title: RNA sequencing of rhesus macaque prefrontal cortex and human embryonic stem cell after sevoflurane exposure

status: Public on Sep 10 2020

city: shanghai

first: yanyong

last: cheng

address: 639 Zhizaoju Road

department: Department of Anesthesiology

institute: Shanghai Ninth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

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

sample_organism:
Macaca mulatta
Homo sapiens

platform_organism:
Macaca mulatta
Homo sapiens

overall_design: Refer to individual Series


title: RNA sequencing of Macaca mulatta prefrontal cortex after sevoflurane exposure

country: China

type: Expression profiling by high throughput sequencing

summary: RNA sequencing analysis of macaque’s prefrontal cortex

overall_design: 6 samples of macaque’s prefrontal cortex were used in this study. There were two groups, Ctrl and Sevoflurane, 3 replicated sample were included in each group.

first: Lei

last: Zhang


title: RNA sequencing of human embryonic stem cell after sevoflurane exposure

summary: RNA sequencing analysis of human embryonic stem cell

overall_design: 2 samples of human embryonic stem cell, Ctrl and Sevoflurane.


title: How to Make an Elephant: Functional Genomic Divergence and the Evolution of Cancer Suppression

city: Salt Lake City

first: Chris

last: Gregg

state: UT

address: 20 South 2030 East

department: Neurobiology and Anatomy

country: USA

institute: University of Utah

summary: Contrast the genomes of different elephants species to find genetic differences underlying species differences like immune system differences that impact disease resistance.

overall_design: Define genes that are differentially expressed between Asian and African Elephants. The Asian elephant is in the SRA database under SRP065915 and BioProject PRJNA301482.

first: Marc

last: Tollis

first: Lisa

last: Abegglen

first: Elliott

last: Ferris


title: Attenuating Hypoxia Driven Malignant Behavior in Glioblastoma with a Novel Hypoxia-Inducible Factor 2 Alpha Inhibitor

city: Winston-Salem

first: Jeff

last: Chou

state: NC

address: Medical Center Blvd

institute: Atrium Health Wake Forest Baptist

overall_design: RNA Seq Analysis of Orthotopic Mice GBM tumors treated with a HIF2a inhibitor, PT2385

first: Hawkins

last: Gregory

first: Sanders

last: Stephanie

first: Renfrow

last: Jaclyn


title: Development of gene expression signatures in the liver cancer cells with FXR overexpression and FXR activation

city: fuzhou

first: xiongfei

last: huang

state: fujian

address: 1 Xue Yuan Road,University Town

institute: :Fujian mecical university

summary: To investigate the role of nuclear receptor FXR during hepatocarcinogenesis, HepG2 cels and SK-Hep-1 cells were transfected with lentiviral mediated FXR overexpressive vector or the negative control. After the cells were treated with FXR agonist GW4064 2uM for 24 h, and total RNA were isolated for detection of gene expression .

overall_design: HepG2 cels and SK-Hep-1 cells were transfected with lentiviral mediated FXR overexpressive vector or the negative control. Then the cells were treated with FXR agonist GW4064 2uM for 24 h, and total RNA were isolated for detection of gene expression .

first: Xiongfei

last: Huang

first: Ningbo

last: Li

first: Yeting

last: Zeng

first: Xinrui

last: Wang


title: Expansion of human colonic organoids from tissue biopsies in a fully defined hydrogel matrix

status: Public on Sep 12 2020

city: Herlev

first: Ole

middle: Haagen

last: Nielsen

address: Borgmester Ib Juuls Vej 1

department: Dept. of Gastroenterology

country: Denmark

institute: Herlev Hospital

summary: Intestinal organoids have widespread applications across a variety of fields, but the dependency on basement membrane extract (BME) has hampered the transition towards clinical utilization. To overcome the limitations of BMEs, we identified an easy-to-use and fully defined extracellular matrix for the culture of human colon organoids established directly from tissue biopsies. Human colonic organoids were established from crypt-derived single cells (from six different patient samples) and cultured in QGel® CN99 or the BME benchmark Matrigel® for six culture passages (median 58 days), after which RNA was harvested for further analysis. The CN99 matrix effectively enabled organoid formation and growth, as well as efficient cell expansion, completely by-passing the use of BME. We expect this fully defined matrix to improve the reproducibility of organoid studies and to advance the translational use of the organoid technology.

overall_design: RNA-seq was performed on an Illumina PE150 system on 12 RNA samples derived from healthy colon organoids from 6 different patients cultured for 6 passages in QGel® CN99 and in Matrigel®. The expression profiles of organoids cultured in the two extracellular matrix conditions were compared.

first: Fredrik

last: Bergenheim

first: Giulia

last: Fregni

first: Cara

middle: F

last: Buchanan

first: Lene

middle: B

last: Riis

first: Mathieu

last: Heulot

first: Jeremy

last: Touati

first: Jakob

last: Seidelin

first: Simone

middle: C

last: Rizzi

middle: H


title: The NKL-code for innate lymphoid cells reveals deregulated expression of NKL homeobox genes HHEX and HLX in ALCL

city: Braunschweig

first: Claudia

last: Pommerenke

address: Inhoffenstraße 7B

country: Germany

institute: Leibniz Institute DSMZ


title: Specific biomarkers Associated with Active and Chronic Renal Lesions in IgA Nephropathy. A Multicenter Study

status: Public on Sep 13 2020

city: Valenzano-Bari

first: Sharon

middle: Natasha

last: Cox

department: Renal Lab

country: Italy

institute: Schena Foundation

summary: Specific molecular biomarkers were detected in kidney biopsy of IgA nephropathy characterizing active (E and C) and chronic (T) renal  lesions compared with other non-IgA glomerulonephritis and living donors

overall_design: RNA was extracted from archival FFPE biopsy samples of 52 IgAN patients, 22 non-IgAN glomerulonephritis (non-IgAN GN) and 7 kidney living donors (LD). Genome-wide gene expression profiles were generated and stringent statistical analysis identified transcripts associated with active and chronic renal lesions. gAN patients were scored using the MEST-C classification by three pathologists (MR, BMA, CG) and stratified into 4 groups with different composite renal lesions: minimal N.22 (M0,1; E0; S0,1; T0; C0); active N. 8 (M0,1; S0,1; T0; E1 and/or C,1,2); chronic N:12 (M0,1; E0; S0,1; T1,2; C0); mixed group of active and chronic lesions N.10(M0,1; E0,1; S0,1; T1,2; C0,1,2).

middle: N

first: Samantha

last: Chiurlia

first: Chiara

last: Divella

first: Michele

last: Rossini

first: Francesco

middle: P

last: Schena

first: Gianluigi

last: Zaza


title: Monocyte Subsets with High Osteoclastogenic Potential and Their Epigenetic Regulation Orchestrated by IRF8 [RNA-Seq sorted cells]

status: Public on Sep 11 2020

city: Baltimore

first: Vivek

last: Thumbigere Math

state: MD

address: 650 W Baltimore Street

department: Periodontics

institute: Universityof Maryland

summary: Currently, it is unclear if all monocyte subsets exhibit osteoclastogenic potential. Furthermore, the role of lineage determining TFs in regulating OC differentiation on a genome-wide scale remains poorly understood. In this study, we utilized a novel Irf8 conditional knockout (Irf8 cKO) mouse model to characterize the importance of IRF8 in OC progenitor development and epigenetic regulation of OC differentiation. To identify global transcriptional program governing the osteoclastogenic potential of Ly6Chi, Ly6Cint, and Ly6C– monocytes, and how it may be further influenced by IRF8 deficiency, we performed RNA-seq on sorted Ly6Chi, Ly6Cint, and Ly6C– cells from WT and Irf8 cKO mice. Cells were analyzed prior to (BMMs) and 4 days after RANKL stimulation (OCs). Here we show that WT Ly6Chi and Ly6Cint monocytes developmentally contain OC-specific transcripts, which are augmented upon RANKL stimulation. Additionally, in the absence of IRF8, OC-specific transcripts in all three monocyte subsets are primed to robustly respond to RANKL stimulation.

overall_design: We performed RNA-seq on sorted Ly6Chi, Ly6Cint, and Ly6C– cells from WT and Irf8 cKO mice. Results include RNA-seq analysis of transcriptional changes in BMMs stimulated with MCSF (day 0) and OCs stimulated with MCSF plus RANKL (day 4). Both male and female mice and cells obtained from both genders were analyzed in this study.

first: Thumbigere-Math

last: Vivek

first: Shetty

last: Amol

first: Das

last: Amitabh

first: Brooks

last: Stephen


title: Monocyte Subsets with High Osteoclastogenic Potential and Their Epigenetic Regulation Orchestrated by IRF8

type: Genome binding/occupancy profiling by high throughput sequencing


title: Differential transcriptional responses in human cardiomyocytes

city: St Louis

first: Tiandao

last: Li

state: MO

address: 4444 Forest Park Ave

institute: Washington University

summary: We report the application of a pericentriolar material 1 (PCM-1) based cardiomyocyte-specific nuclear isolation protocol on human cardiac tissue to specifically ask what transcriptional changes occur in cardiomyocytes of humans with atrial fibrillation. We performed RNA-sequencing on the cardiomyocyte-specific nuclear RNA and found that there are more differentially dysregulated (1343) than similarly regulated transcripts (99) in the right versus left atria. This study is the first of its kind aimed at understanding the transcriptional changes that occur specifically in the left and right atrial cardiomyocytes of humans with atrial fibrillation.

overall_design: Cardiomyocyte nuclear mRNA profiles of human heart tissue samples (RA, LA, RV, LV).

first: Stacey

middle: L

last: Rentschler


title: Effect of Nicotine on neural tube development

city: Institute

first: Sridhar

middle: A

last: Malkaram

state: West Virginia

address: Barron Drive

department: Mathematics and Computer Sciences

institute: West Virginia State University

summary:
Neural tube defects (NTD) occur in 3000 births per year in the US. Several risk factors have been proposed for NTDs including both first hand and passive smoking during the periconceptual period. Previously we reported an increased frequency of cervical region NTD in a chicken model of prenatal nicotine exposure (Bohn, Humphrey et al. 2014; Humprey, Bohn et al. 2014). Here, we will reveal the mechanisms of the insult. The specific aims include: 1) Evaluation of the gene expression changes in the chicken model of nicotine exposure that we developed previosly. Such genome-wide analysis of the expression allows to collect very detailed data regarding the drug impact. To our knowlidge, comparable analysis of nicotine induced changes in gene expression during development of any species has never been conducted. 2) Evaluation of nicotine induced alterations in tadpoles (Xenopus tropica). The frogs will be treated in a manner similar to chicken (the same drug doses and a matched time of sacrifice) and analyzed both histologically and for gene expression. Incorporation of a different group of vertebrates in this study is essential for dissecting the evolutionary conserved role this pathway of interest in development which is another strong aspect of this proposal. We believe, that our comparative approach will allow more effective extrapolation of data from animal models to humans and better understanding of the evolutionary process.
Nicotine is one of the most common developmental insults in humans. The consequences of this exposure  are well-documented. However, the affected pathways are unknown. The identification of the mechanisms of  nicotine induced alterations proposed here is vital for development of better treatment strategies.

overall_design: There are 2 variables, Nicotine treatment  (Nicotine treated and control) and days of incubation (5 days and 7 days).  For each treatment 4 biological replicates were used.

