title: Examining the role of mupirocin-induced nutritional stress in the S. aureus stringent stress response

status: Public on Feb 02 2019

city: Vancouver

first: Erin

last: Gill

state: British Columbia

address: 2259 Lower Mall

country: Canada

institute: University of British Columbia

summary: The stringent response is a conserved stress response employed by various bacteria to respond to and cope with conditions of amino acid starvation, carbon-source, fatty acid, oxygen/iron limitation, heat shock, antimicrobial challenge, and/or other environmental stressors. In S. aureus, the stringent response is mediated in part by enzyme RSH (relA spoT homologue) which synthesizes two nucleotide-based molecules, guanosine tetraphosphate (ppGpp) and pentaphosphate (pppGpp), collectively known as (p) ppGpp. This response is known to result in a number of diverse physiological and metabolic changes which we further characterized in the present study. Specifically, the global transcriptome of the RSH synthase mutant (rshsyn) was compared to the WT parent S. aureus strain (NCTC 8325) by RNA-Seq analysis under both normal and nutrient-limited media conditions. In order to mimic nutrient limitation, bacteria were treated with mupirocin, an antibiotic and isoleucine analogue known to lead to isoleucine starvation. In the WT strain, in response to mupirocin-induced isoleucine starvation, genes encoding protein synthesis machinery were suppressed while genes encoding amino acid biosynthetic machinery were upregulated. This response likely employed to compensate for amino acid deprivation, was not induced in the stringent response mutant. Furthermore, under starvation conditions, biofilm-related genes (i.e. icaA, icaC, fnbA, clfB, emp) were more upregulated in the WT than the stringent response mutant. Moreover, the effect of mupirocin caused a stronger upregulation of several proteases (i.e. sspA, sspP, sppB, aur), lipases (lip, geh) and phenol soluble modulin toxins in the WT as compared to the mutant. Overall, these results suggest that under starvation conditions, RSH plays an important role in helping the cell respond to nutritional stress as well as regulates the expression of numerous colonization and virulence factors.

sample_organism: Staphylococcus aureus subsp. aureus NCTC 8325

overall_design: RNA-Seq profiling of gene expression in Staphylococcus aureus subsp. aureus NCTC8325 with two genotypes grown in two conditions

first: Sarah

middle: C

last: Mansour

middle: E

first: Reza

last: Falsafi

first: Robert

last: Hancock


title: RNA-sequencing of Rabbit Hamstring Allografts

status: Public on Feb 01 2019

city: Rochester

first: Asha

last: Nair

address: 200 1ST ST SW

country: USA

institute: Mayo Clinic

type: Expression profiling by high throughput sequencing

summary: The purpose of this study was to characterize the baseline transcriptional state of semitendinosus autografts in a rabbit model for ACL reconstruction in an effort to guide gene selection for future analyses. These results strengthen the association between genes such as DCN, COL1A1, and COL1A2 and tendon tissues as well as provide the novel addition of further highly expressed tendon characteristic genes such as SPARC and PRELP. These results provide guidance as to which molecules serve as high-signal candidates for future ACL research.

overall_design: RNA sequencing was performed on mRNA extracted from whole semitendinosus autografts from four New Zealand White rabbits and subsequently analyzed using gene enrichment and protein-protein interaction network analysis

first: Daniel

middle: B

last: Saris

first: Mario

last: Hevesi

first: Christopher

last: R Paradise

first: Carlo

last: A Paggi

first: Catalina

last: Galeano-Garces

first: Amel

last: Dudakovic

first: Sanjeev

last: Kakar

first: Timothy

last: Hewett

first: Aaron

middle: J

last: Krych

first: Andre

last: van Wijnen


title: Analysis of whole genome expression change after NPD13668 treatment

city: Nagoya

first: AKIHIRO

last: MURASHIMA

address: 65 Tsurumai-cho, Showa-ku

department: Division of Cancer Biology

country: Japan

institute: Nagoya University Graduate School of Medicine

summary: EZH2 is a catalytic component of polycomb repressive complex 2 (PRC2), which contributes to aggressiveness in many types of cancers. Targeting EZH2/PRC2 has been challenged and now some inhibitors are under clinical trials for cancer treatments. Interestingly, anti-tumor effects of EZH2 is not always depend on H3K27 methyltransferase activity. In order to identify novel inhibitors against EZH2/PRC2, we established a chemical screening system based on measurement of reactivation of promoter activity, which is intrinsically silenced by EZH2/PRC2. We screened more than 300,000 small chemicals and identified 85 chemicals. After validation of reactivation of EZH2/PRC2 target genes, we identified chemical NPD13668 as a potential inhibitor of EZH2/PRC2 activity. To evaluate NPD13668 effect, we analysed whole genome expression change by using SurePrint G3 Human GE 8×60K array slides (G4851B, Agilent Technologies).

overall_design: Microarray experiment was performed as single-color hybridization on SurePrint G3 Human GE 8×60K array.

first: Keiko

last: Shinjo

first: Keisuke

last: Katsushima

first: Tetsuo

last: Ohnuki

first: Akihiro

last: Ito

first: Minoru

last: Yoshida

first: Hiroshi

last: Kimura

first: Yutaka

last: Kondo


title: RNA sequencing of uveal melanona cells treated with VS-4718

city: La Jolla

first: Jorge

middle: Silvio

last: Gutkind

state: CALIFORNIA

address: 3855 Health Sciences Drive

department: Moores Cancer Center

institute: UC San Diego

summary: To identify dysregulated genes in response to short-term FAK inhibition in uveal melanoma cells.

overall_design: 3 independent samples treated with VS-4718 and 3 independent samples treated with vehicle as a control

first: J

middle: S


title: Expression data from skin of patients with adverse drug reactions (ADRs)

city: Zurich

first: Emmanuel

last: Contassot

address: Gloriastrasse 31

department: Dematology

country: Switzerland

institute: University Hospital

summary:
ADRs are immune mediated skin reactions of diverse severity and etiology. The patho-mechanisms are however not well understood.
We used a gene expression array for the comparison of the gene expression profile of 2 cutaneous adverse drug reactions (MPR and AGEP) to normal skin.

overall_design: Total RNA was extracted from 6 mm skin biopsies and subjected to Affymetrix gene expression profiling.


title: Integrating a genome-wide association study with a large-scale transcriptome analysis to predict genetic regions influencing the glycemic index and texture in rice

city: Los Banos

last: Sreenivasulu

address: Metro Manila

country: Philippines

institute: IRRI

summary: Reliably generating rice varieties with low glycemic index (GI) is an important nutritional intervention given the high rates of Type II diabetes incidences in Asia where rice is staple diet. We integrated a genome-wide association study (GWAS) with a transcriptome-wide association study (TWAS) to determine the genetic basis of the GI in rice. GWAS utilized 305 re-sequenced diverse indica panel comprising ~2.4 million single nucleotide polymorphisms (SNPs) enriched in genic regions. A novel association signal was detected at a synonymous SNP in exon 2 of LOC_Os05g03600 for intermediate-to-high GI phenotypic variation. Another major hotspot region was predicted for contributing intermediate-to-high GI variation, involves 26 genes on chromosome 6 (GI6.1). These set of genes included GBSSI, two hydrolase genes, genes involved in signalling and chromatin modification. The TWAS and methylome sequencing data revealed cis-acting functionally relevant genetic variants with differential methylation patterns in the hot spot GI6.1 region, narrowing the target to 13 genes. Conversely, the promoter region of GBSSI and its alternative splicing allele (G allele of Wxa) explained the intermediate-to-high GI variation. A SNP (C>T) at exon-10 was also highlighted in the preceding analyses to influence final viscosity (FV), which is independent of amylose content/GI. The low GI line with GC haplotype confirmed soft texture, while other two low GI lines with GT haplotype were characterized as hard and cohesive. The low GI lines were further confirmed through clinical in vivo studies. Gene regulatory network analysis highlighted the role of the non‑starch polysaccharide pathway in lowering GI.

overall_design: Expression data was obtained from developing grains collected at 16 days after fertilization (DAF) from 195 lines. The grain tissues collected were rapidly frozen in liquid nitrogen, homogenized, subjected to RNA isolation using Qiagen RNeasy Plant Mini Kit, testing the RNA integrity number with 7.0 or above and subjecting it to cDNA synthesis and cRNA labeling using a single-color Low Input Quick Amp Labeling Kit, hybridizing the labeled probe to 60K indica microarrays in SureHyb chamber and scanning the microarrays (with an ozone barrier slide) using SureScan Microarry Scanner following the methods described in Butardo et al., (2017).

first: Roslen

last: Anacleto

first: Saurabh

last: Badoni

first: Sabiha

last: Parween

first: Vito

middle: M

last: Butardo Jr

first: Gopal

last: Misra

first: Rosa

middle: P

last: Cuevas

first: Markus

last: Kuhlmann

first: Trinidad

last: Trinidad

first: Aida

last: Mallillin

first: Cecilia

last: Acuin

first: Anthony

middle: R

last: Bird

first: Matthew

middle: K

last: Morell

first: Nese


title: Environmental and evolutionary drivers of the modular gene regulatory network underlying phenotypic plasticity for stress resistance in the nematode Caenorhabditis remanei

status: Public on Feb 04 2019

city: Saint Paul

first: Kristin

middle: L

last: Sikkink

state: MN

address: 1987 Upper Buford Circle

department: Ecology, Evolution, and Behavior

institute: University of Minnesota

summary: In response to changing environmental conditions, organisms can acclimate through phenotypic plasticity or adapt by evolving mechanisms to cope with novel stressors. Changes in gene expression, whether dynamic or evolved, are an important way in which environmental responses are mediated; however, much is still unknown about how the molecular networks underlying plastic phenotypes evolve. Here, we compare transcriptional responses to acute heat stress among four populations of the nematode Caenorhabditis remanei-one selected to withstand heat stress, one selected under oxidative stress, an unselected control, and the ancestral population. We used a weighted gene coexpression network analysis within these lines to identify transcriptional modules, which are sets of genes that respond similarly to stress via plastic responses, evolutionary responses, or both. The transcriptional response to acute heat stress is dominated by a plastic response that is shared in the ancestor and all evolved populations. However, we also identified several modules that respond to artificial selection by (1) changing the baseline level of expression, (2) altering the magnitude of the plastic response, or (3) a combination of the two. Our findings reveal that while it is possible to perturb the nature of the transcriptional response network with short bouts of intense selection, the overall structure of transcriptional plasticity is dominated by inherent, ancestral regulatory systems.

overall_design: mRNA profiles of ancestral and three experimentally evolved populations of C. remanei reared at 20°C or 30°C, 6 replicates/temperature for each population

first: Rose

last: Reynolds

first: Catherine

last: Ituarte

first: William

middle: A

last: Cresko

first: Patrick

last: Phillips


title: Expression data from Inferior Vena Cava ligation in WT and Cd39-/- mice

city: Ann Arbor

first: Anuli

middle: Caroline

last: Anyanwu

state: MI

address: 2344 Cardiovascular Center SPC 5853 ; 1500 E. Medical Center Drive

department: Cardiology and Internal Medicine

institute: University of Michigan Medical School

summary:
Leukocyte flux contributes to thrombus formation in deep veins under pathologic conditions, but mechanisms which inhibit venous thrombosis are incompletely understood.  Ectonucleotide di(tri)phosphohydrolase 1 (ENTPD1 or Cd39), an ectoenzyme which catabolizes extracellular adenine nucleotides, is embedded on the surface of endothelial cells and leukocytes. We hypothesized that under venous stasis conditions CD39 regulates inflammation at the vein:blood interface in a murine model of deep vein thrombosis.
Gene expression profiling of WT and Cd39-null mice revealed 76 differentially-expressed inflammatory genes that were significantly upregulated in Cd39-deleted mice after venous thrombosis; and validation experiments confirmed high expression of several key inflammatory mediators.

