA-seq for two table grape varieties (Vitis vinifera cv. Victoria and V. vinifera cv. Muscat Superior) at three developmental stages (pre-veraison, post-veraison and full maturity).The transcriptome between summer- and winter- grape berries were compared.

overall_design: Differentially expressed genes between summer- and winter- grape berries were identified by DESeq2. And the transcriptome between summer- and winter- grape berries were compared.

first: Weikai

first: Xianjin

last: Bai

first: Muming

last: Cao

first: Fei

last: He

first: Changqing

last: Duan


title: Honey bee neurogenomic responses to affiliative and agonistic social interactions.

city: Bar Harbor

first: Michael

middle: C.

last: Saul

state: ME

address: 600 Main St

institute: The Jackson Laboratory

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Social interactions can be divided into two categories, affiliative and agonistic. How neurogenomic responses reflect these opposing valences is a central question in the biological embedding of experience. To address this question, we exposed honey bees to a queen larva, which evokes nursing, an affiliative alloparenting interaction, and measured the transcriptomic response of the mushroom body brain region at different times after exposure. Hundreds of genes were differentially expressed at distinct time points, revealing a dynamic temporal patterning of the response. Comparing these results to our previously published research on agonistic aggressive interactions, we found both shared and unique transcriptomic responses to each interaction. The commonly responding gene set was enriched for nuclear receptor signaling, the set specific to nursing was enriched for olfaction and neuron differentiation, and the set enriched for aggression was enriched for cytoskeleton, metabolism, and chromosome organization. Whole brain histone profiling after the affiliative interaction revealed few changes in chromatin accessibility, suggesting that the transcriptomic changes derive from already accessible areas of the genome. Although only one stimulus of each type was studied, we suggest that elements of the observed transcriptomic responses reflect molecular encoding of stimulus valence, thus priming individuals for future encounters. This hypothesis is supported by behavioral analyses showing that bees responding to either the affiliative or agonistic stimulus exhibited a higher probability of repeating the same behavior but a lower probability of performing the opposite behavior. These findings add to our understanding of the biological embedding at the molecular level.

overall_design: There are a total of 8 sets of pooled samples used in the H3K27Ac ChIP-Seq experiment equally balanced between 3 factors: 4 nurturance (N) and 4 control (K); 4 30m and 4 120m; and 4 colony R41 and 4 colony R46.

first: Hagai

middle: Y

last: Shpigler

first: Emma

middle: E

last: Murdoch

first: Frida

last: Corona

first: Amy

last: Cash-Ahmed

first: Christopher

last: Seward

first: Sriram

last: Chandrasekaran

first: Saurabh

last: Sinha

first: Lisa

last: Stubbs

first: Gene

last: Robinson


title: Honey bee neurogenomic responses to affiliative and agonistic social interactions

overall_design: There are a total of 176 samples distributed between 3 factors: nurturance, with 88 nurturance (N) and 88 control (K); time after manipulation, with 58 30m, 60 60m, and 58 120m; and colony, with 60 colony R02, 60 colony R40, and 56 colony R41. The control and nurturance samples are paired by behavioral replicate, and we additionally report time spent in the waxen queen cell for bees exposed to queen cells. After observing the presence of Deformed Wing Virus (DWV) in a prior experiment on the same tissue, we screened each sample here for a proportion of reads aligning to the DWV genome of ≥ 0.005. No samples were excluded.

middle: J


title: Transcriptome profiling reveals PDZ Binding Kinase as a novel biomarker in Peritumoural Brain Zone of Glioblastoma

status: Public on Nov 28 2018

city: Bangalore

first: Ruchi

last: Jain

state: Karnataka

address: C V Raman Road

department: Molecular Reproduction Development and Genetics

institute: Indian Institute of Science

summary: Analysis of gene expression profiles of peritumoural brain zone (PT) in glioblastoma and functional characterization of novel biomarker.

overall_design: Total RNA from the tumour core (TC), Peritumoural Brain Zone (PT) and non-neoplastic brain tissue (control) samples were subjected to Illumina Bead array.

first: Banavathy

last: Kruthika

first: A

last: Arivazhagan

first: R

last: Bharath

first: T

last: Yasha

first: Paturu

last: Kondaiah

first: Vani

last: Santosh


title: Pericentromeric hypomethylation elicits an interferon response in an animal model of ICF syndrome [dsRNA-seq]

city: St. Louis

first: John

middle: R.

last: Edwards

state: MO

address: 660 S. Euclid Ave, Campus Box 8220

department: Center for Pharmacogenomics

institute: Washington University School of Medicine

summary: The goal of this study was to investigate DNA methylation and gene expression changes in a zebrafish model of ICF Syndrome which were generated by mutation of ICF-gene zbtb24. Comparison of gene expression changes between wildtype and zbtb24 homozygous mutants revealed upregulation of interferon response genes following zbtb24 deletion. Upregulation of interferon response genes was blocked by mutation of the dsRNA helicase Mda5.

overall_design: For RNA-seq, gene expression was compared in whole two-week-old zebrafish larvae that were wildtype or homozygous for the zbtb24mk22 mutant allele. We further performed RNA-Seq analysis in three-week-old zebrafish larvae that were WT, mda5mk29/mk29 , zbtb24mk22/mk22  and mda5mk29/mk29 ;zbtb24mk22/mk22. Three samples consisting of pools of 10 larvae were examined for each genotype.  For ERRBS, DNA was separately isolated from the fins of three wildtype and three zbtb24mk22 homozygous mutant adults.

first: Srivarsha

last: Rajshekar

first: Mary

last: Goll


title: Brain transcriptomic differences in response to social opportunity and social challenge in honey bees

first: Michael

last: Saul

overall_design: Refer to individual Series


title: polyA RNA Sequencing Analysis of HTR-8/SVneo cells after lnc-SLC4A1-1 overexpression

status: Public on Nov 27 2018

city: Nanjing

first: Zhenyao

last: Huang

address: Dongshan

institute: Nanjing Medical University

summary: To further evaluate the functional role of lnc- SLC4A1-1, we overexpressed lnc-SLC4A1-1 in HTR-8/SVneo cells and isolated RNA for RNA-seq. RNA-seq was done using TruSeq Stranded mRNA Library Preparation. Briefly, intact RNA was fragmented, end repaired, adapter ligation and PCR amplified following illumina protocol. Libraries were sequencing by illumins Hiseq 3000. After quality control, sequence data were processed with STAR to generate read alignments with hg19. Raw read counts for annotated genes were obtained with featureCounts with default settings, normalized and analyzed using DEGseq.

overall_design: Intact RNA isolated from 6 human HTR-8/SVneo cells was fragmented, end repaired, adapter ligation and PCR amplified following illumina protocol. Libraries were sequencing by illumins Hiseq 2000.

first: Chuncheng

last: Lu


title: Screening of Streptococcus Suis serotype 2 resistance genes with GWAS and transcriptomic microarray analysis

first: Zhe

last: Ma

state: JS

address: Tonwei Road No.1

institute: nanjing agricultural university

type:
Expression profiling by array
SNP genotyping by SNP array


title: Differential expression of heat shock and floral regulatory genes in pseudocarpel initials of mantled female inflorescences from Elaeis guineensis Jacq.

status: Public on Nov 26 2018

city: Bandar Baru Bangi

first: Siew-Eng

last: Ooi

state: Selangor

address: 6 Persiaran Institusi

department: Advanced Biotechnology and Breeding Centre

country: Malaysia

institute: Malaysian Palm Oil Board

summary: Identification of differentially expressed genes from RNA-seq of normal and mantled male floral organs (staminodia) obtained from laser capture microdissection.  Differential expression analysis was also conducted on normal and mantled female floral organs (carpel) using the same approach.

overall_design: Inflorescences at stage 3 floral development were sampled from two normal clonal palms and three mantled clonal palms. Spikelets from these inflorescences were embedded for cryosectioning and targeted stage 3 development florets were identified through microscopy analysis. Three biological replicates per group (normal / mantled); for the mantled group, the biological replicates were obtained from inflorescences sampled from three different palms. For the normal group, two biological replicates were obtained from different parts of one inflorescence of one palm and another biological replicate obtained from an inflorescence of another palm. Normal group was designated as reference group.