first: Natalia

last: Omelchenko

first: Rebecca

last: Barns

first: James

last: Denvir

first: Jian

last: Wang

first: Jun

last: Fan

first: Shuo

last: Wei

first: Donald

last: Primerano

first: Melinda

last: Kreisberg


title: Transcriptional profiling of hepatocyte, reprogrammed hepatocyte, and biliary cells [human]

status: Public on Sep 09 2020

city: New York

first: Jinyang

state: New York

address: 1230 York Ave

institute: The Rockefeller University

summary: Comparison of transcripts between human hepatocytes, human hepatocytes reprogrammed into biliary cells, and human biliary cells shows similarities between reprogrammed cells and the untreated biliary population

overall_design: Human hepatocytes were transplanted into a mouse liver and then reprogramming induced by DDC treatment. Transcripts from human hepatocytes, reprogrammed cells, and biliary cells were then sequenced.

first: Allyson

last: Merrell

first: Ben

last: Stanger


title: An animal study for evaluating the dose-dependent effects of fermented mixed grain enzyme food for adiposity and its metabolic disorders in high-fat-diet induced obese mice

city: Daegu

first: Youngji

last: Han

address: Daehakro 80

country: South Korea

institute: Kyungpook National University

summary: From a long time ago, supplementation of fermented enzyme foods could have worked health effects on the body in the east nevertheless, only a few studies reported functions of them such as weight loss and metabolic syndrome. Thus, it is necessary to be verified whether supplementation of fermented enzyme foods can act in the body as a functional material. Therefore, we investigated the anti-obesity effects of fermented mixed grain with digestive enzymes (FMG) in high-fat diet induced mice. Sixty C57BL/6J mice were divided into six dietary groups and fed a normal diet (ND), a high-fat diet (HFD), Bacilus Coagulans group, steamed grain group, low-dose fermented mixed grain group(L-FMG), high-dose fermented mixed grain group (H-FMG) supplement for 12 weeks. After sacrificing, body weight and body fat mass in H-FMG group were significantly decreased compared to HFD group with a simultaneous decrease in plasma lipids. Also, H-FMG significantly decreased the blood glucose and improved the glucose tolerance compared to HFD group. Moreover high-dose FMG supplementation dramatically decreased the levels of inflammatory cytokines which secreted from adipocyte. Taken together, our findings suggest that H-FMG ameliorate high fat-diet induced obesity and its complication and could be used as a potential preventive agent for obesity.

overall_design: Four-week-old male C57BL/6J mice were obtained from Jackson Laboratory (Bar Harbor, ME, USA). All mice were individually housed under constant temperature (24 ◦C) and 12-h light/dark cycle. After a 1-week acclimation on a normal chow diet, the mice were then randomly divided into six groups, and each group was fed one of the following diets for 12 weeks: Normal diet (ND, 10% kcal from fat, n = 10); High fat diet (HFD, 40% of kcal from fat, n = 10); Bacilus Coagulans group (BC, HFD with 0.3% Bacilus Coagulans (w/w), n = 10); 0.3% Steamed grain group (SMG, HFD with 0.3% steamed grain (w/w), n = 10); Low-dose fermented mixed grain group (L-FMG, HFD with 0.3% fermented mixed grain (w/w)); High-dose fermented mixed grain group (H-FMG, HFD with 0.9 % fermented mixed grain (w/w)).

first: Myung-Sook

last: Choi


title: Contact-dependent traits in Pseudomonas syringae B728a.

status: Public on Sep 14 2020

city: Central Point

first: Monica

middle: Nicole

last: Hernandez

state: OR

address: 569 Hanley Road

institute: Oregon State University

summary: Many bacteria can transition from a planktonic lifestyle to life attached to a surface. Changes in gene expression have been documented in bacteria in mature biofilms, but few studies have looked at gene expression during the initial stages of surface attachment. To investigate this, we performed RNA-Seq using the model organism Pseudomonas syringae B728a which has been found in rivers and lakes but is known for living on the leaf surface. We compared gene expression of wild-type P. syringae B728a cells attached to a filter for 2 hours to the gene expression of wild-type P. syringae B728a cells in King's medium B broth. We found that certain gene catergories were quickly induced when cells were on a surface such as flagellar synthesis and motility while other gene categories were quickly repressed such as phytotoxin synthesis and transport. These fast changes in gene expression suggest that P. syringae B728a uses surface attachment as a potential cue to better adapt to life on a surface.

overall_design: Examination of gene expression in Pseudomonas syringae B728a cells using RNA sequencing. Gene expression of P. syringae B728a cells attached to a filter for 2 hours was compared to gene expression of P. syringae B728a cells in broth culture. Three replicates were used per condition.

first: Steven

middle: E

last: Lindow


title: Next generation sequencing facilitates quantitative analysis of pAd-KLF5- and pAd-Control-infected mouse VSMC transcriptomes

city: Tangshan

first: Dong

last: Ma

state: Hebei

address: No. 21 Bohai Avenue, Caofeidian New Town, Tangshan, Hebei Province

department: School of public health

institute: North China University of Science and Technology

summary:
Purpous: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathway. The goals of this study are to compare different gene expression between pAd-KLF5- and pAd-Control-infected mouse VSMC.
Methods: adenovirus vectors either encoding KLF5 or empty adenovirus vector were transfected into mouse VSMCs. shSirt6 transfected or shControl transfected VSMCs samples were performed RNA sequencing (RNA-seq) analysis, functional enrichment analyses of gene ontology (GO) and gene set enrichment analysis (GSEA).
Results: eIF5a is found to be highly expressed and predictive target of KLF5 in VSMCs. KLF5-enhanced VSMCs demonstrated cell proliferation and were noted to have promoted cell cycle progression between the G2 and M phases. In accordance with the gene set enrichment analysis (GSEA) according to RNA-sequencing, ATP biosynthesis and cell redox homeostasis was upregulated upon KLF5 overexpression.
Conclusion:  These findings provide mechanistic insights into the oncogenic activity of KLF5 for the first time.

overall_design: RNA profiles of test and control samples were generated by deep sequencing, using Illumina HiSeq 4000.

first: Jin-Kun

last: Wen


title: RNA Sequencing Analysis of Wild Type and Myrf +/− mice Retina

city: Guangzhou

first: Xiaowei

last: Yu

address: No.7 jinsui road

institute: Zhongshan ophthalmology center, Sun yat-sen University

summary: We have created a Myrf knockdown (Myrf +/−) mutant mouse strain and investigated the molecular phenotype of reduced MYRF expression in the retina using RNA-sequencing.  As an initial finding, photoreceptor defects with impaired functions of spatial vision and retinal electrophysiology were found in Myrf +/− mice, indicating an important role of MYRF in retinal development.It was revealed through RNA-seq that the expression of phototransduction and estrogen signaling pathways reduced in Myrf +/− mice. Thus, alterations of phototransduction and estrogen signaling pathways seem to play important roles in connecting Myrf deficiency with retinal photoreceptor defects.

overall_design: Retinal RNA profiles of wild type (WT) and Myrf +/− mice

first: Zhigang

first: Nannan

last: Sun


title: DeepH&M: Simultaneous determination of single-CpG hydroxymethylation and methylation levels from enrichment and restriction enzyme sequencing methods

city: SAINT LOUIS

first: Daofeng

last: Li

address: 4515 McKinley Avenue

department: Genetics

institute: Washington University in St. Louis

type: Methylation profiling by high throughput sequencing

summary: Increased appreciation of 5-hydroxymethylation (5hmC) as a stable epigenetic mark, which defines cell identity and disease progress, has engendered a need for cost-effective, but high-resolution 5hmC mapping technology. Current enrichment-based technologies provide cheap, but low-resolution and relative enrichment of 5hmC levels while single base-resolution methods can be prohibitively expensive to scale up to large experiments.  To address this problem, we developed a deep learning-based method “DeepH&M”, which integrates enrichment and restriction enzyme sequencing methods to simultaneously estimate absolute hydroxymethylation and methylation levels at single CpG resolution. Using 7-week-old mouse cerebellum data for training DeepH&M model, we demonstrated that the 5hmC and 5mC levels predicted by DeepH&M were in high concordance with gold standard data predicted by TAB-seq and WGBS. The DeepH&M model can be applied to 7-week old frontal cortex and 79-week cerebellum revealing the robust generalizability of this method to other tissues from various biological time points.

overall_design: WGBS, TAB-seq were generated for 7w and 79w mouse cerebellum and cortex. RNA-seq were generated for 7w and 79w mouse cerebellum.

first: Yu

last: He

first: Ting


title: Transcriptional profile changes in dedifferentiating Müller glia in mammalian cell culture after treatment with an α7 nicotinic acetylcholine receptor agonist

city: Kalamazoo

first: Cindy

last: Linn

state: MI

address: 1903 W. Michigan Avenue

department: Biological Sciences

institute: Western Michigan University

summary:
Purpose: Eye drop application of PNU-282987, an α7 nAChR agonist, causes regeneration through activation of Müller glia (MG) in the adult rodent retina. The goals of this study are to examine the transcrptional changes through RNA-seq after treatment with PNU-282987 in mammalian MG cell culture that result in dedifferentiated MG that have a retinal progentior cell(RPC)-like fate and to vallidate RNA-seq differentially expressed genes with qRT-PCR and immunocytochemistry.
Methods: Retinal pigment epithelium (RPE-J) cells were treated with PNU-282987 for 24 hours and then washed extensivley. These treated RPE cells were co-cultured via a transwell system with MG (rMC-1) cell culture for 0, 12, 24 and 48 hours. RNA was extracted from MG using Zymo Direct-zol RNA miniprep kit and mRNA proflies were generated by GeneWiz with the Illumina NextSeq 550 high-output platform.
Results: Using an optimized data analysis workflow, GeneWiz mapped about 30 million sequence reads per sample to the rat genome (Rnor6.0) and identified over 15,000 transcripts. Deseq2 analysis was performed to determine log 2 fold changes in gene expression compared to DMSO control and found 1050 significantly differentially expressed genes and 12 of these were validated with qRT–PCR to compare trends. Notably, the HB-EGF/Ascl1/Lin28 pathway was signficantly upregulated. ICC showed expression of RPC genes that were also seen in the RNA-seq profile.
Conclusions: PNU-282987 activation of RPE causes signficant transcript profile changes in MG cell culture that leads to upregulation of the HB-EGF/Ascl1/Lin28 pathway that was seen with RNA-seq profiles and validated with qRT-PCR. Further, these gene expression changes lead to dedifferentation of MG to an RPC-like fate and expression of several retinal RPC markers were found in RNA-seq data set and was validated with immunocytochemistry. Our study is the first to show that activaiton of the α7 nAChR on RPE can lead to MG dedifferentiation and that the HB-EGF/Ascl1/Lin28 pathway is upregulated in these cells.

overall_design: RPE-J cell lines were treated with DMSO (vehicle control) or PNU-282987 for 24 hours before being extensivley washed. RPE-J cells were allowed to grow in reponse to treatment for 24 hours before being put into a transwell co-culture system with rMC-1 cells. rMC-1 cells were allowed to be in contact with PNU treated RPE-J cells for 8, 12, 24, 48h or with DMSO treated RPE-J cells for 48h. rMC-1 cells were trypsinized and collected for RNA extraction. RNA was shipped overnight on dry ice to GeneWiz for RNA-seq analysis resulting in Log2 fold changes for differentially expressed genes.

