title: Comparative  transcriptomes analysis at different developmental stages of seed embryo in maize by RNA-sequencing

status: Public on Aug 20 2019

first: Hong

last: Meiyan

address: Xudong 2nd Road

department: Oil Crops Research Institute

institute: Chinese Academy of Agricultural Sciences

summary: we used two contrasting maize genotypes with differential oil accumulation percentage. High oil content (HOC) maize had 11% oil content while low oil content (LOC) maize had significantly lower oil content (5.4%). Transmission electron microscopy revealed a higher accumulation of oil bodies in the HOC maize embryo as compared to LOC maize. Comparative RNA-sequencing analysis at different developmental stages of seed embryo identified 739 genes that are constantly differentially expressed (DEGs) at all the six developmental stages from 15 days after pollination (DAP) to 40 DAP. KEGG enrichment analysis identified fatty acid metabolism and fatty acid biosynthesis as the most enriched biological pathways contributed by these DEGs. Notably, transcriptional changes are more intense at the early stages of embryo development as compared to later stages. In addition, pathways related to oil biosynthesis and their corresponding genes were more enriched at 30 DAP, which seems to be the key stage for oil accumulation. The study also identified 33 key DEGs involved in fatty acid and triacylglycerols biosynthesis, most of them were up-regulated in HOC, which may shape the differential oil contents in the two contrasting maize. Notably, we uncovered that both acyl-CoA-dependent and acyl-CoA-independent processes are essential for the high oil accumulation in maize embryo.

overall_design: Thirty six libraries representing the embryos from the two genotypes collected at six developmental stages and in three replicates were constructed for transcriptome sequencing

first: Xiangxiang

last: zhang

first: Meiyan

last: Hong


title: Expression data from multiple myeloma plasma cells before and after co-culture with osteoclasts

status: Public on Aug 21 2019

city: Little Rock

first: Joshua

last: Epstein

department: Myeloma Institute for Research and Therapy

country: USA

institute: University of Arkansas for Medical Sciances

summary:
To understand how interactions of myeloma cells with osteoclasts and mesenchymal stem cells in the bone marrow affect the clinical course of myeloma, we used microarrays to study changes in gene expression in freshly isolated myeloma plasma cells following co-cultures with osteoclasts (8 experiments) or with mesenchymal stem cells (13 experiments). Interaction with osteoclasts induced changes in the expression of 675 genes, and interaction with mesenchymal stem cells induced changes in the expression of 296 genes. Expression of only 58 genes commonly and similarly changed in both co-culture systems. Among these, we identified genes associated with overall, progression-free, and post-relapse survival, and developed survival prediction models. Gene expression data from 347 patients treated with total therapy 2 protocol, 433 with total therapy 3, and 98 patients who received various treatments (91 of them high-dose therapy with autologous stem cell support) were used for the analysis. Good predictive models were developed only for post-relapse survival, using genes involved in interaction with osteoclasts or with mesenchymal stem cells. The best predictive model used expression of first relapse of 33 probesets whose expression changed in myeloma cells following interaction with osteoclasts, with hazard ratios of 24, 20, and 12 for patients who relapsed following total therapy 2, total therapy 3 and the various other treatments, respectively. Among the probesets used for prediction, only 10, representing 8 genes, were commonly changed after both co-culture systems. These could present favorable target for therapy.

Global gene expression profiling of primary multiple myeloma plasma cells (MMPCs) before and after interaction with osteoclasts (OCs) was done using Affymetrix microarrays.

overall_design: Eight MMPC and OC co-culture experiments were performed using MMPC isolated from 8 patients and OC prepared from 8 different patients.

first: Shmuel

last: Yaccoby


title: The effect of attenuated Salmonella typhimurium on the tumor epithelium in mouse colorectal cancer model

city: Bethesda

first: Daniel

middle: L

last: Kastner

state: MD

address: 9000 Rockville Pike

department: NHGRI

institute: NIH

type: Expression profiling by high throughput sequencing

summary: Bacterial cancer therapy (BCT) shows great promise for treatment of solid tumors, yet basic mechanisms of bacterial-induced tumor suppression remain undefined. We aimed to better understand the tumor epithelium-targeted mechanisms of BCT by using mouse models of intestinal tumorigenesis to assess the effectiveness and mechanisms of treatment with aromatase A-deficient Salmonella typhimurium (STm) delivered by oral gavage.

overall_design: RNAseq using normal colon tissue or colon tumor induced by AOM/DSS, treated or non-treated with aromatase A-deficient STm delivered by oral gavage

first: Hirotsugu

last: Oda

first: Kendle

middle: M

last: Maslowski


title: Polymorphic immune mechanisms regulate commensal repertoire

status: Public on Aug 29 2019

city: Chicago

first: Aly

middle: Azeem

last: Khan

state: IL

address: 6045 S. Kenwood Ave.

institute: University of Chicago

summary: Environmental influences such as infections and dietary changes strongly affect a host’s microbiota. In the steady state, however, host genetics may influence the microbiota composition, as suggested by the greater similarity between the microbiomes of identical twin pairs compared to non-identical twins. Understanding the role of polymorphic mechanisms in regulating the commensal communities is complicated by the variability of human genomes and microbiomes, and by microbial sensitivity to the environment. Animal studies allow genetic modifications, but are also sensitive to influences known as ‘cage’ or ‘legacy’ effects. Here, we analyzed ex-germ-free mice of various genetic backgrounds, including immunodeficient and Major Histocompatibility Complex (MHC)-congenic strains repopulated with identical input microbiota. We found that the host’s genetic polymorphic mechanisms did indeed affect the gut microbiome and that both innate (e.g. anti-microbial peptides, complement, pentraxins and enzymes affecting microbial survival), as well as adaptive (both MHC-dependent and MHC-independent) pathways influenced the microbiota. These polymorphic mechanisms regulated only a limited number of microbial lineages (independently of their abundance). In addition, our comparative analyses suggested that some microbes might benefit from the specific immune responses that they elicit.

overall_design: RNA-seq data of 39 samples from Colon, Ileum and Duodenum/Jejunum from BALB/cJ and C57BL/6J mice were generated.

middle: A

first: Kelly

last: O’Grady

first: Tatyana

last: Golovkina

first: Alexander

last: Chervonsky


title: Mirc11 selectively regulates inflammatory responses of NK cells by targeting ubiquitin modifiers and TRAF6-dependent NF-kB and AP1 activation

city: Milwaukee

first: Robert

last: Burns

state: Wisconsin

address: 8727 W Watertown Plank Rd

institute: Blood Research Institute, Versiti

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

overall_design: Refer to individual Series


title: Mirc11 selectively regulates inflammatory responses of NK cells by targeting ubiquitin modifiers and TRAF6-dependent NF-kB and AP1 activation (RNA-seq: IL-2_expanded_NKG2D_stimulation)

summary:
Lack of Mirc11 significantly reduces NK cell-mediated cytokine production in vivo
Mirc11 cluster targets NF-kB and AP-1-mediated gene transcriptions

overall_design: 3 biological replicates were analyzed for each of 4 conditions (2 genotypes; 2 treatments per genotype)

first: Subramaniam

last: Malarkannan

first: Arash

last: Nanbakhsh


title: Mirc11 selectively regulates inflammatory responses of NK cells by targeting ubiquitin modifiers and TRAF6-dependent NF-kB and AP1 activation (RNA-seq: Listeria_challenge)


city: seoul

first: Hyun-Seob

last: Lee

address: 71 Daehak-ro, Jongno-gu

department: Biomedical research institute

country: South Korea

institute: Seoul national University Hospital

summary:
mRNA-seq analyses for the differentially expressed genes (DEGs) between Parkinsons's disease patient (holding Lin28 R192G hetero mutation)-iPSC (Pt-iPSC) derived neural stem cell vs  Lin28 R192G hetero mutation corrected-iPSC (Corrected Pt-iPSC) derived neural stem cell.
To gain further molecular insight into the observed Lin28R192G mutation in Parkinsons's disease (PD) patient iPSC-derived neural stem cell (NSC) functions, we performed mRNA-sequencing (RNA-seq) analysis of the PD patient (holding Lin28 R192G hetero mutation)-iPSC (Pt-iPSC) derived NSC and  Lin28 R192G hetero mutation corrected-iPSC (Corrected Pt-iPSC) derived NSC.

overall_design: 2 human samples: PD patient (Lin28 R192G het) iPSC derived-NSC (Pt-iPSCs) and  Lin28 R192G het mut-corrected PD patient iPSC derived-NSC (corrected Pt-iPSCs)

first: Mi-Yoon

last: Chang

first: Sang-Hun


title: Molecular insight into the Lin28R192G mutation in human ESCs and Parkinson's disease


title: Molecular insight into the Lin28R192G mutation in human ESCs

summary:
Total RNA-seq analyses for the differentially expressed genes (DEGs) among WT (c42), Lin28 R192G hetero mut hESC (c26_5), and Lin28 R192G homo mut hESC (c38)
To gain further molecular insight into the observed Lin28R192G mutation in human ESCs, we performed total RNA-sequencing (RNA-seq) analysis of the WT, Lin28 R192G hetero mut hESC, and Lin28 R192G homo mut hESC. The genes that are differentially expressed (DEGs) in Lin28 R192G hetero mut and Lin28 R192G homo mut hES compared to WT hESC.

overall_design: 3 human samples: WT hESC (c42), Lin28 R192G hetero mut hESC (c26_5), and Lin28 R192G homo mut hESC (c38)


title: Transcriptomic responses to oil, a pathogen, or both in spleen and liver tissues from juvenile Atlantic croaker (Micropogonias undulatus)

city: Ocean Springs

first: Maria

last: Rodgers

state: Mississippi

address: 103 McIlwain Drive

department: Coastal Sciences

institute: University of Southern Mississippi

summary: The objective of this study was to determine how transcriptomic responses in the spleen and liver are altered in juvenile Micropogonias undulatus exposed to oil, a known fish pathogen (Vibrio anguillarum), or both.