first: Norashikin

last: Sarpan

first: Aziz

middle: A

last: Norazlin

first: Azimi

last: Nuraziyan

first: Meilina

last: Ong-Abdullah


title: Bisulfite sequencing of Sordaria macrospora wild type and asf1 mutant

city: Bochum

first: Minou

last: Nowrousian

address: Universitaetsstr. 150

department: Molecular and Cellular Botany

institute: Ruhr-University Bochum

type: Methylation profiling by high throughput sequencing

summary: The aim of this analysis was to analyze DNA methylation in the wild type and the histone chaperone mutant asf1 of the filamentous fungus Sordaria macrospora.

overall_design: Two independent biological replicates were performed and sequenced each for the wild type and the developmental mutant asf1.


title: Genome-wide location of Candida albicans transcription factor Crz2p

status: Public on Nov 20 2018

city: Paris

first: Sadri

last: ZNAIDI

address: 25 rue du Docteur Roux

department: Mycology Department

country: France

institute: Institut Pasteur

type: Genome binding/occupancy profiling by genome tiling array

summary: Candida albicans is part of the human gastrointestinal (GI) microbiota. To better understand how C. albicans efficiently establishes GI colonisation, we competitively challenged growth of 572 signature-tagged strains (~10% genome coverage), each conditionally overexpressing a single gene, in the murine gut. We identified CRZ2, a transcription factor whose overexpression and deletion respectively increased and decreased early GI colonisation. Using clues from genome-wide expression and gene-set enrichment analyses, we found that the optimal activity of Crz2p occurs under hypoxia at 37°C, as evidenced by both phenotypic and transcriptomic analyses following CRZ2 genetic perturbation. Consistent with early colonisation of the GI tract, we show that CRZ2 overexpression confers resistance to acidic pH and bile salts, suggesting an adaptation to the upper sections of the gut. Genome-wide location analyses revealed that Crz2p directly modulates the expression of many mannosyltransferase- and cell-wall protein-encoding genes, suggesting a link with cell-wall function. We show that CRZ2 overexpression alters cell-wall phosphomannan abundance and increases sensitivity to tunicamycin, suggesting a role in protein glycosylation. Our study reflects the powerful use of gene overexpression as a complementary approach to gene deletion to identify relevant biological pathways involved in C. albicans interaction with the host environment.

overall_design: A total of 2 samples are included, corresponding to 2 biological replicates: samples CRZ2_ChIP_Upper array and CRZ2_ChIP_Lower array.

last: Znaidi


title: Pericentromeric hypomethylation elicits an interferon response in an animal model of ICF syndrome [ssRNA-seq]

middle: G


title: Gene expression profiling shows that a jaz decuple mutation (jazD) promotes expression of defense-related genes while inhibiting expression of growth-related genes

city: East Lansing

first: Qiang

last: Guo

state: MI

address: 612 Wilson Rd

department: Plant Research Laboratories

institute: Michigan State University

summary: The decuple jaz mutation (jazD) affects plant growth and defense. We used RNA-sequencing to query the transcriptomes of a jaz quintuple mutant (jazQ) and jazD, and examined how these mutations alter the expression of growth- and defense-associated genes in comparison to wild-type Col-0 plants. The data highlight how jasmonate pathways contribute to growth and defense.

overall_design: Analysis of Col-0 (wildtype), jazQ, and jazD (three genotypes), with three biological replicates per genotype - 9 total samples.

first: Gregg

last: Howe


title: Screening of Streptococcus Suis serotype 2 resistance genes with GWAS and transcriptomic microarray analysis (mRNA)

summary: Swine streptococcosis has caused great economic loss in the swine industry, and the major pathogen responsible for this disease is Streptococcus Suis serotype 2 (SS2). Disease resistance breeding is a fundamental way of resolving this problem. With the development of GWAS and transcriptomic microarray technology, we now have powerful research tools to identify SS2 resistance genes.  In this research, we generated an F2 generation of SS2 resistant C57BL/6 and SS2 susceptive A/J mice. With the F2 generation of these two mice strains and GWAS analysis, we identified 286 significant mouse genome SNPs sites associated with the SS2 resistance trait. Gene expression profiles for C57BL/6 and A/J were analyzed under SS2 infection pressure by microarray. In total, 251 differentially expressed genes were identified between these two mouse strains during SS2 infection. After combining the GWAS and gene expression profile data, we located two genes that were significantly associated with SS2 resistance, which were the UBA domain containing 1 gene (Ubac1) and Epsin 1 gene (Epn 1). GO classification and over-representation analysis revealed nine up-regulated related to immune function, which could potentially be involved in the C57BL/6 SS2 resistance trait. This is the first study to use both SNP chip and gene express profile chip for SS2 resistance gene identification in mouse, and these results will contribute to Swine SS2 resistance breeding.

overall_design: The SS2 inoculum for experimental infection was adjusted to a concentration of 1×108 CFU/mL. Seventy male and seventy female F2 mice were injected i.p. with a 1 mL inoculum per mouse. F2 mice surviving for fewer than 3 days following infection were regarded as susceptible (22 males and 22 females), while those surviving for more than 15 days were regarded as resistant (23 males and 21 females). Blood samples were collected aseptically from susceptible and resistant F2 mice. Genomic DNA was extracted from blood using TIANamp Genomic DNA Kit, and then amplified and hybridized to an Affymetrix Mouse Diversity Genotyping Array (Affymetrix) according to the manufacturer’s instructions (Affymetrix Inc.).

first: Hongjie

last: Fan


title: Fitness assay of Candida albicans strains grown in vitro or in vivo in a mouse model of gastrointestinal colonization

overall_design:
12 samples in total:
Samples 1-3 (Fitness_in vitro_rep1, rep2 and rep3) are three independent biological replicates of in vitro fitness profiling data.
Samples 4-8 (Fitness_in vivo_+Dox_rep1, rep2, rep3, rep4 and rep5) are 5 independent biological replicates of in vivo fitness profiling data from dox-treated mice.
Samples 9-12 (Fitness_in vivo_-Dox_rep1, rep2, rep3 and rep4) are 4 independent biological replicates of in vivo fitness profiling data from dox-untreated mice.


title: RNA Sequencing Based Transcriptional Overview of Xerotolerance in Cronobacter sakazakii SP291

status: Public on Nov 23 2018

city: Columbia

first: Sathesh

last: Sivasankaran

address: Bond Life Sciences Center Suite 106, 1201 Rollins Street

institute: University of Missouri

summary: Cronobacter sakazakii is a xerotolerant neonatal pathogen epidemiologically linked to powdered infant food formula, often leading to high mortality rates. Here, we used RNA-seq to provide physiological and transcriptional insights into the survival of C. sakazakii in desiccated conditions. Our RNA-seq data shows that about 22% of the total C. sakazakii genes were significantly up-regulated and 9% were down-regulated during desiccation survival. When qRT-PCR was used to validate the RNA-seq data, we found that the primary desiccation response was gradually down-regulated during the tested four hours of desiccation while the secondary response remained constitutively up-regulated. The desiccation tolerance of C. sakazakii was dependent on the immediate microenvironment surrounding the bacterial cell. Removal of TSB salts and that the introduction of sterile infant formula residues in the microenvironment enhanced the desiccation survival of C. sakazakii SP291. The trehalose biosynthetic pathway encoded by otsA and otsB, a prominent secondary bacterial desiccation response, was highly up-regulated in desiccated C. sakazakii. C. sakazakii SP291 ∆otsAB was significantly inhibited compared to the wild type in an eight hour desiccation survival assay confirming the physiological importance of trehalose in desiccation survival. Overall, we provide a comprehensive RNA-seq based transcriptional overview and the phenotypic importance of trehalose metabolism in Cronobacter sakazakii during desiccation.

overall_design: Bacterial transcriptomic profile of desiccated and early stationary phase (ESP; WT) conditions were generated by deep sequencing, in triplicates, using Illumina HiSeq2500.