overall_design: C57BLK6 and CD39 null mice on a C57BLK6 background were either IVC ligated for 48hrs or were shammed. RNA was extracted and hybridized on Affymetrix microarrays. We obtained a n= 4 per group for biological replicates. Technical replication was achieved by pooling four samples for each of the four groups for analysis. We sought to detect gene expression changes at 48 hours following venous stasis-induced thrombosis.


title: Diel and circadian gating of Arabidopsis thermotolerance and transcriptional response to heat stress.

city: Raleigh

first: Dmitry

middle: Olegovich

last: Grinevich

state: NC

address: 120 Broughton Drive, Rm 128

department: Biochemistry

institute: North Carolina State University

summary:
Purpose: To understand time of day variation in Arabidopsis heat shock responses. We have observed significant differences in terms of plant survivability in response to a heat shock across various times of day. Because of this, we believe that transcriptional responses may be a significant underlying factor which contributes to the observed physiology and surivability after heat stress.
Methods: Whole plant tissue mRNA profiles in Col-0 Arabidopsis were generated by deep sequencing using Illumina HiSeq 2500. Tissue samples of four replicates were collected at two times of day (Dawn and Dusk, ZT0/ZT12) and were either control or heat stressed (30oC) for 1 hour. An additional 4 samples were collected in constant light conditions (single replicate) to quantify circadian effects. Sequence reads from each sample were mapped to the TAIR10 reference genome with Tophat2 and counts were obtained using Htseq-count. Differential expression analysis was done using DeSeq2 to calculate differential expression levels of each gene in the dataset.
Results: We identified 5512 differentially expressed transcripts with our DESeq2 based data analysis pipeline that involves characterizing gene expression profiles based on basal expression level, time of differential expression, and direction of differential expression. An additional interaction term analysis revealed 572 genes which showe time of day dependent responses to heat stress, meaning the response to heat stress differs depending on the time of day that the heat stress is perceived by the plant. Downstream analysis using gene ontology analysis tools (Pantherdb.org) and Cytoscape revealed strong differences in terms of response happening in the AM and PM gene expression networks. The significance of this work is that it is the first study to show that there is a significant difference in terms of transcriptional responses to heat stress in Arabidopsis where the differences were quantified by levels of mRNA expression.

overall_design: Whole tissue mRNA profiles were measured by deep sequencing with four replicates in Col-0 ecotype Arabidopsis. Samples collected were control samples at two times of day (dawn and dusk) and heat stressed samples at two times of day (dawn and dusk). Additionally, 4 single replicate samples were collected in contant light conditions (two times of day/control and treatment) to quantify circadian effects. Reads were collected using Illumina Hiseq 2500 and analyzed with dowstream computational analysis.

middle: O

first: Jigar

last: S Desai

first: Kevin

last: Stroup

first: Jiaqi

last: Duan

first: Erin

last: Slabaugh

first: Colleen

last: J Doherty


title: Inhibition of a G9a/DNMT network triggers an immune-mediated bladder cancer regression treated with CM272 (IC50)

city: Madrid

first: Monica

last: Martinez-Fernandez

address: Avda Complutense 40

country: Spain

institute: CIEMAT

summary: Based on the identification of G9a as a potential target in BC, we decided to test the effect of a recently described dual inhibitor against G9a/DNMTs, CM-272, in several BC cell lines

overall_design: Gene expression was compared between bladder cancer cell lines with the same cell lines treated with CM272 (IC50)

first: Cristina

last: Segovia

first: Mónica

last: Martínez-Fernández

first: Carolina

last: Rubio

first: Marta

last: Dueñas

first: Jesús

last: Paramio


title: Inhibition of a G9a/DNMT network triggers an immune-mediated bladder cancer regression

summary: Using a novel immunocompetent quadruple (PtenF/F; Trp53F/F; Rb1F/F;Rbl1-/-) knockout transgenic mouse model of highly aggressive metastatic muscle-invasive BC, we demonstrate that treatment with CM272 and CDDP results in a significant tumor and metastasis regression with a very significant prolonged survival

overall_design: Gene expression was compared between normal bladders from transgenic CKO mice (Rbf/f, Ptenf/f, Tp53f/f, p107-/- ), tumor bladders from CKO inoculated with Adeno-Cre in the bladder, bladders from CKO treated with CM272+CDDP, and metastasis from these mice.


title: Alternative Splicing Variants of Androgen Receptor Altered insulin resistance Gene expression in Human Ovarian Granulosa Cell

city: Hangzhou

first: Chengliang

last: Zhou

state: Zhejiang

address: No. 866th, Yuhangtang Road

department: School of Medicine

country: China

institute: Zhejiang University

summary:
Polycystic ovary syndrome (PCOS) is a complex endocrine disorder, of which the morbidity among women aging from 18 to 44 years old can be as high as 10%. Insulin resistance is an important characteristic of PCOS and affects approximately 65-70% of women with PCOS.
Our previous work identified two AR alternative splicing variants (ASVs) in human granulosa cells (hGCs), Insertion (Ins) and deletion (Del) isoforms, takes up 62% of PCOS specifically. Both isoforms display altered genome-wide recruited genes and genes expressions which are tightly associated with steroidogenesis, folliculogenesis and ovulation. However, the molecular regulatory mechanism of ASVs in hGCs of insulin resistance needs to be illustrated.

overall_design: Here, we used RT-PCR array to detect gene expression relating with insulin resistance in hGCs over-expression with ASVs.

first: Cheng-Liang

first: Qian

last: Yang


title: Developmental and Functional Heterogeneity of White Adipocytes within a Single Fat Depot

city: Boston

first: Grace

last: Daher

address: 1 Joslin Place

institute: Joslin Diabetes Center

summary: We and others have previously observed that adipocytes and preadipocytes taken from different adipose tissue depots are characterized by differential expression of developmental and patterning genes (Dankel et al., 2010; Ferrer-Lorente et al., 2014; Gesta et al., 2006; Lee et al., 2017a; Lee et al., 2013; Macotela et al., 2012; Tchkonia et al., 2007; Yamamoto et al., 2010). To investigate how adipocyte heterogeneity and differences in the expression of developmental genes might impact the biology of adipocytes and preadipocytes, we created preadipocyte cell lines from the stromovascular fraction (SVF) isolated from the scapular white, inguinal, perigonadal, perirenal, and mesenteric fat pads of 6-week old male Immortomouse™ (Jat et al., 1991).During routine culture of the subcutaneous and visceral/perigonadal clonal cell lines, we observed extreme variation in media acidification rates that was unrelated to the fat pad of origin, the differentiation capacity of the cells, or the rate of their proliferation, suggesting metabolic heterogeneity. To further investigate this possibility, 24 clonal cell lines (12 each from subcutaneous and perigonadal fat) were selected based on variable media acidification rates, and their mRNA expression pattern determined by microarray analysis. The expression data was clustered using three different algorythms, and the consensus was used to categorize each type of adipose tissue.

overall_design: Immortomouse™ clonal preadipocyte cell lines were created from the stromovascular fraction (SVF) of the subcutaneous and perigonadal fat of a single 8 week-old male mouse. RNA was extracted, and used to run a microarray. Expression data was then used to cluster the cell lines into groups.

middle: Y

last: Lee

first: Quyen

last: Luong

first: Rita

last: Sharma

first: Jonathan

last: Dreyfuss

first: Siegfried

last: Ussar

first: C

last: Kahn


title: Transcriptional profiling of rice gene expression changes upon co-infection with pathogens Magnapothe oryzae and Xanthomonas oryzae pv. oryzae that causes rice blast and bacterial blight respectively.

city: Hyderabad

first: Ramesh

middle: V.

last: Sonti

state: Andhra Pradesh

address: Uppal Road

department: Plant Microbe Interactions

country: India

institute: Centre for cellular and molecular biology (CCMB)

summary:
Yield loss in crop plants due to biotic stresses is a major problem and pyramiding of R genes is often suggested for sustained and durable resistance against target pests. Information is available for single R gene interaction in rice and other crop plants, but not much data is available for multiple R gene interaction against multiple pathogens/pests. In this study we carried out transcriptional analysis of two rice lines introgressed with either R gene against bacterial blight and gall midge or, against bacterial blight and fungal blast. The gene expression changes were investigated through microarray and the expression pattern upon co-infection with multiple pathogens was analyzed to study the synergistic effect of R gene mediated defense responses as well as to explore the possibility of any antagonism between the R genes as defense pathway employed due to R gene mediated resistance varies as per the attacking pathogen/pest.

Keywords: Expression profiling by array

overall_design: For the experiment, 25 day old rice plants (Rice line RPNF08 carrying bacterial blight resistance gene Xa21, xa13 and rice blast resistance genes Pi54) were infected with the bacterial pathogen Xanthomonas oryzae pv. oryzae (Xoo) and Magnaporthe oryzae that cause bacterial blight and rice blast respectively. Thereafter, total RNA was isolated from tissue samples that were collected from control (uninfected/mock inoculation) and treated plants (infected with the pathogens) at 24 and 72 hours post inoculation. The RNA sample from the two time points were pooled and used for expression analysis using Affymetrix GeneChip System. Three biological replicates were used for the experiment.

first: Roshan

middle: V

last: Maku

first: D

last: Divya

first: Ayyappa

last: Dass

first: R

last: Madhavi

first: G

last: Mallikarjuna

first: P

last: Ramesh

first: M

first: Srinivas

last: Prasad

last: Sundaram

last: Laha

first: A

last: Padmakumari

first: Hitendra

last: Patel

first: Jagadish

last: Bentur


title: Transcriptional profiling of rice gene expression changes upon co-infection with insect Orseola oryza and pathogen Xanthomonas oryzae pv. oryzae that causes gall midge and bacterial blight respectively.

summary:
Yield loss in crop plants due to biotic stresses is a major problem and pyramiding of R genes is often suggested for sustained and durable resistance against target pests. Information is available for single R gene interaction in rice and other crop plants, but not much data is available for multiple R gene interaction against multiple pathogens/pests. In this study we carried out transcriptional analysis of two rice lines introgressed with either R gene against bacterial blight and gall midge or, against bacterial blight and fungal blast. The gene expression changes were investigated through microarray and the expression pattern upon co-infection with multiple pathogens was analyzed to study the synergistic effect of R gene mediated defense responses as well as to explore the possibility of any antagonism between the R genes as defense pathway employed due to R gene mediated resistance variesaccording to the attacking pathogen/pest.