first: Megan

last: Stanchfield

first: Sarah

last: Webster


title: RAPID DEHYDRATION OF GRAPE BERRIES DAMPENS THE POST-RIPENING TRANSCRIPTOMIC PROGRAM AND THE METABOLITEPROFILE EVOLUTION

city: VR

first: Alessandra

last: Amato

address: strada le grazie 15

institute: University of Verona

summary: The postharvest dehydration of grape berries allows theaccumulation of sugars and other solutesand promotes the synthesis of aroma compounds unique to high-quality raisin wines such as thepassito wines made in Italy. These dynamic changes are dependent on environmental parameters such as temperature and relative humidity,as well asendogenous factors such as berry morphology and genotype, but the contribution of each variable isnot well understood.Here wecompared berries subjected to natural or accelerated dehydration, the latterdriven by forced airflow.We followed the evolution of transcript andmetaboliteprofiles and found that accelerated dehydration clearly dampened the natural transcriptomic and metabolomic programs of postharvest berries. We found that slow dehydration over a prolonged duration isnecessary to inducegene expression and metabolite accumulation associated with the final quality traits of dehydrated berries. The accumulation of key metabolites (particularly stilbenoids)during postharvest dehydration isinhibited by rapid dehydration conditions that shorten the berry life time.

overall_design: Transcriptomic changes occurring during post-harvest dehydration conducted in different environmental condition, were inspected by a microarray analysis performed on drying grape berries collected over the processes. At each time points, three biological replicates were collected.

first: Sara

last: Zenoni

first: Erica

last: D'Incà

first: Flavia

last: Guzzo

first: Giovanni

last: Tornielli


title: Leukemias from NP23-NHD13 double transgenic mice - WES study

city: Bethesda

first: Yuelin

middle: Jack

last: Zhu

address: 9000 Rockville Pike

department: Genetics Branch, Center for Cancer Research

institute: NCI

type: Genome variation profiling by high throughput sequencing

summary: Whole exome sequencing (the SureSelectXT Mouse All Exon Kit) was done on leukemias from NP23-NHD13 double transgenic mice with strain background designated “C57Bl6-NIH”.

overall_design: 17 NP23-NHD13 thymic AML mice compared with the WT mice.

first: Peter

middle: D

last: Aplan

first: Subhadip

last: Kundu


title: An antibiofilm effect against Salmonella typhimurium rdar biofilm formation upon treatment with the macrolide clarithromycin

city: Stockholm

first: Ute

last: Römling

address: Solnavägen 9

department: Department of Microbiology, Tumor and Cell Biology

country: Sweden

institute: Karolinska Institutet

summary: Upon biofilm formation, production of extracellular matrix components and alteration in physiology and metabolism allows bacteria to build up multicellular communities which can facilitate nutrient acquisition during unfavorable conditions and provide protection towards various forms of environmental stresses to individual cells. Thus, bacterial cells become tolerant against antimicrobials and the immune system within biofilms. In the current study, we evaluated the antibiofilm activity of the macrolides clarithromycin and azithromycin. Clarithromycin showed antibiofilm activity against rdar (red, dry and rough) biofilm formation of the gastrointestinal pathogen Salmonella typhimurium ATCC14028 Nalr at 1.56 µM subinhibitory concentration in standing culture and dissolved cell aggregates at 15 µM in a microaerophilic environment suggesting that the oxygen level affects the activity of the drug. Treatment with clarithromycin significantly decreased transcription and production of the rdar biofilm activator CsgD, with biofilm genes such as csgB and adrA to be consistently downregulated. While fliA and other flagellar regulon genes were upregulated, apparent motility was downregulated. RNA sequencing showed a holistic cell response upon clarithromycin exposure, whereby not only genes involved in the biofilm-related regulatory pathways, but also genes that likely contribute to intrinsic antimicrobial resistance, and the heat shock stress response were differentially regulated. Most significantly, clarithromycin exposure shifts the cells towards an apparent oxygen- and energy- depleted status, whereby the metabolism that channels into oxidative phosphorylation is downregulated, and energy gain by degradation of propane 1,2-diol, ethanolamine and L-arginine catabolism, potentially also to prevent cytosolic, is upregulated. This analysis will allow the subsequent identification of novel intrinsic antimicrobial resistance determinants.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium

overall_design: RNA isolation from six samples; three samples untreated without clarithromycin, three samples treated with 15 µM clarithromycin. All samples contained 1.5 (v/v) % DMSO.

first: Munirah

last: Zafar

first: Humera

middle: J

last: Choudhary

first: Sulman

last: Shafeeq


title: Organism Dual RNA-Seq Reveals the Control on both Pathogen and Host through BarA/UvrY of Vibrio parahaemolyticus for Successful Infection

city: Macau

first: wenwen

last: Zhang

address: University of Macau,  Avenida de Universidade, Taipa

country: Macau

institute: Zhang Wenwen

summary: Elucidation of host-pathogen interaction is essential for developing effective strategies to combat bacterial infection. Dual RNA-Seq using cultured cells or tissues/organs as the pathogen host has emerged as a novel strategy to understand the response concurrently from both pathogen and host at cellular level. However, bacterial infection mostly causes systematic responses from the host at organism level where the interplay is urgently to be understood but inevitably being neglected by the current practice. Here, we developed an approach that simultaneously monitor the genome-wide infection-linked transcriptional alterations in both pathogenic Vibrio parahaemolyticus and the infection host nematode Caenorhabditis elegans. Besides the dynamic alterations in both transcriptomes of C. elegans and V. parahaemolyticus during infection, we identify a two-component system, BarA/UvrY, that are essential for host colonization. BarA/UvrY not only controls the virulence factors in V. parahaemolyticus including Type III and Type VI secretion systems, but also represses the MAP kinase mediated signaling cascades to attenuate innate immune responses. Thus, our study exemplifies the use of dual RNA-Seq at organism level to uncover previously unrecognized interplay between host and pathogen.

sample_organism:
Vibrio parahaemolyticus
Caenorhabditis elegans

overall_design: Investagation  of  cross-talk between host and pathogen

first: Ruiqiang

last: Xie

first: Jun

last: Zheng


title: Astroglial FMRP deficiency cell-autonomously up-regulates miR-128 and disrupts developmental astroglial mGluR5 signaling (miRNA)

city: Boston

first: Yongjie

last: Yang

state: MA

address: 136 Harrison Ave

institute: Tufts University School of Medicine

summary: The loss of fragile X mental retardation protein (FMRP) causes fragile X syndrome (FXS), the most common inherited intellectual disability. How the loss of FMRP alters protein expression and astroglial functions remains essentially unknown. Here we showed that selective loss of astroglial FMRP in vivo up-regulates a brain-enriched miRNA, miR-128-3p, in mouse and human FMRP-deficient astroglia, which suppresses developmental expression of astroglial metabotropic glutamate receptor 5 (mGluR5), a major receptor in mediating developmental astroglia to neuron communication. Selective in vivo inhibition of miR-128-3p in FMRP-deficient astroglia sufficiently rescues decreased mGluR5 function, while astroglial overexpression of miR-128-3p strongly and selectively diminishes developmental astroglial mGluR5 signaling. Subsequent transcriptome and proteome profiling further suggests that FMRP commonly and preferentially regulates protein expression through posttranscriptional, but not transcriptional, mechanisms in astroglia. Overall, our study defines an FMRP-dependent cell-autonomous miR pathway that selectively alters developmental astroglial mGluR5 signaling, unveiling astroglial molecular mechanisms involved in FXS pathogenesis.

overall_design: miRNA expression was profiled in cortical astroglia of Fmr1+/y and Fmr1−/y mice.

first: Yuqin

last: Men

first: Yongie


title: Gene expression differences among Neuropilin1 (NRP1) knockdown cell lines

city: Xiamen

first: Wanyun

last: Lee

state: Fujian

address: Xiang'an South Road, Xiang'an District

institute: Xiamen University

summary: To further find out candidates down or up regulated by Neuropilin1(NRP1)

overall_design: MDA-MB-231-shctrl,MAD-MB-231-shNRP1,HT29-shctrl and HT29-shNRP1 cell lines were cultured in 6-well plates,collect cells in a cryopreservation tube

first: Zhizhong

last: Lin

last: Li


title: Analysis of mRNA expression in human skin fibroblasts WS1 cells between IFI6-overexpression and control upon irradiation.

city: Suzhou

first: Shuyu

address: Ren Ai Road 199

institute: Suzhou University

summary: This study aims to compared mRNA expression between IFI6-overexpressed WS1 cells and NC by RNA-Seq. In this study, WS1 cells were divided into two groups and each group had four repeats, one group was infected by IFI6-overexpressed lentivirus and another was infected by NC lentivirus. The two groups of cells were then irradiated with a single 5 Gy dose of radiation at a fixed rate of 1.15 Gy/min using an X-ray linear accelerator (Rad Source Technologies Inc., Suwanee, GA, USA). 24 hours post irradiation, WS1 cells from IFI6-overexpression and NC were collected and subjected to mRNA expression analysis.

first: Huimin

last: Jia


title: CUT&Tag for analysis of Nrf2-regulated genes in liver of heat-stressed chicken (Gallus gallus)

city: Shanghai

first: Ding

last: Yu

address: Number 953 Jianchuan Road

institute: Newcore biotechnology

summary: The aim of the present study was to investigated the difference of Nrf2-regulated genes in livers between normal and heat-stressed chickens. The CUT&Tag and high-throughput sequencing technologies were used in this experiment. Results showed that 13171838- 15417444 clean reads were obtained in this study. These data suggested that there were many Nrf2- regulated genes in the liver of heat-stressed chicken.

overall_design: CUT&Tag for analysis of Nrf2-regulated genes in liver between normal and heat-stressed chickens

first: Hong

last: Hu

first: Xi

last: Bai


title: Expression data in EC109 and KYSE510 cells

city: beijing

first: sichong

last: han

address: No. 15 North Third Ring East Road, Chaoyang District

institute: beijing university of chemical technology

summary:
Esophageal cancer is the top 10 global arising common cancer with limited therapeutic strategies, and the general prognosis is poor owing to diagnosis in late stages in many cases. Sulforaphene (SFE) has been possess anticarcinogenic activities in many cancers, however, it is still not clear how SFE can function as an antineoplastic compound in esophageal cancer.
We used microarrays to identify the target genes involved in SFE inhibition of esophageal cancer cell progression.

overall_design: EC109 and KYSE510 cells were cultured and treated with 20 µM SFE or DMSO as negative control for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain the significantly differentially expressed genes between SFE-treated cells and the control group.

first: SiChong

last: Han

first: Zhe

last: Wang


title: Gene expression data from bleomycin-instilled lung tissue or control (Sham) of C57BL/6 mice (wild-type mice and transgenic mice expressing dominant-negative form of p38α or constitutive active form of MKK6 in type II alveolar epithelial cells).

city: Toyama

first: Jun-Dal

last: Kim

state: Toyama

address: 2630 Sugitani

department: Department of Complex Biosystem Research (CBR), Institute of National Medicine (INM)

country: Japan

institute: University of Toyama

summary: Idiopathic pulmonary fibrosis (IPF) is a type of pulmonary fibrosis, a disease that results in scarring and stiffness of lung tissue affecting over 5 million people globally, while the underlying disease mechanisms in IPF are largely unknown.  As an animal model of IPF, a single intratracheal injection of bleomycin (BLM) is generally employed, in which cell death of type II alveolar epithelial cells (AEC II) is a trigger of pulmonary fibrosis. One of mitogen-activated protein kinases, p38 is well known as an important regulator of inflammatory responses and cell fate such as apoptosis, differentiation and tumorgenesis. Given that mice with different intrinsic activity of p38 in AEC II were subjected to BLM instillation and investigated, candidate genes in the development of pulmonary fibrosis would be screened. Here, we provide gene expression profiling of lung tissues using the RNA sequencing for identifying changes in gene expression.