first: Shabarinath

last: Srikumar

first: Yu

last: Cao

first: Qiongqiong

last: Yan

first: Koenraad

last: Van Hoorde

first: Scott

last: Nguyen

first: Shane

last: Cooney

first: Gopal

last: Gopinath

first: Dechamma

last: Muthappa

first: Ben

last: Tall

first: Angelika

last: Lehner

first: Roger

last: Stephan

first: Séamus

last: Fanning


title: Changes in the transcriptome of S. aureus SH1000 containing a nisin resistance mutation in nsaS

status: Public on Nov 19 2018

city: Leeds

first: Christopher

middle: Paul

last: Randall

state: West Yorkshire

address: Clarendon Way

department: Faculty of Biological Sciences

country: United Kingdom

institute: University of Leeds

summary: We have demonstrated previously that high-level resistance to nisin can occur in Staphylococcus aureus as a consequence of a single non-synonymous mutation in nsaS, which encodes a putative sensor kinase. To explore the mechanism by which this mutation confers high-level resistance we compared global transcriptomes of SH1000 and SH1000 (NsaS A208E) using RNAseq. This process identified several genes to be upregulated in SH1000 (NsaS A208E), including members of the NsaRS regulon which encode VraDE and BraDE, two putative ABC-transporters and are known to provide intrinsic nisin resistance. Gene deletion and complementation experiments revealed that both BraDE and VraDE are essential to high-level nisin resistance, with BraDE required for signal transduction through NsaRS, and VraDE directly responsible for nisin detoxification.

overall_design: Total RNA was extracted from explonentially-growing cultures of SH1000 (x2 replicates) and SH1000 (NsaS A208E) (x3 replicates) and was subjected to sequencing using an Illumina NextSeq 500

first: Alex

last: O'Neill

first: Arya

last: Gupta


title: Screening of Streptococcus Suis serotype 2 resistance genes with GWAS and transcriptomic microarray analysis (SNP)

first: Zhe

last: Ma

first: Hongjie

last: Fan


title: Integrated analysis of lncRNA and mRNA reveals the temporal expression patterns during chicken brain development and aging

status: Public on Nov 16 2018

city: Chengdu

first: Xu

last: Zhongxian

address: NO. 211, Huiming Road, Wenjiang District

institute: Sichuan Agricultural University

type: Non-coding RNA profiling by high throughput sequencing

summary: We systematically investigated the lncRNA and mRNA temporal expression profile of the female chicken brain by high-throughput sequencing 8 stages across their entire lifespan. We identified and classified 39,907 putative lncRNAs, and predicted the potential biological functions of lncRNAs based on WGCNA. Temporal expression patterns were investigated based on a set of age-dependent genes, results showed that genes functioned in development, synapse and axon exhibited a progressive decay; genes related to immune response were up-regulated with age, And some genes showed inversion of their temporal profiles. These results demonstrated dynamic changes in lncRNA and mRNA with age, which may reflect changes in regulation of transcriptional networks and provides non-coding RNA gene candidates for further studies. It would be vital significance in avian epidemic prevention and contribute to comprehensively understand the molecular mechanisms of chicken breeding and reproduction. Besides, birds, as important species to bridge the evolutionary gap between mammals and other vertebrates, would contribute to further improve the understanding of the role in evolution.

overall_design: rRNA-deleted RNA-Seq was performed on chicken brain to profile the lncRNAs and mRNAs across the entire life span

first: Zhongxian

last: Xu

first: Diyan

last: Li


title: RNAseq analysis reveals the transcriptional programme of Clostridium difficile in a biologically relevant faecal–stress environment: implications for pathogenicity

status: Public on Nov 12 2018

city: Coleraine

first: Nigel

last: Ternan

state: Co. Londonderry

address: Cromore Road

department: School of Biomedical Sciences

institute: University of Ulster

summary: RNAseq and LC/MS metabolomics analysis of C. difficile strain 630 grown in BHIS media with 50% (vol/vol) faecal water added, compared with control BHIS containing only the additional PBS used for prep of Faecal water. Cells grown in biological triplicates to late log phase (T=6h) prior to harvest. Goal was to determine changes in gene expression caused by exposure to Faecal water, and changes in the metabolite profile of faecal water containing medium when incubated with actively growing C. difficile cells

overall_design: Two condition experiment. BHIS-FW grown vs BHI-PBS grown cells.  Biological replicates: 3 control replicates (BHIS-PBS), 3 experimental replicates (BHIS-FW),  6 x stranded RNAseq lib preps & 3 x MiSeq run performed

first: Nicola

middle: D

last: Moore

first: Deborah

last: Smyth

first: Gordon

last: McDougal

first: James

middle: W

last: Allwood

first: Susan

last: Verrall

last: Dooley

last: Gill

first: Geoff

last: McMullan


title: Transcriptome reprogramming at late stage of desiccation defines the resurrection behavior of Haberlea rhodopensis

first: Chih Ta

last: Lin

address: No.20 Nanxincun, Xiangshan

department: CAS Key Laboratory of Photosynthesis and Molecular Physiology

institute: Institute of Botany Chinese Academy of Sciences

summary:
Water shortage is a major factor that harms agriculture and ecosystems worldwide. Plants display various levels of tolerance to water deficit, but only resurrection plants can survive full desiccation of their vegetative tissues. Haberlea rhodopensis, an endemic plant of the Balkans, is one of the few resurrection plants found in Europe. We performed transcriptomic analyses of this species under slight, severe and full dehydration and recovery to investigate the dynamics of gene expression and associate them with existing physiological and metabolomics data.
De novo assembly yielded a total of 142,479 unigenes with an average sequence length of 1,034 nt. Among them, 18,110 unigenes were differentially expressed. Hierarchical clustering of all differentially expressed genes resulted in seven clusters of dynamic expression patterns. The most significant expression changes, involving more than 15,000 genes, started at severe dehydration (~20% relative water content) and were partially maintained at full desiccation (<10% relative water content). More than a hundred pathways were enriched and functionally organized in a GO/pathway network at the severe dehydration stage. Transcriptomic changes in key pathways were analyzed and discussed in relation to metabolic processes, signal transduction, quality control of protein and DNA repair in this plant during dehydration and rehydration.
Reprograming of the transcriptome occurs during severe dehydration, resulting in a profound alteration of metabolism toward alternative energy supply, hormone signal transduction, and prevention of DNA/protein damage under very low cellular water content, underlying the observed physiological and metabolic responses and the resurrection behavior of H. rhodopensis.

overall_design: cDNA libraries of fully hydrated (fresh) leaves - F (90% RWC), two stages of dehydration (D75, 75% RWC) and (D20, 20% RWC), fully desiccated leaves (DT, 6% RWC) and recovery (R, 90% RWC) were used for sequencing by Illumina HiSeq™ 4000 and transcriptome De novo Assembly.

last: Tao

first: Chih-Ta


title: Genome-wide RBR1 (Retinoblastoma related 1) binding sites in Arabidopsis thaliana dividing cells.

status: Public on Nov 10 2018

city: Hamburg

first: Arp

last: Schnittger

address: Ohnhorststr. 18

institute: Biozentrum Klein Flottbek, University of Hamburg

summary: ChIP-seq experiments using an anti-RBR1 antibody were performed on MM2d cell culture material from Arabidopsis thaliana (3d after sub-culture).

overall_design: Two biological replicates were analysed.

first: Daniel

last: Bouyer

first: Francois

last: Roudier

first: Hirofumi

last: Harashima

first: Maren

last: Heese


title: Xeno-free and Chemically Defined Human System for Culturing Human Epidermal Keratinocytes

status: Public on Nov 06 2018

city: Singapore

first: Aida

last: Moreno-Moral

address: 8 College Road

country: Singapore

institute: Duke-NUS Medical School

summary: Developing an effective xeno-free and defined system for human keratinocyte culture has been one of the fundamental measures in current cellular therapy. For keratinocytes, in particular, such system will not only fulfill clinical safety and quality criteria, it will allow for the management of less severe burns and other skin injuries such as chronic wounds. To date, the expansion of autologous keratinocytes in the clinical settings still relies on 3T3 feeder co-culture system. Here we report a completely xeno-free and defined culture system by using human recombinant laminins as feeder replacement. We have thoroughly characterized the cells cultured in this new system both in vitro and in vivo. We found that laminin-511/-521, and the unanticipated laminin-411/-421, but not -332, -111, -121, -211, or LN-221 support adult human skin keratinocytes and could maintain their self-renewal properties comparable to the 3T3 system. We believe our new culture method should facilitate broader use of cultured epithelial cell products for today’s regenerative medicine.