overall_design: M. undulatus juveniles were exposed to oil, a pathogen (Vibrio anguillarum) or both.  Oil exposure was for 8 days and pathogen exposure was for 1 hour, 24 hours before takedown.  Oil solutions used in exposures were derived from high energy water accommodated fractions (HEWAF) prepared using Macondo well oil from the Deepwater Horizon oil spill following established procedures.  At the end of the experiments, livers and spleen were taken from organisms, RNA was extracted and sequenced.

middle: J

last: Griffitt


title: Gene expression of E.coli challenged green rice leafhopper Nephotettix cincticeps.

city: Tsukuba

first: Yuki

last: Nakamura

state: Ibaraki

address: 1-1 Owashi

country: Japan

institute: National Institute of Agrobiololgical Sciences

summary: The green rice leafhopper Nephotettix cincticeps have two mutualistic symbiotic bacteria (Candidatus Sulcia muelleri and Candidatus Nasuia deltocephalinicola) in its symbiont special organ bacteriome and are also infected to rickettsia. In order to determine immune challenge is induced or not in N. cincticeps, we investigated gene expression of Escherichia coli challenged N. cincticeps.

overall_design: One day adult N. cincticeps females were pricked with E. coli with a sterile needle. Control adults were pricked with sterilized water. Total RNA of five females was extracted after 3 h and 12 h incubation respectively. E.coli challenged and control Nephotettix cincticeps samples were prepared 3 replicates for 3h and 4 replicates for 12h.

first: M

last: Tomizawa

first: Y

first: H

last: Noda


title: CDK12 inhibition in Hep3B, Huh7 and SNU449 cells

city: Amsterdam

first: Cun

last: Wang

address: Plesmanlaan 121,

department: Division of Molecular Carcinogenesis

country: Netherlands

institute: The Netherlands Cancer Institute

summary: Purpose: to analyze gene expression in THZ531 treated liver cancer cells. Methods: Hep3B and Huh7 cells are treated with THZ531 for 24 hours. SNU449 cells are treated with THZ531 for 48 hours. For RNA sequencing, the library was prepared using TruSeq RNA sample prep kit according to the manufacturer’s protocol (Illumina). Gene set enrichment analysis was performed using gene set enrichment analysis software.

overall_design: RNA seq data of Hep3B-control, Hep3B-250nM, Hep3B-500nM, Huh7-control, Huh7-250nM, Huh7-500nM, SNU449-control, SNU449-250nM, SNU449-500nM,  to check the effects of THZ531 on globle gene expression.

first: Cor

last: Lieftink


title: Next generation sequence analysis

city: Thanjavur

first: K

last: Anbarasu

state: TN

address: Periyar Nagar, Vallam

country: India

institute: Periyar Maniammai Institute of Science & Technology

summary: To investigate the transcriptional expression patterns of carotenogenic biosynthetic genes accumulating partially saturated canthaxanthin under acidic stress in Aspergillus carbonarius mutant

overall_design: Transcriptome sequence analysis of mutant Aspergillus carbonarius grown at pH 3.0 and mutant A. carbonarius grown at pH5.5 condtions

last: Ahila

first: Muhil Vannan

last: Seralathan


title: Salivary microRNA expression data from malignant pleural effusion patients and healthy controls

city: Beijing

first: Yuan

last: Yang

address: 8 Gongti Nanlu, Chaoyang District

country: China

institute: Beijing Chaoyang Hospital, Capital Medical University

summary:
Malignant pleural effusion (MPE) is a common medical problem caused by multiple malignancies especially lung cancers and always along with a poor therapeutic outcome.
We investigate the characteristics of salivary microRNAs (miRNAs) of MPE patients and healthy controls, identifying the distinct classes of up-regulated and down-regulated miRNAs during this process

overall_design: Salivary supernatant from 3 MPE patients and 3 healthy controls were collected for RNA extraction.The miRNA profiles of these saliva were detected using the Affymetrix® GeneChip® miRNA 4.0 Arrays (Affymetrix, Santa Clara, CA) for miRNA biomarker signatures discovery.

first: Kan

last: Zhai

first: Huan-Zhong

last: Shi


title: DNA methylation changes in regional lung macrophages are associated with metabolic differences

city: Lebanon

first: Youdinghuan

last: Chen

state: NH

address: Hinman Box 7650

department: Epidemiology

institute: Dartmouth College

summary:
A flexible fiberoptic bronchoscope was inserted trans-orally and advanced through the vocal cords of subjects. Brochoalveolar lavage (BAL) fluid was obtained from tertiary airways in the right upper and lower lobes.
The BAL procedure was performed sequentially in the right upper lobe (RUL) and right lower lobe (RLL) with 20 ml of sterile saline followed by 10 ml of air and this was repeated for a total of 5 times per airway. BAL fluid was then filtered through 2-layer gauze, centrifuged, and washed twice in 0.9% NaCl. Cells were counted with a T10 automated cell counter.
Cytospins were performed using a Shandon Cytospin 3 centrifuge. 75,000 cells resuspended in 200 l of 0.9% NaCl were loaded into a cytology funnel and centrifuged for 10 mins. Cells were allowed to air dry and processed for viewing via Hema 3 Stat pack.
One pair of samples (GEO accessions GSM3610354 [H_1_RLL] and GSM3610362 [H_1_RUL]) from our previous publication, collected and measured in the same manner, was also included in our present analysis.
DNA was extracted from lung macrophages via Qiagen DNeasy Blood and Tissue Kit.  DNA was quantitated on a Qubit 3.0 Fluorometer. Bisulfite conversion of DNA was performed using the Zymo EZ DNA methylation kit. The Illumina MethylationEPIC array hybridization and scanning were performed at the University of Southern California Molecular Genomics Core.

overall_design: BAL fluids from 12 heathy subjects' right upper and lower lung lobe were acquired. A pair of upper and lower-lobe samples from one additional subject (GEO accessions GSM3610354 and GSM3610362) used as a healthy control in our previously published cystic fibrosis manuscript (Chen & Armstrong et al. 2018) was also included in the present analysis.

first: David

last: Armstrong


title: Male Sterility in Maize after Transient Heat Stress during the Tetrad Stage of Pollen Development

city: Gainesville

first: Kevin

last: Begcy

state: Florida

address: 1535 Fifield Hall

institute: University of Florida

summary: we show that a short moderate heat stress during the tetrad stage of pollen development targets vital metabolic pathways ultimately leading to sterility and yield losses in maize.

overall_design: 6 samples (3 replicates each of control vs heat stress)

first: Thomas

last: Dresselhaus

first: Tetyana

last: Nosenko


title: LSD1 inhibition promotes epithelial differentiation through derepression of fate- determining transcription factors [proliferation vs differentiation]

city: Philadelphia

first: Yann

last: Aubert

state: Pennsylvania

address: Biomedical Research Building 421 Curie Blvd

department: Penn Dermatology Research

institute: University of Pennsylvania

summary: Genome-wide gene expression changes triggered by Ca2+-induced differentiation of epidermal progenitors

overall_design: In vitro cultured proliferating human epidermal progenitors were differentiated by treating cell cultures with 1.22mM CaCl2 for 48H.

first: Shaun

last: Egolf

first: Miriam

last: Doepner

first: Amy

last: Anderson

first: Alexandra

last: Maldonado-Lopez

first: Gina

last: Pacella

first: Jessica

last: Lee

first: Eun

middle: K

last: Ko

first: Jonathan

last: Zou

first: Yemin

last: Lan

first: Cory

last: Simpson

first: Todd

last: Ridky

first: Brian

middle: C

last: Capell


title: LSD1 inhibition promotes epithelial differentiation through derepression of fate- determining transcription factors [inhibitors]

summary: We report the impact of the pharmacological inhibition of the Histone 3 Lysine 4 demethylase (H3K4) LSD1 (KDM1A) enzymatic activity on genome-wide gene expression in normal human epidermal keratinocyte (NHEK)

overall_design: Examination of genome-wide gene expression changes triggered by the pharmacological inhibition of LSD1 (KDM1A) Histone 3 Lysine 4 (H3K4) histone demethylase activity in normal human epidermal keratinocyte using 2 different LSD1 inhibitors: GSK-LSD1 (Cayman Chemical, Cat# 16439) or 2-PCPA (BPS Bioscience, Cat# 27305) and different treatment length (2d or 6d).


title: Understanding the Mechanistic Contribution of Herbal Extracts in Compound Kushen Injection with Transcriptome Analysis

city: Adelaide

first: David

middle: L.

last: Adelson

state: South Australia

address: University of Adelaide

department: Molecular and biomedical science

country: Australia

institute: University of Adelaide

summary: Herbal compatibility is the knowledge of which herbs to combine in traditional Chinese medicine (TCM) formulations. The lack of understanding of herbal compatibility is one of the key problems for the application and popularization of TCM in western society. Because of the chemical complexity of herbal medicines, it is simpler to begin to conduct compatibility research based on herbs rather than component plant secondary metabolites. We have used transcriptome analysis to explore the effects and interactions of two plant extracts (Kushen and Baituling) combined in Compound Kushen Injection (CKI). Based on shared chemical compounds and in vitro cytotoxicity comparisons,  we found that both the major compounds in CKI, and the cytotoxicity effects of CKI were mainly derived from the extract of Kushen (Sophorae flavescentis). We generated and analyzed transcriptome data from MDA-MB-231 cells treated with single-herb extracts or CKI and results showed that Kushen contributed to the perturbation of the majority of cytotoxicity/cancer related pathways in CKI such as cell cycle and DNA replication. We also found that Baituling (Heterosmilax yunnanensis Gagnep) could not only enhance the cytotoxic effects of Kushen in CKI, but also activate immune-related pathways. Our analyses predicted that  IL-1[beta] gene expression was upregulated by Baituling in CKI and we confirmed that IL-1[beta] protein expression was increased using an ELISA assay. Altogether, these findings help to explain the rationale for combining Kushen and Baituling in CKI, and show that transcriptome analysis using single herb extracts is an effective method for understanding herbal compatibility in TCM.