overall_design: We sought to obtain changes associated with the fibrotic response in sham and BLM injected mice with the different genotypes. Lung samples at 8 days after BLM instillation were selected for RNA extraction and sequencing on NextSeq 500 (Illumina) and used three biological replicates for each condition.

first: Shuichi

last: Matsuda

first: Yoshitoshi

last: Kasuya


title: Old Mice Have Less Transcriptional Activation But Similar  Periosteal Cell Proliferation Compared to Young-Adult  Mice in Response to in vivo Mechanical Loading

city: St. Louis

first: Christopher

middle: John

last: Chermside-Scabbo

state: Missouri

address: 425 S Euclid Ave

department: Orthopaedic Surgery

institute: WASHINGTON UNIVERSITY in St. Louis

summary: Mechanical loading is a potent strategy to induce bone formation, but with aging, the bone formation response to the same mechanical  stimulus diminishes. Our main objectives were to (i) discover the potential transcriptional differences and (ii) compare the periosteal  cell proliferation between tibias of young-adult and old mice in response to strain-matched mechanical loading. First, to  discover potential age-related transcriptional differences, we performed RNA sequencing (RNA-seq) to compare the loading  responses between tibias of young-adult (5-month) and old (22-month) C57BL/6N female mice following 1, 3, or 5 days of axial loading  (loaded versus non-loaded). Compared to young-adult mice, old mice had less transcriptional activation following loading at each  time point, as measured by the number of differentially expressed genes (DEGs) and the fold-changes of the DEGs. Old mice engaged  fewer pathways and gene ontology (GO) processes, showing less activation of processes related to proliferation and differentiation. In  tibias of young-adult mice, we observed prominent Wnt signaling, extracellular matrix (ECM), and neuronal responses, which were  diminished with aging. Additionally, we identified several targets that may be effective in restoring the mechanoresponsiveness of  aged bone, including nerve growth factor (NGF), Notum, prostaglandin signaling, Nell-1, and the AP-1 family. Second, to directly test  the extent to which periosteal cell proliferation was diminished in old mice, we used bromodeoxyuridine (BrdU) in a separate cohort  of mice to label cells that divided during the 5-day loading interval. Young-adult and old mice had an average of 15.5 and 16.7 BrdU+  surface cells/mm, respectively, suggesting that impaired proliferation in the first 5 days of loading does not explain the diminished  bone formation response with aging. We conclude that old mice have diminished transcriptional activation following mechanical  loading, but periosteal proliferation in the first 5 days of loading does not differ between tibias of young-adult and old mice.

overall_design: Female C57BL/6N mice were obtained at 5-months and 22-months were separated into groups (5 mice/day/age) and loaded for either one, three, or five bouts of daily loading, reflecting distinct phases of the loading response: early mechanosensation (day 1), activation of the bone formation cascade before matrix deposition (day 3), and active bone formation (day 5). Mice were anesthetized (3% isoflurane) and subjected to loading each morning for the specified number of bouts. With the mice prone, the right legs (tibias) were placed vertically in the loading fixture, with the knee positioned superiorly in a semispherical cup (10-mm-diameter) attached to the system actuator, and the foot held in a static fixture inferiorly (20 degrees of dorsiflexion). A preload (−0.5 N) was applied, and tibias were subjected to axial compression for 1200 cycles/day (4-Hz triangle waveform with a 0.1-s rest-insertion after each cycle) using the Electropulse 1000 materials testing. Based on prior strain gauging analyses, age-specific peak forces of −8 N and −7 N were selected for 5-month-old and 22-month-old mice, respectively, to engender average peak periosteal strains of −2200με at the cortical mid-shaft. After each loading bout, buprenorphine was delivered to mitigate pain from loading, and mice were returned to their cages to resume unrestricted activity. The left tibias served as non-loaded, contralateral controls. Left and right tibias were stripped of muscle, cut at the distal tibiofibular junction and 2 mm distal to the tibial plateau, centrifuged to remove the bone marrow, and snap frozen in liquid nitrogen. Samples were pulverized, and total RNA was extracted using TRIzol. Ribosomal RNA (rRNA) was removed using the Ribo-Zero rRNA Removal Kit, and all 60 samples (30 pairs of tibias) were subjected to RNA-seq with the HiSeq 3000 at 1 × 50 bp on 1 μg of RNA. The RNA-seq reads were aligned to the mouse genome (mm10), and gene counts were determined by the number of uniquely aligned, unambiguous reads.

first: Taylor

last: Harris

first: Michael

last: Brodt

first: Ingrid

last: Braenne

first: Bo

last: Zhang

first: Charles

middle: R

last: Farber

first: Matthew

last: Silva


title: Determination of different gene expressions for AngII induced wild-type and smcKlf5-/- mouse abdominal aortic aneurysm

first: Dong

last: Ma

summary: To identify genes that are regulated by KLF5 during vascular smooth muscle cell mitochondrial mophology, redox and ATP, we performed RNA expression profiling using microarray analyses of AAA and normal abdominal aortas from WT (control) and smcKlf5−/− mice. The experiments showed that mitochondrial mophology-, redox- and ATP-related gene expressions markedly differed between AAA and normal aortic tissues.

overall_design: AngII infusion induced gene expression in aortas from  male wild-type and smcKlf5-/- mice was measured at 28 days after exposure to 1000 mg/kg/d AngII.  Three independent experiments were performed for each experiment.

first: Ma

last: Dong

first: Wen

last: Jin-kun


title: Investigation of conventional and unconventional protein secretion using galectin-3

city: Cambridge

first: Davide

last: Chiarugi

address: Box 289, Addenbrooke’s Hospital

department: Metabolic Research Laboratories

country: United Kingdom

institute: WT-MRC Institute of Metabolic Science

summary:
Protein secretion is an essential process in cell biology. The conventional secretion pathway is well known, and involves proteins with a signal sequence being directed into the endoplasmic reticulum. Once in the lumen of the endoplasmic reticulum, proteins are trafficked through the Golgi and remain separate from the cytosol throughout their journey to the outside of the cell.
More recently, proteins without a signal sequence have been found outside the cell. These proteins are secreted unconventionally, and avoid the ER-Golgi route. For both pathways, some aspects remain unclear, particularly surrounding the regulation of protein secretion.
Galectin-3, an unconventionally secreted protein, was used here to investigate both conventional and unconventional protein secretion. The unconventional protein secretion of galectin-3 is poorly understood.  To address this, genetic manipulation of galectin-3 was used to gain insights into the mechanism of galectin-3 secretion. It was found that galectin-3 does not require unfolding or binding to cell surface glycoproteins to be secreted.
Galectin-3 was also used to assess protein secretion using a genome-wide CRISPR screen. As galectin‑3 binds to cell surface glycoproteins, galectin-3 on the cell surface was used to assess secretion of these glycoproteins. Hits were validated by a glycoprotein secretion assay. Using this pipeline, 93 hits were identified as involved in protein secretion, of which 51 were novel hits not previously associated with protein secretion.
Many of the hits identified also resulted in a phenotype of altered Golgi morphology, and five of these were investigated further. Two novel hits that localised to the Golgi were identified, TMEM220 and GPR161. GPR161 likely mediates its effect on Golgi morphology by its interaction with golgin A5.
This thesis presents new insights into both conventional and unconventional protein secretion. Insights into the mechanism for galaectin-3 secretion were revealed. A novel Golgi-localised regulator of secretion, GRP161, was identified, with a mechanism for action suggested. Importantly, the list of 51 novel genes identified will serve as a useful resource for other researchers investigating protein secretion.

overall_design:
Hela-Cas9 cells were transfected with Brunello library
Other data associated with this work, including control samples: Accession number GSE133692

first: Stephanie

last: Popa


title: Astroglial FMRP deficiency cell-autonomously up-regulates miR-128 and disrupts developmental astroglial mGluR5 signaling (RNA-Seq)

first: Yongjie

last: Yang

overall_design: examine the genome-wide mRNA expression profiles in cortical astroglia in Fmr1+/y and Fmr1−/y mice

first: Yuqin

last: Men

first: Albert

last: Tai

first: Ling

last: chen


title: Next Generation Sequencing Facilitates Quantitative Analysis of Transcriptomes in HeLa cells upon Hippo Components Overexpression or Knockout

first: Wentao

last: Yu

address: 320 Yue Yang Road

department: Center for Excellence in Molecular Cell Science,Shanghai Institute of Biochemistry and Cell Biology

institute: Chinese Academy of Sciences

summary:
Purpose: The goals of this study are to compare and integrate NGS-derived transcriptome when Hippo components are manipulated in HeLa cells.
Methods: Total RNAs from three replicates were extracted using TRIzol (Thermo Fisher Scientific) from HeLa cells. RNA quality was assessed using a bioanalyzer (Agilent Technologies). RNA-seq libraries were prepared according to the Illumina TruSeq protocol. Then were pooled for deep sequencing by using Illumina Hiseq Xten (2 × 150) platforms at the Omics Core of Bio-Med Big Data Center, CAS-MPG Partner Institute for Computational Biology, Shanghai, China. Raw read qualities were evaluated with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, v0.11.5). Adaptor sequences and read sequences on both ends with Phred quality scores below 30 were trimmed. Trimmed reads were then mapped with the Hisat2 algorithm (version 2.1.0) to target sequences. Gene expression levels were quantified by the software package HTSeq (v0.6.1p1). The list of differentially expressed genes were generated by DESeq2 with FC：1.5，and adjust p-value<0.05.The significant genes were then compared with each other.
Results: We finally get 558 genes that have dramatical change in different groups.
Conclusions: Our study shows many common genes that can be loyally regulated by Hippo signaling.

overall_design: RNA-seq analysis of HeLa cells in which Hippo components are manipulated.

first: Lingli

last: He

first: Dan

last: Jiang

first: Xiaodong

last: Wang

first: Hua

last: Feng


title: Quantitative Analysis of 4 different type T cells Transcriptomes

city: Seoul

first: Sun-Hee

last: Heo

address: Seoul

institute: Asan Medical Center

summary:
Purpose: Memory T cells has been studied to improve vaccine design and develop adaptive immunotherapy. The goal of this study is to identify specific genes to memory T cells by analysis different types of T cells using transcriptome (RNA-seq) data.
Methods: CD3 positive T cells were isolated from PBMC separated from blood taken from 2 healthy donors (PBMC17003 and PBMC17006). IL-7 and IL-15 were used for differentiation from CD3 positive T cells to memory type T cells. The transcriptome data of memory type T cells was generated by next generation sequencing using Illumina TruSeq Stranded mRNA LT Sample Prep Kit and HiSeq 2500 System. RNA-seq reads were trimmed and aligned to UCSC hg19 reference genome using Bowtie2 aligner. The transcripts were assembled with known transcript and abundance of the transcripts was measured as FPKM value using StringTie program. Filtration was processed by excluding genes with a FPKM value of zero and artifacts such as adaptor sequence, contaminant DNA and PCR duplicates. Differentially expressed genes (DEG) among samples were analyzed with FPKM of each gene.
Results: Four type T cells were sorted after differentiation from CD3 positive T cells to memory type T cells for transcriptome analysis. They are CD8 positive T cells (sample number-1), stem memory T cells (Tscm, sample number-2), central memory T cells (Tcm, sample number-3) and effector memory T cells (Tem, sample number-4). At least 65 million sequence reads per sample were mapped to the human genomic DNA reference (UCSC hg19). More than 15,000 genes were identified after filtration, Log2 transformation of FPKM+1 and quantile normalization. Significant genes in each memory T cells were analyzed by comparing with CD8 T cells in PBMC17003 or PBMC17006. Tscm specific genes were identified 176 in PBMC17003 and 108 in PBMC 17006. Tcm specific genes were 117 in PBMC17003 and 62 in PBMC 17006. DEG of Tem were 191 in PBMC17003 and 109 in PBMC 17006.
Conclusions: This study represents the transcriptomes analysis of different memory T cell using RNA-seq technology. PBMCs obtained from 2 healthy donors were used for differentiation to memory T cells followed by analysis of transcriptome. These RNA-seq data are useful for developing improved vaccine or immunotherapy.

