title: Single-cell transcriptomics of the early developing mouse cerebral cortex disentangles the spatial and temporal components of neuronal fate acquisition

city: Paris

first: Matthieu

middle: X.

last: Moreau

address: 102-108 Rue de la Santé

country: France

institute: Institute of Psychiatry and Neuroscience of Paris, INSERM U1266

summary: The establishment of neuronal diversity in the developing cerebral cortex is currently the focus of much attention. How progenitors that seemingly display limited diversity end up in producing a vast array of neurons remains a puzzling question. The prevailing model that recently emerged suggests that temporal maturation of progenitors in the dorsal pallium is a key driver in the diversification of neuronal output. However, temporal constrains are unlikely to account for all diversity across pallial domains, especially in the ventral and lateral aspects where neurons that will later belong to the olfactory cortex, claustrum and amygdala significantly differ from their neocortical counterparts born at the same time. In this study, we implemented single-cell RNAseq to sample the diversity of progenitors and neurons along the dorso-ventral axis of the pallium. We first identified neuronal types, mapped them on the tissue and performed genetic tracing to determine their ontogenic origin. We then investigated progenitor diversity and extensively characterized genes with variable expression along the dorso-ventral axis. We further identified those subjected to temporal vs spatial regulations. Finally, we reconstructed the developmental trajectories followed by ventral and dorsal pallial neurons to identify gene waves specific of each lineage. Our data suggest a model in which discrete neuronal fate acquisition from a continuous gradient of progenitors results from probabilistic mechanisms with a strong bias imposed on progenitors by both spatial information and temporal maturation.

overall_design: We applied scRNAseq profiling on dissected E12.5 mouse cortex containing subpallial as well as ventral, lateral and dorsal pallial cells

middle: X

first: Yoann

last: Saillour

first: Andrzej

middle: W

last: Cwetsch

first: Alessandra

last: Pierani

first: Frédéric

last: Causeret


title: Loss of claudin-3 impairs hepatic metabolism, biliary-barrier function and cell proliferation in the murine liver

status: Public on Jul 01 2021

city: Bern

first: Daniel

last: Sanchez-Taltavull

address: Murtenstrasse 35

department: Department of BioMedical Research

country: Switzerland

institute: University of Bern

type: Expression profiling by high throughput sequencing

summary: We determined the functional role of the tight junction protein Claudin-3 for overall gene expression in the liver. In the bulk RNAseq, we compare global gene expression in the livers of C57BL/6 wildtype mice and in CLDN3-/- mice. We sequenced both normal liver tissue and regenerating liver tissue.

overall_design: A two-thirds surgical partial hepatectomy was performed in C57BL/6 wildtype mice (CLDN3+/+) and mice with global claudin-3 knock-out (CLDN3-/-). Mouse liver tissue was analyzed at baseline (no surgery) and 48 hours post resection by RNA seq.

first: Deborah

last: Stroka

first: Felix

middle: A

last: Baier


title: Single cell RNA-sequencing on E17.5 mouse lungs and tracheas

city: Los angeles

first: Xue

last: Liu

state: CA

address: AHSP A9404, 127 S. San Vicente Blvd

department: Medicine

country: USA

institute: Cedars-Sinai Medical Center

summary: To identify clear mesenchymal cell clusters, sequencing libraries of embryonic lung cells were prepared using the 10x Genomics Chromium system. After quality control samples were integrated. The cells were visualized in two dimensions according to their gene expression profiles using Uniform Manifold Approximation and Projection (UMAP).

overall_design: We FACS sorted live cells from three E17.5 murine lungs and tracheas. Library preparation and single cell RNA-seq was performed on purified single cells.

first: Paul

last: Noble

first: Dianhua

last: Jiang


title: TEAD inhibition in SCC9 cells

city: Bethesda

first: Ramiro

last: Iglesias-Bartolome

address: 37 Convent Drive

department: LCMB

institute: NIH/NCI

summary: RNA sequencing (RNAseq) of SCC9 cells transduced with TEAD inhibitor protein (TEADi) or control GFP

overall_design: SCC9 cells were transduced in triplicate with adenoviruses expressing  GFP (control) or TEADi and harvested 48hs after transduction

first: Yao

last: Yuan


title: ATACseq samples of Arabidopsis thaliana regenerating root at different time points.

city: New York

first: Kenneth

middle: David

last: Birnbaum

state: NY

address: 12 Waverly Place

department: Biology

institute: New York University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Wounding is a trigger for both regeneration and defense in plants, but it is not clear if the two responses are linked by common activation or represent potential tradeoffs. While plant glutamate-like receptors (GLRs) are known to mediate defense responses, we implicate GLRs in regeneration through dynamic changes in chromatin and transcription in reprogramming cells near wound sites. Here, we show that genetic mutation and pharmacological inhibition of GLRs increases regeneration efficiency in multiple organ repair systems and plant species. Perturbation of GLR-mediated function, possibly by affecting Calcium fluxes, speeds cell division and re-specification of the stem cell niche while dampening a subset of defense responses. We show that the GLRs work through salicylic acid (SA) signaling in their effects on regeneration, with mutants in the SA receptor NPR1 partially resistant to GLR perturbation and hyper regenerative. These findings reveal a conserved mechanism that regulates a tradeoff between defense and regeneration and also offer new strategies to improve regeneration in agricultural and conservation.

overall_design: Chromatin accessibility profiling of root regenerating nuclei isolated at 2.5h, 14h and 16h after root tip excision (using MONOPTEROS(MP):MP::GFP transgenic marker or DAPI stained for uncut controls).

first: Marcela

last: Hernandez-Coronado

first: Poliana

last: Coqueiro

first: Pui-Leng

last: Ip

first: Custódio

middle: O

last: Nunes

first: Ramin

last: Rahni

first: Michael

last: Wudick

last: Lizzio

first: José

last: Feijó

middle: D


title: Modeling Genetic Epileptic Encephalopathies using Brain Organoids

city: Jerusalem

middle: Jacob

last: Steinberg

address: Hebrew University-Hadassah Medical School - Ein Karem Campus

department: Lautenberg Center for Immunology and Cancer Research

country: Israel

institute: The Hebrew University of Jerusalem Israel

summary: We generated cerebral organoids from genetically engineered human embryonic stem cells (hESCs), modeling the devastating WOREE syndrome (DEE28), as a prototype for genetic epileptic encephalopathies (EEs). Transcriptome analysis of mutated organoids compared to the WT revealed molecular changes related to both early infantile EEs and specifically to WOREE syndrome.

overall_design: Transcriptome analysis of WWOX-KO cerebral organoids comprared to age- and batch-matched WT organoids from the hESCs line WiBR3. 4 KO samples and 2 WT samples were included in final analysis, after 2 WT samples failed quality control as described in the manuscript.

middle: J

first: Rami

middle: I

last: Aqeilan


title: Global transcriptomic changes occur in uterine fluid-derived extracellular vesicles (UF-EVs) during the endometrial window for embryo implantation

city: Milan

first: Giulia

middle: Maria

last: Scotti

state: Milan

address: Viale Rita Levi Montalcini, 1

department: National Facility for Data Handling and Analysis

country: Italy

institute: Fondazione Human Technopole

summary:
Purpose: Extracellular vescicles (EVs) of uterine origin have recently been identified, but they are not comprised by current diagnostics on endometrial receptivity. In order to test the possibility to use EVs as biomarker reservoirs for non-invasive monitoring of the endometrial status, we defined two experimental designs: in step a) we aimed at assessing the concordance between the transcriptome of endometrial tissue and uterine fluid-derived EVs (UF-EVs); in step b) we aimed at unraveling the transcriptomic profile of UF-EVs released during the receptive phase and associated with successful implantation
Methods: RNAseq analysis was performed on total RNA isolated from a) endometrial biopsies and UF-EVs concomitantly collected from regularly cycling women; b) UF-EVs collected in the pre-receptive (LH+2) versus the receptive (LH+7) phase of provenly fertile women and in the receptive phase (LH+7) of women undergoing assisted reproduction and transfer of an euploid blastocyst. In the latter group, the outcomes of the following embryo transfer attempt were recorded, in order to compare the transcriptomic profile of women with successful versus failed implantation. Differential Gene Expression (DGE) and Gene Set Enrichment (GSEA) analyses were performed.
Results: In the first experimental design, a highly significant correlation was found between the transcriptional profiles of endometrial tissue biopsies and corresponding UF-EVs (r=0.71 p<0.001; ρ=0.65 p<0.001). In the second experimental design, using a large group of 73 samples, 16,777 genes were overall found to be expressed in UF-EVs. Of these, DGE analysis showed that 942 were up-regulated and 1,305 down-regulated during the receptive phase in women with proven fertility and 97 were up-regulated and 64 down-regulated during the receptive phase of women achieving successful implantation versus women failing to achieve pregnancy in the subsequent cycle. 41 genes had a  statistically significant different expression in both comparisons. We additionally tested wether transcripts used by current  endometrial receptivity tests based on endometrial biopsies (Endometrial Receptivity Assay, ERA test) could also be detected in UF-EVs: out of 238 ERA test gene data-set, GSEA highlighted 219 genes with similar transcriptional profile in UF-EVs. We then performed another comparison adding the list of genes consisting of the ‘metasignature’ transcriptome derived from the published meta-analysis of endometrial receptivity associated transcripts, comprising 57 genes. This last intersection identified 38 genes expressed in UF-EVs that i) show differential expression with the same transcriptional profile (same trends) in both EVs and ERA test assay; ii) belong to the leading edge of genes with the most significant enrichment score in our analysis; iii) are identified as receptivity-associated genes by the current meta-analysis on endometrial transcriptome.
Conclusions: This is the first study showing the capacity of UF-EVs to reflect the endometrial tissue transcriptional status and to establish a signature of genes expressed in UF-EVs that might serve as putative biomarkers for non-invasive endometrial receptivity tests.

overall_design: Firstly In order to assess the concordance between endometrial tissue and uterine fluid-derived EVs (UF-EVs) transcriptome, we simultaneously sequenced RNA species derived from pairwise samples collected from physiologically cycling women (n=10 tissues and n=10 UF-EVs). Secondly, to unravel the transcriptomic profile of EVs released by the endometrium during the window of implantation, we analyzed RNA species of UF-EVs collected from a) provenly fertile women (LH+2 n=13 and LH+7 n=13) and b) a larger population of women undergoing ART and transfer of euploid blastocysts, as a function of pregnancy outcomes (n=49). .

first: Elisa

last: Giacomini

first: Dejan

last: Lazarevic

first: Sofia

last: Makieva

first: Laura

last: Privitera

first: Simona

last: Signorelli

first: Luca

last: Pagliardini

last: Cantone

first: Valentina

last: Bollati

first: Enrico

last: Papaleo

first: Massimo

last: Candiani

first: Giovanni

last: Tonon

first: Paola

last: Viganò


title: Identification and development of DNA methylation biomarkers for Stomach cancers prevalent in Mizoram, India

city: Shillong

first: Srimoyee

last: Ghosh

state: Meghalaya

address: Umshing-Mawkynroh

department: Zoology

country: India

institute: North Eastern Hill University

type: Methylation profiling by genome tiling array

summary: Whole genome DNA methylation profiling of stomach cancer in patients from Mizoram, India. The Illumina Infinium 450k Human DNA methylation Beadchip was used to screen the entire DNA methylation profiles across approximately 485,577 CpGs in matched stomach cancer samples. Samples included 12 paired samples (12 cancer and 12 normal).

overall_design:
Bisulphite converted DNA from the 24 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip

Please note that the samples are arranged pair-wise, i.e, samples 1 & 2 are pair no. 1, samples 3 & 4 are pair no.2 and so on.