overall_design: RNA sequencing and analysis on whole adult human skin or freshly cultured human keratinocytes using two different methods: co-cultured with 3T3 feeder and laminin-coated tissue culture plates.

first: Monica

middle: S

last: Tjin

first: Alvin

last: Chua

first: Bryan

last: Buenaflor

first: Li

last: Chong

first: Enrico

last: Petretto

first: Bien

last: Tan

first: Karl

last: Tryggvason


title: m6A mRNA methylation controls the innate immune response to infection by targeting interferon β

status: Public on Nov 14 2018

city: Rehovot

first: Noam

last: Stern-Ginossar

address: 234 herzel

department: Molecular Genetics

country: Israel

institute: Weizmann Institute

summary: N6-methyladenosine (m6A), the most abundant mRNA modification, was shown to alter the life cycles of diverse DNA and RNA viruses. These effects were proposed to be mediated in a virus-specific manner, through dysregulated methylation of viral RNA. We use RNA-seq to systematically follow differences in gene expression in cells depleted of m6A machinery, compared to control cells, following human cytomegalovirus (HCMV) infection. We show that following viral infection or stimulation of cells with an inactivated virus, depletion of the m6A 'writer' protein METTL3  or 'reader' protein YTHDF2 leads to a dramatic increase in the induction of hundreds of interferon-stimulated genes (ISGs), which constitutes the first line of antiviral defense. Consequently, propagation of different viruses is markedly suppressed in an interferon (IFN)-signaling dependent manner. Furthermore, we used m6A-immunoprecipitation, followed by RNA-seq, to map m6A sites on human and HCMV transcripts, and found that the mRNA of IFNβ, the central cytokine that drives the type I IFN response, is m6A modified, and is stabilized upon repression of METTL3 and YTHDF2.

sample_organism:
Homo sapiens
Human betaherpesvirus 5

platform_organism:
Homo sapiens
Human betaherpesvirus 5

overall_design: mRNA-seq of total mRNA and m6A-immunoprecipitated mRNA from METTL3-depleted and control human fibroblasts, following HCMV infection.

first: Roni

last: Winkler

first: Ella

last: Gillis

first: Aharon

last: Nachshon

first: Schraga

last: Schwartz


title: Genome-Wide Identification and Characterization of microRNAs responding to ABA and GA in maize embryos during seed germination

city: Tai'an

first: Shuxin

last: Zhang

address: DaiZong Street NO.61

institute: Shandong Agricultural University

summary: In this study, Three sRNA libraries were generated and sequenced from embryos treated with GA, ABA and ddH2O (CK). A total of 247 miRNAs (69 known and 178 novel ones) were identified and found that 28 known and 70 novel miRNAs were differentially expressed in embryos with different treatments. Using bioinformatics tool, we predict target genes of the differentially expressed miRNAs. GO enrichment and KEGG pathway analysis for these targets showed that miRNAs differentially expressed in the samples are involved in peroxisome, ribosome and plant hormonal signalling. This study not only improves our knowledge about the roles of miRNAs in maize seed germination but also reveals the potential role of miRNAs in the hormonal responses of different pytohormones.

overall_design: Analysis of miRNA expression in maize embryos after GA and ABA treatment, with water treatment as the control

first: Jisheng

last: Liu


title: Targeting FOXA1-mediated repression of TGF-β signaling suppresses castration-resistant prostate cancer progression [microarray]

status: Public on Nov 01 2018

city: Atlanta

first: Jindan

last: Yu

state: GA

address: E330, 1760 Haygood Dr NE

department: Urology

institute: Emory University

summary: our study establishes FOXA1 as an important regulator of lineage plasticity mediated in part by TGF-β signaling and supports a novel therapeutic strategy to control lineage switching and potentially extend clinical response to antiandrogen therapies.

overall_design: Microarray analysis on LNRII cells with control and TGFB3. Microarray analysis on LNCaP cells with control and FOXA1 knockdown followed by LY2157299 treatment

first: Bing

last: Song


title: Altered expression of the Cdk5 activator-like protein, Cdk5α, causes neurodegeneration, in part by accelerating the rate of aging [head]

status: Public on Nov 07 2018

city: Bethesda

first: Kory

last: Johnson

state: MD

address: 10/3B01, 9000 Rockville Pike

department: DIR IT & Bioinformatics

institute: NINDS/NIH

summary: Aging is the greatest risk factor for neurodegeneration, but the connection between the two processes remains opaque. This is in part for want of a rigorous way to define physiological age, as opposed to chronological age. Here, we develop a comprehensive metric for physiological age in Drosophila, based on genome-wide expression profiling. We applied this metric to a model of adult-onset neurodegeneration, increased or decreased expression of the activating subunit of the Cdk5 protein kinase, encoded by the gene Cdk5α, the ortholog of mammalian p35. Cdk5α-mediated degeneration was associated with a 27-150% acceleration of the intrinsic rate of aging, depending on the tissue and genetic manipulation. Gene ontology analysis and direct experimental tests revealed that affected age-associated processes included numerous core phenotypes of neurodegeneration, including enhanced oxidative stress and impaired proteostasis. Taken together, our results suggest that Cdk5α-mediated neurodegeneration results from accelerated aging, in combination with cell-autonomous neuronal insults. These data fundamentally recast our picture of the relationship between neurodegeneration and its most prominent risk factor, natural aging.

overall_design: 82 Drosophila samples representing two tissue types (head, thorax), four ages (3 Days, 10 Days, 30 Days, 45 Days), four genotypes (control, p35-null, p35-OE, rescue), and two batches (batch 1, batch 2) with one technical replicate sample run between batches.

first: Joshua

last: Spurrier

first: Arvind

last: Kumar Shukla

first: Kristina

last: McLinden

first: Edward

last: Giniger


title: Sphingobium chlorophenolicum Confronts the Stresses Associated with Pentachlorophenol and Four Toxic Downstream Metabolites to Utilize a Suboptimal Nutrient Source [Tn-Seq]

city: Boulder

first: Jake

middle: James

last: Flood

state: CO

address: 347 UCB

department: Molecular, Cellular and Developmental Biology

institute: University of Colorado Boulder

summary: Pentachlorophenol (PCP) is a highly toxic pesticide that was first introduced in the 1930s. The a-proteobacterium Sphingobium chlorophenolicum, which was isolated from PCP-contaminated sediment, has assembled a metabolic pathway capable of mineralizing PCP. Interestingly, this pathway produces four toxic intermediates, which include a chlorinated benzoquinone that is a potent alkylating agent and three chlorinated hydroquinones that produce reactive oxygen species and benzoquinones upon reaction with O2. We sought to identify how the cell tolerates the onslaught of toxic effects associated with these intermediates. RNA-Seq and Tn-Seq were used to probe the response of S. chlorophenolicum to PCP as well as the stresses associated with its exposure and degradation. The results demonstrate that PCP exposure causes dissipation of the proton-motive force and perturbation of the cell envelope, and the downstream intermediates cause oxidative stress. However, the transcriptional response to PCP degradation far exceeds what is actually needed and, for many genes, is actually counter-productive. Prevention of PCP degradation by deletion of the transcriptional regulator, pcpR, increases growth rate in rich medium. These data suggest that, although PCP degradation allows access to a novel nutrient, the benefit of degrading it depends upon the availability of other resources. When resources are abundant, the detrimental effects of the toxic intermediates may outweigh the benefit of the carbon and energy that can be obtained by degrading PCP. However, when resources are scarce, degradation of PCP may provide access to a novel source of carbon and energy as well as detoxification of this anthropogenic pollutant.