overall_design: mRNA profiles of 4 types T cells in PBMC isolated from 2 healthy individuals.

first: Gyungyub

last: Gong

first: HeeJin

last: Lee


title: Single cell RNA sequencing analysis of human embryonic stem cells, human embryoid bodies, human mesenchymal stem cells and  human musculoskeletal stem cells

city: Jeonju-si

first: Myung-Kwan

last: Han

state: Jeollabuk-do

address: Baeje-daero 567

department: Department of Microbiology

institute: Jeonbuk National University Medical School

summary: NOT PROVIDED; REQUESTED

overall_design: We first derived human musculoskeletal stem cells from human embryonic stem cells. Single cell RNA sequencing of human embryonic stem cells, human embryoid bodies, human mesenchymal stem cells and human musculoskeletal stem cells were performed using 10x Genomics Chromium System .


title: Postnatal loss of Arx transcriptional activity in parvalbumin interneurons induces epilepsy-like network abnormalities

city: PHILADELPHIA

first: Ana

middle: Gabriela

last: Cristancho

state: Pennsylvania

address: 3400 Civic Center Blvd

institute: University of Pennsylvania/CHOP

summary: We report the use to RNA-sequencing to understand the role of postnatal Arx in the regulation of PV interneuron function. Total RNA extracted from control and Arx CKO male mice cells were submitted to the Next-Generation Sequencing Core of the University of Pennsylvania for cDNA amplification, library preparation, and sequencing using the Ovation RNA-seq v2 and Rapid DR Multiplexing kits (NuGEN). Whole mRNAseq libraries were prepared from 9 mice (5 control and 4 Arx CKO mice) using the SMARTer Ultra Low RNA Kit for Illumina Sequencing (Clontech, Cat#634936) according to manufacturer’s instructions. Standard methods to assess sample quality (Agilent Bioanalyzer, Kappa Biosystems Library Quantification kit, Qubit® Fluorometer) and measure cDNA concentration were used. A total of 1ng of amplified cDNA for each sample was used as input to build the sequencing libraries. Whole mRNAseq libraries from control and Arx CKO mice were quantified using Agilent Bioanalyzer DNA 7500 chips. Libraries were sequenced on the Illumina HiSeq 4000 2 × 100 (Illumina, San Diego, CA, USA) to generate 150bp paired end reads, yielding approximately 20-40 million reads per sample (~80 million reads per lane).

overall_design: PV interneurons weresorted by FACS in adult mice for RNA-Seq studies. 5 Control mice(PV-CreTdTom) were compared to 4 Arx floxed/Y:PVCreTdTom (Arx CKO) mice for RNA-seq.

first: Donald

last: Joseph

first: Markus

last: Von Deimling

middle: G

first: Eric

last: Marsh


title: SAM treatment of CRC cell lines

city: Budapest

first: Sara

last: Zsigrai

state: Please Select

address: Szentkirályi street

department: 2nd Dept. of Internal Med.

country: Hungary

institute: Semmelweis University

summary: whole-transcriptom analysis of HT-29 and SW480 cells by HTA 2.0 microarray

overall_design: Colorectal cancer cells were treated with S-adenosylmethionine and harvested for gene expression analysis following 48 hours incubation period. HTA 2.0 microarray experiments were performed according to the manufacturer’s instructions. 100 ng input total RNA samples were applied as staring material. For sscDNA synthesis 15 µg cRNA was used and 5.5 µg fragmented and labeled sscDNA sample was hybridized to HTA 2.0 microarrays (Affymetrix) for 16 hours at 45°C with 60 rpm rotation in the Hybridization Oven (Affymetrix). Microarrays were washed and stained with GeneChip® Hybridization, Wash, and Stain Kit reagents according to FS450_0001 protocol using the Fluidics Station 450 instrument (Affymetrix). Scanning was performed with GeneChip Scanner 3000 (Affymetrix).

first: S

first: A

last: Kalmar

first: Z

middle: B

last: Nagy

first: O

last: Galamb

first: G

last: Valcz

first: B

middle: K

last: Barták

first: K

last: Szigeti

last: Tulassay

first: P

last: Igaz

last: Molnar


title: Transcriptome and translatome profiling of Arabidopsis upf1-3 pad4 mutant

city: Brno

first: Vivek

middle: Kumar

last: Raxwal

address: building A26, Kamenice 753/5

department: Plant Molecular Biology

country: Czech Republic

institute: Central European Institute of Technology

summary: Goal of the study is to decipher the role of UPF1 in maintaining  transcriptome and translatome homeostasis in Arabidopsis

overall_design: Leaf from three week old soil grown plants were used to perform ribosome depleted strand specific libraries (Illumina) from RNA isolated from monosomal, polysomal and total RNA. High throughput sequencing libraries were prepared from three biological replicate from pad4(Control) and upf1-3 pad4 mutant plants

first: Craig

last: Simpson

first: Jiradet

last: Gloggnitzer

first: Juan

middle: C

last: Entinze

first: Wenbin

last: Guo

first: Runxuan

last: Zhang

first: John

middle: W

last: Brown

first: Karel

last: Riha


title: Next Generation Sequencing Analysis of exosomes in follicle fluid of PCOS/non-PCOS patients

first: Xin

last: Huang

state: Shanghai

address: No.2699 Gaoke east road

department: Reproductive Medicine Centre

institute: Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine

type: Non-coding RNA profiling by high throughput sequencing

summary:
Purpose: the goals of this study are to identify the transcriptome profiling of exosome derived from follicle fluid of PCOS patients by next-generation sequencing (NGS).
Methods:the transcriptome profiling of exosome derived from follicular fluid of five PCOS and five control patients were generated by deep sequencing, using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays
Results: the transcriptome profiling  including circRNA, lncRNA and mRNA  were comparatively analyzed in the two groups of exosomes (exo-PCOS and exo-control). We focus on the circRNAs profile for further analysis. A circRNA candidate was considered to be differentially expressed if its levels between both experiment groups showed a statistically significant difference (p<0.05) of at least two-fold. Based on this criterion, we identified 16 differentially expressed circRNAs (5 up-regulated and 11 down-regulated circRNAs) between exo-PCOS and exo-control, including 3 annotated exonic circRNAs and 13 novel ones. Clustering analysis based on the differentially expressed circRNAs clustered the exo-PCOS and the exo-control groups (control).
Conclusion: the circRNA expression profile of exosome derived from follicular fluid of five PCOS and five control patients were determined by RNA sequencing technology. 16 circRNAs showed significantly different expression in the exosome of PCOS FF. GO and KEGG pathway analysis indicated that the parental genes of the candidate circRNAs were involved in ovarian steroidogenesis, aldosterone synthesis and secretion, thyroid hormone signaling pathway, ubiquitin mediated proteolysis, Jak-STAT signaling pathway, and endocytosis pathway.

overall_design: Exosomal circRNA profiles of PCOS and control patients were generated by deep sequencing using Illumina.


title: Transcriptional correlates of high norepinephrine content in ovarian carcinomas

city: Los Angeles

first: Steve

last: Cole

state: CA

address: 11-934 Factor Bldg, UCLA

department: Medicine

institute: UCLA School of Medicine

summary: Genome-wide transcriptome profiling was conducted on 97 Stage I-IV ovarian carcinomas classified according to tissue norepinephrine content.

overall_design: To characterize the impact of norepinephrine on ovarian carcinoma biology, we conducted genome-wide transcriptome profiling of 97 clinical ovarian tumors.  Tissue norepinephrine content was assessed by high performance liquid chromatogrphy (0=below median value of 1.05 pg/ml;1=above median).  Covariates included age (years), body mass index (kg / m^2), tumor stage (1-4), and tumor grade (0=low;1=high).


title: Cardiac Mesenchymal Cells from Failing Hearts Limit Ventricular Dilation when Administered Late after Infarction

city: Louisville

first: Steven

last: Jones

state: KY

address: 580 South Preston Street - Rm 321F

department: Diabetes and Obesity Center

institute: University of Louisville

summary: Donor source of cardiac mesenchymal cells influences their expression profile.

overall_design: At 28 days after surgery, cardiac mesenchymal cells were harvested from hearts that had been subjected to Sham occlusion or coronary occlusion followed by reperfusion.

middle: P


title: Gene expression profile of K562 and KBM5 treated with the combination of imatinib and a new demethylating agent, OR-2100

city: Saga

first: Kazuharu

last: Kamachi

department: Hematology and Oncology

institute: Saga university

summary: Treatment with demethylating agents in combination with tyrosine kinase inhibitors have shown improved molecular responses and survival benefits in patients with TKI-resistant or advanced-phase CML. However, little is known regarding underlying mechanism of the combination anti-tumor effect of demethylating agents and tyrosine kinase inhibitors. To analyze the combination effect, we have compared gene expression profiles among chronic myeloid leukemia (CML) cell lines (K562, KBM5) treated with imatinib (IM), a new demethylating agent, OR-2100 (OR21), and these combination therapy.

overall_design: To identify specific gene expressions of the combination therapy of imatinib and OR21 against CML cells, gene array analysis was performed. K562 and KBM5 cells were pre-exposed with OR21 for 3 consecutive days, then followed by IM exposure. Total RNA of each treated cells in each cell line was extracted 24 hours after IM exposure and gene expressions were compared among 4 groups; control (no exposure), OR21, IM, and the combination.

first: H

last: Ureshino

first: T

last: Watanabe

first: N

last: Yoshida

first: Y

last: Yamamoto

last: Kurahashi

first: S

last: Kimura


title: An epigenetic vulnerability in PI3K/AKT inhibition resistant cancers is targetable by both bromodomain and HDAC inhibitors

city: San Antonio

first: Zhenqing

last: Ye

state: TX

address: 8403 Floyd Curl Dr

department: 6Department of Population Health Sciences

institute: UT Health San Antonio

summary: Acquisition of resistance to PI3K/AKT-targeted monotherapy regardless of cancer types implies the existence of common mechanisms. Here we demonstrate that while causing glycolysis crisis, acetyl-CoA shortage and global decrease of histone acetylation, PI3K/AKT inhibitors induce drug resistance by selectively augmenting CBP/p300, H3K27 acetylation and BRD4 binding at genomic loci of a subset of growth factor and receptor (GF/R) genes. BRD4 occupation at these loci and drug resistant cell growth are vulnerable to both bromodomain and HDAC inhibitors. Little or none occupation of HDACs at the GF/R gene loci underscores the paradox that cells respond equivalently to the two classes of inhibitors with opposite modes of action. Targeting this unique epigenetic vulnerability offers a general solution to overcome PI3K/AKT inhibitor resistance in different cancers.

overall_design: ChIP-seqs were performed in the PC-3 control and GDC-R cells treated with iCBP112 or SAHA, using antibody of H3K27-ac, H3K9/K14-ac, H4-ac,CBP/p300, HDAC1/2 and BRD4 (Drosophila S2 cell chromatin was used as spike-in control for H3K27-ac ChIP-seq).

first: Haojie

first: Di

last: Wu

first: Liguo

last: Wang

first: Ting

last: Wei


title: Functional analysis of caspase cleavable proteoforms of the Drosophila GSK-3 gene shaggy.