Keywords: Expression profiling by array

overall_design: For the experiment, 25 day old rice plants (Rice line RPNF05 carrying bacterial blight resistance gene Xa21, xa13, xa5 and gall midge resistance genes Gm1, Gm4, Gm8, gm3) were infected with the bacterial pathogen Xanthomonas oryzae pv. oryzae (Xoo) and the insect pest Orseolia oryzae that cause bacterial blight and gall midge respectively. Thereafter, total RNA was isolated from tissue samples that were collected from control (uninfected) and treated plants (infected with pathogen and pest) at 24 and 72 hours post inoculation. The RNA sample from the two time points were pooled and used for expression analysis using Affymetrix GeneChip System. Three biological replicates were used for the experiment.


title: Gene expression profiling of human brain microvascular pericytes with hypoxia and acidosis stimulation

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary: The objective of the present study is to investigate the effect of a stroke mimic condition on human brain pericytes. Comparative gene expression analysis was performed using cultured human brain microvascular pericytes with 1% oxygen for 24 hours or with acidic condition at pH 6.5 for 24 hours. Gene expression was analyzed using 3D-Gene® Human 25k oligonucleotide microarrays and computational gene expression analysis tools. Incubation of cells under these conditions resulted in significant changes in numerous genes related with glycolysis, immune responses, and angiogenesis.

overall_design: Two-condition experiment, control vs. hypoxia or control vs. acidic condition. Biological replicates: 2 control vs. hypoxia, 2 control vs. acidic condition, independently grown and harvested. Cells were exposed for 24 hours to hypoxia (1%O2, 5% CO2, humidified atmosphere) or acidic medium (pH 6.5). Control cells were kept at pH 7.4, in 20% O2, 5% CO2, humidified atmosphere.

first: Kuniyuki

last: Nakamura

first: Masahiro

last: Kamouchi

first: Tetsuro

last: Ago

first: Takanari

last: Kitazono


title: A microarray to characterize the immune response of adult zebrafish to a low dose Mycobacterium marinum infection

city: Tampere

first: Markus

middle: Juhani Tapani

last: Ojanen

address: Arvo Ylpön katu 34

country: Finland

institute: Tampere University

summary: Zebrafish Mycobacterium marinum infection has been widely used to model human tuberculosis because these two diseases share common features, e.g. latency, granuloma formation and reactivation. Here we infected adult zebrafish with a low dose of M. marinum, which usually leads to a chronic infection. At 14 days post infection we performed microarray analysis to characterize the immune response against this infection. Analysis was done using total RNA extracted from the abdominal organs of zebrafish. Our aim was to find novel genes underlying host defense mechanisms against M. marinum infection in zebrafish, and thus to produce novel information that is valuable when developing new treatments for human tuberculosis.

overall_design: Identification of the up- and downregulated genes in Mycobacterium marinum infection in zebrafish. 5 samples were analyzed, 2 samples (biological replicates) collected from wild-type AB zebrafish infected with Mycobacterium marinum and 3 from PBS injected zebrafish.

first: Sanna-Kaisa

middle: E

last: Harjula

first: Mika

last: Rämet


title: Lysolecithin as feed additive enhances collagen expression and villus length in the jejunum of broiler chickens

city: Charlottesville

first: Stephen

last: Turner

state: VA

address: 1670 Discovery Drive

institute: Signature Science, LLC

summary: Adding lysolecithin to feed has reportedly improved the performance of broiler chickens. Lysolecithin is generated by phospholipase catalyzed hydrolysis of lecithin. The enzymatic reaction converts phospholipids into lysophospholipids, with lysophosphatidylcholine (LPC) the primary product. Here we compared supplementation with a commercial lysolecithin (Lysoforte(R) Kemin Industries, Inc., Des Moines, IA) with comparable levels of purified LPC for effects on broilers. Despite no differences in weight gain during the starter period, we discovered a significant increase in average villus length in the jejunum with lysolecithin, but not with LPC. High-throughput gene expression microarray analyses revealed many more genes were regulated in the epithelium of jejunum by lysolecithin compared to LPC. The most upregulated genes and pathways were for collagen, extracellular matrix and integrins. Staining sections of jejunum with Sirius Red confirmed the increased deposition of collagen fibrils in villi of broilers fed lysolecithin but not LPC. Thus, lysolecithin elicits gene expression in the intestinal epithelium leading to enhanced collagen deposition and villus length. LPC alone as a supplement does not mimic these responses. Feed supplementation with lysolecithin triggers changes in the intestinal epithelium with the potential to improve overall gut health and performance.

overall_design: Control group (T1) was provided feed without supplement and was compared to four treatment groups provided feed with either purified LPC, isolated from lysolecithin by column chromatography, (T2, T3) or lysolecithin (T4, T5), each at two different application levels.  T2 (LPC-low) contained 9.5 g/T of LPC supplemented as 500 g/T of purified LPC plus carrier.  T3 (LPC-high) contained 19 g/T of LPC supplemented as 1,000 g/T of purified LPC plus carrier. T4 (lysolecithin-low) contained 9.5 g/T of LPC supplemented as 250 g/T of lysolecithin. T5 (lysolecithin-high) contained 19 g/T of LPC supplemented as 500 g/T of lysolecithin. Lysoforte (as 50% w/w lysolecithin on carrier) and purified LPC were provided by Kemin Industries Inc., Des Moines, Iowa, USA. Pure LPC was applied to a carrier prior to mixing with feed to ensure homogeneous distribution within the feed. Gene expression was analyzed separately in each tissue for differential expression between treatments.

first: David

last: Brautigan

first: Rasia

last: Li

first: Ewa

last: Kubicka

middle: D

first: Javier

last: Garcia

first: Melodie

last: Weintraut

first: Eric

last: Wong


title: Role of HBO1 (KAT7/MYST2) in ovarian cancer cell line SKOV-3

city: Houston

first: Paul

last: Webb

address: 6670 Bertner Ave

department: Genomic Medicine

institute: Houston Methodist Research Institute

summary: Analysis of change in transcriptosome after HBO1 knockdown in SKOV-3 ovarian cancer cell line

overall_design: Total RNA was obtained from SKOV-3 cell line, transfected with siCtrl and siHBO. siHBO1 samples were compared to siCtrl samples.

first: Marcos

last: Quintela


title: Role of HBO1 (KAT7/MYST2) in ovarian cancer cell line UWB1.289

summary: Analysis of change in transcriptosome after HBO1 knockdown in UWB1.289 ovarian cancer cell line

overall_design: Total RNA was obtained from UWB1.289 cell line, transfected with siCtrl and siHBO. siHBO1 samples were compared to siCtrl samples.


title: Aryl hydrocarbon receptor antagonism allows sustained culture of leukemia progenitor cells from acute myeloid leukemia patients

city: Hamilton

first: Mickie

last: Bhatia

state: Ontario

address: 1200 Main Street West

department: Stem Cell and Cancer Research Institute (SCC-RI)

institute: McMaster University

summary:
Hematopoietic progenitors from AML patients express the aryl hydrocarbon receptor signaling pathway. Independent of in vivo engraftability to detect leukemic stem cells, AHR antagonism allows in vitro survival and expansion of AML progenitors, while retaining patient-to-patient heterogeneity.
Based on AML expression data, we show that AHR antagonism disrupts the AHR signaling pathway but it doesn't affect the overall genomic profile of the samples

overall_design: Primary human mononuclear (Ficoll-separated) AML cells were treated with DMSO vehicle control or purine derivative and AHR antagonist (PD-AHA) analog to stemregenin 1 for 24 h in a serum-free media supplemented with stem cell factor, FLT3 ligand and thrombopoietin

first: Fanny

last: Casado

first: Borhane

last: Guezguez

first: Jamie

last: McNicol

first: Aline

last: Fiebig-Comyn

first: Zoya

last: Shapovalova

first: Kyle

last: Salci

first: Tony

middle: J

last: Collins


title: Transcriptomic and proteomic profiling of Rhodospirillum rubrum M68 cultivated in MELiSSA related culture conditions

city: Mol

first: Rob

last: Van Houdt

address: Boeretang 200

department: Interdisciplinary Biosciences

country: Belgium

institute: SCK-CEN

summary:
In the context of the Micro-Ecological Life Support System Alternative (MELiSSA) project, the quorum sensing system (QS) of R. rubrum S1H has been shown to rely on acyl homoserine lactones (AHLs) as communication signals. In addition, previous studies in our lab have suggested that pigment content and photosynthetic membrane production could be under the control of QS. In the present study, the transcriptomic and proteomic profiles of a QS-deficient mutant (R. rubrum strain M68) that does not produce AHLs as the WT strain (R. rubrum S1H) were compared when cultivated in light anaerobic conditions using acetate as carbon source.
Transcriptomic and proteomic approaches revealed that 330 genes and 217 proteins were differentially expressed in M68 compared to S1H, indicating that several operons were QS-regulated i.e. flagellar assembly, chemotaxis, photosynthesis, electron transport, stress proteins. These results showed the importance of a functional QS system in R. rubrum.

overall_design: Comparison of the expression of two R. rubrum cultures

first: Sandra

last: Condori Catachura

first: Natalie

last: Leys

first: Felice

last: Mastroleo


title: Application of a NanoString Technology-based TP53 Functional Assay for Prediction of Chemotherapy Response of Muscle-invasive Bladder Cancer

city: Sacramento

first: Clifford

middle: G.

last: Tepper

state: CA

address: 4645 2nd Avenue, Room 2300A

department: Biochemistry and Molecular Medicine

institute: UC Davis School of Medicine

summary: Platinum-based treatment (e.g., cisplatin, carboplatin) is generally the first-line chemotherapy for muscle-invasive bladder cancer (MIBC) and mediates regression in approximately 50% of the patients. The goal of this study was to improve the response rate to platinum-based treatment by developing a genomics-based method capable of classifying MIBC patients as being either likely to respond to therapy versus not likely to respond. Aberrations in TP53 and its downstream effectors play a key role in promoting bladder cancer progression, however, TP53 mutation status is neither an independent indicator of treatment response nor survival in MIBC. The hypothesis of this study was that evaluating overall TP53 function would be informative in predicting responsiveness to therapy. Towards this goal, we developed a custom-designed “TP53 functional miRGE assay”, which assesses TP53 function by simultaneously measuring the expression of 105 TP53-responsive mRNAs and miRNAs using NanoString nCounter technology. Expression profiling was performed on a panel of 34 therapy-naïve MIBC specimens with known outcomes of either being responsive or resistant. Clustering analysis identified a 7-gene subset of TP53 network genes (BAK1, BAX, BBC3, CDKN1A, MDM2, PMAIP1, TP53), which identified patients who did not respond to chemotherapy with 92.3% accuracy. Furthermore, higher TP53 function was associated more with resistant MIBCs in that these exhibited higher relative expression of TP53 target genes. Our results demonstrate a 7-gene TP53 functional assay using NanoString technology has the potential to predict patient response to platinum-based chemotherapy, and that validation of this method using a larger patient sample set is warranted.