first: Frederick

last: Lamare


title: Lineage selective cardiac GATA4 chromatin occupancy [embryo]

city: Boston

first: William

middle: T

last: Pu

state: MA

address: 300 Longwood Ave

institute: Children's Hospital Boston

summary: We used cre-directed biotinylation of a GATA4 knockin allele with an AviTag epitope tag to measure GATA4 chromatin occupancy in endocardial and cardiomyocyte lineages in the E12.5 heart. These data are complemented by lineage selective measurement of gene expression and chromatin accessibility. Cardiomyocyte accessibility and gene expression data were reported in GSE124008.

overall_design: GATA4 lineage-selective bioChIP-seq; ATAC-seq; RNA-seq

first: Pingzhu

last: Zhou


title: Chloride Intracellular Channel Knockdown in Drosophila Alters the Transcriptome, Sensitivity to Ethanol Sedation, and Oxidation-Reduction Processes

city: Richmond

first: Michael

last: Miles

state: VA

department: Pharmacology and Toxicology

institute: Virginia Commonwealth Univ.

summary: Chloride intracellular channels (CLICs) are a unique family of evolutionarily conserved metamorphic proteins, switching between stable conformations based on redox conditions. CLICs have been implicated in a wide variety biological processes including ion channel activity, apoptosis, membrane trafficking, and enzymatic oxidoreductase activity. Understanding the molecular mechanisms by which CLICs engage in these activities is an area of active research. Here, the sole Drosophila melanogaster ortholog, Clic, was targeted for RNAi knockdown to identify genes and biological processes associated with Clic expression. Clic knockdown had a substantial impact on global transcription, altering expression of over 9% of transcribed Drosophila genes. Overrepresentation analysis of differentially expressed genes identified enrichment of 23 Gene Ontology terms including Cytoplasmic Translation, Oxidation-Reduction Process, Heme Binding, Membrane, Cell Junction, and Nucleolus. The top term, Cytoplasmic Translation, was enriched almost exclusively with downregulated genes. Drosophila Clic and vertebrate ortholog Clic4 have previously been tied to ethanol sensitivity and ethanol-regulated expression. Clic knockdown-responsive genes from the present study were found to overlap significantly with gene sets from 4 independently published studies related to ethanol exposure and sensitivity in Drosophila. Bioinformatic analysis of genes shared between these studies revealed an enrichment of genes related to amino acid metabolism, protein processing, oxidation-reduction processes, and lipid particles among others. To determine whether the modulation of ethanol sensitivity by Clic may be related to co-regulated oxidation-reduction processes, we evaluated the effect of hyperoxia on ethanol sedation in Clic knockdown flies. Consistent with previous findings, Clic knockdown reduced acute ethanol sedation sensitivity in flies housed under nomoxia. However, this effect was reversed by exposure to hyperoxia, suggesting a common set of molecular-genetic mechanism may modulate each of these processes. This study suggests that Drosophila Clic has a major influence on regulation of oxidative stress signaling and that this function overlaps with the molecular mechanisms of acute ethanol sensitivity in the fly.

overall_design: Flies harboring the neuron-selective elav-Gal4 driver and/or Clic UAS-RNAi transgenev105975 were reared and crossed as previously described (Chan et al. 2014). Tissue samples were obtained from whole fly head homogenates and processed as described previously (Jones et al. 2014).

first: Rory

middle: M

last: Weston

first: Mike

last: Grotewiel

middle: F


title: Combined immunotherapy potentiates CD8+ cytotoxic T-cell infiltration in a spontaneous mouse model of immune-excluded gastric cancer

city: Geneva

first: Celine

last: Delucinge

address: 1 rue Michel Servet

department: iGE3 Genomics Platform

institute: University of Geneva

summary: In this study, we characterized the transgenic mouse model of stomach adenocarcinoma CEA424-SV40 T Ag. Transgenic mice, generated in Prof Wolfgang Zimmermann’s lab (Ludwig-Maximilian University, Munich) (Tompson et al. Int J Cancer, 2000), produce spontaneous tumors in the pyloric region of the stomach in a time-dependent stage wise process. Combining multiple techniques, including transcriptomic analysis, we investigated the composition of the tumor microenvironment over time. We found that gastric tumors in CEA424-SV40 Tag present features of an immunosuppressive environment and are refractory to different immunotherapies. Comparing the expression profiles of tumors at early (day 60) and late stage (day80) we observed overexpression of stroma remodelling signatures, predicting poor overall survival in human patients of stomach adenocarcinoma. Finally, we demonstrated that combination of stroma-targeted T cell activation and PD-L1 inhibition potentiated CD8+ T cell migration to tumors. Our data demonstrate that the CEA424-SV40 T Ag model is clinically relevant and constitute an ideal platform to develop new immunotherapies, such as tumor-targeted stimulation of T cells combined with immune checkpoint blockade.

overall_design: Total RNA was exctracted from bulk pyloric tissue collected from 60 or 80 days-old wild-type C57BL/6 mice or CEA424-SV40 T Ag transgenic mice, and profiled by RNA-seq

first: Viola

last: Puddinu

first: Nathalie

last: Seinhoff

first: Sara

last: Colombetti

first: Carole

last: Bourquin


title: Heart fibroblasts from Siah-knockout mice in hypoxia

city: Giessen

first: Jochen

last: Wilhelm

state: Hessen

address: Aulweg 132

department: Institute for Lung Health

country: Germany

institute: Justus-Liebig University Giessen

summary: Heart fibroblasts from wildtype mice and Siah2-/- knockout mice were isolated and cultured. The cells were either left untreated or incubated for 6 hs under hypoxic conditions. One experiment consists of wildtype cells (normoxia/hypoxia) and Siah2 knockout cells (normoxia/hypoxia) = 4 samples. To allow statistical analysis of the data set the experiment was repeated once under identical conditions.

overall_design: 4 groups, each with 2 biological replicates.

first: Lienhard

last: Schmitz


title: siRNA sequencing of Aedes aegypti from two regions of the Americas reveals insect-specific virus profiles with geographic structure

city: Fort Collins

first: Ken

middle: E

last: Olson

state: CO

address: 3185 Rampart Road

department: Microbiology, Immunology, Pathology

institute: Colorado State University

type: Non-coding RNA profiling by high throughput sequencing

summary: We performed small RNA sequencing on recently colonized female Aedes aegypti from Mexico and Brazil. We compare small RNA profiles in midguts and abdomens (without ovaries) either non-bloodfed or 48 hours post non-infectious bloodmeal.

overall_design: Small RNA profiles of Ae. aegypti midgut and abdomen tissues from Mexico vs. Brazil, either before or after a bloodmeal.

first: Nelson

last: Lau

first: Adeline

last: Williams

first: Qicheng

last: Ma


title: LncRNA expression profile in triple negative breast cancer (TNBC)

city: Harbin

first: Aixin

last: Hao

address: 26 Hexing Road

country: China

institute: Northeast Forestry University

type:
Expression profiling by array
Non-coding RNA profiling by array

summary: To identify novel TNBC-relevant lncRNAs, we performed lncRNA microarray analysis using 5 TNBC tissues and their matched adjacent non-cancerous tissues by Arraystar Human LncRNA Microarray V3.0.

overall_design: LncRNA expression profiling analysis of 10 samples including 5 TNBC tissues and their matched adjacent normal breast tissues by Arraystar Human LncRNA Microarray V3.0.

first: Yu

last: Wang

first: Guangchao

last: Sui


title: Consequences of a low protein diet in the liver and longissimus dorsi transcriptome of Duroc x Iberian crossbred pigs

city: Zafra

first: María

middle: Muñoz

last: Muñoz

state: Badajoz

address: Centro I+D en Cerdo Ibérico, carretera Ex-101, km 4.7

country: Spain

institute: INIA

summary: Low protein diets supplied during the growing period of pigs can diminish their growth rate and increase the intramuscular fat (IMF) content which affects the sensorial and technological characteristics of the traits. In the present study, the effects of a low protein diet supplied during the growing diet of Duroc x Iberian crossbred pigs on several phenotypic traits and liver and longissimus dorsi transcriptome, were analysed 20 days after the differential treatment was started (EARLY) and at the end of it (FINAL). A total of 20 crossbred pigs were assigned to two different dietary treatments during the growing period: a control diet (C) and a low protein diet (LP) with the same energy and lower levels of raw protein (11%) and lysine (0.60%). The transcriptomes of liver and longissimus dorsi were quantified through RNAseq. A total of 134 differentially expressed annotated genes and new isoforms (DEGs) between C and LP diets in liver of EARLY animals; 480 DEGs in liver of LATE animals, and 128 DEGs and 68 DEGs in longissimus dorsi of EARLY and LATE animals were detected. The functional analyses revealed that low protein diet diminishes the expression in liver of genes codifying for proteins involved in immune system both in EARLY and LATE animals, affects the expression of genes involved in cholesterol homeostasis in liver and in the energy process and growth in longissimus dorsi. Pigs fed with LP diet had not higher IMF content than C ones, although some lipogenesis genes such as FASN, SCD or SREBF1 were higher expressed on their liver. A low protein diet supplied during growing period affects multiple biological process that could compromise the immune and energy state of the Duroc x Iberian crossbred pigs. These results point out that we should be very cautious before implementing this type of regime in Duroc x Iberian pigs.

overall_design: A total of 20 Duroc x Iberian crossbred pigs were assigned to two different dietary treatments during the growing period: a control diet (C) and a low protein diet (LP) with the same energy and lower levels of raw protein (11%) and lysine (0.60%). A total of 10 animals (5 per diet) were slaughtered 20 days after the differential diet treatment started (EARLY), and the remaining 10, at the end of the growing period (LATE). Liver and longissimus dorsi samples were taken after the slaughter, the RNA was extracted and pair-end libraries were constructed.

first: Miguel

last: Fernández-Barroso

first: Adrían

last: López-García

first: Carmen

last: Caraballo

first: Yolanda

last: Nuñez

first: Elena

last: González

first: Juan

last: García-Casco


title: Dissecting the yeast heat shock response by CRISPRi/a

city: Heidelberg

first: Cosimo

last: Jann

address: Meyerhofstr. 1

department: Genome Biology

institute: EMBL Heidelberg

summary: CRISPRi screens on the repression of 129 protein kinases and 161 transcription factors in S. cerevisiae. We quantify perturbation effects on cellular fitness at 23, 30 and 38°C, expression of the SSA1 Hsp70 chaperone (as proxy for heat shock response activity) and thermotolerance. The integration of these phenotypes allowed us to identify core signaling pathways of the HSR and their contributions to temperature-associated growth and heat resistance.

overall_design: CRISPR interference screens in S. cerevisiae in bulk yeast populations on five selection conditions: competitive growth assays over 1.5-2 days at temperatures 23, 30 and 38°C, survival of a lethal heat shock (150 min at 50°C, including recovery without maintaining CRISPRi induction), and chaperone expression as a proxy for heat shock response activity (FACS-based collection of cells by their cellular Hsp70 GFP reporter intensity).

first: Andreas

last: Johansson

first: Justin

last: Smith

first: Leopold

last: Parts

first: Lars

last: Steinmetz


title: Neonatal Blood Spots from the Emory University African American Microbiome in Pregnancy Cohort

city: Atlanta

first: Anna

middle: K

last: Knight

state: Georgia

address: 101 Woodruff Circle NE

institute: Emory University

summary: Newborn screening blood spots were obtained for neonates born to women enrolled in the Emory University African American Microbiome in Pregnacy Cohort

overall_design: DNA methylation was assesed on the MethylationEPIC array.