last: Russell

address: Downing Street

institute: University of Cambridge

summary: A comparison of the embryonic transcriptome of wild type embryos (sggisoD-DS-SFS  ) with embryos harbouring mutated DEVD caspase recognition sites ( sggisoD-cI-DS-SFS ) in a major shaggy isoforms class to examine the role of caspase cleavage in sgg function. The unique N-terminal exon undegoing caspase cleavage is tagged with DsRED at its N-terminus and StrepII-Flag-StrepII upstream of caspase cleavage sites for the wild type and caspase insensitive variant versions.

overall_design: Drosophila lines were engineered using CRISPR-Cas9 to carry N-terminal DsRed and internal StrepII-Flag-StrepII tags; one line is otherwise wild type, sgg[isoD-DS-SFS] the other is mutated for 2 consensus caspase recognition sites sgg[isoD-CI-DS-SFS]. RNA from 3 independent stage matched embryo collections for each line were processed for RNA-seq.

first: Dagmara

last: Korona

first: Bettina

last: Fischer


title: IFI16 functions as an antiviral factor during influenza virus infection by binding viral RNA and enhancing the RIG-I signaling (RNA-seq)

city: Bei jing

first: zhimin

last: jiang

address: No.2 Yuanmingyuan West Road, Haidian District, Beijing

department: college of Veterinary medicine

institute: China agriculture university

summary: RIG-I is thought to be the most important sensor of influenza virus infection and plays critical roles in the recognition of cytoplasmic dsRNA and activation of type I IFNs and initiates the innate antiviral immune responses. How the binding of viral RNA to and activation of RIG-I are regulated remains enigmatic. Here, by an affinity proteomics approach with viral RNA as the bait, we found that IFI16, previously identified as a DNA sensor, was significantly induced both in vitro and in vivo during influenza virus infection. Using an IFI16 knockout cells and p204-deficient mice model, we demonstrated that IFI16 enhanced RIG-I-mediated production of type I IFNs and thereby inhibited viral replication during influenza virus infection. Furthermore, we showed that IFI16 regulated the RIG-I signaling by enhancing its transcriptional expression through recruitment of RNA Pol II to the RIG-I promoter. We also verified that IFI16 directly interacted with both viral RNA by HINa domain and associated with RIG-I through its PYRIN domain as well as promoted influenza virus-induced K63-linked polyubiquitination of RIG-I. In addition, we found that IFI16 lost its ability to inhibit viral replication in the absence of RIG-I in virus-infected cells. These results indicate that IFI16 is a key regulator of the RIG-I signaling during antiviral innate immune responses, which highlights a novel mechanism of IFI16 in IAV and other RNA viruses infection, expands our knowledge in antiviral innate immunity, and suggests its possible use as a new strategies to manipulate antiviral responses.

overall_design: To investigate the endogenous-derived IFI16 in IAV infection, we infected IFI16+/+ and IFI16-/- A549 cells with PR8 virus at an MOI of 1 for 12h. And then, the cells were collected and the total RNA was extracted and analyzed by RNA-seq.

first: Zhimin

last: Jiang

first: Fanhua


title: Transcriptome sequencing of two Baikal (Eulimnogammarus verrucosus and E. cyaneus) and one Holarctic (Gammarus lacustris) amphipod species exposed to 1.5 and 12 degree Celsius

city: Leipzig

first: Polina

last: Lipaeva

address: Permoserstraße 15

department: Biotox

institute: Helmholtz Centre for Environmental Research - UFZ

summary: This project aims to find the molecular changes driving the cold stress response of freshwater amphipods with different overwintering strategies

sample_organism:
Eulimnogammarus verrucosus
Gammarus lacustris
Eulimnogammarus cyaneus

overall_design: After preacclimation at 6 degrees C for two weeks, three amphipod species were exposed to 1.5 and 12 degrees C for 30 days. At each temperature point, there were 4 replicates of each amphipod species analyzed. Animals were pooled; pools of E. verrucosus, E. cyaneus, and G. lacustris contained 3, 12-15, and 10-12 animals, respectively. De novo transcriptome assembly was performed using Trinity. Redundant transcripts were removed with cd-hit-est. Misassembled or incomplete contigs were filtered out with TransRate. Only transcripts with matches to metazoan sequences were retained. Transcript quantification was performed with salmon and further processed with the DESeq2 package for R.

first: Daria

last: Bedulina

last: Drozdova

first: Elizaveta

last: Kondrateva

first: Till

last: Luckenbach

first: Stephan

last: Schreiber

first: Peter

last: Stadler

first: Maxim

last: Timofeyev

first: Kseniya

last: Vereshchagina


title: Pattern occupation of HDACs on chromatin determines PI3K/AKT inhibitor resistance in cancers [RNA-seq]

first: Zhenqing

last: Ye

summary: Blocking BRD4 or HDACs induces paradoxically similar gene expression, comparably attenuates PI3K/AKT inhibitor resistance in multiple cancer cells.

overall_design: Examination of RNA expression in: GDC-0068 resistant PC-3 (PC-3-GDC-R) cells and control PC-3 (PC-3-control) cells.

first: Haojie

last: Huang

last: Wu


title: RNA-seq analysis CFPAC-1-siNC and CFPAC-1-siUBE2C

city: Chongqing

first: wang

last: xianxing

address: No. 2 Tiansheng Rd., Beibei District

institute: State Key Laboratory of Silkworm Genome Biology, the Institute of Sericulture and Systems Biology, Southwest University

summary: The transcriptome sequencing results were used to determine the association between UBE2C and pancreatic cancer. First, the RNA-seq data revealed that the expression of 2332 genes were different in the siUBE2C group compared with the negative control group. There were 363 genes and 152 genes with two-fold increased and decreased expression, respectively. The top 30 GO terms enriched among all differentially expressed genes included biological processes (attachment of spindle microtubules to kinetochore, regulation of attachment of spindle microtubules to kinetochore, protein localization to chromosome), cellular components (condensed nuclear chromosome, condensed chromosome outer kinetochore) and molecular functions (single-stranded DNA-dependent ATPase activity, intestinal epithelial cell maturation). The major enriched pathways were the cell cycle pathway and the p53 signaling pathway.

overall_design: After transfecting CFPAC-1 cells with siUBE2C for 36 hours, total RNA was extracted and performed RNA-seq, contained three siUBE2C-treated samples and three matched control samples(siNC).

first: Huaizhi

last: Wang

first: Xianxing

first: Liangyu

last: Yin

first: Ludi

last: Yang

first: Yao

last: Zheng

first: Songsong

last: Liu

first: Jiali

first: Hongjuan

last: Cui


title: Visualization and Sequencing of Accessible Chromatin Reveals Cell Cycle and Post-HDAC inhibitor Treatment Dynamics

city: Ipswich

first: Sriharsa

last: Pradhan

address: 240 County Road

institute: New England Biolabs

summary: Chromatin accessibility in the nucleus is a predictor of gene expression, cell division and cell type specificity. NicE-viewSeq (Nicking Enzyme assisted viewing and Sequencing) allows accessible chromatin visualization and sequencing with lower mitochondrial DNA and duplicated sequences compared to ATACsee. Using NicE-viewSeq we interrogated cell cycle G1, S and G2M specific accessible chromatin in mammalian cells. Despite DNA replication and subsequent condensation of chromatin to chromosome, chromatin accessibility remained subtly altered and generally preserved. Genome-wide alteration of accessibility for TSS and enhancer gradually decreased as the cell progressed from G1 to G2M, with distinctive differential accessibility near consensus transcription factors sites. Inhibition of histone deacetylase promoted accessible chromatin of the gene body, correlating with apoptotic gene expression. In addition, reduced chromatin accessibility for MYC oncogene pathway correlated with gene down regulation. Surprisingly, repetitive RNA expression remained unaltered following histone acetylation mediated increased accessibility. Therefore, we suggest that subtle changes in chromatin accessibility is a prerequisite during cell cycle and histone deacetylase inhibitor mediated therapeutics.

overall_design: HCT116, HeLa, HUT78 and HT1080 cell line were routinely grown in McCoy's and DMEM media with 10% fetal bovine serum respectively, media being replaced every 3 days. Cell cycle studies were performed in HCT116 and HeLa. Cells were sorted using FACS and also used nocodazole. HUT78 were treated with 1 micromolar of Romidepsin for 6 hours.

first: Vishnu

last: Udayakumar

first: Pierre

last: Esteve


title: Bromodomain and HDAC inhibitors equivalently suppress PI3K/AKT inhibition resistance in cancers

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

overall_design: Refer to individual Series


title: Endothelial mutagenesis screen identifies genetic risk factors in the development vascular anomalies

first: Safiyyah

last: Ziyad

address: 621 Charles E. Young Drive, South

department: Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles


title: Endothelial mutagenesis screen identifies genetic risk factors in the development vascular anomalies [muscle]

summary: mRNA transcriptional comparison between two pieces of tissue from three SBxVEC-Cre+ animals and three control animals

first: Trent

last: Su

first: M

middle: L

last: Iruela-Arispe


title: Single-cell analysis of tumor progression reveals the function, structure, and evolution of cancer archetypes

city: New York

first: Maayan

last: Baron

state: NY

address: 435 E. 30th Street, 8th Floor

institute: NYU

summary: The classic cancer evolution model posits that driver mutations sweep the population sequentially as the complete set of hallmarks are assembled by the neoplastic clone. However, recent work has challenged this model revealing that most tumors contain highly complex dynamics with genetic diversity reflecting distinct clonal architectures. The functional and phenotypic heterogeneity also has been shown to have a crucial influence on the fate of the tumor5–10. However, it is not well understood how distinct tumor clonal populations coexist and function. Here, we study tumor architecture at the level of individual cells by sampling a zebrafish melanoma tumor over time and space. We found that cancer transcriptional programs can be classified to three archetypes, each exploiting the existing neural crest, mature melanocytes, and stress modules, and distinct intra-tumor locations. Strikingly, these archetypes are conserved in human melanoma. Further, we found that the cancer cells are comprised of two distinct clones, where one expresses a unique archetype. Over time, we found that the cells of this clone adapt by exhibiting a more similar profile to the corresponding archetype.

overall_design: Single-cell RNA sequencing of zebrafish tumor cells from 2 zebrafish at multiple time points.


title: Genome-wide microRNA profiling and target gene prediction in different embryonic muscle developmental stage of duck breast

status: Public on Sep 08 2020

city: Nanchang

first: Biao

last: Chen

address: Zhimin street, Jingkai district

institute: Jiangxi Agricultural University

summary: The objective of this study is to profile microRNA expressed in embryonic breast muscle of duck, analyze the conservation across multiple species and identify candidate microRNAs associated with duck muscle development. microRNA sequencing analysis was performed using female breast muscle samples at embryonic stage 13th day (E13) and embryonic stage 19th day (E19).

overall_design: microRNA sequencing in female muscle samples at embryonic stage 13th day (E13) and embryonic stage 19th day (E19).

first: Sanfeng


title: Pattern occupation of HDACs on chromatin determines PI3K/AKT inhibitor resistance in cancers [ChIP-seq]

first: Zhenqing

last: Ye

overall_design: To determine the distribution changes of H3K27-ac and BRD4 in PC-3-GDC-R cells (w/o iCBP112 and SAHA treatments), we performed ChIP-seq for H3K27ac and BRD4 in PC-3-control+vehicle, PC-3-GDC-R+vehicle, PC-3-GDC-R+iCBP112 and PC-3-GDC-R+SAHA cells.