overall_design: Muscle-invasive bladder cancer (MIBC) samples were obtained from patients prior to neoadjuvant chemotherapy (NAC) in accordance with a UC Davis Institutional Review Board (IRB)-approved protocol. The specimens were then processed for standard pathologic analysis, and total RNA was isolated from the formalin-fixed paraffin-embedded (FFPE) specimens. Total RNA samples (150 ng) were analyzed with a custom-designed miRGE assay CodeSet for expression profiling of TP53 pathway mRNAs (n=96) and miRNAs (n=10) using an nCounter Analysis System (NanoString Technologies, Seattle, WA), which performs all processing steps, including target and reporter probe hybridization, probe-target tripartite complex purification and immobilization, and counting. The raw data for each sample were output as Reporter Code Count (RCC) files that contain the counts for each gene in the sample. Data analysis was performed with nSolver Software (NanoString Technologies) and the following processing steps: quality control (i.e., for imaging, binding density, positive control linearity, and positive control limit of detection), background subtraction (negative control subtraction), normalization (geometric mean), fold change estimation, and agglomeration clustering. Samples that required a normalization factor of >10 were flagged and removed from further analysis.

middle: G

first: Ralph

middle: W

last: de Vere White


title: Transcript profiling of Pinus sylvestris trees as a response to Heterobasidion annosum infection under field conditions

city: Helsinki

first: Tommaso

last: Raffaello

address: Latokartanonkaari 7 PO Box 27

department: Forest Sciences

institute: University of Helsinki

summary: In conifer forests of Northern Europe, a pathogenic fungus Heterobasidion annosum attacks the roots of Scots pine and causes mortality. Trees with infection grow slower and produce less timber with reduced quality. Despite applied control methods, such as switching tree species to a non-host species, or stump treatment, root and butt rot continues to be a serious forest health problem. Disease resistance breeding is a less-applied control method which has potential to improve tree health. However, neither conifer genotypes with absolute resistance to Heterobasidion sp. nor robust selection markers for resistance breeding have been found. We studied the responses of various Scots pine genotypes to Heterobasidion annosum infection and mechanic damage in drained peatland. Stems and roots of mature naturally regenerated Scots pine trees growing in drained peatland were either artificially infected with H. annosum or wounded and inoculated with sterile inoculum. Untreated trees from the study sites served as controls. Responses of different Scots pine genotypes to pathogen infection as determined by lesion size were recorded from samples harvested four months after inoculation, and least susceptible and highly susceptible genotypes were selected from the study material. Analysis of terpenoids from both least susceptible and highly susceptible pine genotypes by gas chromatography coupled with mass spectrometry indicates that some monoterpenes and sesquiterpenes are differentially induced depending on the susceptibility level. Transcriptomic microarray analysis was therefore conducted with RNA from stems of the least susceptible and highly susceptible Scots pine genotypes. Gene expression data from cDNA microarray were analysed by comparisons between the treatments, and the genotypes with different resistance level. The aim of the study is to highlight transcripts specific to differing levels of susceptibility.

overall_design: We performed 24 hybridizations (NimbleGen) with samples derived from untreated trees (control) growing in drained peatland (3 replicates) and in mineral soil (3 replicates), artificially wounded trees growing in drained peatland (3 replicates) and in mineral soil (3 replicates), artificially infected trees growing in drained peatland (3 replicates) and in mineral soil (3 replicates). Replicate samples originate from the same individual tree. Samples were harvested 4 months after the inoculations. All samples were labeled with Cy3.

first: Susanna

last: Keriö

first: Andriy

last: Kovalchuk

first: Emad

last: Jaber

first: Walter

last: Lorenz

first: Jarmo

last: Holopainen

first: Jeffrey

last: Dean

first: Fred

last: Asiegbu


title: Human neural progenitor cell differentiation in vitro

city: Seattle

first: Elaine

middle: M.

last: Faustman

state: WA

address: 4225 Roosevelt Way NE, #100

department: Environmental and Occupational Health Sciences

institute: University of Washington

summary:
This experiment was designed to characterize the temporal gene expression dynamics of differentiating human neural progenitor cells through time in culture.
In vitro models of neuronal differentiation are emerging as an important tool for high-throughput and high-content screening in neurodevelopmental toxicology. However, little has been done to characterize normal temporal pathway dynamics of differentiation in vitro or to anchor processes captured in vitro to developmental processes in vivo that are vulnerable to toxicant perturbation. We cultured human neural progenitor cell (hNPCs) up to 21 days in differentiation conditions, examining changes in morphology, protein expression and global gene expression. Over time, hNPCs acquired morphological characteristics of mature neuronal networks and increased protein expression of neuronal markers, including beta tubulin III, MAP2, and alpha-synuclein. Significantly changed genes were organized according to temporal expression patterns using K-means clustering, revealing 3 phases of gene expression. Quantitative pathway analysis identified gene ontology (GO) terms enriched among genes expressed in each of these phases and created a quantitative summary of temporal pathway trends in vitro. These observations of morphology, protein and gene expression provide a timeline of progression through differentiation, facilitating identification of key phases of sensitivity. We compared gene expression in vitro with publicly available gene expression data from developing human brain tissue in vivo and found substantial concordance in relative gene expression intensity. Genes highly expressed in both samples were enriched for key processes of brain development, including proliferation, migration, differentiation, synapse formation, and neurotransmission. GO terms enriched among genes highly expressed only in vivo or only in vitro reveal important differences between systems. For example, genes highly expressed in vitro are enriched for more stress and apoptosis pathways. This analysis provides a temporal roadmap of in vitro neuronal differentiation and anchors gene expression patterns in vitro to gene expression during sensitive windows of in vivo development. By anchoring in vitro dynamics to in vivo reference points, this work clarifies the extent to which fundamental processes of brain development are captured in our model.

overall_design: hNPCs were cultured in vitro in differentiation conditions. To characterize temporal gene expression dynamics in differentiating cultures, gene expression was measured 0, 1, 3, 7, 14 and 21 days following initiation of differentiation. Three replicate samples from independent experiments were collected for each timepoint.

last: Wegner

first: Ian

last: Stanaway

middle: M


title: Comparison of the in vivo transcriptome of the myometrium exposed to mifepristone vs vehicle

city: Nottingham

first: Marios

last: Georgiou

address: Queen's Medical Centre

department: School of Life Sciences

country: United Kingdom

institute: University of Nottingham

summary:
Circulating progesterone (P4) levels decline before the onset of parturition in most animals, but not in humans. This has led to the suggestion that there is functional withdrawal of P4 action at the myometrial level prior to labor onset. However, to date, no evidence of a loss of P4 function has been provided.
Mifepristone is a mixed progesterone and glucocorticoid receptor antagonist that is frequently used to induce human labor. However, its effect on the myometrial tissue transcriptome hs not been determined. In this study, we aimed to identify the effects of mifepristone treatment on the pregnant myometrium at term in order to better understand the possible mechanisms underlying the loss of P4 function in human labor.

overall_design: Biopsies obtained from non-laboring women at elective Caesarean section at term were dissected into 3x3x3mm^3 explants and plated in DMEM supplemented with penicillin/streptomycin. Explants were immediately treated with ethanol vehicle or 1 µM mifepristone for a period of 9 hours.

first: Ektoras

middle: X

first: Kaiyu

last: Lei

first: Mark

middle: R

last: Johnson

first: Marcos

middle: C

last: Uribe


title: Concentration dependent gene expression in zebrafish embryos after PCE exposure

status: Public on Jan 31 2019

city: Koblenz

first: Andreas

last: Schüttler

address: Am Mainzer Tor 1

department: Department Biochemistry and Ecotoxicology

country: Germany

institute: German Federal Institute of Hydrology

summary: The dataset contained concentration course exposures of 24hpf old zebrafish embryos with tetrachloroethylene (PCE). The exposure duration was set to 12h and 24h and the concentrations were chosen to be not higher than the LC10.

overall_design: Zebrafish embryos were treated with 6 different concentrations of PCE. Two biological replicates were analyzed regarding the treatment and 4 replicates for untreated embryos for each exposure duration. One replicate of each treatment was additionally treated with a constant concentration of a nanomaterial (Carbo Iron 10 mg/l) which was proven to cause no effects at all at the lethal and sublethal level (including the gene expression).

first: Wibke

last: Busch


title: Role of HBO1 (KAT7/MYST2) in ovarian cancer cell line OVCAR-3

first: Paul

last: Webb

summary: Analysis of change in transcriptosome after HBO1 knockdown in OVCAR-3 ovarian cancer cell line

overall_design: Total RNA was obtained from OVCAR-3 cell line, transfected with siCtrl and siHBO. siHBO1 samples were compared to siCtrl samples.

first: Webb

last: Paul

first: Quintela

last: Marcos


title: Epigenetic regulation of NfatC1 transcription and osteoclastogenesis by nicotinamide phosphoribosyl transferase in the pathogenesis of arthritis

city: Kansas City

first: Daniel

middle: Paul

last: Heruth

state: MO

address: 4th Floor PRC, 2401 Gillham Road

department: Pediatrics

institute: Children's Mercy

summary: Nicotinamide phosphoribosyltransferase (NAMPT) functions in NAD synthesis, apoptosis, and inflammation. Dysregulation of NAMPT has been associated with several inflammatory diseases, including rheumatoid arthritis (RA). The purpose of this study was to investigate NAMPT’s role in arthritis using mouse and cellular models. Collagen-induced arthritis (CIA) in DBA/1J Nampt+/- mice was evaluated by ELISA, micro-CT and RNA-sequencing (RNA-seq). In vitro Nampt loss-of-function and gain-of-function studies on osteoclastogenesis were examined by TRAP staining, nascent RNA capture, luciferase reporter assays, and ChIP-PCR. Nampt-deficient mice presented with suppressed inflammatory bone destruction and disease progression in a CIA mouse model. Nampt expression was required for the epigenetic regulation of the Nfatc1 promoter and osteoclastogenesis. Finally, RNA-seq identified 690 differentially expressed genes in whole ankle joints which associated (P<0.05) with Nampt expression and CIA. Selected target was validated by RT-PCR or functional characterization. We have provided evidence that NAMPT functions as a genetic risk factor and a potential therapeutic target to RA.

overall_design: Paired-end sequencing of RNA isolated from whole ankle joints of Nampt+/+ and Nampt+/- mice with and without CIA

first: Xuanan

last: Li

first: Shamima

last: Islam

first: Min

last: Xiong

first: Ndona

middle: N

last: Nsumu

last: Lee Jr

first: Li

middle: Q

last: Zhang

first: Yasuyoshi

last: Ueki

middle: P

first: Guang

middle: H

first: Shui

last: Ye


title: Interferon and inflammasome networks are associated with lower neutralizing antibody responses to Yellow Fever vaccination

city: Cleveland

first: Ali

last: Filali

address: 10900  Euclid Avenue

department: Pathology

institute: CWRU

summary: The immune response to vaccines is critically dependent on multiple host and environmental factors including acute and chronic infections as well as metabolic and/or pathophysiological states of the host. In this study, we used computational systems biology to analyze a cohort of Ugandan subjects following immunization with the Yellow Fever vaccine (YF-17D) to identify pre-vaccination molecular and cellular mechanisms that are associated with the response to the vaccine. By integrating gene expression profiling, cell subset phenotyping and cytokine measurements, we highlight the upregulated levels of interferon-regulated, and inflammasome genes and proteins at the time of vaccination as negative correlates of the antibody response to the YF-17D vaccine. We show that this innate immune response is associated with higher levels of genes that interact  with bacterial components and with increased frequencies of Tr1 CD39+  IL-10 producing cells. Our results provide a framework to define the influence of environmental parameters present prior to vaccination on the response to vaccines in human populations

overall_design: Pre-vaccination transcriptomic profiling and other immune parameters have been investigated in association with   the immune response, at Day 80 post vaccination, to Yellow Fever vaccine (YF-17D) in a cohort of 36  recruited in Entebee (Uganda)

first: A

last: Filali-Mouhim

first: G

last: Canderan

first: F

last: Lefebvre

first: E

last: Muyanja

first: P

last: Cartwright

first: R

last: Balderas

first: M

last: Cameron

middle: K

last: Haddad

first: L

last: Trautmann

last: Kaleebu

last: Sabbagh

last: Fast

last: Sekaly


title: Analysis of vastus lateralis muscle from 30 human subjects classified by metabolic flexibility

city: Baton Rouge

first: Jaycob

last: Warfel

state: Louisiana

address: 6400 Perkins Road

department: RNA Homeostasis

institute: PBRC

summary: To determine the transcriptomic effects on skeletal muscle gene expression between metabolically flexible and inflexible subjects, we assessed vastus lateralis muscle from 15 males and 15 females using a serial analysis of gene expression strategy. Complementary bioinformatics pathway enrichment studies were performed which indicated that differentially expressed genes between genotypes were predominantly related to various processes include carbohydrate metabolism, lipid metabolism, amino acid metabolism, cell proliferation, and apoptosis.