overall_design: High-depth paired-end RNA-seq from  MDA-MB 231 adenocarcinoma cell line. Each sample contains 3 biological replicates.

first: Hanyuan

last: Shen


title: Avian Tembusu virus infection of chicken HD11 cells

city: Xi'an

first: Hai

last: Li

address: No.76 Yanta West Road

department: Department of Pathogenic Microbiology and Immunology

institute: Xi'an Jiaotong University

summary: We sequenced mRNA from HD11 cells infected with TMUV at 12 hpi and 24 hpi.

overall_design: Examination of mRNA levels in individual condition were compared

first: Shengwang

last: Liu


title: LSD1 inhibition promotes epithelial differentiation through derepression of fate- determining transcription factors

first: Yann

last: Aubert

type: Genome binding/occupancy profiling by high throughput sequencing


title: LSD1 inhibition promotes epithelial differentiation through derepression of fate- determining transcription factors [ChIP-seq]

summary: We report the impact of the pharmacological inhibition of the Histone 3 Lysine 4 demethylase (H3K4) LSD1 (KDM1A) enzymatic activity on its binding genome wide and how it impacts genome-wide H3K4me1 and H3K4me2 deposition in Normal Human Epidermal Keratinocytes (NHEK)

overall_design:
Examination of LSD1 (KDM1A) genome-wide binding and H3K4me1/H3K4me2 deposition upon pharmacological inhibition of LSD1 enzymatic activity in normal human epidermal keratinocytes (NHEK)

Please note that each processed data was generated from both *4624 and *4625 replicates and is linked to the corresponding *4624 sample records.

first: Shaun

last: Egolf


title: Tropifexor-Mediated Abrogation of Steatohepatitis and Fibrosis Is Associated With Antioxidative Gene Expression Profile in Rodents

city: San Diego

first: Bin

last: Fang

state: CA

address: 10675 John Jay Hopkins Dr

department: Discovery Science

institute: Novartis

summary: Farnesoid X receptor (FXR) agonism is emerging as an important potential therapeutic mechanism of action for multiple chronic liver diseases. The bile acid–derived FXR agonist obeticholic acid (OCA; 6-ethyl chenodeoxycholic acid) has shown promise in a phase 2 study in patients with nonalcoholic steatohepatitis (NASH). Here, we report efficacy of a novel, non–bile acid FXR agonist tropifexor (LJN452) in two distinct preclinical models of NASH. The efficacy of tropifexor at <1 mg/kg doses was superior to that of OCA at 25 mg/kg in the liver in both NASH models. In a chemical and dietary model of NASH (STAM model), tropifexor reversed established fibrosis and reduced nonalcoholic fatty liver disease activity score and hepatic triglycerides. In an insulin-resistant, obese NASH model (AMLN), tropifexor markedly reduced steatohepatitis, fibrosis, and profibrogenic gene expression. Transcriptome analysis of livers from AMLN mice revealed 461 differentially expressed genes following tropifexor treatment, which included a combination of signatures associated with reduction of oxidative stress, fibrogenesis, and inflammation. Conclusion: Based on the preclinical validation in animal models, tropifexor is a promising investigational therapy that is currently under phase 2 development for NASH.

overall_design: Liver mRNA profiles of male C57BL/6 mice aged ~6 weeks and maintained on a high-fat (40% kcal; Primex), high-fructose (22% by weight), and high-cholesterol (2% by weight) diet (Research Diets Inc., New Brunswick, NJ; cat. no. D09100301) for 26 weeks to induce NASH. Control animals received low-fat diet (10% kcal) with no fructose or cholesterol (Research Diets; cat. no. D09100304). From week 26, animals received tropifexor (0.1, 0.3, or 0.9 mg/kg) or OCA (25 mg/kg) qd orally for 4 weeks.

first: Eloy

middle: D

last: Hernandez

first: Lianxing

last: Zheng

first: Young

last: Kim

first: Bo

first: Reginald

last: Valdez

first: William

middle: F

last: Dietrich

first: Paul

middle: V

last: Rucker

first: Donatella

last: Chianelli

first: James

last: Schmeits

first: Dingjiu

last: Bao

first: Jocelyn

last: Zoll

first: Claire

last: Dubois

first: Glenn

last: Federe

first: Lihao

last: Chen

first: Sean

middle: B

last: Joseph

first: Lloyd

last: Klickstein

first: John

last: Walker

first: Valentina

last: Molteni

first: Peter

last: McNamara

first: Shelly

last: Meeusen

last: Tully

first: Michael

last: Badman

first: Jie

last: Xu

first: Bryan

last: Laffitte


title: Glial transcriptome responses to chronic intermittent ethanol exposure

city: Austin

first: Emma

last: Erickson

state: TX

address: 2500 Speedway MBB 1.124

department: Neuroscience

institute: University of Texas at Austin

summary:
Purpose: Identify the specific transcriptome alterations in astrocytes and microglia isolated from mouse prefrontal cortex (PFC) following a chronic intermittent ethanol vapor exposure paradigm
Methods: We performed RNA-sequencing on astrocytes, microglia, and total homogenate tissue isolated from the PFC of C57BL/6J mice following chronic intermittent ethanol vapor exposure
Results: We identified common neuroimmune gene expression response between cell types in response to CIE, unique networks of correlated genes differentially expressed in specific cell types, along with candidate pathways, biological processes and highly connected cell-type specific genes
Conclusions: This study sheds light on the cell-specific effects of chronic ethanol and provides novel molecular targets for understanding ethanol dependence

overall_design: Illumina RNA-sequencing of isolated astrocytes, microglia and total homogenate from mouse PFC following chronic intermittent ethanol vapor exposure

first: R

last: Mayfield


title: Asymmetrical methyltransferase PRMT3 regulates human mesenchymal stem cell osteogenesis via miR-3648

city: Chengdu

first: xiaomeng

last: liu

address: No.55,Section 4,South Renmin Road

country: Colombia

institute: Sichuan Cancer Hospital & Institute, Sichuan Cancer Center

summary: Histone arginine methylation, which is catalyzed by protein arginine methyltransferases (PRMTs), plays a key regulatory role in various biological processes, including signal transduction, RNA splicing, transcription and chromatin remodeling, and DNA repair. Several PRMTs are involved in skeletal development; however, their role in the osteogenic differentiation of mesenchymal stem cells (MSCs) is not completely clear. In this study, we aimed to elucidate the function of PRMT3, a type-I PRMT that catalyzes the formation of ω-mono- or asymmetric dimethyl arginine, in MSC osteogenesis. We found that PRMT3 is involved in MSC osteogenic commitment and bone remodeling. Then we did PRMT3 and H4R3me2a ChIP-seq in MSC to find the possible target genes.

overall_design: PRMT3 and H4R3me2a ChIP-seq experiments in MSC showed the possible target genes of PRMT3 and H4R3me2a which gave the clues on how PRMT3 regulated human MSC osteogenesis.

first: Min

last: Zhang

first: Xiaomeng

last: Liu

first: Ping

first: Yongsheng

last: Zhou


title: Mapping Histone Modifications in Single Cells Using an Antibody-guided Transposase

city: Bethesda

first: Keji

last: Zhao

address: Building 10 Room 7B06A

department: National Heart, Lung, and Blood Institute

institute: national Institute of Health

summary: We describe a novel method of mapping genome-wide distributions of epigenetic marks in single cells using a Tn5 transposase complex conjugated to Protein A. This construct is guided to chromatin by an associated antibody, allowing sequence tag insertion and chromatin fragmentation specifically at genomic sites presenting the relevant antigen. This method is capable of processing thousands of individual cells in a single day of bench work.

first: Carter

last: Benjamin

first: Wai Lim

last: Ku

first: Jee Youn

last: Kang

first: Gangqing

last: Hu

first: Jonathan

last: Perrie

first: Qingsong

last: Tang


title: Expression data from SIX1 knocked-down HKc/DR cells

city: Columbia

first: Diego

last: Altomare

state: SC

address: 715 Sumter Street, Room 617

department: Department of Drug Discovery and Biomedical Sciences

institute: University of South Carolina

summary: The homeodomain transcription factor SIX1 plays a critical role in embryogenesis, is not expressed in normal adult tissue, but is expressed in many malignancies, including cervical cancer. SIX1 drives the progression of HPV16-immortalized human keratinocytes (HKc/HPV16) toward malignancy: HKc/HPV16 express high levels of SIX1 mRNA and protein; overexpression of SIX1 in HKc/HPV16 produces pre-malignant, differentiation-resistant lines (HKc/DR); SIX1 overexpression in HKc/DR induces tumorigenicity. In this paper, we explore the consequences of inhibition of SIX1 expression in premalignant HKc/DR. Only partial inhibition of SIX1 expression could be obtained in HKc/DR by RNA interference. Decreased SIX1 expression (up to 80%) in HKc/DR resulted in slower proliferation, decreased HPV16-E6/E7 mRNA levels, and increased p53 protein levels. Gene expression changes induced in HKc/DR by anti-SIX1 shRNA were indicative of mesenchymal-epithelial transition (EMT) and changes in TGF-beta signaling. We conclude that HPV16-transformed cells depend on SIX1 for survival, continuous HPV16 E6/E7 gene expression and EMT.

overall_design: Three-condition, one-color experiment. HKc/DR cells were transfected with control or one of two different SIX1-targeting siRNA duplexes and gene expression was performed on RNA isolated from them. 4 biological replicates per each experimental group.

first: Maria

last: Hosseinipour

first: Lucia

last: Pirisi


title: Gene expression profiling in Hepa1c1c7 transfected Cd74 or Tmem54.

first: Keiko

last: Nohara

address: 16-2 Onogawa

department: Center for Health and Environmental Risk Research

institute: National Institute for Environmental Studies

summary: To analyse Cd74 and Tmem54 function as tumor associated genes, we carried out overexpression analysis of Cd74 or Tmem54 using Hepa1c1c7 and  investigated downstream genes expression by microarray.