first: Haojie

last: Huang

first: Di


title: High throughput joint profiling of chromatin accessibility and protein levels in single cells [marrow]

first: Caleb

last: Lareau

address: 417 E 68th St, Zuckerman - ZRC 1132

institute: Memorial Sloan Kettering

summary: Recent technological advances have enabled massively parallel single-cell Assay for Transposase Accessible Chromatin by sequencing (scATAC-seq) to simultaneously profile the epigenomic landscape in thousands of individual cells. scATAC-seq methods sample genomic DNA accessible to transposases, but have not previously been combined with measurement of protein levels.  Here, we present ATAC with Select Antigen Profiling by sequencing, ASAP-seq, a tool to simultaneously profile accessible chromatin and protein levels in thousands of single cells, pairing sparse scATAC data with robust detection of hundreds of cell surface and intracellular protein markers, and optionally, enriched mtDNA coverage for lineage tracing (mtscATAC-seq) with minimal impact on ATAC-seq data quality. ASAP-seq makes use of a novel bridging approach to utilize existing commercially available antibody:oligo conjugates developed for CITE-seq and related technologies. We demonstrate the utility of ASAP-seq in the context of hematopoietic differentiation, cell surface marker dynamics following peripheral blood mononuclear cell stimulation, and as a combinatorial decoder of multiplexed perturbations in primary T cells.

overall_design: A bone marrow sample stained with a 242-antibody panel was used to apply ASAP-seq and resolve cell heterogeneity and composition in combination with mtDNA-based lineage tracing

first: Eleni

last: Mimitou

first: Kelvin

first: Leif

last: Ludwig

first: Peter

last: Smibert


title: Transcriptional profile of B cells isolated from blood, heart, lung, and liver

city: St Louis

first: Luigi

last: Adamo

address: 660 South Euclid Ave

department: Internal Medicine - Cardiovascular Division

institute: Washington University In St Louis

summary: We have shown previously that myocardial-associated B cells are transcriptionally distinct from circulating B cells. To investigate whether the sub-populations of B cells identified in the heart might not be unique to the heart, we investigated the transcriptional profile of B cells isolated from blood, heart, lung, and liver.

overall_design: We performed single cell sequencing of FACS-sorted B cells isolated from blood, and perfused heart, liver, and lung. Samples were collected from the same mice, at the same time, and underwent the same digestion and staining protocols. To identify the tissue origin of the B cells, samples were stained with Hashtag antibodies, processed within the same 10X cDNA library and sequenced together to eliminate potential “batch” artifacts. We used the Chromium Single Cell 5′ Chromium instrument (from 10x Genomics) to perform single cell transcriptional profiling analyses.

first: Cibele

last: Rocha-Resende

first: Wei

last: Yang

first: Douglas

last: Mann


title: High throughput joint profiling of chromatin accessibility and protein levels in single cells [PBMC stimulation]

overall_design: Control and stimulated with aCD3/CD28 PBMC samples were stained with a 227-antibody panel and used to apply CITE-seq and ASAP-seq to simultaneously measure changes in protein, mRNA levels, and chromatin accessibility.


title: Transcriptional profile of B cells isolated from neonatal and adult hearts

summary: We have identified four distinct B cell subgroups within the naïve murine heart, whose relative expression changed markedly throughout development, including CD19+CD11b+CD5+, CD19+CD11b+CD5-, CD19+CD11b-CD21+CD23+, and CD19+CD11b-CD21-CD23- B cells. In order to gain further insight into the identity of the various myocardial B cells subsets, we performed single cell RNA sequencing (scRNAseq) of neonatal (2 weeks) and adult (8 weeks) myocardial B cells. We combined 10X single cell gene expression analysis with immunostaining using TotalSeq antibodies against CD11b, CD23, and CD21.

overall_design: We performed transcriptional profiling of cardiac B cells isolated from 6 neonatal (2 weeks old) and 6 adult (8 weeks old) wild-type mice. We used the Chromium Single Cell 3′ v3 Chromium instrument (from 10x Genomics) to perform single cell transcriptional profiling analyses.


title: High throughput joint profiling of chromatin accessibility and protein levels in single cells [Species mix]

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Mixed human and mouse cells were used to test the method's ability to detect antibody tags with specificity. A 50:50 cell mix was stained with a cocktail of human and mouse a-CD29 before fixation and lysis. Permeabilized cells were processed according to 10x scATAC workflow with the addition of a bridge oligo during the barcoding reaction in droplets to allow capture and barcoding of antibody tags.


title: High throughput joint profiling of chromatin accessibility and protein levels in single cells [Tcell KO]

overall_design: Sorted human T-cells from 3 biological donors were activated and target genes were perturbed using CRISPR / Cas9. Gene KOs were generated in a pooled fashion using gRNAs targeting CD4 (HTO2), ZAP70 (HTO4), NFKB2 (HTO5), CD3E (HTO3 + HTO13), CD3E+CD4 (HTO3 + HTO12) and 2 non-targeting controls (NTCs; HTO1). Different gRNA replicates were encoded using HTO12 and HTO13 for CD4, ZAP70, NFKB2, and NTC conditions. Changes in chromatin accessibility and protein abundance were determined concomitantly in single cells.


title: mTOR inhibition by INK128 extends ovarian functions in aging and premature aging mice following germline stem cell transplantation

city: TianJin

first: Heng

last: Dai

state: TianJin

address: NanKai District NanKai University

institute: NanKai University

summary: Germline stem cell transplantation in combination with mTOR inhibition by INK128 can improve and extend ovarian and endocrine functions of aging and particularly premature aging mice.

overall_design: We collected the transplanted rOvaries of premature aging mice，compared the groups fed with INK128 and those without INK128 , and performed RNA sequencing analysis to explore the mechanism of INK128 extending ovarian function

first: Dai

last: Heng

first: Xiaoyan

last: Sheng

first: Chenglei

last: Tian

first: Jie

last: Li

first: Linlin

last: Liu

first: Mo

last: Gou

first: Lin


title: Elucidation of remdesivir cytotoxicity pathways through genome-wide CRISPR/Cas9 screening and transcriptomics

city: Boston

first: Richard

middle: I

last: Sherwood

address: 77 Avenue Louis Pasteur

department: Division of Genetics, Department of Medicine

institute: Brighan and Women's Hospital and Harvard Medical School

summary: The adenosine analogue remdesivir has emerged as a front-line antiviral treatment for SARS-CoV-2, with preliminary evidence that it reduces the duration and severity of illness. As clinical trials are ongoing, the full side effect profile of remdesivir is not yet known. Prior clinical studies have identified adverse events, and remdesivir has been shown to inhibit mitochondrial RNA polymerase in biochemical experiments, yet little is known about the specific genetic pathways involved in cellular remdesivir metabolism and cytotoxicity. Through genome-wide CRISPR/Cas9 screening (data not provided here) and RNA sequencing, we identify specific genes and pathways implicated in remdesivir metabolism. We show that remdesivir treatment leads to a global repression of mitochondrial respiratory activity. Further, we show that loss of the mitochondrial nucleoside transporter SLC29A3 or the mitochondrial adenylate kinase AK2 provide 10-72-fold mitigation of remdesivir toxicity  while conserving its antiviral potency. This work provides candidate gene targets to reduce remdesivir toxicity and provides a proof-of-principle for the use of CRISPR/Cas9 screening to elucidate mechanisms of drug cytotoxicity.

overall_design: RNA-sequencing of on liver and intestinal cell lines treated with remdesivir or Hydroxychloroquine (HCQ).

first: Ersin

last: Akinci

first: Minsun

last: Cha

first: Marisa

last: Hamilton

last: Lin

first: Grace

middle: H

last: Yeo

first: Heysol

last: Bermudez-Cabrera

first: Larissa

last: Zanetti

first: Minja

last: Velimirovic

first: Benyapa

last: Khowpinitchai

first: James

last: Fife

first: Miha

last: Sovrovic

first: Rikita

last: Jodhani

first: Robert

last: Davey

first: Christopher

middle: A

last: Cassa


title: Endothelial mutagenesis screen identifies genetic risk factors in the development vascular anomalies [adipose]

first: Safiyyah

last: Ziyad

summary: mRNA transcriptional comparison between two pieces of VA from eight SBxVEC-Cre+ animals and four control animals

first: Trent

last: Tsu

first: M

last: Iruela-Arispe


title: Genome-wide mapping of the heterochromatin mark H3K9me2 in loss-of-function mutant worms

city: London

first: Ruben

last: Esse

address: Guy's Hospital, Great Maze Pond

department: Department of Medical and Molecular Genetics

institute: King’s College London

summary: Histone modification marks such as H3K4me1 and H3K27ac have been used to map putative enhancers, but these marks represent only a fraction of the full repertoire of histone modifications decorating these regulatory regions. In mammals, methylation of histone H3 on lysine 79 (H3K79me), deposited by the methyltransferase DOT1L, is present at enhancers. In C. elegans, putative enhancers have been predicted based on chromatin modifications and regions of chromatin accessibility. Our own overlap analysis has revealed that both DOT-1.1, the C. elegans DOT1L homologue, and its major interacting partner, the chromatin-binding factor ZFP-1 (AF10 in mammals), are enriched at both distal and intragenic enhancers. Previous work has shown that Dot1 proteins prevent encroachment of heterochromatin to actively transcribed regions in yeast and in MLL-rearranged leukemias. Here we find that, in C. elegans, loss of DOT-1.1 is accompanied by ectopic H3K9me2, a hallmark of heterochromatin, at distal and intragenic enhancers. This observation suggests a new role for DOT1L in the control of heterochromatin formation at enhancers, which may partake on the control of developmentally regulated genes.

overall_design: Profiling of H3K9me2 in wild-type (WT) and mutant (zfp-1, ced-3, dot-1.1; ced-3, rde-1; dot-1.1, and rde-4; dot-1.1) third larval (L3) stage Caenorhabditis elegans

first: Alla

last: Grishok


title: MM_0565 orchestrates CRISPR-based immunity in Methanosarcina mazei by transcriptional regulation of components essential for the adaptation

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

institute: ZB MED - Information Centre for Life Sciences

summary: CRISPR loci are found in bacterial and archaeal genomes where they provide the molecular machinery for acquisition of immunity against foreign DNA. In addition to the cas genes fundamentally required for CRISPR activity, a second class of genes is associated with the CRISPR loci, of which many have no reported function in CRISPR-mediated immunity. Here, we characterize MM_0565 of Methanosarcina mazei Gö1 associated to the type I-B CRISPR-locus providing evidence for its relevance in regulating this system. We show that MM_0565 is composed of a modified Rossmann-like fold and a winged helix-turn-helix domain and forms a dimer in solution. While direct effects on CRISPR-Cas transcription were not detected by genetic approaches, binding to the leader region of both CRISPR-Cas systems was observed by microscale thermophoresis and electromobility shift assays. Overexpression of MM_0565 however, strongly induced transcription of the cas1-solo gene located in the recently reported casposon, the gene product of which shows high similarity to classical Cas1 proteins. Based on our findings we hypothesize that Cas1-solo is involved in the adaptation of CRISPR-mediated immunity in M. mazei, and that MM_0565 modulates the activity of the CRISPR systems amongst potential other hypnotized actions by activating the transcription of the cas1-solo gene.

overall_design: Investigation of differential-gene expression profiles of a MM565 overproduction M. mazei strain (OP_MM565) and a vector control strain (pWM321), using duplicates.