first: Alicia

first: Anne

middle: L

last: Dunlop


title: ChIPseq identification of DDIT3 genomic binding sites - correlations with gene expression data reveal dimerization partners and target genes

city: Gothenburg

first: Ayman

last: Osman

address: Medicinaregatan 1F

department: Laboratory medicine

country: Sweden

institute: Gothenburg University

summary: This study inverstigate the properties of the DDIT3 binding and involvement of DDIT3 in transcriptional regulation.

overall_design: We used ChIP-seq of DDIT3 oncoprotein in sarcoma cells to study the DDIT3 DNA binding sites.

first: Pierre

last: Åman


title: Gene expression profile of chemically induced expandable cardiovascular progenitor cells derived from mouse fibroblasts

city: Guangzhou

first: tao

last: xu

state: Guangdong

address: North Campus, Sun Yat-*Sen University, No. 74, 2nd Yat-*Sen Road/Street，Yuexiu District, Guangzhou City, Guangdong Province

department: ZHONGSHAN SCHOOL OF MEDICINE

institute: SUN YAT-SEN UNIVERSITY

summary: Cardiovascular progenitor cells (CPCs) can be reprogrammed from somatic fibroblasts by combinations of genes, providing a new avenue for cardiac regenerative therapy. Here we developed a strategy to capture chemically induced CPCs (ciCPCs) during the small molecule-induced cardiac reprogramming of mouse fibroblasts and expand these ciCPCs for a long-term in a chemically defined condition. RNA-seq analysis has been used to compare the expression profile of ciCPCs at early and late passages.

overall_design: To study the characteristics of ciCPCs during their long-term expansion, we collected ciCPCs at both early (P3) and late (P20) passages.

first: Jia

last: Wang

last: Cao

first: Tao

last: Xu


title: Nurse cell-derived small RNAs define paternal epigenetic inheritance in Arabidopsis

city: Norwich

first: Xiaoqi

last: Feng

state: Norfolk

address: Norwich Research Park

department: Cell and Developmental Biology

country: United Kingdom

institute: John Innes Centre

type: Methylation profiling by high throughput sequencing

summary: We report here that gentic methylation in the male germline, from meiocytes to sperm, is established by siRNAs transcribed from transposons with imperfect sequence homology. These siRNAs are synthesized by meiocyte nurse cells (tapetum) via activity of the chromatin remodeler CLASSY3, which is specifically expressed in tapetal cells. Plants that produce siRNAs only in the tapetum have broadly normal DNA methylation of the entire germline. Finally, we also report that these nurse cell-derived siRNAs (niRNAs) silence germline transposons, thereby safeguarding genome integrity. Our results reveal the crucial role of tapetal niRNAs in germline methylation reprogramming, which is remarkably analogous to piRNA-mediated reprogramming in animal germlines.

overall_design: Profiling of methylome and sRNAome in meiocyte and tapetum in Arabidopsis

first: Jincheng

last: Long

first: James

last: Walker

first: Wenjing

last: She

first: Billy

last: Aldridge

first: Hongbo

last: Gao

first: Samual

last: Deans

first: Martin

last: Vickers


title: Integrated metabolomic and transcriptomic analysis reveals metabolic adaptation of rats to Abcg2/Abcb1a knockout

city: Memphis

first: Geoffrey

last: Neale

state: TN

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

summary: Breast Cancer Resistance Protein (Bcrp) and P-glycoprotein (Pgp) are xenobiotic efflux transporters that limit permeability of their substrates in the gastrointestinal system and brain, and increase drug clearance in liver and kidney. Bcrp and Pgp are also known to transport different endogenous metabolites such as riboflavin, urate, sulfated steroids and glucocorticoids. However, a systemic approach to understand the endogenous substrates and function of these transporters is still lacking. We hypothesized that Bcrp and Pgp have important endogenous functions and play a crucial role in maintaining metabolomic homeostasis in the biological system. To understand the impact of Bcrp and Pgp on endogenous metabolome, we performed untargeted metabolomics of CSF and plasma of male Sprague Dawley (SD) rats (WT) and SD rats lacking both Bcrp and Pgp (double knock-out, dKO rats) (n= 8 per genotype). In addition, we performed genome-wide microarray analysis of brain frontal cortex, kidney and liver from the same animals to analyze changes in gene expression (n=5 per genotype). Our results indicate distinct differences in metabolites and gene expression between WT and dKO rats. Rank order based on both fold change (>1.5 or <0.67) and significance (p <0.05) identified 29 metabolites in CSF and 47 metabolites in plasma as most significantly altered between WT and dKO rats, which includes, among other biochemicals, known substrates of Bcrp e.g., riboflavin, urate, daidzein and its metabolites. Significantly altered metabolites in plasma as well as CSF showed signatures of altered fatty acid metabolism and oxidative stress, which was further supported by the pathway analysis of significantly altered genes. These findings may lead to new insights in understanding the endogenous function of Bcrp and Pgp transporters and identification of functional biomarkers of these transporters

overall_design: We performed microarray analysis to compare the global expression profiles in tissues from WT and Bcrp/Pgp double knock-out rats. Expression profiling was performed in biological replicates of the frontal cortex of the brain (WT: n = 5, dKO: n = 5),  liver (WT: n = 5, dKO: n = 5) and kidney (WT: n = 5, dKO: n = 5) using the Affymetrix  Rat Gene 2.0 ST Array.

first: Samit

last: Ganguly

first: Erin

middle: G

last: Schuetz


title: Characteristics of microRNAs Profile in Five Pairs of Early Gastric Cancer Tissues and Matched Adjacent Normal Mucosa Tissues.

city: Lanzhou

first: Yuping

state: Gansu

address: Donggang West Road, Chengguan District

department: Department of Gastroenterology

institute: The First Hospital of Lanzhou University

summary: Gastric cancer is one of the most common malignant tumors. Asia has a high incidence of gastric cancer globally. South Korea, Mongolia, Japan and China are the four countries with the highest incidence of gastric cancer in the world. Gansu province in China has the estimated age-standardized incidence rates and mortality rates by Chinese standard population of 62.34/100,000 and 36.94/100,000, respectively, in 2012, which are much higher than the average level of China (22.06/100,000 and 15.16/100,000) in the same year. As a high incidence area of gastric cancer in China, Wuwei city in Gansu province has the prevalence of gastric cancer almost 5 times higher than the average level nationwide. In this study, the cancer tissues and matched adjacent normal mucosa tissues of 5 patients with early gastric cancers who were treated with ESD in Gansu Wuwei Tumor Hospital and the First Hospital of Lanzhou University were collected. All of the patients are from Gansu, China. MicroRNA array was used to find the differences in microRNAs expression profile between the early gastric cancer tissues and the para-cancer normal tissues. It is expected to explore the reasons of the abnormal high incidence of gastric cancer in Gansu Province, China, from the aspect of microRNAs expression profile characteristics.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Tissues are the cancer tissues and matched adjacent normal mucosa tissues of 5 patients with early gastric cancers who were treated with ESD in Gansu Wuwei Tumor Hospital and the First Hospital of Lanzhou University. They were collected in the year of 2014 and 2015. All carcinomas were pathologically diagnosed. The specimens were stored and transported at -80℃. MicroRNA array was performed by Aksomics company in Shanghai, using miRCURY LNA microRNA Array, 7th generation - hsa, mmu & rno (Exiqon A/S), the microRNA array product.


title: Bioplatforms Australia: Antibiotic Resistant Sepsis Pathogens Framework Initiative - Streptococcus pneumoniae 180/15

city: Sydney

last: Bioplatforms Australia

state: NSW

address: Level 4, Building 4WW, Research Park Drive, Macquarie University

country: Australia

institute: Bioplatforms Australia

summary: The Antibiotic Resistant Sepsis Pathogens Framework Initiative aims to develop a framework dataset of 5 sepsis pathogens (5 strains each) using an integrated application of genomic, transcriptomic, metabolomic and proteomic  technologies. The pathogens included in this initiative are: Escherichia coli, Klebsiella pneumoniae complex, Staphylococcus aureus, Streptococcus pyogenes, and Streptococcus pneumoniae. This submission pertains to strain 180-15.

overall_design:
18 samples, 3 conditions, 6 biological replicates per condition.
contributor: Bioplatforms Australia Antibiotic Resistant Sepsis Pathogens Framework Initiative


title: Bioplatforms Australia: Antibiotic Resistant Sepsis Pathogens Framework Initiative - Streptococcus pneumoniae 180/2

summary: The Antibiotic Resistant Sepsis Pathogens Framework Initiative aims to develop a framework dataset of 5 sepsis pathogens (5 strains each) using an integrated application of genomic, transcriptomic, metabolomic and proteomic  technologies. The pathogens included in this initiative are: Escherichia coli, Klebsiella pneumoniae complex, Staphylococcus aureus, Streptococcus pyogenes, and Streptococcus pneumoniae. This submission pertains to strain 180-2.


title: Effect of NKX2-5 or ETS1 on GATA4 pioneer activity [fibroblast]

first: William

last: Pu

summary: GATA4 is a pioneer transcription factor. The mechanisms by which pioneer factors select and occupy specific loci, open chromatin, and activate enhancers is not well understood. To address the influence of partner, non-pioneer factors on pioneer factor activity, we analyzed the effect of NKX2-5 or ETS1 on GATA4 pioneer activity. NIH3T3 cells were transduced with lentivirus to obtain stable cell lines that express GFP (control), GATA4 (G), NKX2-5 (N), ETS1 (E), GATA4+NKX2-5 (GN), and GATA4+ETS1 (GE). We measured chromatin accessibility using ATAC-seq, and enhancer activation using H3K27ac. From these measurements we determined GATA4, GATA4+ETS, and GATA4+NKX2-5 pioneer binding, pioneer opening, and pioneer enhancer activation. Our results show that ETS1 or NKX2-5 alter GATA4 pioneer binding, opening, and enhancer activation.

overall_design:
NIH3T3 cells were transduced with lentivirus to obtain stable cell lines that express GFP (control), GATA4 (G), NKX2-5 (N), ETS1 (E), GATA4+NKX2-5 (GN), and GATA4+ETS1 (GE). We measured chromatin accessibility using ATAC-seq, and enhancer activation using H3K27ac. From these measurements we determined GATA4, GATA4+ETS, and GATA4+NKX2-5 pioneer binding, pioneer opening, and pioneer enhancer activation.
We obtained three replicates per sample.

first: Pingzhu

last: Zhou


title: Single-cell analysis reveals cellular heterogeneity and molecular determinants of hypothalamic leptin-receptor cells

city: Utrecht

first: Onur

last: BASAK

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

summary: Hypothalamic nuclei which regulate homeostatic functions express leptin receptor (LepR), the primary target of the satiety hormone leptin. Single-cell RNA sequencing (scRNA-seq) has facilitated the discovery of a variety of hypothalamic cell types. However, low abundance of LepR transcripts prevented further characterization of LepR cells. Therefore, we perform scRNA-seq on isolated LepR cells and identify eight neuronal clusters, including three uncharacterized Trh-expressing populations as well as 17 non-neuronal populations including tanycytes, oligodendrocytes and endothelial cells. This includes food restriction to measure the response of Lepr positive cells to fasting. Using FACS sorting into 384 well plates and Celseq2 method, we generated a high-quality dataset containing a median of 12,082 unique counts and 4,756 genes per cell.