overall_design: Vastus laterlis muscles were taken from 30 human subjects classified as either metabolically flexible or inflexible based upon differences between 24hr and sleep respiratory quotient. Total RNA was prepared using Trizol, RNA concentration was determined usign a nanodrop UV spectrophotometer, and 500ng RNA per sample was used for sequencing library construction.

first: Bolormaa

last: Vandanmagsar

first: Shawna

middle: E

last: Wicks

first: Robert

last: Noland

first: Randall

middle: L

last: Mynatt

first: Sujoy

last: Ghosh

first: Susan

middle: S

last: Newman

first: Richard

last: Carmouche

first: Claudia

last: Kruger

first: J

last: Salbaum

first: Eric

last: Ravussin


title: Transcriptome Profile of Cultured Adult Mouse Cardiomyocytes Overexpressing JP2 or JP2NT

city: Iowa City

first: Long-Sheng

last: Song

state: Iowa

address: 285 Newton Road

department: Department of Internal Medicine

institute: University of Iowa

summary: Calpain mediated cleavage transforms the full-length junctophilin 2 (JP2) from a structural protein into a transcriptional regulator (JP2 N-terminal trancate - JP2NT). We used affymetrix Genechip to reveal the differentially expressed transcripts induced by overexpression of JP2NT and JP2 in adult cultured mouse cardiomyocytes.

overall_design: Adult mouse ventricle cardiomyocytes were isolated and cultured. JP2 and JP2NT were expressed in these cells via Adenovirus. Empty adenovirus infected cells were used as control.

first: Ang

last: Guo

first: Yunhao

last: Wang

first: Fenghuang

last: Zhan


title: Bioenergetic Activity is Correlated with Apomeiosis in Sorghum Ovules

status: Public on Jan 30 2019

city: Logan

first: John

middle: G.

last: Carman

state: UT

address: 4820 Old Main Hill

department: Plants, Soils and Climate Department

institute: Utah State University

summary: Apomixis in angiosperms terminates sexual reproduction and produces a clonal egg (apomeiosis), which undergoes parthenogenesis, and an embryo sac, which produces endosperm with or without fertilization. Progeny of apomictic plants are maternal, a property viewed by seed producers as a potential tool for producing hybrid seed. Apomixis does not occur in major crops, but sexual termination and apomeiosis (aposporous embryo sac formation) do occur in certain sorghum lines at low frequencies. We identified in sorghum differentially expressed genes (DEG) and significant gene ontology (GO) categories that differentiated ovules of an aposporous (13.6 %) F2 sib from those of a sexual F2 sib at the megasporocyte to early embryo sac formation stages. GO terms indicated that ovules of the aposporous sib experienced elevated glucose levels. These induced ethylene and glucose signaling cascades that appeared to activate the growth modulator TORC1 by silencing the energy sensor SnRK1 and by producing reactive oxygen species scavengers that silenced the stress sensor SnRK2.

overall_design:
Saturated loop design: two sibs from an F2 population, 151 and 264, with 13.6 and 0.0 % aposporous embryo sac formation, respectively (BMC Plant Biol 11, 9. doi: 10.1186/1471-2229-11-9) were selected for gene expression profiling of ovule tissues. Twenty tiller-propagated clones of each were grown. Three germline stages were chosen for profiling: early MMC, early meiocyte, and mid ES stages. Ovules were excised from pistils, and 30 samples (90-150 ovules each), five for each sib by stage combination, were collected for a total of 601, 699 and 499 ovules and 508, 604 and 499 ovules for the MMC, meiocyte and early ES stages of sexual sib 264 and aposporous sib 151, respectively. A saturated loop design was used to distribute the 30 sib/stage/replication samples (2:3:5) evenly among the 15 arrays.
both channels of the array were used for data collection.


title: Transcriptomic analysis of Baltic cod (Gadus morhua) liver infected with Contracaecum osculatum third stage larvae indicates parasitic effects on growth and immune response

city: Copenhagen

first: Huria

last: Marnis

address: Stigbøjlen 7

department: Veterinary and Animals science

country: Denmark

institute: Copenhagen university

summary:
Purpose: To investigate any association between parasite infection and physiological status of the host we performed a comparative transcriptomic analysis of liver obtained from C. osculatum infected and non-infected cod.
Methods: Samples for transcriptomic analyses were collected from cod caught by local fishermen.  Infected cod: Live cod (ten specimens) obtained by trawling along the Coastline of Bornholm were brought ashore (Nexø, Bornholm island, Denmark) and stocked in fish tanks (volume 8 cubic meter) supplied with running saltwater from the Baltic (salinity 8 ppt, temperature 10 °C). Non-infected cod: Live cod (ten specimens) were caught on the coastline of Zealand and stocked in similar fish tanks at the fish keeping facility (Blue Planet, Kastrup, Denmark). Total RNA was extracted using RTN350 (Sigma-Aldrich), according to the manufacturer’s instruction and subsequently, DNase treated with DNase I (Thermo Scientific, USA). Quality and integrity of the total RNA were checked on an Agilent Bioanalyzer 2100 total RNA Nano series II chip (Agilent, Amstelveen, Netherlands). Illumina RNAseq libraries were prepared from 500 ng total RNA using the Illumina TruSeqTM Stranded mRNA LT Sample Prep Kit according to the manufacturer’s instructions (Illumina Inc. San Diego, CA, USA). All RNAseq libraries (150-750 bp inserts) were sequenced on an Illumina HiSeq2500 sequencer as 1 x 50 nucleotides single-end reads according to the manufacturer’s protocol. Image analysis and base calling were done using the Illumina pipeline. Reads were aligned to the Rainbow trout reference genome (http://www.genoscope.cns.fr/trout/data/) using TopHat (version 2.0.5) and on average 53.4% of the RNAseq reads could be mapped. The resulting files were filtered using SAMtools (version 0.1.18) to exclude secondary alignment of reads. For statistical comparison of gene expression levels between groups, aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq (version 0.5.3p9). To make comparisons across samples possible, these fragment counts were corrected for the total amount of sequencing performed for each sample. As a correction scalling factor, we employed library size estimates determined using the R/Bioconductor (release 2.11) package DESeq. Read counts were normalized by dividing the raw counts obtained from HTSeq by its scale factor. Correction for false positives is included in the statistical analysis of gene expression through DESeq. The cut-off for significance was set to adjusted p<0.05 and at least 2-fold change.
Results: A total of 47,025 unigenes were identified from cod liver, of which 2,085 (4.43%) unigenes were differentially expressed in the infected liver when compared to non-infected. Of the differentially expressed unigenes (DEGs) 1,240 unigenes were up-regulated while 796 were down-regulated. The Gene Ontology (GO) enrichment analysis showed that 845 DEGs were highly represented in cellular process and single-organism process, cell and cell part, binding and catalytic activity. As determined by the Kyoto Encyclopedia of Gene and Genomes (KEGG) Pathways analysis, 241 DEGs were involved in 753 pathways. Eighty DEGs were related to metabolic pathways including carbohydrate, lipid, and amino acid metabolism. Twenty-four regulated genes were playing a role in immune response such as complement and coagulation cascades, B-cell receptor signalling, chemokine signalling and twenty-five genes (most of which were down-regulated) were associated with growth of Baltic cod
Conclusion: a transcriptomic profile of rainbow trout gills exposed to the parasitic I. multifiliis was reported for the first time. A total of 3,355 differentially expressed unigenes were identified. Of these were 1,184 unigenes (mapped to 952 genes) annotated 282 KEGG pathways and 268 unigenes were associated with 16 immune pathways. Most unigenes were related to innate immune system pathways (Chemokine signaling pathway, Platelet activation, Toll-like receptor signaling pathway, NOD-like receptor signaling pathway, and Leukocyte transendothelial migration) although a number of unigenes was related to adaptive responses (antigen processing and presentation, T and B cell receptor signaling pathway). The present study gave a far better resolution of the immune response of rainbow trout exposed to a parasitic protozoan than has ever been presented previously. The identification of a series of immune genes involved in several but important was useful for understanding of immune mechanism of the rainbow trout responding to the parasite I. multifiliis. Our results provide tools to link innate and adaptive immune elements in the process and present basic information which will be useful in the future studies related to immunoprophylaxis.

overall_design: Transcriptome profiling of Baltic cod liver infected by Contracaecum osculatum was generated by Next Generation Sequencing, in 10 replicates, using Illumina HiSeq2500 sequencer.

first: Per

last: Kania

first: Khairul

last: Syahputra

first: Shaozhi

last: Zuo

first: Ron

last: Dirks

first: Kurt

last: Buchmann


title: Development of high-density genetic map by transcriptome sequencing

city: Changsha

first: Touming

last: Liu

address: NO.348, western road of xianjia lake

department: Institute of Bast Fiber Crops

institute: Chinese Academy of Agricultural Sciences

summary: Ramie is an important industrial fiber crop, and the fiber yield and its related traits are the most valuable traits in ramie production. However, the genetic basis for these traits is still poorly understood. Herein, a high-density genetic map with 1085 markers spanning 2,118.8 cM was constructed using a population derived from two parents, cultivated ramie Zhongsizhu 1 (ZSZ1) and its wild progenitor B. nivea var. tenacissima (BNT). The fiber yield (FY) and its four related traits—stem diameter (SD) and length (SL), stem bark weight (BW) and thickness (BT)—were performed for quantitative trait locus (QTL) analysis, resulting in eight, six, six, three, and ten QTLs for SD, SL, BW, BD and FY traits, respectively. These 33 QTLs were mapped into 11 genomic regions, thus forming 11 QTL clusters; there were 11 QTLs identified their beneficial alleles from the wild species BNT. Interestingly, all QTLs in Cluster 8 and Cluster 10 displayed overdominance, indicating that these two regions were likely heterotic loci. In addition, there were five fiber yield-related genes identified to undergo positive selection in previous study, and they were found to locate into the genomic region near to the QTLs of this study. The genetic dissection for FY and its related traits improved our understanding to the genetic basis of these traits, as well to their domestication in ramie. The identification of many QTLs and the discovery of beneficial alleles from wild species provided a basis for the improvement of yield traits in ramie breeding.