overall_design: Transposon mutant libraries were created in wild type S. chlorophenolicum and in S. chlorophenolicum ∆pcpB (a mutant which cannot degrade PCP). Libraries were grown in the absence or presence of 200 µM pentachlorophenol for 22-24 generations. Libraries were then subjected to Tn-Seq analysis for fitness determinations of individual mutants. This analysis allowed us to determine genes important for fitness during exposure to PCP as well as specifically those important during degradation of PCP.

first: Shelley

last: Copley


title: Genome-Wide Analysis of Transcriptional Changes and Genes that Contribute to Fitness during Degradation of the Anthropogenic Pollutant Pentachlorophenol by Sphingobium chlorophenolicum

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

overall_design: Refer to individual Series


title: The mice uterine gene expression landscape from early to late pregnancy

city: Amsterdam

first: Febilla

last: Fernando

address: Meibergdreef 9

department: Reproductive Biology Laboratory

country: Netherlands

institute: Academic Medical Center

summary: To define the vast landscape of mice pregnancy and labor/parturition associated gene expression transitions, wild type FVB mice uterine tissues from the non-pregnant state (NP) and at E6.5, E8.5, E10.5, E15.5 and E17.5 were analysed using gene expression microarray

overall_design: FVB mice (WT) uterine tissues from the non-pregnant state (NP) and at E6.5, E8.5, E10.5, E12.5, E15.5 and E17.5 with four to five uterine samples per time point were used and gene expression data was generated using the Illumina Mouse Ref-8.v2 platform

first: Souad

last: Boussata

first: Joris

last: van der Post

first: Gijs

middle: B

last: Afink

first: Carrie

last: Ris-Stalpers


title: Altered expression of the Cdk5 activator-like protein, Cdk5α, causes neurodegeneration, in part by accelerating the rate of aging [thorax]

middle: R


title: Sphingobium chlorophenolicum Confronts the Stresses Associated with Pentachlorophenol and Four Toxic Downstream Metabolites to Utilize a Suboptimal Nutrient Source [RNA-seq]

overall_design: RNA-seq analysis of Sphingobium chlorophenolicum after a 15-minute exposures to one of the following stresses: 200 µM pentachlorophenol, 5 mM toluene, 39.1 µM CCCP, 20 µM paraquat, or 1 mM methylglyoxal, or a 5-hour exposure to 200 µM pentachlorophenol. All were repeated in triplicate.


title: Identification of the EmrR regulon in Chromobacterium violaceum

city: Ribeirao Preto

first: Jose

middle: Freire

last: da Silva Neto

state: Sao Paulo SP

address: Av Bandeirantes 3900

department: Biologia Celular e Molecular e Bioagentes Patogenicos

institute: Universidade de Sao Paulo

summary: Antibiotic resistance can arise by several mechanisms, including mutation in transcription factors that regulate drug efflux pumps. In this work, we identified EmrR as a MarR family transcription factor involved in antibiotic resistance in Chromobacterium violaceum, a Gram-negative bacterium that occurs in soil and water and can act as a human opportunistic pathogen. Antibiogram and minimum inhibitory concentration (MIC) assays showed that the ΔemrR mutant presented increased resistance to the antibiotic nalidixic acid in respect to the wild-type strain. The emrR gene is near to a putative operon emrCAB, which encode the efflux pump EmrCAB. DNA Microarray analysis showed that EmrR represses the emrCAB operon and some other putative transporters. Northern blot assays validated that EmrR represses the emrCAB operon and this repression can be released by salicylate, but not other compounds such as nalidixic acid or ethidium bromide. Electrophoretic mobility shift assays (EMSA) showed that EmrR binds directly to the promoter regions of emrR, emrCAB and other genes to exert negative regulation. Therefore, in response to compounds as salicylate, EmrR derepresses the operon emrCAB causing overexpression of the efflux pump EmrCAB and increased resistance to nalidixic acid in C. violaceum.

overall_design: The experimental procedure compares WT control vs. emrR mutant. Comparison was performed using three biological replicates.

first: Kelly

last: Barroso

first: Maristela

last: Previato-Mello

first: Bianca

last: Batista

first: José

middle: F


title: ChIP-seq for embryonic chicken feather samples

status: Public on Oct 31 2018

city: Los Angeles

first: Randall

middle: B.

last: Widelitz

state: California

address: 2011 Zonal Ave HMR 305

department: Department of Pathology

institute: University of Southern California

summary: Study of H3K4me3 profile patterns during early feather development

overall_design: H3K4me3 ChIP-seq was performed to document E7 (H&H 31) and E9 (H&H 35) feather development. There are 2 replicates for each sample group.


title: Expression data from wt, Lkb1 conditional knock out and LPS treated DC

status: Public on Oct 29 2018

city: Tianjin

first: Xiaoming

last: Feng

address: 288 Nanjing Road

institute: Institute of Hematology and Hospital of Blood Disease, Chinese Academy of Medical Sciences

summary:
To dissect the molecular mechanism by which Lkb1 controls DC function, we performed transcriptional profiling of DCs sorted from Lkb1f/f, LPS-treated mice and Cd11cCreLkb1f/f mice.
We used microarrays to detail the global programme of gene expression underlying cellularisation and identified

overall_design: DCs were sorted from spleen of Lkb1f/f mice, LPS-treated mice, Cd11cCreLkb1f/f mice for RNA extraction and hybridization

first: Dong

last: Kui


title: Expression data from prostate cancer LNCaP-AdtHs cells in response to androgen, ADT, normoxia, or hypoxia

status: Public on Oct 30 2018

city: Portland

first: David

last: Qian

address: 3303 SW Bond Ave, CH14R

institute: Oregon Health & Science University

summary:
Androgen and hypoxia are two cancer hallmark pathways; both exert biological effects primarily via the regulation of gene expression
We used gene expression array to determine the global gene expression changes due to androgen, castration (androgen-free) in normoxia and hypoxia conditions. Microarray assays were performed in the OHSU Gene Profiling Shared Resource

overall_design: Androgen responsive human prostate cancer LNCaP-AdtHs cells were cultured in four conditions: with 5% charcoal-stripped FBS (CSS) (ADT), 5% CSS + 1nM synthetic androgen R1881 (R1881) in 20% oxygen (normoxia) or in 1% oxygen (hypoxia).

middle: Z


title: Comparative gene expression analysis in the Arabidopsis thaliana root apex using RNA-seq and microarray transcriptome profiles [RNA-seq]

city: Gainesville

first: Robert

middle: J.

last: Ferl

state: Florida

address: 1301 Fifield Hall PO Box 110690

department: Horticultural Sciences

institute: University of Florida

summary:
The root apex is an important section of the plant root, involved in environmental sensing and cellular development. Analyzing the gene profile of root apex in diverse environments is important and challenging, especially when the samples are limiting and precious, such as in spaceflight. The feasibility of using tiny root sections for transcriptome analysis was examined in this study.To understand the gene expression profiles of the root apex, Arabidopsis thaliana Col-0 roots were sectioned into Zone-I (0.5 mm, root cap and meristematic zone) and Zone-II (1.5 mm, transition, elongation and growth terminating zone). Gene expression was analyzed using microarray and RNA seq.Both the techniques, arrays and RNA-Seq identified 4180 common genes as differentially expressed (with > two-fold changes) between the zones. In addition, 771 unique genes and 19 novel TARs were identified by RNA-Seq as differentially expressed which were not detected in the arrays.
Single root tip zones can be used for full transcriptome analysis; further, the root apex zones are functionally very distinct from each other. RNA-Seq provided novel information about the transcripts compared to the arrays. These data will help optimize transcriptome techniques for dealing with small, rare samples.

overall_design: Arabidopsis thaliana var. Columbia (COL-0) seedlings were grown on sterile solid media plates containing 0.5 % phytagel. The plates were vertically placed in growth chambers with continuous light (80-100 µmol m -2) at a constant temperature of 19° C. Eight day old seedlings were harvested into RNA-later solution in a 50 mL centrifuge tubes and stored at -20 °C freezer. The root tips were dissected into zone-I: 0.5mm from the tip including the root cap and root division zones, and zone-II: 1.5mm sections including root elongation and root hair zone. Microarray and sequencing experiments were performed.