overall_design:
Multiplexed (384) single cell libraries of sorted Lepr cells of the hypothalamus of Lepr-cre;Rosa-LSL-tdTomato animals, library 1
Multiplexed (384) single cell libraries of sorted Lepr cells of the hypothalamus of Lepr-cre;Rosa-LSL-tdTomato animals, library 2
Multiplexed (384) single cell libraries of sorted Lepr cells of the hypothalamus of Lepr-cre;Rosa-LSL-tdTomato animals, library 3
Multiplexed (384) single cell libraries of sorted Lepr cells of the hypothalamus of Lepr-cre;Rosa-LSL-tdTomato animals following 24 of fasting, library 4

first: N

last: Kakava-Georgiadou

first: J

last: Severens

first: A

last: Jørgensen

first: K

last: Garner

first: M

middle: C

first: V

last: Drkelic

first: R

last: van Dijk

first: T

middle: H

last: Pers

first: O

last: Basak

last: Adan


title: Induced muscle progenitor cells

city: Cambridge

first: Jocelyn

last: Charlton

address: 7 Divinity Avenue

department: Stem Cell and Regenerative Biology

institute: Harvard University

summary: Dissecting mechanisms by which MyoD and small molecules convert fibroblasts to muscle progenitor cells.

overall_design: RRBS was performed for 13 samples in duplicate.

first: Masaki

last: Yagi

first: Alexander

last: Meissner

first: Konrad

last: Hochedlinger


title: Bioplatforms Australia: Antibiotic Resistant Sepsis Pathogens Framework Initiative - Streptococcus pneumoniae 4559

last: Bioplatforms Australia

summary: The Antibiotic Resistant Sepsis Pathogens Framework Initiative aims to develop a framework dataset of 5 sepsis pathogens (5 strains each) using an integrated application of genomic, transcriptomic, metabolomic and proteomic  technologies. The pathogens included in this initiative are: Escherichia coli, Klebsiella pneumoniae complex, Staphylococcus aureus, Streptococcus pyogenes, and Streptococcus pneumoniae. This submission pertains to strain 4559.


title: Amniotic fluid cells chromatin accessibility in Turner's syndrome

city: Xiamen

first: zhiwei

last: zeng

address: Jimei

institute: huaqiao university

summary: Turner syndrome is a relatively rare condition that is usually associated with the loss of all or part of an X chromosome. Amniotic fluid is a complicated biological material, could contribute to the understanding of turner syndrome pathogenesis. In this study, ATAC-seq analysis of Turner syndrome (45X) and Female (46XX) amniotic fluid cells was applied to illustrate that genome wide chromatin accessible landscapes. Our results show that Turner Syndrome has higher chromatin accessibility than Female on autosomes and has lower chromosome accessibility on the X chromosome. We identified candidate genomic regions and transcript factors that may play an important role in Turner syndrome pathogenesis. Our analysis suggests that the phenotype of Turner Syndrome should be the result of abnormal regulation of gene expression in the whole genome, not just the result of insufficient doses of X chromosome haploids.

overall_design: ATAC-seq  of Turner syndrome amniotic fluid cells

first: Zhiwei

last: Zeng

last: Miao

first: Tao

last: Sun


title: Expression profile of plasma exosomal microRNAs in women with polycystic ovary syndrome and control women

city: Jinan

first: Xiao

last: Jiang

address: 157 Jingliu Road

summary: Polycystic ovary syndrome (PCOS) is a highly prevalent endocrine-metabolic disorder. Epigenetic etiology is suggested to play an important role in PCOS pathogenesis, since it is hard to elucidate completely by genetic variations.   Exosomal microRNAs (miRNAs) have recently been identified as a novel mechanism of intercellular communication, and a more stable regulator of gene expression compared with free miRNAs. The aim of this study is to detect the different expression profile of plasma exosomal miRNAs between PCOS patients and healthy controls.

overall_design: Plasma exosomal miRNA profiles from 15 PCOS women and 15 control women. All participants were recruited in Center for Reproductive Medicine, Shandong University, from January to June in 2017.

first: Linlin

last: Cui


title: Expression data from the complex I mutant gas-1 (fc21)  C. elegans worms in comparison to wildtype N2 Bristol worm and under the inluence combination drug therapy

city: Philadelphia

first: Zhe

last: Zhang

state: PA

address: Translational Research Lab

institute: University of Pennsylvania

summary: We studied genome-wide expression profiles of C. elegans young adult worms, complex I mutant gas-1(fc21) compare to the wild type N2 Bristol worm and the effect of combination drug treatment on the gene expression profile in gas-1(fc21).

overall_design: 4 biological replicates of wildtype (N2 Bristol) synchronized worms grown on OP50 bacteria, 4 biological replicates of the complex I  mutant C. elegans synchronized young adults and 4 biological replicates of synchronized complex I mutant worm treated with the different drug combination  were used as sources of total RNA.  Comparison of the data was intended to reveal causes of different antioxidant drug treatment on gene expresssion profile  in the complex I mutant gas-1(fc21) worms.

first: Marni

last: Falk

first: Erzsebet

last: Polyak

first: Sujay

last: Guha


title: IGF2BP1 is required for hepatic outgrowth during early liver development in zebrafish

city: Kunming

first: Junjie

last: Wu

address: No. 66 Gaoyao Village

institute: Yunnan Institute of Fishery Sciences Research

summary: IGF2BPs, a subclass of RNA-binding proteins, regulate cellular differentiation, proliferation and migration during mutiple organs development, but its function still remains unclear. Here, we provide the in vivo evidence that Igf2bp1 is pivotal during liver development by using zebrafish as a model organism. Whole-mount in situ hybridization showed that igf2bp1 was highly expressed in liver, and the morpholino knockdown had no effect on hepatoblast differentiation, but the liver size was significantly reduced. Data from microarray analysis indicated that the hepatic outgrowth defect in igf2bp1 konckdown embroys could be attributed to the significantly down-regulated of several important genes related to liver development, such as epo, cxcl8, socs1a, uox, ripk1, itgb1 and arhgef7. Besides, the igf2bp1Δ5 mutant, obtained by CRISPR/Cas9, showed the same phenotype with morpholino knockdown. Altogether, our researchs demonstrate that Igf2bp1 is a critical regulator during liver development by modulating several genes related to hepatic outgrowth.

overall_design: The Zebrafish (V3) Gene Expression Microarray (4 x 44K, Agilent Technologies) was carried out to screen the differentially expressed gene between igf2bp1 morpholino and standard control embryos at 72 hpf.

first: Chang

last: Lu

first: Zhigang

last: Shen

first: Xiaohui

last: Li

first: Wenjie

last: Guo


title: Transcriptomic profiling of circulating T follicular helper cells in kidney transplant recipients

city: Pittsburgh

first: Uma

last: Chandran

address: 5150 Center Ave

department: BioMedical Informatics

institute: University of Pittsburgh

summary: We compared the transcriptomic profile between patients without donor-specific HLA antibodies (DSA-), patients with donor-specific HLA antibodies without antibody-mediated rejection (DSA+ ABMR-) and patients  with donor-specific HLA antibodies and antibody-mediated rejection (DSA+ ABMR+). We found that patient with DSA+ ABMR+ had a distinct transcriptomic profile compared to DSA- and DSA+ ABMR-, characterized by upregulation of genes encoding for germinal center T follicular helper cells function, T-B cell interaction and costimulatory molecules.

overall_design: We analysed N=3 samples per group of patients (DSA-, DSA+ABMR-, DSA+ ABMR+), without replicates

first: Kevin

last: Louis

first: Diana

last: Metes

last: Chang


title: Bioplatforms Australia: Antibiotic Resistant Sepsis Pathogens Framework Initiative - Streptococcus pneumoniae 947

last: Bioplatforms Australia

summary: The Antibiotic Resistant Sepsis Pathogens Framework Initiative aims to develop a framework dataset of 5 sepsis pathogens (5 strains each) using an integrated application of genomic, transcriptomic, metabolomic and proteomic  technologies. The pathogens included in this initiative are: Escherichia coli, Klebsiella pneumoniae complex, Staphylococcus aureus, Streptococcus pyogenes, and Streptococcus pneumoniae. This submission pertains to strain 947.


title: DNA methylation of a 3' cis-element promotes gene activation

city: Fuzhou

first: mao

last: fei

state: Fujian

address: Shangxiadianlu NO.15

department: National Engineering Research Center of JUNCAO

institute: Fujian Agriculture and Forestry University

summary: In our study, we identified a new transgenerational epigenetic mutant in rice, Epi-LF (Epi-LongFeng). The metastable phenotype of Epi-lf resembles that of rice Epi-d1, and the inheritance is largely similar to that of the agoutiAy mouse mutant. We found that in Epi-lf,mCHH methylation was present in a 155-bp sequence of DNA in close proximity to the 3' end of the LF gene, but the abundance of the siRNAs corresponding to this region was not significantly different from that of the wild type (WT), suggesting that this is a mCHH island like modification. In addition, ectopic mCHH modifications accumulated in the sporophytic tissues and embryos of the Epi-lf mutants. The majority of these ectopic CHH regions did not fit with the OsDRM2 (Domain Rearranged Methylase2)-mediated CHH methylation of genomic regions, suggesting that unknown genetic factors may co-ordinate DNA demethylation and methylation, especially for non-CG methylation.

overall_design: We sequenced transcriptome, methylome and small RNA in different tissues of Eip-lf mutants and wild-type rice

first: Yongtao

first: Xingming

last: Hu

first: Jiawen

last: Cheng

first: Wumei

last: Wang

first: Lan

first: Guosheng

last: xiong

first: Jiang

first: Guojun

last: Dong

first: Dali

last: Zeng

first: Zefu

first: Yongjun

last: Lin

first: Yufeng

first: Longbiao

first: Qian

last: Qian


title: Transcriptomics Expression Analysis of the effects of UV radiations on Normal Human Dermal Fibroblast Cells

city: St. John's

first: Akinola

middle: Adekoya

last: Alafiatayo

state: Newfoundland and Labrador

address: 300 Prince Philip Drive

department: Faculty of Medicine, Division of Biomedical Sciences (Genetics)

country: Canada

institute: Memorial University of Newfoundland

summary: Chronic exposure to sunlight is linked to premature aging (photoaging) and UV radiations is implicated to be the main contributor of this phenomenon. It causes changes to dermal collgen through two major pathways; promotion of collagen breakdown and lost of collagen content via the inhibition of collagen biosynthesis. The absorption of UV radiations by skin molecules generates reactive oxygen species (ROS) which lead to oxidative damage of cellular components such as cell walls, lipid membranes, mitochondria and DNA. Therefore, this research involve the identification of key genes in biological processes through high throughput RNA Sequencing technology to identify genes and pathways underlying skin aging health and diseases due to UV exposure, ultimately leading to novel ways of managing, diagnose, treat and prevent/slow down skin aging illnesses/wrinkles.The results from this study produces huge amount of  differential expressed genes (DEG) as a result of UV exposure which were subsquently validated with qPCR.

overall_design: mRNA expression profiling from cultured human dermal fibroblast cells exposed to UV radiations (Treated) and non-exposed (Control) were generated by high throughput sequencing using Illumina HiSeq®4000.

first: A

middle: A

first: Lai

last: Song

first: Syahida

last: Ahmad

first: Maziah

last: Mahmood

first: Noor

last: Shaharuddin


title: Next Generation Sequencing Facilitates Quantitative Analysis of the effects of TNFa treatment on sorted mouse lung ILC2 Transcriptomes

city: Los Angeles

first: Benjamin

middle: Pierre

last: Hurrell

state: CA

address: 1450 Biggy Street

department: MMI

institute: University of Southern California

summary: TNFa induces secretion of ILC2 effector cytokines ex vivo. Increased ILC2 activation leads to the development of airway hyperreactiviy and lung inflammation. Targeting TNFa may therefore represent a novel therapeutic target to treat asthma.

overall_design: mRNA profiles of sorted mouse lung ILC2s treated either with PBS or TNFa were generated by deep sequencing, in triplicate, using a NextSeq 500 (Illumina) system.