overall_design: The clean reads from the transcriptome of 111 F2 families and two parents were aligned to the ramie genome, then to identify SNPs and develop genetic map.


title: Transcriptome analysis of Novosphingobium sp. THN1 during  microcystin-LR degradation under different carbon concentrations

city: Wuhan

first: Juanping

state: Hubei

address: No. 7 Donghu South Road, Wuchang District

institute: Institute of Hydrobiology, Chinese Academy of Sciences

summary: The bacterium Novosphingobium sp. THN1 (THN1) is capable of degrading microcystin-LR (MCLR). To get an insight into genes expression during MCLR degradation and  the regulation of different carbon concentrations on MCLR degradation, we performed RNA-seq of THN1 during MCLR degradation under different carbon concentrations.

overall_design: Transcriptomes of THN1 at 2h and 0h of MCLR degradation under R2A and 40%C_R2A medium were generated by deep sequencing, in triplicate, using Illumina Hiseq.


title: Transcriptome sequencing to unravel the molecular mechanisms underlying the cuticle liquefaction of Antheraea pernyi following Antheraea pernyi nucleopolyhedrovirus challenge

city: Weifang

first: Wang

last: Guobao

address: No.5147 Dongfeng East Street

institute: Weifang University

summary:
Purpose:  The goal of this study is to analyze  the transcriptome profile changes of the cuticles between ApNPV-infected and non-infected A. pernyi larvae for investigating themolecular mechanisms of cuticle liquefaction of A. pernyi induced by ApNPV infection.
Methods:The A. pernyi cuticles infected by ApNPV and normal samples were generated by deep sequencing, in triplicate, using Illumina Hiseq 4000. The high-quality reads were obtained by removing the reads that contained adaptor contamination, low quality bases and undetermined bases.The  transcriptome were de novo assembly.
Results:The RNA-seq data generated 57332226, 48859400, 50197630 and 52086538, 52447736, 47585326 raw reads from ApNPV-infected and control groups, respectively. After data filtering, 55715544, 48130252, 49354556, 51102012, 51633978, 46798094 clean reads were obtained (Table1). Using the Trinity de novo assembly programme, all short-read sequences were assembled into 87036 transcripts and 50126 unigenes.
Conclusions:We systematically analyzed the gene expressional profiles and obtained both up- and down-regulated genes in ApNPV-infected cuticle compared with control. Meanwhile, we screened the chitin metabolism-related differentially expressed genes (DEGs) from the transcriptome data, and further characterized those DEGs based on their expression profiles challenged by ApNPV. Our research findings lay the foundation for further research on the molecular mechanisms of liquefaction induced by viral infection in insect.

overall_design: The  cuticle mRNA profiles of ApNPV-infected/Control were generated by deep sequencing, in triplicate, using Illumina Hiseq 4000.

first: Guobao

first: Shuang

first: Li

last: Qin


title: Transcriptomic analysis of Quercus mongolica leaves: de novo assembly, functional annotation and molecular markers mining

status: Public on Jan 29 2019

summary:
Purpose:  The goal of this study is to provided a comprehensive genomic information for functional genomic studies in Q. mongolica.
Methods:The  Quercus mongolica leaves were generated by deep sequencing, using Illumina Hiseq 4000. The high-quality reads were obtained by removing the reads that contained adaptor contamination, low quality bases and undetermined bases.The  transcriptome were de novo assembly.
Results:A total of 52934562 raw reads were obtained from Illumina sequencing platform. After filtering out the low quality reads, we obtained 52076914 clean reads, which assembled into 39130 transcripts with a mean length of 742 bp and GC content of 42.12%, and 24196 unigenes with a mean length of 732 bp and GC content of 42.34%, based on Trinity assembly platform.
Conclusions:RNA-Seq was applied to polyadenylate-enriched mRNAs from leaves of Q. mongolica to obtain the transcriptome. De novo assembly was then applied followed by gene annotation and functional classification. The SSRs and SNPs were also obtained using assembled transcripts as reference sequences. The results of this study lay the foundation for further research on genetic diversity of Quercus.

overall_design: The mRNA profile of Quercus mongolica leaf was generated by deep sequencing using Illumina Hiseq 4000.


title: Unravelling the cellular and humoral immune responses of Antheraea pernyi hemolymph to Antheraea pernyi nucleopolyhedrovirus infection

summary:
Purpose: With the advent of next generation sequencing technologies, several researches have been focused on the molecular mechanism underlying the innate immunity of insects based on the changes of gene expression profiles in hemolymph. The goal of this study is to detect the differences in transcript levels in A. pernyi hemolymph in response to ApNPV.
Methods:The A. pernyi hemolymph infected by ApNPV and normal samples were generated by deep sequencing, in triplicate, using Illumina Hiseq 4000. The high-quality reads were obtained by removing the reads that contained adaptor contamination, low quality bases and undetermined bases.The  transcriptome were de novo assembly.
Results:We constructed six cDNA libraries using RNA samples from the hemolymph in ApNPV-infected and non-infected A. pernyi larvae with three replicates for each group. A total of 50459962, 49797542, 54402474 and 56342454, 56036432, 55471402 raw reads in ApNPV-infected and control groups were generated. After filtering, 48009732, 47241848, 51319586 and 53555764, 53364108, 53077540 clean reads were obtained. All short-read sequences were assembled into 49966 transcripts and 37498 unigenes.
Conclusions: The transcriptome sequences were de novo assembled. The differentially expressed genes (DEGs) including both up- and down-regulated genes were obtained. We focused on the innate immunity related DEGs, and screened numerous of DEGs involved in cellular and humoral immune related pathways via bioinformatic analysis. The results of this study lay the foundation for a better understanding of the molecular mechanisms of cellular and humoral immunity of A. pernyi.

overall_design: The  hemolymph mRNA profiles of ApNPV-infected/Control were generated by deep sequencing, in triplicate, using Illumina Hiseq 4000.


title: Identification of drought resistance related factors in Quercus liaotungensis leaf via transcriptome sequencing

summary:
Purpose:  The goal of this study is to screen the candidate genes involved in drought avoidance of Q. liaotungensis
Methods:The  Q. liaotungensis leaves were generated by deep sequencing, using Illumina Hiseq 4000. The high-quality reads were obtained by removing the reads that contained adaptor contamination, low quality bases and undetermined bases.The  transcriptome were de novo assembly.
Results:A total of 54153182 raw reads were obtained from Illumina sequencing platform, and 53021436 clean reads were generated after filtering out the low quality reads. The clean reads were assembled into 41207 transcripts with median length 704 and GC content 42.17%, and 25593 unigenes with median length 687 and GC content 42.31%, based on Trinity assembly platform
Conclusions:RNA-Seq was applied to polyadenylate-enriched mRNAs from leaves of Q. liaotungensis to obtain the transcriptome. De novo assembly was then applied followed by gene annotation and functional classification. The SSRs and SNPs were also obtained using assembled transcripts as reference sequences. The results of this study lay the foundation for further research on genetic diversity of Quercus.

overall_design: The mRNA profile of Q. liaotungensis leaf was generated by deep sequencing using Illumina Hiseq 4000.


title: Differential expression of miRNAs in IFN-gamma treated SWAN-71 versus untreated control by next generation sequencing

city: New Delhi

first: Satish

middle: Kumar

last: Gupta

address: Aruna Asaf Ali Marg

institute: NAtional Institute of Immunology

type: Non-coding RNA profiling by high throughput sequencing

summary: The goal of this study is to compare miRNAs expressed by IFN-gamma treated SWAN-71 cells to miRNAs expressed in untreated control SWAN-71 cells to identify micro RNAs which play a role during IFN-gamma-mediated SWAN-71 cells invasion

overall_design: cDNA libraries were made from total RNA of untreated control and 24 h IFN-gamma treated samples by TruSeq Small RNA Sample prep kit. Deep sequencing of cDNA libraries were performed with the help of Illumina Genome analyzer IIx. Raw sequence data was imported into the CLC Genomics Workbench 6.5.1. The sequence reads were trimmed for adapter sequences and low quality base. The trimmed raw sequences were subjected to miRNA-sequence analysis, by mapping them to miRBase release 21.

last: Kumar Gupta

first: Sonam

last: Verma


title: Differential expression of miRNAs in HGF treated SWAN-71 versus untreated control by next generation sequencing

summary: The goal of this study is to compare miRNAs expressed by HGF treated SWAN-71 cells to miRNAs expressed in untreated control SWAN-71 cells to identify micro RNAs which play a role during HGF-mediated SWAN-71 cell invasion

overall_design: cDNA libraries were made from total RNA of untreated control and 24 h HGF treated samples by TruSeq Small RNA Sample prep kit. Deep sequencing of cDNA libraries were performed with the help of Illumina Genome analyzer IIx. Raw sequence data was imported into the CLC Genomics Workbench 6.5.1. The sequence reads were trimmed for adapter sequences and low quality base. The trimmed raw sequences were subjected to miRNA-sequence analysis, by mapping them to miRBase release 21.

first: Piyush

last: Chaudhary


title: Gene expression in Jurkat T cell lines

city: London

first: Paul

last: Lavender

address: 5th Floor, Tower Wing, Great Maze Pond

department: School of Immunology and Microbial Sciences

institute: King's College London

summary: Jurkat cell lines were generated to stably express CD46 protein expressing either cytoplasmic tail 1 or 2 (BC1  or BC2). The transcription profile of these unactivated stable lines were compared with unactivated Jurkat cells.

overall_design: Toral RNA was isolated and gene array analyses pereformed as technical replicates of three.

first: Claudia

last: Kemper


title: Vav Knockout in Raw264.7 macrohages

city: Xinxiang

first: Rong

last: Huang

address: 601 Jinsui Road

institute: Xinxiang Medical University

summary:
The scavenger receptor CD36 plays critical roles in lipid uptake and triggering of inflammatory response, via activation of guanine nucleotide exchange factor Vav.
We used microarrays to detail the different up-regulated or down-regulate genes among three vav familymembers.

overall_design: 12 samples are analyzed.Sample 1-3 are Vav1 Knockout cells.Sample 4-6 are Vav2 Knockout cells.Sample 7-9 are Vav3 Knockout cells.Sample 10-12 are Wildtype Raw264.7 cells as control group.

first: Liaoxun

last: Lu


title: Differential expression of miRNAs in HGF treated HTR-8/SVneo versus untreated control by next generation sequencing

summary: The goal of this study is to compare miRNAs expressed by HGF treated HTR-8/SVneo cells to miRNAs expressed in untreated control HTR-8/SVneo cells to identify micro RNAs which play a role during HGF-mediated HTR-8/SVneo cells invasion


title: Differential expression of miRNAs inEGF treated SWAN-71 versus untreated control by next generation sequencing

summary: The goal of this study is to compare miRNAs expressed by EGF treated SWAN-71 cells to miRNAs expressed in untreated control SWAN-71 cells to identify micro RNAs which play a role during EGF-mediated SWAN-71 cell invasion

overall_design: cDNA libraries were made from total RNA of untreated control and 24 hEGF treated samples by TruSeq Small RNA Sample prep kit. Deep sequencing of cDNA libraries were performed with the help of Illumina Genome analyzer IIx. Raw sequence data was imported into the CLC Genomics Workbench 6.5.1. The sequence reads were trimmed for adapter sequences and low quality base. The trimmed raw sequences were subjected to miRNA-sequence analysis, by mapping them to miRBase release 21.