first: Aparna

last: Krishnamurthy

first: Anna-Lisa

last: Paul


title: Comparing RNA-Seq and microarray gene expression data in two zones of the Arabidopsis root apex relevant to spaceflight

status: Public on Oct 27 2018


title: Comparative gene expression analysis in the Arabidopsis thaliana root apex using RNA-seq and microarray transcriptome profiles [microarray]


title: Decidualization of human endometrial stromal fibroblasts is a multi-phasic process involving distinct transcriptional programs

status: Public on Oct 25 2018

city: West Haven

first: Kalle

middle: T

last: Rytkönen

state: CT

address: 840 West Campus Drive

department: EEB, Systems Biology institute

institute: Yale University

summary: We sequenced mRNA from endometrial stromal fibroblasts and decidual stromal cells after 3 day and 8 days decidualization treatment

overall_design: We sequenced mRNA from endometrial stromal fibroblasts (n=3), and after 3days (n=3) or 8 days (n=2) in vitro decidulization with cAMP and progesterone (MPA)


title: Altered expression of K13 disrupts DNA replication and repair in Plasmodium falciparum

city: Tampa

first: Rays

last: Jiang

state: FL

address: 4202 E Fowler Ave

department: Department of Global Health

institute: University of South Florida College of Public Health

summary:
Background: Plasmodium falciparum has evolved resistance to the artemisinin component of the frontline antimalarial treatment Artemisinin-based Combination Therapy in South East Asia. Millions of lives will be at risk if resistance spreads to Africa. Single non-synonymous mutations in the propeller region of PF3D7_1343700, “K13”are implicated in resistance. In this work, we use transcriptional profiling to characterize a laboratory-generated k13 insertional mutant previously demonstrated to have increased sensitivity to artemisinins to explore the functional role of k13.
Results: A set of RNA-seq and microarray experiments confirmed that the expression profile of k13 is specifically altered during the early ring and early trophozoite stages of the mutant intraerythrocytic development cycle. The down-regulation of k13 in this mutant during the early ring stage is associated with a transcriptome shift towards a more trophozoite-like state. To discover the specific downstream effect of k13 dysregulation, we developed a new computational method to search for differential gene expression while accounting for the temporal sequence of transcription. We found that the strongest biological signature of the transcriptome shift is an up-regulation of DNA replication and repair genes during the early ring developmental stage and a down-regulation of DNA replication and repair genes during the early trophozoite stage; by contrast, the expressions of housekeeping genes are unchanged. This effect, due to k13 dysregulation, is antagonistic, such that k13 levels are negatively correlated with DNA replication and repair gene expression.
Conclusion: Because a hypothesized mode of action of artemisinins is oxidative stress our results support a role for k13 as a stress response regulator, consistent with the role of its human homolog Keap1, that regulates DNA replication and repair genes in response to oxidative stress.

overall_design: The parasite strains NF54 and PB58  (the K13 mutant) were maintained in identical standard culture conditions and synchronized by 3 rounds of sorbitol synchronization. The time points collected were 6 (n=3), 12 (n=2), 24 (n=5), 38 (n=3), and 48 (n=3 for wild-type and n=2 for K13 mutant) hours after time zero. Time zero was defined as the time when the synchronized culture was half late schizonts and half early rings.

first: Justin

last: Gibbons

first: Katrina

last: Button-Simons

first: Swamy

last: Adapa

first: Suzzane

last: Li

first: Maxwell

last: Pietsch

first: Min

last: Zhang

first: Xiangyun

last: Liao

first: John

middle: H

last: Adams

first: Michael

last: Ferdig


title: Dysregulated neutrophil responses and neutrophil extracellular trap formation and degradation in PAPA syndrome

status: Public on Oct 23 2018

first: Hong-wei

last: Sun

address: 9000 Rockville Pile

department: Office of Science & Technology

institute: NIAMS

summary: Pyogenic arthritis, pyoderma gangrenosum and acne (PAPA) syndrome is characterized by flares of sterile arthritis with neutrophil infiltrate and the overproduction of Interleukin (IL)-1β. The purpose of this study was to elucidate the potential role of neutrophil subsets and neutrophil extracellular traps (NETs) in the pathogenesis of PAPA. The transcriptome of PAPA normal-dense neutrophils, autologous LDGs, and healthy control normal-dense neutrophils was characterized using RNASeq. The transcriptome of a PAPA skin biopsy and a healthy control skin sample was elucidated using RNASeq.

overall_design: This dataset includes a total of 5 individual samples. This study sought to characterize PAPA normal-dense neutrophils, autologous LDGs, and healthy control normal-dense neutrophils and determine their transcriptomic profiles. We also wanted to characterize the transcriptomic profile of PAPA skin compared to a healthy control skin.

first: P

last: Mistry

first: C

last: Carmona-Rivera

first: N

last: Seto

first: A

middle: K

last: Ombrello

last: Hoffmann

last: Jones

first: D

middle: L

last: Stone

middle: M

last: Carlucci

first: S

last: Dell'Orso

first: G

last: Gutierrez-Cruz

first: H

last: Kastner

first: I

last: Aksentijevich

first: M

middle: J

last: Kaplan


title: RNA sequencing (RNA-seq) analysis of 35SARF18-OE-2 and Col.

status: Public on Oct 16 2018

city: Jinan

first: Yuebin

last: Jia

address: 88 Cultural east road

institute: Shandong University

summary: The goals of this study are to find the target gene of ARF18, to explain why the ARF18 overexpression line has smaller leaves. Library construction and sequencing were performed as described elsewhere, based on RNA extracted with the TRIzol reagent (Invitrogen, Carlsbad, CA, USA) from 7-day-old seedlings of 35S-ARF18-OE-2 and Col. The RNA was purified by electrophoresis through a TBE-urea polyacrylamide gel. The gel regions harboring 18-30 nt fragments were excised and the RNA recovered. The resulting population of sRNAs was 5’ and 3’ RNA adaptor-ligated using T4 RNA ligase and amplified for 18 PCR cycles. The amplicons were purified and sequenced using an Illumina/Solexa Genome Analyzer (Beijing Genomics Institute, Shenzhen, China). Raw reads were trimmed by removing low-quality and adaptor sequences, and then they were aligned to the Arabidopsis genome using SOAP2 software. Transcript frequency was calculated using the reads per kilobase per million reads method. Differentially transcribed genes were identified using a method modified from Audic and Claverie (1997). Significance was based on the p value and the false discovery rate (FDR) (Audic and Claverie, 1997). The chosen thresholds were FDR ≤ 0.001 and |log2| ≥ 1. We identified 113 differentially expressed genes, of which 49 genes are up-regulated, and 94 genes are down-regulated.

overall_design: The RNA was extracted from 7-day-old seedlings of Col and 35SARF18-OE-2 for deep sequencing.

first: Xiangpei

last: Kong


title: Epidermal growth factor activates β-catenin via integrin-linked kinase to control proliferation of mesenchymal stromal cells.

status: Public on Oct 24 2018

city: York

first: Katherine

last: Newling

address: Wentworth Way

department: Biology

institute: University of York

summary: Mesenchymal stromal cells (MSCs) are located in bone marrow where they help to maintain bone homeostasis and repair through the ability to expand in response to mitotic stimuli and differentiate into skeletal linages. The signalling mechanisms that enable precise control of MSC function remain unclear. Here, we have identified a non-canonical epidermal growth factor (EGF) signalling pathway in MSCs, which acts via integrin-linked kinase (ILK) to activate β-catenin, a key component of Wnt signalling. EGF induces nuclear translocation of β-catenin in MSCs but does not drive T cell factor (TCF)-mediated transactivation of Wnt target genes, and we demonstrate by Design of Experiments statistical analysis that the EGF/β-catenin and Wnt/β-catenin pathways do not cross-talk following co-stimulation with multiple concentrations of both ligands. By examining EGF-regulated genes in MSCs by RNA-Sequencing, we identified gene sets that were exclusively regulated by the EGF/b-catenin pathway, which were distinct from canonical EGF-regulated genes. In contrast, the expression of subsets of canonical EGF signalling gene targets were significantly influenced by b-catenin activation. These newly-identified EGF signalling pathways cooperate to enable EGF-mediated proliferation of MSCs by alleviating the suppression of cell cycle pathways induced by canonical EGF signalling.