overall_design: Overexpression of Cd74 in Hepa1c1c7 cells increased Trib3 expression and suppressed expression of tumor suppressor genes Id3 and Atoh8.


title: Gene expression profiles of liver tissues (normal, non-tumor and tumor tisuues) of F2 males of C3H mice born to F1 mice gestationally exposed to arsenite

summary: We have employed microarray analysis to detect gene expression changes that were affected in the F2 mice of arsenite group.

overall_design: Examination of liver gene expressions in normal tissues (N), non-tumor tissues (Tn) and tumor tissues (Tt) of control (CC) and arsenite (AA) group, respectively (N=3/group, total 18 samples) . The gene expression data in CCN and CCTt (N=3) were already publicly avairable at Gene Expression Omnibus (GEO), accession number GSE104627.  We upload the rest of liver gene expression data in CCTn, AAN, AATn and AATt (N = 3).


title: ROLE OF EXOSOMAL miRNAs IN METASTATIC POST-TRANSPLANT COLORECTAL CARCINOMA UNDER RAPAMYCIN AND CYCLOSPORINE

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

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

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

platform_organism:
Homo sapiens
synthetic construct

overall_design: Refer to individual Series


title: The DNA methylation profiles of liver tissues (normal, non-tumor and tumor tisuues) of F2 males of C3H mice born to F1 mice gestationally exposed to arsenite

type: Methylation profiling by high throughput sequencing

summary:
Background: Previously, we showed that gestational arsenite (As) exposure of F0 females increases hepatic tumors in the F2 males in C3H mice.  However, the mechanisms have not yet been clarified.
Methods: We detected genome wide site-specific DNA methylation by using reduced representative bisulfite sequence (RRBS) method. We used the data uploaded here and those with GSE Series accession number GSE111420 (CCN and CCTt) to detect differential methyrated cytosines between control groups and arsenite groups.
Results: We clarified that DNA methylation of Tmem54 and Cd74 around TSS were downregulated and their gene expressions were accordingly upregulated in the liver tumor tissues of F2 males of arsenite group.
Conclusions: Our study proposes novel DNA methylation dependent pathways which increase liver tumors in the F2 males of arsenite group.

overall_design: Examination of liver DNA methylation modifications (normal tissues (N), non-tumor tissues (Tn), tumor tissues (Tt) of control (CC) and arsenite (AA) group, respectively (N=3/group, total 18 samples)) . These methylation status in CCN and CCTt (N=3) were already publicly avairable at Gene Expression Omnibus (GEO), accession number GSE111420.  We uploaded the rest liver DNA methylation status in CCTn, AAN, AATn and AATt (N = 3).


title: ROLE OF EXOSOMAL miRNAs IN METASTATIC POST-TRANSPLANT COLORECTAL CARCINOMA UNDER RAPAMYCIN AND CYCLOSPORINE (Clariom_S_Human)

summary: Immunosuppression plays a crucial role in the development of cancer which remains a major cause of mortality in kidney transplant recipients. Cancer Exosomes (Exos) are extracellular vesicles described as modulators of tumor invasion and metastasis. This paper describes the effect of RAPA and CsA, two immunosuppressive drugs with different oncogenic proprieties, in Exos of colorectal cancer (CRC) cell lines. RAPA induces an increased Exos production and an overexpression of miR-6127, miR-6746-5p, and miR-6787-5p in Exos from a metastatic cell line. These miRNAs produce a significant down-regulation of epigenetic genes involved in cell cycle, chromatin and DNA regulation pre-metastatic niche. Our results describe a potential mechanism by RAPA in modulating pre-metastatic niche in post-transplant metastatic CRC through these exosomal miRNAs.

overall_design: IMR90 cell lines were transfected by 3 mirnas separately and together with replicates. Also Untreated cell line is included in the transcriptomic analysis.

first: V

last: Tubita

first: M

last: Ramirez-Bajo

first: F

last: Diekmann

first: I

last: Revuelta


title: Transcript profiles of developing Arabidopsis dgat1-1 mutant seed

city: Manhattan

first: Timothy

last: Durrett

state: KS

address: 1711 Claflin Road

department: Biochemistry and Molecular Biophysics

institute: Kansas State University

summary: Global transcript profiling of Arabidopsis dgat1-1 seed at different stages of embryo development was used to identify differentially expressed genes in the mutant compared to wild-type (Col-0) seed. These genes provided information about the remodeling of lipid metabolism and TAG synthesis in response to the lack of DGAT1 activity.

overall_design: In depth transcriptome profile was generated using RNA-Seq for total RNA extracted from different seed development stages 8, 12, 16 Days after flowering (DAF). Samples were collected from wild type (WT) and dgat1-1 genotypes, with three biological replicates for each time point/genotype combination. RNA was sequenced at the Genomics Core at the University of Kansas Medical Center. The mRNA fraction was enriched with oligo dT capture, sized, reverse transcribed into cDNA and ligated with the appropriate indexed adaptors using the TruSeq Stranded mRNA Sample Preparation Kit (Illumina). Following Agilent Bioanalyzer QC of the library preparation and library quantification using the Roche Lightcycler96 with KAPA SYBR Fast Universal qPCR kit (KAPA Biosystems), the RNA-Seq libraries were adjusted to a 4nM concentration and pooled for multiplexed sequencing. Libraries were denatured and based on qPCR results, diluted to the appropriate concentration, followed by clonal clustering onto the sequencing flow cell using the TruSeq Paired-End (PE) Cluster Kit v3-cBot-HS (Illumina). The clonal clustering procedure was automated using the Illumina cBOT Cluster Station. The clustered flow cell was sequenced on an Illumina HiSeq 2500 Sequencing System using the TruSeq SBS Kit v3-HS (Illumina) to obtain 100bp pair-end reads, which were trimmed and quality assessed before assembly against the Arabidopsis reference genome (Araport 11) using CLC genomics workbench (v 7.5.1)

middle: P

first: Karanbir

last: Aulakh


title: Dcr1-GFP is functional for 22-23 nt small RNAs production

city: Paris

first: Maxime

last: Wery

address: 26 rue d'Ulm

country: France

institute: Institut Curie

type: Non-coding RNA profiling by high throughput sequencing

summary: Antisense (as)lncRNAs are extensively degraded by the nuclear exosome and the cytoplasmic exoribonuclease Xrn1 in the budding yeast Saccharomyces cerevisiae, lacking RNA interference (RNAi). Whether the ribonuclease III Dicer affects aslncRNAs in close RNAi-capable relatives remains unknown. Using genome-wide RNA profiling, here we show that aslncRNAs are primarily targeted by the exosome and Xrn1 in the RNAi-capable budding yeast Naumovozyma castellii, Dicer only affecting Xrn1-sensitive lncRNAs (XUTs) levels in Xrn1-deficient cells. The dcr1 and xrn1 mutants display synergic growth defects, indicating that Dicer becomes critical in the absence of Xrn1. Small RNA sequencing showed that Dicer processes aslncRNAs into small RNAs, with a preference for asXUTs. Consistently, Dicer localizes into the cytoplasm. Finally, we observed an expansion of the exosome-sensitive antisense transcriptome in N. castellii compared to S. cerevisiae, suggesting that the presence of cytoplasmic RNAi has reinforced the nuclear RNA surveillance machinery to temper aslncRNAs expression. Our data provide fundamental insights into aslncRNAs metabolism and open perspectives into the possible evolutionary contribution of RNAi in shaping the aslncRNAs transcriptome.

overall_design: Small RNA-Seq analysis in Dcr1-GFP cells of N. castellii.

first: Ugo

last: Szachnowski

first: Sara

last: Andus

first: Dominika

last: Foretek

first: Antonin

last: Morillon


title: Transcriptomic changes induced by Curcumin loaded solid nanoparticles and radiation in breast cells

city: Cefalù

first: Valentina

last: Bravatà

address: Contrada Pietrapollastra Pisciotto

country: Italy

institute: IBSBC CNR

summary: In breast cancer (BC) care, radiotherapy is considered an efficient treatment. However, approximately 90% of BC-related deaths are due to the metastatic tumor progression. Then, it is strongly desirable to improve tumors radiosensitivity using molecules with synergistic action. In this study, we developed curcumin-loaded solid nanoparticles (Cur-SLN) in order to increase curcumin bioavailability and evaluated their radiosensitizing ability in comparison to curcumin free (Cur), by using an in vitro approach on BC models. Precisely, here we analyzed the transcriptomic profiles induced by Cur-SLN treatments, in non tumorigenic MCF10A and tumorigenic MCF7 and MDA-MB-231 BC cell lines,  highlighting the networks responsible of its radiosensitization ability.  Curcumin loaded- SLN can be suggested in future preclinical and clinical  studies to test its concomitant use during radiotherapy treatments with the double implications of being a radiosensitizing molecule against cancer cells, with a protective role against IR side effects.

overall_design: We performed two-color hybridization experiments using Agilent Technologies whole human genome 4x44K microarrays after curcumin and radiation (photons) treatment in non- tumorigenic (MCF10A) and in tumorigenic breast (MCF7 and MDA-MB-231) immortalized cell lines. New Samples were named as follow: MCF10A_curcumin_2Gy; MCF7_curcumin_2Gy; MDA-MB-231_curcumin_2Gy


title: Comparing the effects of microbiota-directed therapeutic foods in gnotobiotic mice, gnotobiotic piglets and undernourished children

city: St. Louis

first: Jeanette

last: Gehrig

state: Missouri

address: 4515 McKinley

summary: We illustrate an approach for integrating preclinical gnotobiotic animal models with human studies to understand the contributions of perturbed gut microbiota development to childhood undernutrition, and to identify new microbiota-directed therapeutic concepts/leads. Combining metabolomic and proteomic analyses of serially collected plasma samples with metagenomic analyses of serially collected fecal samples, we characterized the biological state of Bangladeshi children with severe acute malnutrition (SAM) as they transitioned to moderate acute malnutrition (MAM) after standard treatment. Gnotobiotic mice were subsequently colonized with a defined consortium of bacterial strains representing different stages of microbiota development in healthy children from Bangladesh. Administering different combinations of Bangladeshi complementary food ingredients to colonized mice and germ-free controls revealed diet-dependent changes in representation and metabolism of targeted weaning-phase strains, including accompanying increases in branched-chain amino acids, plus diet- and colonization-dependent augmentation of IGF-1/mTOR signaling. Host and microbial effects of microbiota-directed complementary food (MDCF) prototypes were subsequently examined in gnotobiotic mice colonized with post-SAM MAM microbiota and in gnotobiotic piglets colonized with a defined consortium of targeted age- and growth-discriminatory bacteria. Finally, ar andomized, double-blind study revealed a lead MDCF that affected the representation of targeted bacterial taxa and increased levels of biomarkers and mediators of growth, bone formation, neurodevelopment, and immune function.