first: Ankita

last: Malik


title: RNA-seq analysis of FACS-sorted control and Tsc2 cKO nociceptors with and without sciatic nerve crush

status: Public on Jan 26 2019

city: St Louis

first: Dan

last: Carlin

address: 660 S Euclid Ave / Campus Box 8108

department: Neuroscience

institute: Washington University in St Louis

summary: The goals of this study are to compare the transcriptomes of control heterozygous and Tuberous sclerosis 2 (Tsc2) homozygous nociceptors 3 days after sciatic nerve injury that have been enriched by fluorescence-associated cell sorting (FACS) with the aim of identifying differences in genes associated with axon regeneration. Nav1.8-Cre transgenic mice were used to delete Tsc2 as well as express Green fluorescent protein from the Rosa26 locus. Tsc2 deletion constitutively activates mTORC1 signaling cell autonomously. Dissociated dorsal root ganglia from adult mice were FACS-sorted for GFP and analyzed by RNA-seq. We find that the expression of a number of regeneration-associated transcription factors including cJun, Atf3, Sox11 and other are upregulated in Tsc2 mutant neurons in the absence of an injury. Additionally, the target genes of several other normally expressed regeneration-associated transcription factors are differentially expressed in Tsc2 mutant neurons, such as Creb1 and Klf’s. We conclude Tsc2 deletion and consequent mTORC1 activation establishes a pro-regenerative gene expression profile in nociceptors in the absence of an injury.

overall_design: L4 dorsal root ganglia contralateral and ipsilateral to sciatic nerve crush were harvested 3 days post-injury from mice with Nav1.8-Cre mediated expression of GFP from Rosa26 locus as well as heterozgous (control) or homozygous (cKO) deletion of Tsc2 were FACS-sorted by GFP expression for 3 technical replicates of 100 cells each. RNA-seq data from 4 biological replicates was collected.

first: Alexandra

last: Halevi

first: Eric

last: Ewan

first: Amy

last: Moore

first: Valeria

last: Cavalli


title: Regulation of lineage segregation, pluripotency and X chromosome inactivation in the pig revealed by scRNA-Seq

first: Fei

last: Sang

address: QMC

summary: we report single cell expression profiles of embryonic cells (from day 5 to 11) of pig embryo development.

overall_design: single cell transcriptomes were generated from 220 cells obtained from 28 embryos (15 male and 13 female)

first: Ramiro

last: Alberio


title: Differential expression of miRNAs in IFN-gamma treated HTR-8/SVneo versus untreated control by next generation sequencing

summary: The goal of this study is to compare miRNAs expressed by IFN-gamma treated HTR-8/SVneo cells to miRNAs expressed in untreated control HTR-8/SVneo cells to identify micro RNAs which play a role during IFN-gamma-mediated HTR-8/SVneo cells invasion


title: Mycobacterium tuberculosis response to environmental potassium

city: Boston

first: Shumin

last: Tan

state: MA

address: 150 Harrison Ave

department: Molecular Biology and Microbiology

institute: Tufts University School of Medicine

summary: The purpose of this study was to identify genes that are differentially expressed under conditions of potassium limitation, to elucidate how Mycobacterium tuberculosis (Mtb) senses and responds to ionic changes, and the role of these responses in host colonization.

overall_design: Mtb strain CDC1551 wild type was grown to an OD600 of 0.6 in standing vented T-75 flasks before being subcultured to an OD600 of 0.3 in standing vented T-25 flasks of either standard 7H9, pH 7 or 0 mM K+ 7H9, pH 7 media. Exposure was for 4 hours in a humidified, 37C, 5% CO2 incubator before RNA was extracted. RNA was prepared by removing the rRNA and library prepping with a TruSeq Stranded kit (Illumina) before high-throughput sequencing with an Illumina HiSeq 2500 (High Output v4) (100 bp single end reads, one lane). Two biological samples per condition were sequenced.

first: Nathan

middle: J

last: MacGilvary


title: A halotolerant growth promoting rhizobacteria triggers induced systemic resistance in plants and defends against fungal infection

city: Bhavnagar

first: Sandeep

last: Sharma

state: Gujarat

address: Waghawadi Road

department: Department of Biotechnology & Phycology

institute: CSIR-CSMCRI

summary: RNA sequencing of peanut roots treated or untreated with rhizobacteria, MBE02

overall_design: mRNA profiles of peanut roots treated with MBE02 rhizobacteria and compared with non-treated control. Two samples for each treatment were processed for RNA sequencing

first: Chen

last: Chen

first: Shree

last: Pandey


title: Expression data from Saccharomyces cerevisiae strains deleted for the nucleoporin Nup84

status: Public on Jan 25 2019

city: Seville

first: Andrés

last: Aguilera

address: Av. Américo Vespucio 24

department: Genome BIology

institute: CABIMER, Universidad de Sevilla

summary:
the nuclear pore complex (NPC) is emerging as an important mediator of cellular processes beyond molecule transport, including control of gene expression, replication and DNA repair.
We used microarrays to study the global impact of Nup84 in gene expression, in particular expression of DNA repair genes.

platform_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

overall_design: S. cerevisiae strains were grown in YPD liquid culture, total RNA was isolated and hybridized on Affymetrix microarrays

first: José

last: Santos-Pereira

first: Hélène

last: Gaillard


title: Single-cell profiling of the myeloid landscape identifies cell subsets with distinct fates during neuroinflammation

city: Freiburg

first: Sagar

address: Hugstetter Straße 55

department: Department of Internal Medicine II

institute: University Medical Center Freiburg

summary: The innate immune cell compartment is highly diverse in the healthy central nervous system (CNS) including parenchymal and non-parenchymal macrophages. However, this complexity is increased in inflammatory settings by the recruitment of circulating myeloid cells. It is unclear which disease-specific myeloid subsets exist and what their transcriptional profiles and dynamics during CNS pathology are. By combining deep single-cell transcriptome analysis, fate mapping, in vivo imaging, clonal analysis, and transgenic lines, we comprehensively characterized unappreciated myeloid subsets in several CNS compartments during neuroinflammation. During inflammation, CNS macrophage subsets undergo self-renewal, and random proliferation shifted towards clonal expansion. Finally, functional studies demonstrated that endogenous CNS tissue macrophages are redundant for antigen presentation. Our results highlight myeloid cell diversity and provide insights into the brain’s innate immune system.

overall_design: CD45+ cells isolated from different CNS compartments (including leptomeninges, perivascular space and parenchyma, and choroid plexus) and Ly6Chigh and Ly6Clow monocytes from blood were FACS-sorted in 384-well plates and used for scRNAseq. All myeloid cells were sorted from C57BL/6N mice with 8-10 weeks of age at naive stage or at different stages of Experimental Autoimmune Encephalomyelitis (preclinical, onset and peak of the disease). Data are representative of 16-18 mice from three independent experiments. mCEL-Seq2 protocol was used for single cell sequencing (Hashimshony et al. 2016, Herman et al. 2018).

first: Marta

last: Costa Jordão

first: Roman

last: Sankowski

last: Sagar

first: Dominic

last: Gruen

first: Marco

last: Prinz


title: DOF2.1 controls vascular cell proliferation downstream of TMO5/LHW

status: Public on Jan 24 2019

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

summary: As plant cells are fixed within their tissue context, a precise control of cell division orientation is crucial to generate complex three-dimensional organs. The transcription factor complex formed by TARGET OF MONOPTEROS5 (TMO5) and LONESOME HIGHWAY (LHW) triggers a change in cell division orientation leading to radial expansion, at least in part by activating local cytokinin biosynthesis. However, it remains unclear how cytokinin controls these oriented cell divisions. Here, we analyzed the transcriptional responses upon simultaneous induction of both TMO5 and LHW in detail. Using inferred network analysis, we identify AT2G28510/DOF2.1 as a cytokinin-dependent downstream target gene of the TMO5/LHW heterodimer complex. We further show that DOF2.1 is specifically required and sufficient for vascular cell proliferation without inducing other cytokinin-dependent effects such as the inhibition of vascular differentiation. In summary, we have identified DOF2.1 as a TMO5/LHW target gene, specifically responsible for controlling vascular cell proliferation leading to radial expansion.

overall_design: 4-day-old pRPS5A::TMO5:GR x pRPS5A::LHW:GR (dGR) plants grown on MS were treated with dexamethasone (DEX) compounds for the indicated time, whereafter root meristems were harvested, and total RNA was isolated that was subjected to gene expression profiling.

first: Wouter

last: Smet

first: Mark

middle: V

last: Boekschoten

first: Bert

last: De Rybel


title: Tracking of epigenetic changes during hematopoietic differentiation of induced pluripotent stem cells

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

institute: RWTH Aachen University

type: Methylation profiling by genome tiling array

summary: Differentiation of induced pluripotent stem cells (iPSCs) toward hematopoietic progenitor cells (HPCs) raises high hopes for disease modelling, drug screening, and cellular therapy. Various differentiation protocols have been established to generate iPSC-derived HPCs (iHPCs) that resemble their primary counterparts in morphology and immunophenotype, whereas a systematic epigenetic comparison was yet elusive. In this study, we compared genome wide DNA methylation (DNAm) patterns of iHPCs with various different hematopoietic subsets. Furthermore, we analyzed if additional co-culture for two weeks with syngenic primary mesenchymal stromal cells (MSCs) or iPSC-derived MSCs (iMSCs) further supports epigenetic maturation toward hematopoietic lineage. After 20 days of in vitro differentiation cells revealed typical hematopoietic morphology, CD45 expression and colony forming unit (CFU) potential. DNAm changes were particularly observed in genes that are associated with hematopoietic differentiation. On the other hand, the epigenetic profiles of iHPCs remained overall very distinct from normal hematopoiesis. Co-culture with MSCs or iMSCs enhanced proliferation of iHPCs and maintenance of CFU potential. However, morphology, immunophenotype, and DNAm profiles did not indicate that additional culture expansion with stromal support increases hematopoietic differentiation. In conclusion, differentiation of iPSCs towards hematopoietic lineage remains epigenetically incomplete. These results substantiate the need to elaborate advanced differentiation regimen while DNAm profiles provide a suitable measure to track this process.

overall_design: DNA from iPSC-derived hematopoietic progenitor cells was isolated after 20 days of differentiation or after additional 14 days of culture expansion on either tissue culture plastic or in co-culture with bone marrow derived MSCs or iPSC-derived MSCs. DNA was bisulfite converted and hybridized to the Illumina Infinium MethylationEPIC BeadChip.

first: Olivia

last: Cypris

first: Joana

last: Frobel

first: Shivam

last: Rai

first: Julia

last: Franzen

first: Stephanie

last: Sontag

last: Goetzke

first: Marcelo

middle: A

last: Szymanski de Toledo

first: Martin

last: Zenke


title: Neuroblast-specific open chromatin allows the temporal transcription factor, Hunchback, to bind neuroblast-specific loci

city: Eugene

first: Sonia

last: Sen

state: OR

address: 1440 Franklin Blvd

department: ION/IMB

institute: University of Oregon

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Integration of spatial and temporal identity during Drosophila neurogenesis is due to spatial factors generating neuroblast-specific chromatin thereby biasing subsequent temporal transcription factor binding and producing neuroblast-specific neurons.