middle: P


title: Integrated analysis of RNA-seq and microRNA-seq depicts miRNA-mRNA networks involved in stripe patterns of Botia superciliaris skin

city: Yaan

first: jideng

last: Ma

address: Xinkang road

institute: Sichuan Agricultural University(SICAU),

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

overall_design: Refer to individual Series


title: Breast tumor stiffness instructs bone metastasis via mechanical memory

city: Tucson

first: Casey

last: Romanoski

state: AZ

address: 1657 E. Helen St.

department: Cellular & Molecular Medicine

institute: University of Arizona

summary: The mechanical microenvironment of primary breast tumors plays a substantial role in promoting tumor progression. While the transitory response of cancer cells to pathological stiffness in their native microenvironment has been well described, it is unclear whether mechanical stimuli in the primary tumor influence distant, late-stage metastatic phenotypes in absentia. Here, we show that primary tumor stiffness promotes stable yet non-genetically heritable phenotypes in breast cancer cells. This “mechanical memory” instructs cancer cells to adopt and maintain increased cytoskeletal dynamics, traction force, and 3D invasion in vitro, in addition to promoting osteolytic bone metastasis in vivo. We established a “mechanical conditioning score” comprised of mechanically-regulated genes as a proxy measurement of tumor stiffness response, and we show that it is associated with bone metastasis in patients. Using a discovery approach, we mechanistically traced mechanical memory in part to ERK-mediated mechanotransductive activation of RUNX2, an osteogenic gene bookmarker and bone metastasis driver. This combination of traits allows for the stable transactivation of osteolytic target genes which persists after cancer cells disseminate from their activating microenvironment. Using genetic, epigenetic, and functional approaches, RUNX2-mediated mechanical memory can be stimulated, repressed, selected, or extended. In concert with previous studies detailing how biochemical properties of the primary tumor stroma influence distinct metastatic phenotypes, the impact of local biomechanical properties we present here support a generalized model of cancer progression in which the integrated properties of the primary tumor microenvironment govern cell behavior in the metastatic microenvironment.

overall_design: Two mechanical conditions were used to grow SUM159 cells: soft (0.5 kPa) and stiff (8.0 kPa) with three biological replicates.

first: Ghassan

last: Mouneimne


title: Next Generation Sequencing of whole SAS and FaDu spheroids transcriptomes treated with Hyperthermia (HT) and Radiation therapy (RT)

city: Dresden

first: Oleg

last: Chen

address: Handelallee 26

institute: OncoRay

summary: By employing a global gene expression profiling, we performed the differential gene expression analysis and the analysis of the molecular pathways which are deregulated in Hyperthermia (HT) and Radiation therapy (RT) treated SAS and FaDu spheroids from the head-and-neck cancer cell lines. The RNA-Seq analysis was done on FaDu and SAS spheroids treated with clinically relevant HT dose of 42.5°C for 60 minutes alone or in combination of single dose irradiation of 7 and 10 Gy for FaDu and SAS, respectively. The main pathways and networks modulated by the treatments (0.5 h after treatment) were identiﬁed using Gene Ontology (GO) enrichment analysis.

overall_design: Direct comparisons of the total genome of Control, RT, HT and HT+RT treated FaDu and SAS spheroids were performed using the Illumina NovaSeq™ 6000 System. Differential gene expression and pathways analysis were done in the format Control versus each Treatment groups (HT, RT and HR+RT) for defined spheroids and also for SAS Control vs. FaDu Control samples. Each of 8 samples has been prepared in 3 replicates.

first: Soňa

last: Michlíková

first: Damian

middle: D

last: McLeod

first: Leoni

last: Kunz-Schughart


title: Integrated analysis of RNA-seq and microRNA-seq depicts miRNA-mRNA networks involved in stripe patterns of Botia superciliaris skin [miRNA-seq]

summary:
 Purpose:In order to elucidate the molecular mechanism of the stripe patterns in B. superciliaris skin.These results will enhance understanding of molecular mechanisms underlying skin pigmentation and facilitate molecular-assisted selection of highly valued skin colors.
Methods:In this study, Illumina sequencing was employed to identify the mRNAs and miRNAs involved in stripe pattern formation in B. superciliaris skin. target prediction revealed a variety of putative target genes; differentially expressed mRNAs and miRNAs patterns were observed in 5 mRNAs and mir-217 by qRT-PCR.
Results:Based on the zebrafish genome, a total of 44,206,176 and 46,941,318 high-quality transcriptome reads were generated, which resulted in 134,586 unigenes that were used as reference sequences. A total of 24,113 genes exhibited significantly different expression patterns (fold-change ≥ 2 or ≤ 0.5 and q ≤ 0.05), including 15,117 up-regulated genes and 8,996 down-regulated genes associated with black and yellow stripes.These genes were enriched in 65 GO terms and 7 KEGG pathways (q ≤ 0.05), which included melanogenesis, and contained  32 up-regulated genes and 12 down-regulated genes. High-throughput miRNA sequencing identified a total of 355 miRNAs, which included 38 novel miRNAs. Furthermore, 87 differentially expressed miRNAs that contained 50 up-regulated and 37 down-regulated miRNAs were identified in different color skin
Conclusions:This study provides novel insight into the mechanism that produces different color stripes in B. superciliaris by combining RNA-seq with small RNA-seq. 5 genes and 1 miRNAs were selected arbitrarily for verification . Compared with previous fish studies, revealed that these DE mRNAs and miRNAs are likely involved in melanin  synthesis, and the quantitative mRNA/miRNA data and pathway information presented here provide a strong basis for elucidation of the detailed functions of mRNAs and miRNAs associated with black and yellow stripe formation in aquarium fish.

overall_design: Black and yellow skin tissue samples were collected from 6 individuals . and mRNA and miRNA library construction and sequencing

first: Jian

last: Zhou

first: Han

last: Zhao


title: Integrated analysis of RNA-seq and microRNA-seq depicts miRNA-mRNA networks involved in stripe patterns of Botia superciliaris skin [RNA-seq]

summary:
Purpose:In order to elucidate the molecular mechanism of the stripe patterns in B. superciliaris skin.These results will enhance understanding of molecular mechanisms underlying skin pigmentation and facilitate molecular-assisted selection of highly valued skin colors.
Methods:In this study, Illumina sequencing was employed to identify the mRNAs and miRNAs involved in stripe pattern formation in B. superciliaris skin. target prediction revealed a variety of putative target genes; differentially expressed mRNAs and miRNAs patterns were observed in 5 mRNAs and mir-217 by qRT-PCR.
Results:Based on the zebrafish genome, a total of 44,206,176 and 46,941,318 high-quality transcriptome reads were generated, which resulted in 134,586 unigenes that were used as reference sequences. A total of 24,113 genes exhibited significantly different expression patterns (fold-change ≥ 2 or ≤ 0.5 and q ≤ 0.05), including 15,117 up-regulated genes and 8,996 down-regulated genes associated with black and yellow stripes.These genes were enriched in 65 GO terms and 7 KEGG pathways (q ≤ 0.05), which included melanogenesis, and contained  32 up-regulated genes and 12 down-regulated genes. High-throughput miRNA sequencing identified a total of 355 miRNAs, which included 38 novel miRNAs. Furthermore, 87 differentially expressed miRNAs that contained 50 up-regulated and 37 down-regulated miRNAs were identified in different color skin
Conclusions:This study provides novel insight into the mechanism that produces different color stripes in B. superciliaris by combining RNA-seq with small RNA-seq. 5 genes and 1 miRNAs were selected arbitrarily for verification . Compared with previous fish studies, revealed that these DE mRNAs and miRNAs are likely involved in melanin  synthesis, and the quantitative mRNA/miRNA data and pathway information presented here provide a strong basis for elucidation of the detailed functions of mRNAs and miRNAs associated with black and yellow stripe formation in aquarium fish.


title: Development of 2D organotypic rat liver co-culture models for assessing hepatotoxicant modes of action

city: Research Triangle Park

first: Michael

middle: B.

last: Black

state: North Carolina

address: 100 Capitola Dr., Suite 106

institute: Scitovation, LLC.

summary: In both the regulatory and commercial arenas, the goal is to move away from time consuming, costly in-life rodent studies and towards safety assessment strategies that rely on testing species-relevant cells in vitro.  The liver has been a major focus of these efforts, yet there are currently no in vitro alternatives for hepatotoxicity testing accepted by regulators, and the assays that do exist typically utilize hepatocyte monolayer culture. While hepatocytes have been the primary component of in vitro hepatotoxicity assay development, the non-parenchymal cells (NPCs) (i.e., hepatic stellate cells, Kupffer cells, and liver sinusoidal endothelial cells) also play a critical role in the progression of liver pathologies. The goal of this study was to develop an organotypic co-culture system that could read out the various mechanisms of action observed in vivo, as well as maintain metabolic capability and extended viability to allow for repeat dosing.  We developed a two-dimensional 96-well plate-based co-culture system that includes primary rat hepatocytes, stellate, Kupffer, and endothelial cells that supports hepatocyte viability and phenotype stability for up to eight days.  Importantly, markers of hepatocyte differentiation and polarity are maintained in co-culture, but hepatocyte monocultures with no other cell types lose phenotypic markers after prolonged culture.  This co-culture model was leveraged to assess the effects of known hepatotoxic stimuli, and the co-culture model resulted in responses that were more representative of the in vivo phenotypes.

overall_design: Freshly isolated male rat Sprague Dawley hepatocytes and non-parenchymal cells were obtained from Lonza (Walkersville, MD) as described.  The cells were cultured in either 2D mono- or co-culture and treated with either Ketoconazole (1, 10, 30 µM), GW7647 (0.01, 0.1, 1 µM), Gemfibrozil (10, 100, 1000 µM), or Phenobarbital (0.1, 1, 10 mM). The cells were treated 24 hours prior to sample collection at 3 timepoints (days 1, 3, and 7 post plating).  After 24 hours, the cells were lysed in TempO-Seq buffer and libraries were prepared for sequencing per manufacturer’s protocols (n=4 biological replicates).

middle: B

first: Jessica

last: Hartman


title: Gefitinib treatment in human  EGFR-driven-Gefitinib resistant tumoral cell line

city: Montpellier

first: Jacques

last: Colinge

address: 208, avenue des Apothicaires

institute: Inserm

summary:
In order to analyze the molecular effect of the combination of Notch inhibitors and EGFR inhibitors on resistance to TKI,
we performed RNA-seq gene expression profiling of PC9 resistant to Gefitinib cells treated with different combinations.

overall_design: Cells were treated with each drug alone (DBZ for Notch inhibition or Gefitinib for EGFR inhibition) or a combination of both drugs.

first: Antonio

last: Maraver

first: Emilie

last: Bousquet

first: Sara

last: Bernardo


title: Differential gene expression of peripheral blood NKp65+ and NKp65- lymphocytes

city: Frankfurt am Main

first: Alexander

last: Steinle

address: Theodor-Stern-Kai 7

department: Institute for Molecular Medicine

institute: Goethe-University Frankfurt am Main

summary: We report differential gene expression in human peripheral blood NK cell enriched cytokine activated NKp65+ vs NKp65- innate lymphocytes.