overall_design: 191 plasma samples total were measured from non-fasted venous blood, collected in EDTA-coated tubes, and rapidly cryoperserved before transfer to Washington University School of Medicine in St. Louis. The different groups include healthy (n = 21), ready-to-use supplementary food (RUSF) pre- (n = 14) and post-treatment (n = 14), microbiota-directed complementary food formulation 1 (MDCF1) pre- (n = 16) and post-treatment (n = 16), MDCF2 pre- (n = 16) and post-treatment (n = 16), MDCF3 pre- (n = 16) and post-treatment (n = 16), severe acute malnutrition (SAM, n = 30), post-SAM moderate acute malnutrition (post-SAM MAM) immediately after discharge from acute stabilizaiton (n = 8), and post-SAM MAM 6 months after discharge from acute stabilization (n = 8).


title: ROLE OF EXOSOMAL miRNAs IN METASTATIC POST-TRANSPLANT COLORECTAL CARCINOMA UNDER RAPAMYCIN AND CYCLOSPORINE (miRNA-4)

overall_design: HCT166 and SW480 cell lines were treated with Rapamycin and cyclosporine using two replicates.Untreated cell lines were also included.


title: Genome‐wide analysis reveals miR‐3184‐5p and miR‐181c‐3p as a critical regulator for adipocytes‐associated breast cancer

city: Mysuru

first: Ravi

last: Kasiappan

state: Karnataka

address: Department of Biochemistry

department: Biochemistry

institute: CSIR-Central Food Technological Research Institute

summary: The purpose of this study is to identify miRNA expression changes in adipocyte-associated breast cancer microenvironment by using indirect in vitro co-culture system. We performed small RNA small RNA deep sequencing in human breast cancer cells and breast cancer cells co-cultured with mature adipocytes. We identified 98 differentially expressed miRNAs in breast cancer cells co-cultured with adipocytes using small RNA deep sequencing.

overall_design: microRNA profiles of breast cancer cells and breast cancer cells cocultured with mature adipocytes for 5 days were generated by deep sequencing using Illumina paltform.

first: Dheeran

last: Rajarajan

first: Sweetha

last: Selvarajan

first: Mamilla

last: Charan Raja

first: Santanu

last: Kar Mahapatra


title: Complement induced aberrant epigenetic modifications in renal tubular epithelial cells and accelerates senescence after kidney transplantation by Wnt pathway

city: Bari

first: Fabio

last: Sallustio

state: Bari

address: Piazza G. Cesare N°11

institute: University of Bari

type: Methylation profiling by genome tiling array

summary: Epigenetic mechanisms as DNA methylation can affect allograft outcome after kidney transplantation, accelerating renal aging. Complement system is the major player of ischemia reperfusion (I/R) injury and Renal Proximal Tubular Cells (RPTEC) are known to express C5a receptor (C5aR). However, little is known about the downstream effect of C5a-C5aR interaction. We performed a whole-genome DNA methylation analysis on C5a stimulated RPTEC and found several regions regulating genes involved in cell cycle control, DNA damage checkpoints and WNT signaling. These most represented genes were BCL9, CYP1B1 and CDK6. We showed that C5a induced-aberrant gene methylation significantly influences the expression of these genes. Moreover, the stimulation of RTEC by C5a led to senescence by up-regulating SA-β Gal positivity and increasing p53 gene and p21 protein level. IL-6, MCP-1, CTGF gene levels increase indicated the tubular SASP (Senescence associated Secretory Phenotype) acquirement. In accordance, in a swine model of I/R injury, we found that the increase expression of WNT4/βcatenin expression correlated with the augment in SA-β Gal, p21, p16 and IL-6 positivity after 24h from reperfusion. The treatment with C1-INH, a complement inhibitor, efficiently antagonized SASP restoring SA-β Gal, p21, p16, IL-6 expression at basal level and abrogating the WNT4/βcatenin activation. Thus, C5a affects the DNA methylation of genes involved in tubular senescence leading to a persistent, low-grade, inflammatory state called inflammaging. Targeting epigenetic programs may offer novels strategies to protect tubular cells from aging and promote kidney repair and recovery.

overall_design: Bisulphite converted DNA from Renal cells were hybridized to the Illumina Infinium HumanMethylation450 BeadChip

first: Giuseppe

last: Castellano

first: Rossana

last: Franzin

first: Alessandra

last: Stasi


title: Organoid-induced differentiation of conventional T cells from human pluripotent stem cells

city: Los Angeles

first: Gay

middle: Miriam

last: Crooks

state: California

address: 610 Charles E. Young Drive, East

department: Pathology & Laboratory Med

institute: University of California Los Angeles

summary: Generation of T cells from pluripotent stem cells (PSC) has the potential to transform adoptive immunotherapy for cancer into universal donor, off-the-shelf cellular therapies.  However, differentiation of human PSCs into fully mature T cells has been challenging with existing methods. We report that a 3D organoid method permitted efficient differentiation of human embryonic stem cell and induced pluripotent stem cell-derived mesoderm progenitors to mature, functional conventional T cells with a diverse T cell receptor (TCR) repertoire. This continuous culture system supported both hematopoietic induction and terminal differentiation to naïve, conventional CD3+CD8αβ+ and CD3+CD4+ T cells. Introduction of a Class I-restricted TCR in PSCs produced antigen-specific CD8αβ+ T cells lacking endogenous TCR expression. Functional assays and RNA sequencing aligned PSC-derived T cells with primary naïve conventional CD8+ T cells. The organoid system presented here provides an effective and scalable platform to generate functional mature T cells from human PSCs.

overall_design: Our goal was to analyze and compare transcriptome of human naïve T cells generated in Artificial Thymic Organoids (ATOs) from PSC  with human naïve T cells from thymus and Cord blood ATOs.

first: Amelie

last: Montel-Hagen

first: Christopher

middle: S

last: Seet

first: Suwen

last: Li

first: Brent

last: Chick

first: Yuhua

last: Zhu

first: Patrick

last: Chang

first: Shawn

last: Lopez

first: Steven

last: Tsai

first: Chong

last: He

first: Chee

last: Chin

first: David

last: Casero


title: Impact of subclinical endometritis on circulating white blood cells and endometrium of dairy holstein cows at postpartum period

city: Jouy-en-Josas

first: Mariam

last: Raliou

address: Allée de Vilvert

department: PHASE

institute: INRAE

summary: Cattle with subclinical endometritis (SCE) are sub-fertile, but there is no predictive or diagnosis tool for subclinical uterine disease. The hypothesis for this study was that endometrial inflammation is reflected in peripheral blood leucocytes gene expression. Transcriptome patterns in healthy cows and in cows with SCE at 45-55 days postpartum were evaluated using circulating white blood cells and endometrial biopsies samples collected from the same animals. Bioinformatics analyses of microarray-based transcriptional data identified gene profiles associated with distinct biological functions in circulating white blood cells and endometrium. In circulating white blood cells SCE promote a pro-inflammatory environment related to the activation of inflammation, whereas in the endometrium functions also related to tissue remodeling. Nineteen differentially expressed genes were altered both in circulating white blood cells and in the endometrium of SCE cows compared with healthy cows. Among these genes, transcript abundance of immune factors C3, C2, LTF, PF4 and TRAPPC13 were up-regulated in SCE cows at 45-55 days postpartum. Moreover, the mRNA expression of C3, CXCL8, LTF, TLR2 and TRAPPC13 was temporally regulated during the postpartum period in circulating white blood cells from healthy cows compared with SCE cows. This observation might indicate an advantageous activation of the immune system in healthy animals. The transcript abundance of these genes might also be used as an indicator for subsequent postpartum uterine health.

overall_design: Eight total RNA samples isolated from endometrial biopsy samples collected from subclinical (n =4) and healthy animals (n = 4) and 8 total RNA samples isolated from PAXgene blood samples from the same animals were hybridized.Transcriptional profiling was performed using a custom bovine array generated by merging oligonucleotides set of the Agilent bovine 44K microarray (Gene Expression Omnibus accession no 023647_B. Taurus Oligo Microarray V2_1 and V2_4) with a non-commercial bovine INRA 22K (13,257-element bovine oligonucleotides array, National Center for Biotechnology Information Gene Expression Omnibus accession no. GPL2853). A Custom bovine Gene Expression array 8x60K designed on bovine annotated Ensembl transcripts (http://www.ensembl.org/index.html, genome assembly UMD3.1) completed with 2100 Ensembl references representing 1632 NCB1 specific transcripts (https://www.ncbi.nlm.nih.gov/) found on the INRA 22K array. For each transcript gene (3 independent X 2) 60-mer oligonucleotides (probes) were designed using Agilent software, eArray (https://earray.chem.agilent.com/earray/). This custom bovine gene expression array containing 19,479 transcripts was manufactured by Agilent SurePrint Technology using In situ synthesis Printing Process. RNA labeling was performed according to Agilent protocol “One-Color Microarray-Based Gene Expression Analysis – Low Input Quick Amp Labelling” version 6.5, May 2010 (Cat # G4140-90050).