first: Andrea

last: Ulbricht

first: Lisa

last: Nickel

first: Katrin

last: Weidenbach

first: Herman

middle: V

last: Gebauer

first: Claudia

last: Kießling

middle: U

first: Ruth

last: Schmitz


title: Relative MicroRNA expresssion profile of porcine embryonic and somatic cells

city: Seoul

first: Chang-Kyu

last: Lee

address: 1 Gwanak-ro, Gwanak-gu

department: Department of Agricultural Biotechnology

institute: Seoul National University

summary: MicroRNAs (miRNAs) have been revealed to control the amount of mRNAs. miRNAs were known to be involved in the derivation and maintenance of pluripotent cells. However, the miRNA profile of pig pluripotent cells has not been defined well. Here, we report expression profiles of pluripotent and somatic (or differentiated) cells in pig to discover cell type-specific miRNAs for pluripotent and differentiated cells. Two blastocysts (BL) samples and embryonic stem cell-like (ES-like) cells were used for pluripotent cells. We selected embryoid bodies (EB) and fetal fibroblasts (PFF) as somatic cells. miRNAs were extracted from samples, then libraries were prepared to analyze miRNAs. We classified miRNAs into two categories, known and novel miRNAs. 72, 28, 19, 39 known miRNAs were relatively high in BL, ES-like, EB, and PFF, respectively. Also, expression levels of 15 and 22 known miRNAs were relatively high in pluripotent and differentiated cells. miRNAs that are well-known to control pluripotency did not found in our data. However, the list of cell type-specific miRNAs can be utilized to induce or maintain pluripotency in further studies. Therefore, our work will promote the application of miRNAs on pluripotency study in the pig.

overall_design: MicroRNA expression profiling of two PA blastocyst samples and three cell line samples (pig ES-like cells, Ebmryoid body from ES-like cells, pig fetal fibroblasts)

first: Jong-Nam

last: Oh

first: Dongchan

last: Son

first: Kwang-Hwan

last: Choi

first: Jae

middle: Y

last: Hwang

first: Dong-Kyung


title: Single cell transcriptome of fresh and UM171-expanded CD34+ cord blood cells

city: Montreal

first: Guy

last: Sauvageau

state: QC

address: 2950, Chemin de Polytechnique

country: Canada

institute: Institute for Research in Immunology and Cancer

summary: Single cell analysis (10X Chromium) to identify blood stem cell specific transcripts.

overall_design: 10X Chromium 3' v2


title: Shock waves induce an evolutionary conserved mechanism of spinal cord regeneration via Toll-like receptor 3

city: Innsbruck

first: Can

last: Gollmann-Tepeköylü

address: Anichstraße 35

department: Department for Cardiac Surgery

country: Austria

institute: Medical University of Innsbruck

summary: Shock wave therapy (SWT) is improving motor function and decreasing lesion size in wild-type but not Tlr3-/- mice via IL6 dependent differentiation of neuronal progenitor cells. Both SWT and TLR3 stimulation enhance neuronal sprouting and survival, even in human spinal cord cultures. We could also identify tlr3 as a  crucial enhancer of spinal cord generation in zebrafish. In order to substantiate underlying mechanisms of  the SWT for spinal cords, cultured human neurons (neuroblastoma cell line) were treated with SWT and gene expression profiling were performed by RNAseq.

overall_design: Gene expression profiling of neurons (neuroblastoma cell lineSG-SY5Y) treated with shock wave tretared exosomes

first: Hubert

last: Hackl

first: Johannes

last: Holfeld


title: Genome wide chromatin accessibilty changes associated with JUN and SHH expression in human SSCL patients

city: Stanford

first: Gerlinde

last: Wernig

address: 265 Campus Drive

department: Pathology

institute: Institute for Regenerative Medicine and Stem Cell Research, Stanford University School of Medicine

summary: We found that JUN and SHH expression is increased in many human fibrotic diseases and that systemic induction of Jun in mice resulted in development of fibrosis of multiple organs. To identify the changes in chromatin accessibility associated with JUN and SHH, we worked with primary SSCL dermal fibroblasts that have normal or Knock-out levels of JUN expression and vismodegib treatment then performed ATAC-seq analysis in all of them.

overall_design: To confirm the key role of JUN and SHH in SSCL process, chromatin accessibility and structure change profile in JUN loss-of-function and vismodegib treatment in primary human SSCL dermal fibroblasts were evaluated by ATAC-seq using Nextseq 500.

first: Lu

last: Cui

first: Tristan

last: Lerbs


title: Single-cell RNA-sequencing of control aortic isografts of mouse models

first: Jiacheng

last: Deng

state: Not Applicable

address: James Black Centre, 125 Coldharbour Lane

institute: King's College London

summary: We reported the transcriptional profiling of cells from aortic isografts by single-cell RNA sequencing.

overall_design: This entry contains 10X Single-cell RNA-seq data of cells from 2-week and 4-week aortic isografts.

first: Cai

last: Jingjing

first: Deng

last: Jiacheng

first: Gu

last: Wenduo

first: Xu

last: Qingbo


title: High throughput joint profiling of chromatin accessibility and protein levels in single cells [PBMCs]

first: Caleb

last: Lareau

state: New York

overall_design: PBMCs were used in a series of experiments to technically characterize and advance ASAP-seq. Hashing, different conditions of lysis, staining with different conjugate families and intracellular staining were tested.

first: Eleni

last: Mimitou

first: Kelvin

last: Chen

first: Leif

last: Ludwig

first: Peter

last: Smibert


title: T47D cells; Anastrozole RNA-seq

city: Rochester

first: Hu

last: Li

state: MN

address: 200 First Street, Gonda Building G19-408

department: Molecular Pharmacology & Experimental Therapeutics

institute: Mayo Clinic

summary: The objective of the RNAseq is to identify genes regulated by anastrozole, and the difference in genes regulated by anastrozole and estradiol.

overall_design: T47D cells were treated with vehicle, anastrozole, estradiol, or the combination of anastrozole and estradiol, in triplicates. Vehicle treatment serves as control.

first: Junmei

last: Cairns


title: Differential contribution of bone marrow derived-monocytes to the lung tissue resident alveolar macrophages and persistent lung inflammation with chronic air pollution exposure

city: Cleveland

first: Ernest

middle: R

last: Chan

state: OH

address: 10900 Euclid Ave, Robbins E211

department: PQHS

institute: CWRU

summary: Chronic exposure to ambient particulate matter <2.5µ (PM2.5) has been linked to cardiopulmonary disease. Tissue-resident (TR) alveolar macrophages (AΦ) are long lived, self-renew and critical to the health impact of inhalational insults. There is inadequate understanding of the impact of PM2.5 exposure on nature/time course of transcriptional responses and the proliferation/maintenance of AΦ including the contribution from bone marrow (BM) over chronic time periods. We investigated the effects of exposure to real-world concentrated PM2.5 or filtered air (FA) in chimeric (CD45.2/CD45.1) mice. Here, we show that PM2.5 exposure induces an influx of BM-derived monocytes to lungs at 4-weeks, with no contribution to TR-AΦ population. Chronic (32-weeks) PM2.5 exposure resulted in enhanced apoptosis (Annexin V+) and decreased proliferation (BrdU+) of TR-AΦ and presence of BM-AΦ in inflamed lungs. RNA-seq analysis of flow sorted TR-AΦ and BM-AΦ from 4 and 32-weeks exposed mice, revealed a unique time dependent pattern of differentially expressed genes, with PM2.5 exposure with a pro-inflammatory bias. PM2.5 exposure resulted in pulmonary fibrosis and reduced alveolar fraction which corresponded to protracted lung inflammation. Our findings suggest a time dependent PM2.5 entrainment of a BM-derived monocytes infiltration into PM2.5 exposed lungs with an inflammatory phenotype, that together with enhanced apoptosis of TR-AΦ and pro-inflammatory polarization may contribute to perpetuation of chronic inflammation and lung fibrosis.

overall_design: RNA sequencing of alveolar macrophages and monocytes of CD45.1 and CD45.2 origin from PM2.5 or FA exposed mice for 4 and 32 weeks.

first: Roopesh

middle: S

last: Gangwar

first: Vinesh

last: Vinayachandran

first: E

first: Shyam

last: Biswal

first: Sanjay

last: Rajagopalan


title: Single-Cell RNA-seq Reveals Obesity-Induced Alterations in the BRAC1 Mutant Mammary Tumor Microenvironment

city: Baltimore

first: Pang-Kuo

last: Lo

state: Maryland

address: 108 N. Greene St.

department: Biochemistry and Molecular Biology

institute: University of Maryland School of Medicine

summary: In this study, we conducted single-cell RNA sequencing (scRNA-seq) studies to investigate the impact of high-fat diet (HFD)-induced obesity on transcriptomic landscapes of stromal and immune cells in mammary glands of Brca1-/-;p53+/- mice, an animal breast cancer model. The scRNA-seq profiling data showed that five different subtypes of stromal fibroblasts existed in mouse mammary glands. HFD-induced obesity led to upregulated expression of extracellular matrix (ECM) genes (Col3a1, Col6a3, Eln, and Sparc) and downregulated expression of immunoregulatory genes (Iigp1, Ccl2, and Cxcl10) in these stromal subtype cells. These findings, taken together, suggest that obesity alters the ECM composition and immune ecosystem through modulating the functionality of mammary stromal cells. Moreover, scRNA-seq analysis of mammary immune cells indicated that HFD-induced obesity promoted the generation and/or recruiting of pro-tumorigenic M2 macrophages in mammary glands.

overall_design: Single-cell RNA-seq profiling analysis of stromal and immune cells in mammary glands isolated from either normal or obese C57BL6 Brca1-/-;p53+/- mice.

first: Qun

last: Zhou


title: Colon, rectum and rectal tumor organoids. Effects of calcitriol (active form of Vitamin D) treatment

city: madrid

first: Alba

last: Costales

state: madrid

address: Arturo Duperier, 4

department: cancer genetics

country: Spain

institute: IIB

summary: We have established three-dimensional (3D) organoids from healthy colon and rectum tissue and from tumor tissue of patients with rectal cancer. Global transcriptomic analyses reveal differences in gene expression between these stem cell-derived cultures and distinct response to vitamin D.

overall_design: 1,25(OH)2D3 and vehicle treated organoids from colon, rectum and rectal tumor tissue are RNA-sequenced

first: A

last: Costales-Carrera

last: Fernández-Barral

first: O

last: Domínguez

last: Burgos

last: Barbáchano

last: Muñoz


title: Circulating miR-16-5p, miR-92a-3p, and miR-451a in plasma from lung cancer patients: potential application in early detection and a regulatory role in tumorigenesis pathways.

city: Botucatu

first: Tainara

middle: Francini

last: Felix

state: SP

address: Av. Prof. Mário Rubens Guimarães Montenegro, s/n, s/n

department: Surgery and Orthopedics

country: Brazil

institute: UNESP

summary: Micro(mi)RNAs, potent gene expression regulators associated with tumorigenesis, are stable, abundant circulating molecules,that are detectable in plasma. Thus, miRNAs could potentially be useful in early lung cancer detection.We aimed to identify circulating miRNA signatures in plasma from patients with lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC), and to verify whether miRNAs regulate pathways of lung oncogenesis.

overall_design: RNA isolated from 139 plasma samples (40 LUAD;38 LUSC;61 healthy/non-diseased individuals) were divided into discovery (38 patients; 7 controls including 21 samples, for expression quantification usingan 800-miRNA panel; NanostringnCounter®)and validation (40 patients; 40 controls; TaqMan®RT-qPCR)cohorts. Elastic net, Maximizing-R-Square Analysis (MARSA), and C-Statistics were applied for miRNA signature identification.

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