overall_design: Peripheral blood lymphocytes of 4 healthy donors enriched for NK cell like cells were stimulated in vitro with cytokines (IL-2/-12/-18) for 4 days and emerging NKp65+NKp44+ as well as NKp65-NKp44+ cells were FACSorted and subsequently

first: I

last: Kühnel

last: Vogler

first: C

last: Döring

first: A


title: Onecut1 and Otx2 directly regulate multiple genes expressed early in cone and horizontal cell development [scRNA-seq]

city: BOSTON

first: CHANGHEE

last: LEE

state: MA

address: 77 AVENUE LOUIS PASTEUR

department: Genetics

institute: Harvard Medical School

summary: The development of the retina into a highly organized structure occurs via the production of over 100 cell types from a pool of retinal progenitor cells (RPCs). While some RPCs are capable of making many types of retinal cell types, some terminally dividing RPCs are restricted to the production of specific types of daughter cells. Notably, although such restrictions can be limited to the production of a very specific single cell type, in other cases, production of two very different cell types, such as a photoreceptor and an interneuron, occurs. How specific types of RPCs make specific types of neuron is not fully understood. Combining RNA-seq and ATAC-seq, we compared the transcriptome and chromatin profiles between one type of biased RPC and other types of  RPCs. The biased RPC that was studied is one that we previously defined by its expression of a cis-regulatory module (CRM) for the thyroid hormone receptor beta gene (Thrb), the earliest known marker of cone photoreceptors. In this earlier study, we found that Otx2 and Onecut1 drove expression of this Thrb CRM, as well as regulated expression of the Thrb gene. Here we explored the roles of these Otx2 and Oc1 further. We discovered that their roles extend well beyond regulating Thrb. They collaborate to regulate multiple genes important in cone development and/or function, including Rxrg, a known partner of Thrb. We also identified several new enhancers of genes active in developing cones. These data expand our understanding of the gene regulatory network (GRN) for cone development and contribute new CRMs for vectors that are expressed only in cones, as well as enable the genesis of cones from stem cells, for their use in retinal disease cell and gene therapies.

overall_design: RNA-seq for ThrbPos and ThrbNeg cells in chick

first: Nicolas

last: Lonfat

first: Su

last: Wang

first: ChangHee

last: Lee

first: Jiho

last: Choi

first: Peter

middle: J

last: Park

first: Connie

last: Cepko


title: Genome-wide identification of miRNAs in C. chinense and C. frutescens

city: New Delhi

first: Nirala

last: Ramchiary

address: lab-229, school of life sciences, JNU, New Delhi - 110067

department: School of life sciences

institute: Jawaharlal Nehru University

summary: Profiling of small RNAs identified a total of 359 and 357 conserved; and 490 and 155 novel miRNAs in C. chinense and C. frutescens, respectively. Based on the sequence similarity observed on alignment with already reported plant miRNAs, conserved and novel miRNAs were identified in both the species. The target prediction analysis reveals vital role of miRNAs in regulating genes involved in transcriptions, protein modification, signal transduction and metabolism. Several miRNAs were expressed in a tissue-specific/preferential manner indicating their involvement in tissue/organ development.

sample_organism:
Capsicum frutescens
Capsicum chinense

platform_organism:
Capsicum frutescens
Capsicum chinense

overall_design: Examination of small RNAs sampled from stem, flower, fruits and leaf tissues of C. chinense and C. frutescens.

first: Sushil

last: Chhapekar

first: Nitin

last: Kumar


title: Genome-wide analysis for joint tissues of Fas (ligand) mutant mice during autoantibody induced arthritis

city: Jongro-gu

first: Dongjin

last: Jeong

state: Seoul

address: 103 Daehak-ro

country: South Korea

institute: Seoul National University

summary: Analysis on gene expression between RA-induced WT, Fas^lpr/lpr, and Fas^gld/gld mice. Data shows different expression pattern between Fas^gld/gld joint and Fas^lpr/lpr(or WT) mice. The reseults indicate sFasL-dependent, but Fas-independent gene expression during AIA

overall_design: Total RNA obtained from mouse joint tissues from K/BxN sera(100uL x 2 times) injected C57BL/6, Fas^lpr/lpr, and Fas^gld/gld mice. Harvested at day 10

first: Hye-Sung

last: Kim

first: Doo-Hyun

last: Chung


title: Examine the impact of germ line insulin suppression on embryo gene expression.

city: Dallas

first: Matt

last: Sieber

state: Texas

address: 5323 Harry Hines blvd, MC 9040 ND12.214

institute: UT Southwestern Medical Center

summary: These expeirments compare the polyA selected RNA isolated from progeny 16-20hr old embryos from GFP expressing (control) and InR-DN expressing oocytes.

overall_design: In this experiment we collected 16hr old embryo derived from GFP expressing oocytes and InR-DN expressing oocytes and conducted mRNA seq to indentify genes differentailly regulated in progeny reporgammed by insulin suppression in the maternal germline.

first: Matthew


title: RNA-seq analysis of OE_REP2 and OE_NC in the U-2 OS cell.

city: guangzhou

first: xu

middle: man

last: hao

state: China

address: 132 East Waihuan Rd, Rm 438 Higher Education Mega

department: School of Life Sciences

institute: sun yet-sen university

summary: Analysis of genes rhythmically expressed in OE_REP2 and OE_NC U-2 OS cell

overall_design: Total RNA obtained from isolated U-2 OS cell(OE_REP2 and OE_NC)

first: Guobin

last: Huang

first: Jinhu

last: Guo


title: Bioplatforms Australia: Antibiotic Resistant Sepsis Pathogens Framework Initiative - Streptococcus pneumoniae 4496

city: Sydney

last: Bioplatforms Australia

address: Level 4, Building 4WW, Research Park Drive, Macquarie University

institute: Bioplatforms Australia

summary: The Antibiotic Resistant Sepsis Pathogens Framework Initiative aims to develop a framework dataset of 5 sepsis pathogens (5 strains each) using an integrated application of genomic, transcriptomic, metabolomic and proteomic  technologies. The pathogens included in this initiative are: Escherichia coli, Klebsiella pneumoniae complex, Staphylococcus aureus, Streptococcus pyogenes, and Streptococcus pneumoniae. This submission pertains to strain 4496.

overall_design:
18 samples, 3 conditions, 6 biological replicates per condition.
contributor: Bioplatforms Australia Antibiotic Resistant Sepsis Pathogens Framework Initiative


title: RNA-seq of the testis sample of ICI mice treated with gut microbiota transplant 2wks

city: Qingdao

first: Yong

last: Zhao

state: Shandong

address: 700 Changcheng Road

department: College of Life Sciences

institute: Qingdao Agricultural University

summary: We profiled a RNA-seq on ICR mouse testis. The mice were treated with one dose of busulfan at 3 weeks of age. Then the mice were treated with gut microbiota for 2 weeks. Then after another 3 weeks, testis samples were collected. Then RNA was isoltated from the cultured testis to do RNA-seq.

first: Pengfei

last: Zhang

first: Wei

last: Shen

first: Hongfu


title: ChIP-Seq analysis of H3K27ac following HDAC1,2 inhibition

city: salt lake city

first: Srividya

last: Bhaskara

state: Utah

address: 2000 circle of hope

department: University of Utah

institute: University of Utah

summary: The goal of this study is to examine H3K27ac genome-wide in leukemic cells treated with HDAC1,2 inhibitor

overall_design: SupB15 cells were treated with 2uM ACY0135 for 36hr. SupB15 cells were mixed with Drosophila S2 cells at a ratio of 2:1. CHIP with H3K27ac antibody was performed as described in the manuscript. The sequencing was perfomed with 3 DMSO control samples and 3 ACY1035 treated samples.

first: S


title: Genome-wide nuclesome occupancy following HDAC1,2 inhibitor treatment

summary: The goal of this study is to identify nucleoosme occupancies in leukemic cells treated with HDAC1,2 inhibitor

overall_design: SupB15 cells were treated with 2uM ACY0135 for 62hr. SupB15 cells were mixed with Drosophila S2 cells at a ratio of 4:1. Mnase digestion was performed as described in the manuscript. The sequencing was perfomed with 3 DMSO control samples and 3 ACY1035 treated samples.


title: Genome-wide nuclesome occupancy following HDAC inhbitor and/or doxorubicin treatment

summary: The goal of this study is to identify nucleosome occupancies in leukemic cells treated with either HDAC inhibitor or doxorubicin or HDAC inhibitor plus doxorubicin

overall_design: The sequencing was performed with 2 DMSO control samples, 3 HDAC inhibitor treated samples, 3 doxorubicin treated samples and 3 HDAC inhibitor + doxorubicin treated samples


title: Gene expression in the colon tumor of AOM/DSS-treated RBJ-/- mice

city: Shanghai

first: Taoyong

last: Chen

address: 800 Xiangyin Road

institute: Second Military Medical University

summary: The purpose of this study was to determine which genes are differentially regulated by the Ras-related small GTPase RBJ after induction by AOM/DSS treatment in the colon of C57BL/6 mice compared to RBJ+/+ mice. The results demonstrate decreased induction of cell proliferation-associated genes in RBJ-/- mice than in RBJ+/+ mice on day 80 after AOM/DSS treatment. The majority of differentially expressed genes are regulated by MEK/ERK signaling pathway. Thus RBJ may be involved in the regulation of tumor progression and tumorigenesis.

overall_design: RBJ+/+ and RBJ-/- mice (5/group) were either untreated or treated with AOM (12 mg/kg) on day 0. On day 7, 3 cycles of DSS (2.5% in drinking water; 7 days/cycle) were itiated, each separated by 14 days of vehicle control (water). Mice were sacrificed on day 80 day after AOM treatments.Tumor tissues in distal colon of the mice were prepared for total RNA individually. Equal amounts of RNA derived from 3 individual mice per group were mixed together, and assayed for gene expression using Affymetrix mouse 430 2.0 arrays.

first: Mingjin

last: Yang

first: Zhou

last: Yu

first: Songqing

last: Tang

first: Xuetao

last: Cao


title: Next Generation Sequencing of RNA from HDAC inhibitor and/or doxorubicin treated samples

summary:
Our study represents the first detailed analysis of transcriptomes in HDAC inhibitor and doxorubicin treated leukemic cells.
The goal of this study is to identify gene expression patterns in HDAC and/or doxorubicin treated leukemic cells

overall_design:
SupB15 cells were treated with either 1035 or doxorubicin or the combination of 1035 and doxorubicin.
The sequencing was performed with two independent samples per treatment


title: Pharmacogenetics and Drug Discovery for Anthracycline-Induced Cardiotoxicity Enabled by Sinoatrial Node-like Cells Derived from Human Pluripotent Stem Cells [SNP array]

city: New York

first: Shuibing

state: NY

address: A 827B, 1300 York Ave

department: Surgery

institute: Weill Cornell Medical College

type:
Genome variation profiling by SNP array
SNP genotyping by SNP array

summary: The sinoatrial node (SAN) is the primary pacemaker of the heart. The human SAN is poorly understood due to limited primary tissue access and lack of robust in vitro derivation methods. We developed an efficient strategy, using a dual SHOX2:GFP; MYH6:mCherry knock-in reporter line, to generate and purify human pluripotent stem cell-derived SAN cells (hPSC-SAN), displaying molecular and electrophysiological characteristics of bona-fide nodal cells. We modeled cell type specific toxicity upon treatment with doxorubicin (DOXO) using hPSC-SAN generated from a library of induced pluripotent stem cells (iPSCs).  We discovered 3 new genetic loci associated with increased sensitivity to DOXO-induced hPSC-SAN death. Genetic variants in these loci were associated with significantly higher early arrhythmia risk in patients receiving DOXO, confirmed by an unbiased PheWAS analysis. Finally, the in vitro DOXO assay enabled an unbiased drug screening platform and identification of physcion as a candidate therapeutic that can partially block DOXO-mediated cardiac toxicity.

overall_design: Human induced pluripotent stem cells were derived from individuals and sequenced for SNPs information.


title: Analysis of genome maintenance in Philadelphia-positive leukemia following HDAC inhibition and doxorubicin treatment