first: Olivier

last: Sandra


title: Transcriptome analysis of histone demethylase Kdm2a knockout in mouse embryonic stem cells

city: Tianjin

first: Sha

last: Zhou

address: Nankai University

department: The State Key Laboratory of Medicinal Chemical Biology

institute: Nankai University

summary: H3K36 methylation plays an important role in gene regulation. The role of H3K36 demethylase Kdm2b has been well studied. However, the role of Kdm2a in embryonic stem cells are still unkonwn. To study the function of Kdm2a in embryonic stem cells. We used CRISPR-gRNA system to knockout Kdm2a. We analyzed the gene expression change and identified target genes and repeats of Kdm2a. We uncovered a novel role of Kdm2a in regulating gene expression in embryonic stem cells.

overall_design: The transcriptome of wild-type mouse embryonic stem cells and Kdm2a knockout mouse embryonic stem cells were analyzed by RNA-seq. The expression change of genes and transposable elements were analyze to study the role of Kdm2a in mouse embryonic stem cells

first: Yongwang

last: Zhang

first: Xinyi

last: Lu


title: The Signature of Glucocorticoid Receptor -Dependent Hypertrophic Transcriptome in Cardiomyocytes

city: Newark

first: Danish

last: Sayed

state: NJ

address: 185 south orange avenue

department: CBMM

institute: Rutgers-NJMS


title: Gene expression of Rickettsia infected green rice leafhopper Nephotettix cincticeps.

city: Tsukuba

first: Yuki

last: Nakamura

address: 1-1 Owashi

institute: National Institute of Agrobiololgical Sciences

summary: The green rice leafhopper Nephotettix cincticeps have two mutualistic symbiotic bacteria (Candidatus Sulcia muelleri and Candidatus Nasuia deltocephalinicola) in its symbiont special organ bacteriome and are also infected to rickettsia. In order to determine immune challenge is induced or not by rickettsia infection in N. cincticeps, we investigated gene expression between rickettsia-infected and rifampicin treated uninfected N. cincticeps colonies.

overall_design: One day adult N. cincticeps females were dissected and separated into cephalothoracic region and abdomen. After PCR checked with cephalothoracic DNA, each five uninfected and Rickettsia infected N. cincticeps abdomen were extracted total RNA.

first: M

last: Tomizawa

first: Y

first: H

last: Noda


title: The Signature of Glucocorticoid Receptor -Dependent Hypertrophic Transcriptome in Cardiomyocytes [ChIP-Seq]

summary: We examined Glucocorticoid receptor binding sites in isolated neonatal cardiomyocytes treated with Dexamethasone (100nM) for 1hr or Ethanol using GR-ChIP-Seq.

overall_design: Examination of genomic GR binding in cardiomyocytes with Dex treatment by ChIP-Seq


title: The Signature of Glucocorticoid Receptor -Dependent Hypertrophic Transcriptome in Cardiomyocytes [RNA-Seq]

summary: We examined Glucocorticoid receptor binding sites in isolated neonatal cardiomyocytes treated with Dexamethasone (100nM) for 1hr or Ethanol using GR-ChIP-Seq. In addition to determine the change in the resulting transcriptional status of genes we performed RNAseq in cardiomyocytes treated with Dexamethasone (100nM) or Ethanol for 1hr or 24hrs.

overall_design: Examination of GR-dependent change in cardiac transcriptome by RNAseq


title: Von Hippel-Lindau (VHL) mutations disrupt vascular patterning and maturation via Notch

city: NASHVILLE

first: Aguirre

last: de Cubas

address: 2220 Pierce Ave

department: Hematology and Oncology

institute: Vanderbilt University Medical Center

summary: Von Hippel-Lindau (VHL) gene mutations induce neural tissue hemangioblastomas as well as highly vascularized clear cell renal cell carcinomas (ccRCCs).  Pathological vessel remodeling arises from mis-regulation of hypoxia inducible factors and vascular endothelial growth factor, among other genes.  Variation in disease penetrance has long been recognized in relation to genotype. We show Vhl mutations also disrupt Notch signaling, causing mutation-specific vascular abnormalities e.g. type 1 (null) vs. type 2B (murine G518A representing human R167Q).  In conditional mutation retina vasculature, Vhl null mutation (i.e. UBCCreER/+; Vhlfl/fl) had little effect on initial vessel branching, but severely reduced arterial and venous branching at later stages.  Interestingly, this mutation accelerated arterial maturation, as observed in retina vessel morphology and aberrant a-smooth muscle actin localization, particularly in vascular pericytes.  RNA sequencing analysis identified gene expression changes within several key pathways including Notch and smooth muscle cell contractility. Notch inhibition failed to reverse later-stage branching defects but rescued the accelerated arterialization.  Retinal vessels harboring the type 2B Vhl mutation (i.e. UBCCreER/+; Vhlfl/2B) displayed stage-specific changes in vessel branching and an advanced progression toward an arterial phenotype.  Disrupting Notch signaling in 2B mutants increased both artery and vein branching, and restored arterial maturation toward non-mutant levels.  By revealing differential effects of the null and type 2B Vhl mutations on vessel branching and maturation, these data may provide insight into the variability of VHL-associated vascular changes, particularly the heterogeneity and aggressiveness in ccRCC vessel growth, as well as suggest Notch pathway targets for treating VHL syndrome.

overall_design: A total of eight mouse retinas (n=8) were submitted for RNAseq. There are four experimental groups with 2 replicates for each: 1) WT CreER VHL lox/lox; 2)WT CreER VHL2b/lox; 3) UBC CreER VHL lox/lox; and 4) UBC CreER VHL2b/lox

first: W

last: Rathmell

first: John

last: Chappell


title: Genome-wide CRISPR knockout to screen for essential targets for HCC cell growth

city: Singapore

first: Yu

last: Wang

address: 11 Hospital Drive

country: Singapore

institute: National University of Singapore

summary: We performed genome-wide functional knockout screens using GECKOv2 library to identify essential growth targets in two hepatocellular carcinoma (HCC) cell lines, HCCLM3 and SNU449. We compared the gRNA present at the end of 10 passages (End Point) vs. that at Time zero in these two cell lines separately then overlap for common targets.

overall_design: End Point vs. Time Zero.

first: Kam

last: Hui


title: Transcriptome analysis in Neobractatin treated cells

city: Shanghai

first: ZhaoQing

last: Zheng

address: 1200, CaiLun Rd

institute: Shanghai University of Traditional Chinese Medicine

summary: The goal of this study is to use RNA seq and rMATS analysis to identify the anticancer mechanism of novel compounds

overall_design: HeLa cells were treated with DMSO or compound NBT for 8 h with three biological replicates

first: Yuanzhi

last: Lao

first: Zhaoqing


title: Transcriptomic insight into pathogenicity-associated facters of Conidiobolus obscurus an obligate aphid-pathogenic fungus from Entomophthoromycota

city: Hangzhou

first: Xiang

state: Zhejiang

address: No. 666 Wusu

institute: Zhejiang Agricultural and Forestry University

summary: a de novo transcriptomic analysis to reveal key virulence factors of the aphid pathogen C. obscurus. The transcript levels of the related genes in the samples of in vitro fungal culture and mycotized cadavers were analyzed

overall_design: mRNA profiles of in vitro fungal culture and mycotized cadavers were generated by deep sequencing , in triplicate, using Illumina HiSeqTM 4000

first: Linlin

last: Pan


title: Rheumatoid arthritis and response to LLDT-8: Fibroblast-like Synoviocytes

city: San Diego

first: Shicheng

last: Guo

address: 8730 Costa Verde

institute: MCRI, SHSCI, GHH, UCSD

summary:
Objective: Tripterygium is a traditional Chinese medicine which has widely been used in the treatment of rheumatic disease. (5R)-5-hydroxytriptolide (LLDT-8) is an extracted compound from Tripterygium, which has been showed lower cytotoxicity and relatively higher immunosuppressive activity. However, the knowledge on its genomic impact is still limited.

Methods: The purpose of our study was to assess the effects of LLDT-8 on transcriptome including mRNAs and lncRNAs in rheumatoid arthritis fibroblast-like synoviocytes cell by a custom genome-wide microarray assay.

Results: Our work showed that 394 significantly differentially expressed gene including 281 significantly down-regulated and 113 significantly up-regulated after the treatment of LLDT-8. Also, KEGG pathway analysis showed 20 pathways were significantly enriched (P-value <0.05, FDR correction). Morever, the top 4 enriched pathway were significant relevant to Immune reaction, including cytokine-cytokine receptor interaction (P-value=4.61×10-13), rheumatoid arthritis (P-value=1.90×10-6), chemokine signaling pathway (P-value=1.01×10-5) and TNF signaling pathway (P-value=2.79×10-4). Furthermore, we identified 1,716 highly correlated lncRNA-mRNA pairs from the selected top lncRNA and mRNA, and 70 pairs of them were located in the same Chromosome.