overall_design: Examination of Dam and Dam:Hb binding in two neuroblast lineages

first: Chris

last: Doe


title: Effect of heat stress on mouse testicular peritubular myoid cells [miRNA-seq]

city: Beijing

first: Su-Ren

last: Chen

address: 1Beichen West Road, Chaoyang District

department: State Key Laboratory of Stem Cell and Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

summary: We performed miRNA-Seq of untreated testicular peritubular myoid cells (NC_1, NC_2, NC_3), and peritubular myoid cells that were collected 1 hour (H1_1, H1_2, H1_3) and 6 hours (H6_1, H6_2, H6_3) after heat treatment using BGISEQ-500 platform (BGI, China).

overall_design: The mouse testicular peritubular myoid cells were isolated as our previously described (PMID: 30306767). Heat treatment was performed as our previously described (PMID: 23759306).

first: Su

first: Xiang

last: Wu


title: Site-specific manipulation of Arabidopsis loci using CRISPR-Cas9 SunTag systems

status: Public on Jan 22 2019

city: Los Angeles

first: Ashot

last: Papikian

address: 4045 Terasaki Life Sciences Building

institute: University of California, Los Angeles

type: Methylation profiling by high throughput sequencing

summary: Understanding genomic functions requires site-specific manipulation of loci via efficient protein effector targeting systems. However, few approaches for targeted manipulation of the epigenome are available in plants. Here, we adapt the dCas9-SunTag system to engineer targeted gene activation and DNA methylation in Arabidopsis. We demonstrate that a dCas9-SunTag system utilizing the transcriptional activator VP64 drives robust and specific activation of several loci, including protein coding genes and transposable elements, in diverse chromatin contexts. In addition, we present a CRISPR-based methylation targeting system for plants, utilizing a SunTag system with the catalytic domain of the Nicotiana tabacum DRM methyltransferase, which efficiently targets DNA methylation to specific loci, including the FWA promoter, triggering a developmental phenotype, and the SUPERMAN promoter. These SunTag systems represent valuable tools for the site-specific manipulation of plant epigenomes.

overall_design: 48 BS-seq libraries, 2 ChIP-seq libraries, 72 RNA-seq libraries

first: Wanlu

last: Liu


title: Effect of heat stress on mouse testicular peritubular myoid cells

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

overall_design: Refer to individual Series


title: TET2 binding to enhancers facilitates transcription factor recruitment in hematopoietic cells [ATAC-Seq]

city: Dundee

first: Kasper

middle: Dindler

last: Rasmussen

address: Dow Street

department: Division of Molecular, Cellular, and Developmental Biology (MCDB)

institute: School of Life Sciences, University of Dundee

summary: The epigenetic regulator TET2 is frequently mutated in hematological diseases. Mutations have been shown to arise in hematopoietic stem cells early in disease development, lead to altered DNA methylation landscapes and to an increased risk of hematopoietic malignancy. Here, we show by genome-wide mapping of TET2 binding sites in different cell types that TET2 localizes to regions of open chromatin and cell-type specific enhancers. We find that deletion of Tet2 in native hematopoiesis as well as fully transformed Acute Myeloid Leukemia (AML) results in changes in transcription factor (TF) activity within these regions, and we provide evidence that loss of TET2 leads to attenuation of chromatin binding of members of the basic helix-loop-helix (bHLH) TF family. Together, these findings demonstrate that TET2 activity shapes the local chromatin environment at enhancers to facilitate TF binding and provide a compelling example of how epigenetic dysregulation can affect gene expression patterns and drive disease development.

overall_design: Analysis of chromatin accessibility using ATAC-seq in various cell types with and without TET2 knockout

middle: D

first: Ivan

last: Berest

first: Sandra

last: Kessler

first: Koutarou

last: Nishimura

first: Lucía

last: Simón-Carrasco

first: George

last: Vassiliou

first: Marianne

middle: T

last: Pedersen

first: Jesper

last: Christensen

first: Judith

middle: B

last: Zaugg

first: Kristian

last: Helin


title: TET2 binding to enhancers facilitates transcription factor recruitment in hematopoietic cells [TET2 ChIP-seq ES cells]

overall_design: ChIP-seq analysis of embryonic stem cells expressing wildtype TET2 or a FLAG-tagged TET2 expressed from the endogenous Tet2 locus. TET2 binding sites were defined by enrichment over non-specific ChIP enriched regions identified in Tet2 knockout cells or parental cells without FLAG-tagged TET2.


title: TET2 binding to enhancers facilitates transcription factor recruitment in hematopoietic cells [RNA-Seq]

overall_design: RNA-seq analysis of hematopoietic cells with and without full-length TET2


title: Promoter-proximal pausing mediated by the exon junction complex regulates splicing [HA ChIP]

city: Lausanne

first: Jean-Yves

last: Roignant

address: genopode building

institute: University of Lausanne

summary: Promoter-proximal pausing of RNA polymerase II (Pol II) is a widespread transcriptional regulatory step across metazoans. Here we find that the nuclear exon junction complex (pre-EJC) is a critical and conserved regulator of this process. Depletion of pre-EJC subunits leads to a global decrease in Pol II pausing and to premature entry into elongation. This effect occurs, at least in part, via non-canonical recruitment of pre-EJC components at promoters. Failure to recruit the pre-EJC at promoters results in increased binding of the positive transcription elongation complex (P-TEFb) and in enhanced Pol II release. Notably, restoring pausing is sufficient to rescue exon skipping and the photoreceptor differentiation defect associated with depletion of pre-EJC components in vivo. We propose that the pre-EJC serves as an early transcriptional checkpoint to prevent premature entry into elongation, ensuring proper recruitment of RNA processing components that are necessary for exon definition.

overall_design: HA ChIP in control and Mago-HA tagged S2R+ cells

first: Akhtar

last: Junaid

first: Kreim

last: Nastasja


title: TET2 binding to enhancers facilitates transcription factor recruitment in hematopoietic cells [TET2 ChIP-seq hematopoietic cells]

overall_design: ChIP-seq analysis of hematopoietic cells with and without full-length TET2


title: Gene expression profiling of mesenchymal stem cells from bone marrow of multiple myeloma patients and normal donors

status: Public on Jan 21 2019

city: São Paulo

first: Rodrigo

last: Fernando

state: SP

address: 824 Doutor Diogo de Faria, 5th floor

country: Brazil

institute: Federal University of São Paulo

summary: A growing body of evidence points to the essential role of bone marrow (BM) tumor microenvironment in Multiple Myeloma (MM) maintenance and progression.  Mesenchymal stem cells (MSC) are one of the most important players in this scenario. Through direct and indirect interactions, these cells support MM cells by promoting increase of proliferation, migration, survival, and drug resistance. Additionally, an increasing number of evidence has been demonstrating that MSC from MM patients (MM-MSC) have several abnormalities when compared with their normal counterpart from normal donors (ND-MSC). Therefore, the aimed of our study was to explore the differences between MM-MSC and ND-MSC through gene expression analysis.

overall_design: MSC were isolated from 4 untreated multiple myeloma patients and 4 normal donors (not matched by age nor gender). The experiments were done in technical triplicates. Total RNA from MSC was isolated and hybridyzed on Affymetrix GeneChip® Human Exon 1.0 ST Array. Amplification, hybridization and scanning were done according to standard Affymetrix protocols (www.affymetrix.com). CEL files were normalized with RMA method.

first: R

middle: C

first: D

middle: R

last: Mazzotti

first: H

last: Azevedo

first: A

middle: F

last: Sandes

first: E

middle: G

last: Rizzatti

first: M

last: Oliveira

first: V

last: Fook-Alves

middle: I

last: Eugênio

first: F

last: Carvalho

last: Dalboni

last: Martins

first: G

middle: W

last: Colleoni


title: TET2 binding to enhancers facilitates transcription factor recruitment in hematopoietic cells

first: Kasper

last: Rasmussen


title: RNA-seq and miRNA-seq of testicular peritubular myoid cells, other testicular cells, and other tissue smooth muscle-like cells

status: Public on Jan 19 2019

first: Su-Ren

last: Chen


title: Chromatin architecture reorganisation during neuronal cell differentiation in Drosophila genome

status: Public on Jan 18 2019

first: Nicolae Radu

last: Zabet

address: 4 Newark Street

department: Blizard Institute, Barts and The London School of Medicine and Dentistry

institute: Queen Mary University of London

summary: Compartmentalisation of the genome as topologically associating domains (TADs) may have a regulatory role in development and cellular functioning, but the mechanism involved in TAD establishment is still unclear. Here, we present the first high-resolution contact map of Drosophila melanogaster neuronal cells (BG3) and identify different classes of TADs by comparing this to genome organisation in embryonic cells (Kc167). We find new interactions during differentiation in neuronal cells, which are reflected as enhanced long-range interactions. This is supported by pronounced enrichment of CTCF at TAD borders. Furthermore, we observed strong divergent transcription, together with RNA Polymerase II occupancy, and an increase in DNA accessibility at the TAD borders. Interestingly, TAD borders that are specific to neuronal cells are enriched in enhancers controlled by neuronal specific transcription factors. Our results suggest that TADs are dynamic across developmental stages and reflect the interplay between insulators, transcriptional states and enhancer activities.

overall_design: Comparison of Hi-C data in Drosophila melanogaster cell lines: BG3 (derived from larval central nervous system) and Kc167 (embryo derived)

first: Nicolae

first: Keerthi

last: Chathoth


title: Molecular interactions between Hel2 and RNA supporting ribosome-associated quality control [II]

city: Edinburgh

first: Marie-Luise

last: Winz

address: Max Born Crescent

department: Wellcome Centre for Cell Biology

institute: University of Edinburgh

summary: Ribosome-associated quality control (RQC) pathways monitor and respond to stalling of translating ribosomes. Using a newly developed technique based on in vivo UV crosslinking and mass spectrometry, we identify a C-terminal region in Hel2/Rqt1 as an RNA binding domain, with amino acids L501/K502 directly interacting with RNA. In vivo crosslinking of Hel2 revealed binding to 18S rRNA and translating mRNAs. Consistent with the 18S binding site located between mRNA entrance and exit channels, Hel2 preferentially bound mRNA both upstream and downstream of the termination codon. A C-terminal truncation that deleted L501/K502, abolished crosslinking to 18S rRNA, altered mRNA binding patterns, and reduced Hel2 function comparable to hel2∆. Asc1, also participates in RQC and ASC1 deletion impaired Hel2 18S and mRNA binding. We conclude that Hel2 is recruited or stabilized on translating 40S ribosomal subunits by interactions with 18S rRNA and Asc1. Ribosome-bound Hel2 interacts with mRNA, predominately during translation termination.

overall_design: CRAC was performed with yeast BY4741 strains containing HTP-tagged Hel2 (only version, under native promotor) in either wildtype, truncated or mutated version, in wt background or asc1-delta background.

first: Lauri

last: Peil

first: Tomasz

last: Turowski

first: Juri

last: Rappsilber

first: David

last: Tollervey