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

overall_design: Refer to individual Series


title: Next Generation Sequencing Quantitative Analysis of PCB-exposed and Sham-exposed Rats Liver, Brain, Thymus and Spleen Transcriptomes

status: Public on Jun 30 2021

city: Iowa City

first: Peter

middle: S

last: Thorne

state: IA

address: 51 Newton Rd

department: Occupational and Environmental Health

institute: University of Iowa

summary: Our goal was to investigate the transcriptomes changes on rats liver, brain, thymus, and spleen after exposure to an indoor school air mixture (SAM+) of polychlorinated biphenyls (PCBs). Female Sprague-Dawley rats were exposed to SAM+ at a concentration of 45.5±5.9 µg/m^3 Σ209PCB or filtered air (sham group) 4 h/day, 6 days/week for 13 weeks using nose-only exposure systems. Twenty-four hours after the final exposure, rats were euthanized by carbon dioxide inhalation followed by cervical dislocation. Cardiac blood was collected and organs were excised and stored at -80 °C until analysis.

overall_design: We analyzed 3 samples for each tissue type in each group, a total of 24 samples.

first: Hui

last: Wang

first: Andrea

last: Adamcakova-Dodd

first: Mary

last: Boes


title: Potential Roles of H2A.Z Ubiquitination

city: Nanning

first: Zhenxing

state: Guangxi

address: Zhongshan Street

department: Center for Genomic and Personalized Medicine

institute: Guangxi Medicla University

summary: Nucleosome is a highly dynamic macromolecular complex that is assembled and remodeled by the replacement of major histone variant H2A.Z, thereby affecting nucleosome structure and stability.Here we established two cell lines stably overexpressing wild-type H2A.Z and mutant H2A.Z with ubiquitination deficiency to explore the potential effects caused by H2A.Z ubiquitination. Intriguingly, H2A.Z ubiquitination was first revealed to enhance the stability of H2A-H2A.Z heterotypic nucleosomes.  Chromatin immunoprecipitation (ChIP) coupled with high-throughput sequencing (ChIP-Seq) further revealed that H2A.Z ubiquitination played a crucial role in the transcriptional regulation.

overall_design: (1) we successfully established two cell lines with overexpression of wild-type H2A.Z and mutant H2A.Z with ubiquitination deficiency. (2) The clonogenic ability of established H2A.Z-knockout (H2A.Z-KO) cell line was overexpressed with the H2A.Z (wt) and H2A.Z (mut) vector to evaluate the rescue effects of clonogenic ability. (3) Separation of Mononucleosomes and Identification of H2A-H2A.Z Heterotypic Nucleosomes. (4) H2A.Z Ubiquitination Promotes the Formation and Stability of H2A-H2A.Z Heterotypic Nucleosomes using Co-IP. (5)  Characterization of non-UbH2A.Z and UbH2A.Z-interacting Proteins using silver staining and mass spectrometry. (6)  Chromatin immunoprecipitation (ChIP) coupled with high-throughput sequencing (ChIP-Seq) further revealed that H2A.Z ubiquitination played a crucial role in the transcriptional regulation.

first: Gao

last: jiamin

first: Lu

last: qinchen

last: xianguo

first: Wang

last: qiuyan


title: Dual role of Integrin alpha-6 in glioblastoma: supporting stemness in proneural stem-like cells while inducing radioresistance in mesenchymal stem-like cells

city: Orsay

first: Giorgio

last: Seano

address: Centre Universitaire, Bâtiment 110

institute: Institut Curie

summary: Therapeutic resistance after multimodal therapy is the most relevant cause of glioblastoma (GBM) recurrence. Extensive cellular heterogeneity, mainly driven by the presence of GBM stem-like cells (GSC), strongly correlates with patients’ prognosis and limited response to therapies. Defining the mechanisms which drive stemness and control responsiveness to therapy in a GSC-specific manner is therefore mandatory. Here we investigated the role of integrin a6 (ITGA6) in controlling stemness and resistance to radiotherapy in proneural and mesenchymal GSCs subtypes. Using cell sorting, gene silencing, RNA-Seq and in vitro assays, we verified that ITGA6 expression seems crucial for proliferation and stemness of proneural GSCs, while it appears not to be relevant in mesenchymal GSCs under basal conditions. However, when challenged with a fractionated protocol of radiation therapy, comparable to that employed in the clinical setting, mesenchymal GSCs turned out to be dependent on integrin a6 for survival. Specifically, GSCs with reduced levels of ITGA6 displayed a clear reduction of DNA-damage response and perturbation of cell cycle pathways. These data indicate that ITGA6 inhibition is able to overcome the radioresistance of mesenchymal GSCs, while it reduces proliferation and stemness in proneural GSCs. Therefore, integrin a6 controls crucial characteristics across GBM subtypes in GBM heterogeneous biology and thus may represent a promising target to improve patient outcomes

overall_design: mRNA profiles of MES-GSC CTL or KD for integrin alpha6

first: Elisabetta

last: Stanzani

first: Guillaume

last: Bourmeau

first: Oceane

last: Anezo


title: Complement gene expression in the mouse brain after open-head TBI

city: Charleston

first: Amer

last: Toutonji

state: SC

address: 173 Ashley Ave, CRI204

institute: Medical University of South Carolina

summary: Expression of 59 complemet genes at day 3, day 7, day 28, year 1, and year 2 post injury

overall_design: There are 3 replicates/group. The 8 groups are: sham brains (12-week-old, 1-year-old and 2-year-old), TBI brains (days 3, 7, and 28 post injury and year 1, and 2 post injury)

first: Stephen

last: Tomlinson


title: Neuroinflammatory gene expression in the mouse brain after open-head TBI

summary: Expression of 757 neuroinflammaiton-associated genes in vehicle and complement inhibitor treated TBI brains at days 3, 7 and 28 post injury

overall_design: There are 3 replicates/group. The 7 groups are: sham brains (controls), PBS-treated TBI brains (days 3, 7, and 28 post injury), and CR2-Crry treated TBI brains (days 3, 7, and 28 post injury).


title: Transcriptomic Analysis of Gene Networks Regulated by U11 Small Nuclear RNA in Bladder Cancer

summary: U11 may alter gene expression by affecting the PI3K-Akt signaling pathway and NF-kappa B signaling pathway, regulating alternative splicing events of FN1 and RPL22L1, and ultimately leading to the development of bladder cancer.

overall_design: Small nuclear RNA is a class of non-coding RNA that widely exist in the nucleus of eukaryotes. Accumulated evidence showed that small nuclear RNA involves in the development of tumors. To explore the effect of gene network regulated by U11 small nuclear RNA on the occurrence and development of bladder cancer. U11 small nuclear RNA knockout and overexpression were performed on T24 bladder cancer cell line, and the gene expression of U11 knockout group, overexpression group and untreated control group were analyzed by RNA sequencing. The dysregulated expressed genes in the U11 knockout and overexpression groups were mainly enriched in tumor-related pathways, such as NF-kappa B signaling pathway, Bladder cancer and PI3K-Akt signaling pathway

first: Xi

first: Yaobang

first: Shaomei

first: Chao

last: Feng

first: Lixin

last: Pan

first: Qinchen

last: Lu

first: Yuting

last: Tao


title: Notch1 switches progenitor competence in inducing medulloblastoma

city: Trento

first: Luca

last: Tiberi

state: TN

address: via Sommarive, 9

department: Department of Cellular, Computational and Integrative Biology - CIBIO

institute: University of Trento

summary: The identity of the cell of origin is a key determinant of cancer subtype, progression and prognosis. Group 3 medulloblastoma (MB) is a malignant childhood brain cancer with poor prognosis and few candidates as putative cell of origin. We overexpressed the Group 3 MB genetic drivers MYC and Gfi1 in different candidate cells of origin in the postnatal mouse cerebellum. We found that S100b+ cells are competent to initiate Group 3 MB and we observed that S100b+ cells have higher levels of Notch1 pathway activity compared to Math1+ cells. Interestingly, we found that additional activation of Notch1 in Math1+ and Sox2+ cells was sufficient to induce Group 3 MB upon MYC/Gfi1 expression. Taken together, our data suggest that the Notch1 pathway plays a critical role in Group 3 MB initiation.

overall_design: RNA-sequencing profiles of medulloblastoma samples induced by N1ICD+MYC/Gfi1 (in Math1+ cells) and MYC/Gfi1 (in S100b+ cells) compared with previously published Group 3 MB mouse models (MYC/Gfi1, MYC/Otx2)

first: Claudio

last: Ballabio

first: Matteo

last: Gianesello

first: Konstantin

last: Okonechnikov


title: INTEGRATIVE MULTI-OMICS REVEAL A TWO-ANALYTE BLOOD-BASED SIGNATURE FOR TB DIAGNOSIS IN ADVANCED HIV

city: Salvador

first: Artur

middle: Trancoso Lopo

last: Queiroz

address: Rua Waldemar Falcão, 121

country: Brazil

institute: Instituto Gonçalo Moniz

summary: Tuberculosis (TB) accounts for disproportionate morbidity and mortality among persons living with HIV (PLWH). Conventional methods of TB diagnosis, including smear microscopy and Xpert MTB/RIF, have lower sensitivity in PLWH. Novel high-throughput approaches, such as miRNAomics and metabolomics, may advance our ability to diagnose subclinical and difficult to diagnose TB, especially in very advanced HIV. We conducted a case-control study leveraging REMEMBER, a multi-country, open-label randomized controlled trial comparing 4-drug empiric standard TB treatment with isoniazid preventive therapy in PLWH initiating ART with CD4 cell counts <50 cells/uL. Twenty-three cases of incident TB were site-matched with 32 controls to identify miRNAs, cytokines/chemokines, and metabolites associated with the development of newly diagnosed TB in PLWH. Differentially expressed miRNA analysis revealed 11 altered miRNAs with a fold change higher than ±1.4 in cases relative to controls (p<0.05). Differentially altered metabolite analysis showed no significant alterations in metabolites between cases and controls. We found higher TNFα and IP-10/CXCL10 in cases (p=0.011, p=0.0005), and higher MDC/CCL22 in controls (p=0.0072). A decision tree algorithm identified gamma-glutamylthreonine and hsa-miR-215-5p as the optimal variables to classify incident TB cases (AUC 0.965). hsa-miR-215-5p, which targets genes in the TGF-β signaling pathway, was downregulated in cases. Gamma-glutamylthreonine, a breakdown product of protein catabolism, was less abundant in cases. To our knowledge, this is one of the first uses of a multi-omics approach to identify incident TB in a severely immunosuppressed PLWH study.