Conclusion: The results indicated that the LLDT-8 would mainly influence the RA cells in the process of immune network regulation.

overall_design: Five rheumatoid arthritis fibroblast-like synoviocytes cell in control and treatment (100nm/ml LLDT-8 ) group were measured by custom genome-wide microarray assay.

first: Dongyi

last: He


title: Identification and functional analysis of a potential key lncRNA in aged mice with postoperative cognitive dysfunction

city: Chengdu

first: Ming

last: Li

address: Ke Yuan Nan lu 88

department: Department of Anesthesiolog

institute: Sichuan University

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

summary:
Postoperative cognitive decline (POCD) is emerging as a significant complication of surgery in elderly patients. However, the molecular mechanisms of POCD are elusive. Here we applied microarray analyses to identify long non-coding RNA (lncRNA) and mRNA expression profiles in hippocampal tissues from a mouse model of POCD and control mice. A total of 869 lncRNAs and 690 mRNAs were differentially expressed between POCD and control mice.
Subsequently, six dysregulated lncRNAs and six mRNAs were confirmed via quantitative real-time polymerase chain reaction (qRT-PCR) in 8 paired samples. Then, Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed to probe the vital functions of dysregulated genes.

overall_design: We randomly selected 6 C57 male mice (age 16-18 months) and divided them into two groups: control group (n=3) and surgery group (n=3). The surgical procedures of unilateral nephrectomy were performed to simulate a mouse model of POCD. The hippocampal tissues of the surgery and control group mice were harvested on day 3 after the surgery for RNA extraction and hybridization. The RNA labeling and array hybridization were performed by KangChen Bio-tech, Shanghai, PR China.

first: Chan

last: Chen

first: Tao

last: Zhu

first: Rui

last: Gao

first: Fangzhou


title: BS008, an amiloride derivative, can regulate the alternative splicing of multiple gene transcripts in cancer cells

city: Taichung

first: Chien Chih

last: Lee

address: 2 Yuh-Der Road

country: Taiwan

institute: China Medical University Hospital

summary: Alternative splicing (AS) is a process that enables a mRNA to generate different protein isoforms that may have different biological functions or properties. Cancer cells often use this maneuverability to produce proteins that contribute to growth and survival. In previous study, we found that the antihypertensive drug amiloride has a novel biological function that regulates the AS on human cancer cells. However, it also showed that the effective concentration of amiloride in cancer treatment is too high to limit its use in future therapeutic application. In this study, we therefore used computational algorithms to predict the potential amiloride derivatives and found that BS008 is the most promising compound in all derivatives. The results demonstrated that BS008 can modulate the AS of apoptotic gene transcripts, including HIPK3, SMAC, and BCLX in cancer cells. Splicing regulatory involved a variety of histone modifications and splicing factors, and accompanied the changed of phosphorylation state of SR proteins during the splicing process. Inhibition of protein phosphatase-1 with okadaic acid pretreatment partially alleviated the effects of BS008 on the AS of HIPK3 and SMAC transcripts, as well as on the phosphorylation levels of SRSF3. RNA sequencing further discovered that the AS of many other apoptosis-related gene transcripts such as AATF, ATM, AIFM1, NFKB1, and API5 was modulated by BS008. We extended the study to apoptosis-associated molecules, and detected decreased levels of BCLX and increased levels of BAX and active CASPASE-3 in BS008-induced apoptosis. In vivo experiments indicated that the treatment of tumor-bearing mice with BS008 resulted in a marked decrease in tumor size. The combination BS008/sorafenib enhances anti-tumor activity of sorafenib and allows dose reduction of sorafenib without compromising its anti-tumor activity. In conclusion, these findings suggested that BS008, an amiloride derivative, may provide therapeutic potential for cancer treatment in future.

overall_design: Examination of the global genes with altered alternative splicing in BS008-treated Huh-7 cells.

first: Jan-Gowth

last: Chang

first: Chien-Chih


title: Expression data from young and old nucleus pulposus stem cells

status: Public on Aug 19 2019

city: Guangzhou

first: Cheng

last: Shi

address: Baiyun Road

institute: Guangdong General hospital

summary:
Nucleus pulposus stem cells is the endogenous stem cell in nucleus pulposus tissues(NPMSCs). The senescene of NPMSCs will cause its malfunction and further induce intervertebral disc degeneration.The expression of specific sets of genes will altered during aging. Thus, identify these key regulater genes is important.
We used microarrays to detail the global programme of gene expression underlying NPMSCs aging and identified distinct classes of up and down-regulated genes during this process

overall_design: First, we isolated and identified NPMSCs form the tail discs of Young (3months) and old (24months) SD rats.mRNAs were extrated by Trizol method.Then, a rat GeneChip Clariom™ S Array was used to detect different expression mRNA between the young and old samples. Additionally, molecular function and pathway analysis were also performed.

first: Shi

last: Cheng


title: microRNA expression data from nucleated cells excluding tumor cells in malignant pleural effusion (MPE) from WT and IL-10 knock out (IL-10-/-)

city: Beijing

first: Xin-Yu

address: Gongti Nan Road

institute: Beijing Chao-yang hospital

summary:
The interactions between tumor cells and the host vasculature and immune cells results in increased net fluid production via enhanced plasma extravasation into the pleural space.Understanding the regulatory mechanism of IL-10 in MPE formation is essential both for deciphering how IL-10 acts in regulating tumor immunity and for discovering key molecular targets for intervention in advanced cancers.
We investigate the characteristic of  microRNAs (miRNAs) in IL-10 induced murine MPE. Identifing the distinct classes of up-regulated and down-regulated miRNAs during this process.

overall_design: The nucleated cells, excluding tumor cells, from MPE of WT and IL-10-/- mice  were collected for RNA extraction.The miRNA profiles of these cells were detected using GeneChip® miRNA 4.0 Array (Affymetrix, Santa Clara, CA).

first: Kan

last: Zhai

first: Huan-Zhong


title: Genome-wide copy number profiling of MCF-7 and fulvestrant-resistant MCF-7/FR cells by SNP microarray.

city: Lebanon

first: Todd

last: Miller

address: DHMC One Medical Center Dr, HB-7936

institute: Geisel School of Medicine at Dartmouth

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

summary: Estrogens have been shown to elicit anti-cancer effects against estrogen receptor alpha (ER)-positive breast cancer. We sought to determine the underlying mechanism of therapeutic response. Response to 17b-estradiol was assessed in ER+ breast cancer models with resistance to estrogen deprivation: WHIM16 patient-derived xenografts, C7-2-HI and C4-HI murine mammary adenocarcinomas, and long-term estrogen-deprived MCF-7 cells. As another means to reactivate ER, the anti-estrogen fulvestrant was withdrawn from fulvestrant-resistant MCF-7 cells. Transcriptional, growth, apoptosis, and molecular alterations in response to ER reactivation were measured. 17b-estradiol treatment and fulvestrant withdrawal induced transcriptional activation of ER, and cells adapted to estrogen deprivation or fulvestrant were hypersensitive to 17b-estradiol. ER transcriptional response was followed by an unfolded protein response and apoptosis. Such apoptosis was dependent upon the unfolded protein response, p53, and JNK signaling. Anti-cancer effects were most evident in models exhibiting genomic amplification of the gene encoding ER (ESR1), suggesting that engagement of ER at high levels is cytotoxic. These data indicate that long-term adaptation to estrogen deprivation or ER inhibition alters sensitivity to ER reactivation. In such adapted cells, 17b-estradiol treatment and anti-estrogen withdrawal hyperactivate ER, which drives an unfolded protein response activation and subsequent growth inhibition and apoptosis. 17b-estradiol treatment should be considered as an alternative therapy for anti-estrogen-resistant disease, particularly in patients with tumors harboring ESR1 amplification or overexpression. Furthermore, therapeutic strategies that enhance an unfolded protein response may enhance the therapeutic effects of ER reactivation.

overall_design: Genomic DNA from MCF-7 cells and fulvestrant-resistant MCF-7/FR cells was analyzed by Affymetrix SNP 6 microarray to determine copy number variations.

middle: W

first: Sarah

middle: R

last: Hosford


title: SC-beta Cell in vivo Maturation

city: Cambridge

first: Jeffrey

last: Davis

state: MA

address: 500 Main Street

department: Koch Institute

institute: MIT

summary: Stem cell-derived β (SC-β) cells are an emerging regenerative therapy to compensate for loss of functional β cell mass in diabetes. Glucose-stimulated insulin secretion in SC-β cells is variable in vitro but stabilizes after transplantation and maturation under the kidney capsule of mice. We identified mechanisms correlated with functional maturation using RNA-sequencing and co-expression network analysis. In vivo maturation enhanced glucose-stimulated but not basal insulin secretion, up-regulated β cell hormones IAPP and ADCYAP1, increased expression of maturation markers MAFA, UCN3, and SIX2, and resolved endocrine identity of incompletely specified polyhormonal cells produced during differentiation. Transplantation promoted calcium signalling, induced exocytotic machinery supporting hormone secretion and improved stimulus-secretion coupling that fine-tunes insulin secretion. Growth hormone signalling emerged as candidate driver of in vivo maturation and was confirmed in vitro. Also, a large co-expression module correlated with HbA1c and was enriched in genes up-regulated during in vivo maturation but down-regulated in hyperglycaemic and palmitate stress conditions, suggesting that transcriptional maturation of SC-β cells in vivo mirrors processes lost in diabetic β cells.

overall_design:
RNA-Seq of TSQ-sorted SC-beta cells before and after transplantation
Cells were dissociated in Accutase and sorted for TSQ/PI/GFP before and after 6 weeks of maturation in vivo in immune compromised SCID-Beige mice
*** The authors state "Due to Swedish law, the patient consent, and the risk that the sequencing data contains personally-identifiable information and hereditary mutations, we cannot deposit the short sequencing read data in a repository."
Thus, this submission is incomplete.

first: Maria

last: Ryaboshapkina


title: Fulvestrant withdrawal from fulvestrant-resistant MCF-7/FR cells

overall_design: MCF-7/FR cells were treated in triplicate with fulvestrant withdrawal for 0-14 days, and RNA was harvested in 2-day intervals.


title: Fate mapping via Ms4a3 expression history traces monocyte-derived cells

first: Jinmiao

address: 8A Biomedical Grove, #04-06 Immunos

institute: Singapore Immunology Network

summary: We performed a single-cell transcriptomic analysis of monocyte and monocyte progenitors by single-cell mRNA sequencing (scRNA-seq) using the C1 Fluidigm platform. We sorted BM cMoPs (Lin−CD117+CD115+CD135−Ly6C+), BM Ly6C+ monocytes (Lin−CD117-CD115+CD135−Ly6C+) and blood Ly6Chi monocytes (CD115+CD11b+Ly6Chi) from wild-type (WT) C57BL/6 mice by fluorescence-activated cell sorting (FACS)  and generated transcriptional profiles for each individual cell (n = 38 for blood Ly6Chi monocytes, n = 66 for BM cMoPs, n = 57 for BM Ly6C+ monocytes).