overall_design: Examination of expression profiles of 3 samples of untreated MSCs, 3 samples EGF treated, 3 samples EGF + IWR-1 treated MSCs using RNA-seq analysis

first: Paul

last: Genever

first: Charlotte

last: Knight

first: Sally

last: James

first: David

last: Kuntin

first: James

last: Fox

first: Sam

last: Hollings

first: Rebecca

last: Pennock


title: A single Gal4-like transcription factor activates the Crabtree effect in Komagataella phaffii

status: Public on Oct 19 2018

city: Vienna

first: Nadine

middle: Elpida

last: Tatto

address: Muthgasse 18

department: Department of Biotechnology

country: Austria

institute: University of Natural Resources and Life Sciences

summary: The Crabtree phenotype defines whether a yeast can perform simultaneous respiration and fermentation under aerobic conditions at high growth rates, a phenomenon that resembles the Warburg effect in cancer cells. Whole genome duplication, global promoter rewiring and loss of respiratory complex I are the main molecular events that contributed to the evolution of Crabtree effect. Here we show that overexpression of a single Gal4-like transcription factor is sufficient to convert Crabtree-negative Komagataella phaffii (Pichia pastoris) into a Crabtree positive yeast. We report the transcriptome profile (RNASeq) of the Δgal4-like and Gal4-like overexpression K. phaffii strains. Upregulation of the glycolytic genes and a significant increase in glucose uptake rate due to the overexpression of the Gal4-like transcription factor caused an overflow metabolism, triggering both short-term and long-term Crabtree phenotypes. This indicates that a single mutation leading to overexpression of one gene may have been sufficient as a first molecular event towards respiro-fermentative metabolism in the course of yeast evolution.

overall_design: Investigation of the transcriptome profile of the control, Gal4-like overexpression and Δgal4-like K. phaffii strains in triplicates.

first: Özge

last: Ata

first: Corinna

last: Rebnegger

middle: E

first: Minoska

last: Valli

first: Teresa

last: Mairinger

first: Stephan

last: Hann

first: Matthias

last: Steiger

first: Pinar

last: Calik

first: Diethard

last: Mattanovich


title: Single-cell level transcriptomic anaylsis of the homeostatic and regenerating axolotl limb

city: Lund

first: Nicholas

middle: D

last: Leigh

state: Skåne

address: BMC A12, Sölvegatan 17

department: Laboratory Medicine

country: Sweden

institute: Lund University

summary: Regeneration of complex multi-tissue structures, such as limbs, requires the coordinated effort of multiple cell types. In axolotl limb regeneration, the wound epidermis and blastema have been extensively studied via histology, grafting, and bulk-tissue RNA-sequencing. However, studying the contributions of these tissues is hindered due to limited information regarding the molecular identity of the cell types in regenerating limbs. By performing unbiased single-cell RNA-sequencing on over 25,000 cells from axolotl limbs, we identify a plethora of cellular diversity within epidermal, mesenchymal, and hematopoietic lineages in homeostatic and regenerating limbs. We identify regeneration-induced genes, develop putative trajectories for blastema cell differentiation, and propose the molecular identity and origin of fibroblast-derived blastema progenitor cells residing in homeostatic limbs. This work will enable application of molecular techniques to assess the contribution of these populations to limb regeneration.  It will also facilitate work aimed at identifying transcripts and cells critical for limb regeneration.

overall_design: A timecourse of single-cell transcriptomic data for the regenerating axolotl limb was obtained. Samples were collected at 3 days post amputation (dpa) (wound healing, 3 samples), 14 dpa (early-bud blastema, 2 samples), and 23 dpa (medium-bud blastema, 6 samples). Additonally, two sets of transcriptomic data was collected from 2 samples of intact (homeostatic) limb and 3 samples of intact limb contralateral to an early-bud blastema (14dpa) (not the same early-bud blastema as samples S3-14 and S5-14). All samples were collected on inDrops.

first: Jessica

last: Whited


title: Timing and order of the molecular events marking the onset of berry ripening in grapevine [BHLH OE]

status: Public on Oct 15 2018

city: Verona

first: Silvia

last: Dal Santo

address: Strada Le Grazie, 15

country: Italy

institute: University of Verona

summary: Grapevine (Vitis vinifera L.) is a model for the investigation of physiological and biochemical changes during the formation and ripening of non-climacteric fleshy fruits. However, the order and complexity of the molecular events during fruit development remain poorly understood. To identify the key molecular events controlling berry formation and ripening, we created a highly detailed transcriptomic and metabolomic map of berry development, based on samples collected every week from fruit-set to maturity in two grapevine genotypes for three consecutive years, resulting in 219 samples. Major transcriptomic changes were represented by coordinated waves of gene expression associated with early development, veraison (onset of ripening)/mid-ripening and late-ripening and were consistent across vintages. The two genotypes were clearly distinguished by metabolite profiles and transcriptional changes occurring primarily at the veraison/mid-ripening phase. Co-expression analysis identified a core network of transcripts as well as variations in the within-module connections representing varietal differences. By focusing on transcriptome rearrangements close to veraison, we identified two rapid and successive shared transitions involving genes whose expression profiles precisely locate the timing of the molecular reprogramming of berry development. Functional analyses of two transcription factors, markers of the first transition, suggested that they participate in a hierarchical cascade of gene activation at the onset of ripening. This study defined the initial transcriptional events that mark and trigger the onset of ripening and the molecular network that characterizes the whole process of berry development, providing a framework to model fruit development and maturation in grapevine.

overall_design: For transient transformation of Vitis vinifera cv. Sultana, the 35S:VvBHLH075 construct was transferred to Agrobacterium tumefaciens strain C58C1 by electroporation. As control, Agrobacterium was also transformed with an empty GoldenBraid 2.0 vector (pDGBΩ1). Seven in vitro six-week-old plants of grapevine cv. Sultana were immersed in each bacterial suspension and vacuum infiltrated (2 X 2 min at 90kPa). After agroinfiltration, plantlets were allowed to recover in vitro for seven days before collecting material for RNA extraction and transcriptomic analysis.

first: Marianna

last: Fasoli

first: Chandra

last: Richter

first: Sara

last: Zenoni

first: Edoardo

last: Bertini

first: Nicola

last: Vitulo

first: Nick

last: Dokoozlian

first: Mario

last: Pezzotti

first: Giovanni

last: Tornielli


title: Timing and order of the molecular events marking the onset of berry ripening in grapevine [WRKY19 OE]

overall_design: For transient transformation of Vitis vinifera cv. Sultana, the 35S:VvWRKY19 construct was transferred to Agrobacterium tumefaciens strain C58C1 by electroporation. As control, Agrobacterium was also transformed with an empty GoldenBraid 2.0 vector (pDGBΩ1). Seven in vitro six-week-old plants of grapevine cv. Sultana were immersed in each bacterial suspension and vacuum infiltrated (2 X 2 min at 90kPa). After agroinfiltration, plantlets were allowed to recover in vitro for seven days before collecting material for RNA extraction and transcriptomic analysis.


title: Neurohormonal signalling via a cytosolic sulfotransferase controls insulin sensitivity of C. elegans

status: Public on Oct 14 2018

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

state: MA

institute: Koch Institute

summary: Insulin and insulin-like growth factor signalling regulates a broad spectrum of growth and metabolic responses to a variety of internal and environmental stimuli. Such responses can be tailored so that changes in insulin signalling result in distinct physiological responses to different stimuli. For example, the inhibition of insulin-like signalling is key in the responses of the nematode C. elegans to both osmotic stress and starvation, but these two stresses result in responses that are both physiologically and molecularly distinct. How does reduced insulin-like signalling elicit different responses to different environmental stimuli? We report that neurohormonal signalling involving the C. elegans cytosolic sulfotransferase SSU-1 controls developmental arrest in response to osmotic stress but does not control the distinct developmental arrest that occurs in response to starvation. SSU-1 functions in a single pair of sensory neurons to control intercellular signalling -- likely by catalyzing the synthesis of a steroid hormone -- via the nuclear hormone receptor NHR-1. SSU-1-controlled signalling antagonizes insulin-like signalling and hence modulates insulin sensitivity. In short, we describe a previously unknown neurohormonal signalling pathway that is required specifically for some but not all consequences of reduced insulin-like signalling. In mammals, the nervous system plays a similarly important yet poorly understood role in modulating insulin sensitivity. Our results suggest that the mammalian nervous system might regulate insulin sensitivity via sulfotransferase-controlled neurohormonal signalling.