overall_design: Evaluation of TB infection on HIV subjects using Multi-Omics

first: Sonya

last: Krishnan

middle: T

first: Amita

last: Gupta

first: Nikhil

last: Gupte

first: Gregory

last: Bisson

first: Johnstone

last: Kumwenda

first: Kogieleum

last: Naidoo

first: Lerato

last: Mohapi

first: Vidya

last: Mave

first: Rosie

last: Mngqibisa

first: Javier

middle: R

last: Lama

first: Mina

last: Hosseinipour

first: Bruno

last: Andrade

first: Petros

last: Karakousis


title: Gene expression changes in rat lung induced by six pyrrolizidine alkaloids

city: Berlin

first: Heike

last: Sprenger

address: Max-Dohrn-Strasse 8-10

department: Food Safety

institute: German Federal Institute for Risk Assessment

summary:
Pyrrolizidine alkaloids (PAs) are secondary plant metabolites that can be found worldwide. They can have an impact to human health by inducing acute toxic effects like veno-occlusive disease in the liver and pulmonary arterial hypertension in the lung. The study focuses on the identification of gene expression changes in vivo in rat lungs after treatment with six structurally different PAs (echimidine, heliotrine, lasiocarpine, senecionine, senkirkine or platyphylline). Rats were treated by gavage daily with 3.3 mg/kg body weight PAs for 28 days. After this subacute exposure the transcriptional changes in the lung were investigated by whole genome microarray analysis.
Transcriptomic analysis with six structurally different PA heliotrine, echimidine, lasiocarpine, senecionine, senkirkine, and platyphylline after subacute treatment of rats

overall_design: 48 array samples (each condition: lung of four animals): Five PAs (echimidine, heliotrine, lasiocarpine, senecionine, senkirkine) + five control samples + one dose of non-toxic PA platyphylline

first: Julia

last: Buchmüller

first: Stefanie

last: Hessel-Pras


title: Transcriptomic analysis of pig intestinal explants exposed or not to deoxynivalenol

city: Toulouse

first: Philippe

last: Pinton

address: 180 Chemin de Tournefeuille

department: TOXALIM

institute: INRAE

summary: Intestinal explants from 5-weeks old piglets were exposed 4h to control or 10 µM deoxynivalenol-contaminated cell culture medium. Explants were nitrogen frozen. RNA were extracted, quantified and their quality was checked with Tapestation 4200 device. RNA samples were used to perform a microarray experiment

overall_design: Intestinal explants were prepared from 5-weeks old piglets. They were exposed 4h to control or 10 µM deoxynivalenol-contaminated cell culture medium. DMSO  used as vehicule was added at the same concentration in control medium.

first: Imourana

last: Alassane-Kpembi

first: Claire

last: Naylies

first: Yannick

last: Lippi


title: Ectopic expression of viral circRNAs in SLK cell line

city: Baltimore

first: Myong-Hee

last: Sung

state: MD

address: 251 Bayview Boulevard, Room 06C226

department: National Institute on Aging

institute: NIH

summary: Total RNA was extracted from SLK cells that constitutively express select KSHV circular RNAs, and transcriptome analysis was performed by deep-sequencing (PE150).

overall_design: Triplicate of SLK cells lines that are expressing circGFP, kcirc54, or kcirc55, as describved in Tagawa et al., Proc Natl Acad Sci USA. 115 (2018) 12805–12810. doi:10.1073/pnas.1816183115.

first: Jerico

last: Santos

first: Takanobu

last: Tagawa

first: Joseph

middle: M

last: Ziegelbauer


title: Back-splice junctions of KSHV circular RNAs

summary: Total RNA of KSHV-infected cells were extracted and RT-PCR was performed using viral circRNA specific divergent primers. Amplicons were sequenced with MiSeq.

overall_design: iSLK-BAC16 and TREx-BCBL1 RTA cell lines were reactivated for lytic infection using Doxicyclin and sodium butyrate for two days followed by RNA extraction and RT-PCR. Amplicons were purified and library preparation was performed followed by deep-sequencing (single-end, 300 nt).

first: Sarah

last: Dremel


title: circRNA-sequencing of a lymph node in a primary effusion lymphoma patient

summary: Total RNA was extracted from a lymph node of a primary effusion lymphoma patient and treated with Rnase R to degrade linear, but not circular, RNA followed by deep-sequencing (PE150).

overall_design: A clinical lymph node sample was dissected from a patient with primary effusion lymphoma for RNA extraction, RNase R treatment, and RNA-Seq.

first: Vishal

last: Koparde


title: Differential expression of genes in roots of rice seedlings with contrasting response under low nitrogen

city: Hyderabad

first: C

middle: N

last: Neeraja

state: Telangana

address: Principal Scientist, ICAR-IIRR, Rajendranagar, Hyderabad 500030

department: Crop improvement

institute: ICAR-Indian Institute of Rice Research

summary: Gene expression study using rice microarray were conducted in root samples of two genotypes, Prasanna and Varadhan at seedling stage under hydroponics with supplemented nitrogen and without nitrogen. The roots displayed morphological differences in terms of root length and overall structure. Higher number of gene families for transporters, transcription factors and some nitrogen uptake transporters were up-regulated in the efficient genotype without nitrogen supplementation. The data overall presents up and downregulated genes, metabolic pathways operated in two genotypes with and without nitrogen supplementation.

overall_design:
14 days seedling in hydroponics, Two replication each, Prasanna and Varadhan IIRR released varieties. NICRA
[contributor]  National Initiative on Climate Resilient Agriculture (NICRA), Indian Council of Agricultural Research (ICAR), Ministry of Agriculture, Govt. of India [F. No. Phy/ NICRA/2011-2012].


title: Differential expression of genes in shoot samples of rice seedlings with contrasting response under low nitrogen

summary: Microarray based expression study in two rice contrasting genotypes  under low nitrogen hydroponics condition microarray revealed upregulated transporter genes for nitrogen uptake in shoot tissues

overall_design:
14 days seedling in hydroponics, Two replication each, Prasanna and Varadhan IIRR released varieties. NICRA
contributor: National Initiative on Climate Resilient Agriculture (NICRA), Indian Council of Agricultural Research (ICAR), Ministry of Agriculture, Govt. of India [F. No. Phy/ NICRA/2011-2012].


title: Molecular etiology behind spaceflight-induced impediment of male mouse bone fracture repair

city: Silver Spring

first: Aarti

last: Gautam

address: 503 Robert Grant Avenue

department: Medical Readiness Systems Biology

institute: WRAIR

summary:
Spaceflight triggers molecular signal of apoptosis and inhibits cell migration to impede bone fracture repair in male mice Activated apoptosis and inhibited cell migration.
Adverse impacts of spaceflight on musculoskeletal health increases the risk of bone fracture and impaired healing. Its yet elusive molecular comprehension warrants an immediate attention in the advent of increasingly frequent space travels. Here we examined the effect of spaceflight on bone healing using a 2mm femoral segmental bone defect (SBD) model. Forty, 9-week old, C57BL/6J male mice were randomized by cage into spaceflight or ground groups; 10 mice from spaceflight or ground groups, respectively underwent SBD surgery and rest served as unoperated sham controls. Surgery/sham procedures occurred 4 days prior to launch, thereafter the spaceflight mice were housed in the rodent habitat at International Space Station for around 4 weeks before their euthanasia. Feeding on same diet, the ground sham/surgery mice were in equivalent housing condition. The right leg femur from half of the spaceflight and ground groups were investigated by micro-computed tomography (µCT). In parallel, the callus regions from surgery groups and corresponding femoral segments in sham mice were probed by global transcriptomics and metabolomics assay. µCT confirmed escalated bone loss in sham spaceflight; and a concomitant trend towards habituation was highlighted by gene-metabolite networks linked to active cellular homeostasis and inhibited morbidity signal in sham spaceflight. The morbidity signal was switched in the spaceflight surgery mice and µCT analyses of spaceflight callus revealed an increased trabeculae spacing and decreased trabecular connectivity. Activated apoptotic signal in spaceflight callus was synchronized with inhibited cell migration signal that was critical for wounds to recruit growth factors, cytokines, and angiogenic agents. A major pro-apoptotic and anti-migration signal, namely RANK-NFκB axis emerged as the central node in spaceflight callus. Concluding, SBD in spaceflight triggered a unique biomolecular mechanism to meet failed regeneration, which merits a customized intervention strategy.

overall_design: Here we examined the effect of spaceflight on bone healing using a 2mm femoral segmental bone defect (SBD) model. Forty, 9-week old, C57BL/6J male mice were randomized by cage into spaceflight or ground groups; 10 mice from spaceflight or ground groups, respectively underwent SBD surgery and rest served as unoperated sham controls. 15 Samples were analyzed ( n=8 Ground, n=7 Flight)

first: Nabarun

last: Chakraborty

first: Ariane

last: Zamarioli

first: Ross

last: Campbell

first: Stephen

last: Mendenhall

first: Paul

last: Childress

first: George

last: Dimitrov

first: Bintu

last: Sowe

first: Aamir

last: Tucker

first: Liming

last: Zhao

first: Rasha

last: Hammamieh

first: Melissa

last: Kacena


title: Distinct gene expression profiles between preterm- and adult-derived intestinal enteroids exposed to Enterococcus faecalis: A pilot study

city: Newcastle

first: Simon

last: Cockell

address: Framlington Place

institute: Newcastle University

summary: To determine if intestinal derived organoids are different between preterm infants and adults

overall_design: 43 samples prepared for bulk RNA Sequencing on the Illumina Novaseq

first: Christopher

last: Stewart

first: Andrea

middle: C

last: Masi


title: RNA sequencing-based analysis of transcriptional reprogramming of primary human monocyte-derived macrophages infected with Mycobacterium tuberculosis

first: Monika

last: Looney

address: 1503 E Jefferson Street

institute: Johns Hopkins University

summary: Primary human monocytes were isolated from four healthy human blood donors. Monocytes were isolated from PBMC buffy coats using plastic adherence for 4 hours. Monocytes were allowed to differentiate into macrophages over a period of 1 week. Macrophages from each of the 4 donors were split into two groups - uninfected and infected with Mycobacterium tuberculosis (Mtb). Cells in the infection group were infected with Mtb for 48 hours at a multiplicity of infection (MOI) of 10. Following incubation, uninfected and infected cells were harvested for RNA. RNA was used for next-generation RNA sequencing. Raw RNA sequencing data was processed using a HISAT2, Stringtie, Ballgown, DESeq2 pipeline. Processed data was used to measure differential expression between uninfected and infected macrophages.

overall_design: RNA sequencing of primary human monocyte-derived macrophages infected with Mtb, strain H37Rv for 48 hours at a MOI of 10.

first: Petros

last: Karakousis


title: SDG708 role in drought tolerance in rice

first: Liufan

last: Yin

state: Shanghai

address: No. 2005, Songhu Road

department: School of Life Science

institute: Fudan University

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

overall_design: Refer to individual Series


title: Integrative Analysis of Sorghum Bicolor Green Prop Roots Under Elevated CO2 and Water Deficit Conditions

city: Rio de Janeiro

first: Luis

middle: Willian

last: Pacheco Arge

state: Rio de Janeiro

address: Av. Carlos Chagas Filho, 373

department: Genetica

institute: UFRJ

summary: Elevated CO2 (E[CO2]) improves the biomass and yield when combined with water-stress in C4 plants. Although several studies described the molecular response of the C4 plant Sorghum bicolor during drought exposure, none reported its combinatorial effect with E[CO2] in the roots. We decided to perform a molecular analysis using green prop roots, the portion of the radicular system photosynthetically active and more sensible to drought. Whole-transcriptome analysis identified 394 up- and 1,471 down-regulated genes. Among the E[CO2] induced pathways, photosynthesis stood out. Carbon fixation, phenylpropanoid, phenolic compounds, and fatty acid biosynthesis-related pathways were repressed. Protein family analysis showed induction of chlorophyll a-b binding protein family, and repression of glutathione-related enzymes. Protein-protein interaction networks exhibited well-defined clusters, including genes related to cell organization and biogenesis, oxireduction process, and photosynthesis being induced. The findings suggest that the E[CO2] mitigates the water deficit by antioxidant and osmoregulation activity, as well as by accumulation of sugaralcohols in the green prop roots, which may be responsible by the increase in biomass together with the cell proliferation. The higher carbon uptake explains the increase in photosynthetic and primary metabolism activities. Our data revealed that green prop roots present an intriguing metabolism under water deficit and E[CO2], showing its crucial role in the drought tolerance acquisition in a predicted future global atmosphere.

overall_design: Sorghum bicolor plants under elevated CO2 and drought stress versus plants under normal concentration of CO2 and drought stress.

first: Tamires

last: Rodrigues

middle: W

last: Arge

first: Marcio

last: Alves-Ferreira