overall_design: Gene expression analysis of two or three biological replicates of wild type N2 nematodes, ssu1 mutant nematodes or daf-16 mutant nematodes grown in 50 mM or 500 mM NaCl media.

middle: O

last: Burton

first: Vivek

last: Dwivedi

first: Kirk

last: Burkhart

first: Rebecca

last: Kaplan

first: L

last: Baugh

first: H

last: Horvitz


title: Genome-wide characterization of cis-acting DNA targets of ZmbZIP22 in maize

status: Public on Oct 12 2018

city: Beijing

first: Chaobin

last: Li

state: Beijing

address: 2 Yuanmingyuan West Road, NMICC Building

institute: China Agricultural University

summary: A new factor binds to the 27-kD γ-zein gene promoter was identified through probe affinity purification and mass spectrometry analysis. This new factor belongs to bZIP type TF (hence named as ZmbZIP22). Chromatin immunoprecipitation coupled to high-throughput sequencing (ChIP-Seq) analysis with two biological replicates was performed to determine the DNA binding targets of ZmbZIP22. ChIP-Seq analysis detected 1,550 DNA binding sites distributed over 514 genes. We identified ACAGCTCA as the most conserved ZmbZIP22 binding motif. We confirmed that ZmbZIP22 binds the 27-kD γ-zein gene promoter in vivo, and also identified additional direct targets of ZmbZIP22.

overall_design: Examination of 15 days after pollination (DAP) wild type maize endosperm in duplicate with ZmbZIP22 specific antibody and IgG serves as control.

first: Rentao

last: Song


title: Next Generation Sequencing Facilitates Quantitative Analysis of WT and zmbzip22 mutant Transcriptomes

summary: Analysis of gene expression level. The hypothesis tested in the present study was that zmbzip22 mutant affects nutrient metabolism and stress response.

overall_design: mRNA profiles of 15 DAP wild type (WT) and zmbzip22 mutant were generated by deep sequencing, in triplicate, using Illumina Hiseq 2500 (Zea mays).


title: Genetic ablation of NFAT5/TonEBP in smooth muscle cells impairs flow- and pressure-induced arterial remodeling in mice

status: Public on Oct 10 2018

city: Mannheim

first: Carolina

last: Delatorre

address: Theodor-Kutzer-Ufer 1-3

institute: University Heidelberg

summary:
To study the impact of the transcription factor NFAT5 on the vascular smooth muscle cell (VSMC) transcriptome, genetic ablation of floxed nfat5 in mouse aortic smooth muscle cells was achieved by transducing them with an adenoviral vector to express Cre-recombinase (Ad-Cre) under control of a CMV promoter.
Empty vector adenovirus (Ad-PL) was used as control.

overall_design: 4 samples of Ad-PL- and 4 samples of Ad-Cre-treated VSMCs were processed for RNA extraction

first: Thomas

last: Korff


title: RIG-I and MDA5 fRIP during KSHV lytic reactivation

status: Public on Oct 11 2018

city: Nashville

first: Jeff

last: Rathmell

state: TN

address: 1211 Medical Center Drive

department: PMI

institute: Vanderbilt University Medical Center

summary: The RIG-I like receptors (RLRs) RIG-I and MDA5 are cytosolic RNA helicases best characterized as restriction factors for RNA viruses. However, evidence suggests RLRs participate in innate immune recognition of other pathogens, including DNA viruses. Kaposi's sarcoma-associated herpesvirus (KSHV) is a human gammaherpesvirus and the etiological agent of Kaposi's sarcoma and primary effusion lymphoma (PEL). We demonstrate that RIG-I and MDA5 restrict KSHV lytic reactivation in PEL. By performing fRIP-Seq, we define the in vivo RLR substrates and demonstrate that RIG-I and MDA5-mediated restriction is facilitated exclusively by the recognition of host-derived RNAs.

overall_design: Inducible F-RIG-I and F-MDA5 BC-3 cells, as well as control BC-3 cells were treated with 1 μg/ml of doxycycline, 20ng/ml tetradecanoyl phorbol acetate and 0.1 mM sodium butyrate for 48 h. Flag fRIP was performed and RNA was submitted for high throughput sequencing.

first: Yang

last: Zhao

first: Xiang

last: Ye


title: Drug-induced change in gene expression across NCI-60 cell lines after exposure to 15 anticancer agents for 2, 6 and 24h (sorafenib)

status: Public on Oct 09 2018

city: Rockville

first: Anne

last: Monks

address: 9609 Medical Center Dr

department: Developmental Therapeutics Program

institute: National Cancer Institute

summary: To identify patterns of drug-induced gene modulation that occur across different cell types, we measured gene expression changes across NCI-60 cell lines after exposure to 15 anticancer agents.  The results were integrated into a database and set of interactive analysis tools, the NCI Transcriptional Pharmacodynamics Workbench (NCI TPW), intended to allow exploration of gene expression modulation, including by molecular pathway, drug target, and association with drug sensitivity.  We identified common transcriptional responses across drugs and cell types and uncovered cell signaling pathway–specific gene expression changes associated with drug sensitivity.  We also demonstrated the value of this tool for investigating clinically relevant molecular hypotheses, utilizing the NCI TPW to assess drug-induced expression changes in genes associated with immune function and epithelial-mesenchymal transition, and to identify candidate biomarkers for drug activity.  The NCI TPW provides a comprehensive resource to facilitate understanding of tumor cell characteristics that define sensitivity to anticancer drugs.

overall_design: To compare and contrast transcriptional responses over time, in the NCI-60 cell line panel after treatment with 15 anticancer agents.

first: Yingdong

first: Curtis

last: Hose

first: Hossein

last: Hamed

first: Julia

last: Krushkal

first: Jianwen

last: Fang

first: Dmitriy

last: Sonkin

first: Eric

middle: C

last: Polley

first: Laura

last: Fogli

first: Mariam

last: Konate

first: Sarah

middle: B

last: Miller

first: Melanie

middle: A

last: Simpson

first: Andrea

middle: R

last: Voth

first: Ming-Chung

first: Alida

last: Palmisano

first: Erik

last: Harris

first: Xiaolin

last: Wu

first: John

last: Connelly

first: Annamaria

last: Rapisarda

first: Beverly

last: Teicher

first: Richard

last: Simon

first: James

last: Doroshow


title: Drug-induced change in gene expression across NCI-60 cell lines after exposure to 15 anticancer agents for 2, 6 and 24h (topotecan)

first: Anne

last: Monks

first: Yingdong

last: Zhao

first: Curtis

last: Hose

first: Hossein

last: Hamed

first: Julia

last: Krushkal

first: Jianwen

last: Li


title: Drug-induced change in gene expression across NCI-60 cell lines after exposure to 15 anticancer agents for 2, 6 and 24h (sunitinib)

last: Fang

first: Dmitriy

last: Sonkin

first: Eric

last: Polley

first: Laura

last: Fogli

first: Mariam

last: Konate

first: Sarah

last: Miller

first: Melanie


title: Drug-induced change in gene expression across NCI-60 cell lines after exposure to 15 anticancer agents for 2, 6 and 24h (vorinostat)

last: Simpson

first: Andrea

last: Voth

first: Ming-Chung

first: Alida

last: Palmisano

first: Erik

last: Harris

first: Xiaolin

last: Wu

first: John

last: Connelly


title: Drug-induced change in gene expression across NCI-60 cell lines after exposure to 15 anticancer agents for 2, 6 and 24h (sirolimus)

first: Anne

last: Monks

first: Yingdong

last: Zhao

first: Annamaria

last: Rapisarda

first: Beverly

last: Teicher

first: Richard

last: Simon

first: James

last: Doroshow