overall_design: Gene profiles of ex vivo sorted single cell mouse bone marrow progenitor populations were obtained by C1 single cell mRNA sequencing.

first: Andreas

last: Schlitzer

first: Florent

last: Ginhoux


title: Integrative Epigenomic and Transcriptomic Analysis Reveals Robust Metabolic Switching During Intermittent Fasting in the Brain

first: Gavin

last: Ng

address: Block MD9, Level 4  2 Medical Drive  117597

department: Physiology

summary: Intermittent fasting (IF) is a dietary regimen aimed to restrict energy intake via alternate periods of ad libitum food consumption and fasting, without compromise of nutritional composition intake. Prophylactic IF have been well-established in many animal studies to promote longevity as well as ameliorate the development and manifestation of age-related diseases such as cardiovascular, neurodegenerative as well as metabolic diseases. However, while vast experimental evidences have pointed out that IF is able to exert plethora effects against these diseases, understanding with regards to the underlying mechanisms remain in their infancy. Recently, an emerging area of research in the field of epigenetics have been shown to be a cornerstone in mediating the interaction between environmental factors and genome status. IF is a lifestyle intervention that may serves as potential environmental influences over the epigenome status of individuals. However, there is no current information available that shows that IF can induce epigenetic changes. Here, we show that IF is able to influence the modulation of histone H3 lysine 9 trimethylation (H3K9me3) epigenetic mark in C57/BL6 male mice cerebellum, which in turn helps to control a plethora of transcriptomic changes involved in robust metabolic switching processes commonly observed during IF. Interestingly, both epigenomic and transcriptomic modulation are still observed following a refeeding regimen, which may suggest the possibility of epigenetic maintenance induced by IF at this epigenetic locus. However, we found a loss of H3K9me3 maintenance of transcriptomic changes after abolishment of IF. Collectively, our study helps to characterize a novel mechanism of IF in the epigenetic-transcriptomic axis, which control a myriad of metabolic process changes that provide better understanding of IF-induced effects.

overall_design: C57/BL6NTac male mice (InVivos Pte Ltd, Singapore) were raised to three-month-old with ad libitum access to food using standard Teklad Global 18% protein rodent diet (Envigo, United Kingdom) and water. Mice were then randomly assigned and subjected to ad libitum (AL) feeding, or IF for 16 h per day (IF16) or for 24 h on alternate days (i.e. ‘every other day’; EOD) for three months. Mice placed under IF16 regimen had access to food at 7 am and then removed at 3pm for 16 h daily.  For EOD regimen mice, food was provided at 7 am and removed at 7 am the next day for a further 24 h. All mice had AL access to water, with AL mice having free access to both food and water. During refeeding regimen, these three groups of mice were further subjected to AL access to both food and water for two months. Following which, ChIP and RNA sequencing are performed on these frozen samples.

middle: Y

first: Dominic

last: Sheng

first: Sung

last: Kang

first: David

last: Fann

first: Joonki

last: Kim

first: Asfa

last: Alli-Shaik

first: Vardan

last: Karamyan

first: Eitan

last: Okun

first: Christopher

middle: G

last: Sobey

first: Thameem

last: Dheen

first: Jayantha

last: Gunaratne

first: Mark

last: Mattson

first: Roger

last: Foo

first: Dong-Gyu

last: Jo

first: Thiruma

last: Arumugam


title: Molecular singularities in a pheromone sensor triumvirate desynchronize the competence-predation interplay in the human commensal Streptococcus salivarius

city: Lausanne

first: Johann

last: Mignolet

address: Biophore Quartier UNIL-SORGE

department: DMF

country: Switzerland

institute: UNIL

summary: The human oral cavity is one of the most competing environments, considering the extent and diversity of the bacterial community that colonizes it, as well as the multiple stresses to which it is subjected. The commensal species Streptococcus salivarius is one of the first colonizers of the oral mucosa (tongue, gums, inner cheeks and tooth enamel) in infants and remains predominant throughout the life of an adult. In order to adapt to diverse and variable environmental conditions, S. salivarius triggers in a coordinated way two bacterial developmental processes: competence (acquisition of extracellular DNA and new genetic traits) and predation (secretion of cytotoxic molecule), via ComR, a transcription factor activatable by a "pheromone" peptide. Nevertheless, the activation of other transcriptional regulators can uncouple these 2 mechanisms to allow, for example, only the production of toxins without triggering the competence phase.

overall_design: Examination of mRNA transcriptional profiles in WT and 2 deletion and 2 overexpression mutant strains.

first: Guillaume

last: Cerckel

first: Julien

last: Damoczi

first: Laura

last: Ledesma-Garcia

first: Tom

last: Coenye

first: Pascal

last: Hols


title: Glioma Stem Cell Specific Super Enhancer Drives Polyunsaturated Fatty Acid Synthesis to Support EGFR Signaling

first: Jeremy

last: Rich

address: 9500 Gilman Drive #0695

institute: University of California, San Diego

summary: Glioblastoma ranks among the most aggressive and lethal of all human cancers. Functionally defined glioma stem cells (GSCs) contribute to this poor prognosis by driving therapeutic resistance and maintenance of cellular heterogeneity. To understand the molecular processes essential for GSC maintenance and tumorigenicity, we interrogated the super-enhancer landscapes of primary glioblastoma specimens and in vitro GSCs. GSCs epigenetically upregulated ELOVL2, a key polyunsaturated fatty acid synthesis enzyme. Targeting ELOVL2 inhibited glioblastoma cell growth and tumor initiation. ELOVL2 depletion altered cellular membrane phospholipid composition, disrupted membrane structural properties, and diminished EGFR signaling through control of fatty acid elongation. In support of the translational potential of these findings, dual targeting of polyunsaturated fatty acid synthesis and EGFR signaling had a combinatorial cytotoxic effect on GSCs.

overall_design: Two patient-derived glioma stem cells (GSC387 and GSC3565) were transduced with two independent non-overlapping shRNAs targeting ELOVL2 (shELOVL2.308 and shELOVL2.843) or a non-targeting control shRNA (shCONT). 6 total samples were analyzed with 1 technical replicate per group

first: Ryan

last: Gimple

first: Leo

last: Kim

first: Briana

last: Prager

first: Stephen

last: Mack

first: Qi

last: Xie

middle: N


title: Long noncoding RNA CCDC144NL-AS1 knockdown induces naïve-like state conversion of human pluripotent stem cells

first: Kunshan

last: Zhang

address: 389 Xincun Road

department: Stem cell Translational Research center

institute: Tongji Hospital, Tongji University

summary: Human naïve pluripotency state cells can be derived from direct isolation of inner cell mass or primed-to-naïve resetting of human embryonic stem cells (hESCs) through different combinations of transcription factors, small molecular inhibitors and growth factors. Long noncoding RNAs (lncRNAs) have been identified to be crucial in diverse biological processes, including pluripotency regulatory circuit of mouse pluripotent stem cells (PSCs), but few are involved in human PSCs’ regulation of pluripotency and naïve pluripotency derivation. This study initially planned to discover more lncRNAs possibly playing significant roles in the regulation of human PSCs’ pluripotency, but accidently identified a lncRNA whose knockdown in human PSCs induced naïve-like pluripotency conversion. The results indicated that knockdown of CCDC144NL-AS1 induces naïve-like state conversion of human PSCs in the absence of additional transcription factors or small molecular inhibitors. CCDC144NL-AS1-KD human PSCs reveal naïve-like pluripotency features, such as elevated expression of naïve pluripotency associated genes, increased developmental capacity, analogous transcriptional profiles to human naïve PSCs, and global reduction of repressive chromatin modification marks. Furthermore, CCDC144NL-AS1-KD human PSCs display inhibition of MAPK (ERK), accumulation of active β-catenin, and upregulation of some LIF/STAT3 target genes, and all of these are concordant with previous reported traits of human naïve PSCs.

overall_design: The transcriptional profiles of CCDC144NL-AS1-KD-H9, NC-H9, CCDC144NL-AS1-KD-H14, NC-H14, CCDC144NL-AS1-KD-HDF-iPS, NC-HDF-iPS cells were generated by deep sequencing, the epigenetic landscape of CCDC144NL-AS1-KD-H9 cells and NC-H9 cells were analysed by chromatin immunoprecipitation followed by deep sequencing (ChIP-Seq) of H3k4me3 and H3K27me3, using the Illumina platform.

first: Yingying

last: Wang

first: Yuping

last: Luo

first: Siguang

last: Li


title: Gonadal transcriptome analysis of common carp

city: Hyderabad

first: Balasubramanian

last: Senthilkumaran

state: Telangana

address: School of Life Sciences Gachibowli

department: Animal Biology

institute: University of Hyderabad

summary: De novo assembly of immature gonadal transcriptome was performed to identify genes involved in gonadal development. A total of 81,757 and 43,257 transcripts were obtained from the immature testicular and ovarian transcriptomes, respectively. About 84,367 unigenes were constructed after removing redundancy which were a representation of both the gonadal transcriptomes. About 298 differentially expressed genes were identified. The present study identified certain important genes/factors involved in the gonadal development of C. carpio which may provide insights into the understanding of sex differentiation and gonadal development processes.

overall_design: Testis and Ovary samples from juvenile common carp

first: Arumugam

last: Anitha

first: Yugantak

last: Gupta

first: Seetharam

last: Deepa


title: Production of 14α-hydroxysteroids by a recombinant Saccharomyces cerevisiae biocatalyst expressing fungal steroid 14α-hydroxylation system

status: Public on Aug 18 2019

first: feiyu

last: fan

state: Tianjin

address: 32 West 7th Avenue, Tianjin Airport Economic Area

department: Key Laboratory of Systems Microbial Biotechnology

institute: Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences.

summary:
Purpose: In order to identify genes for  steroid 14α-hydroxylase P450lun and its associated redox partner CPRlun in filamentous fungus Cochliobolus lunatus ATCC#12017
Methods: Strand-specific RNA-seq libraries were constructed for two samples, including (I) Mycelia of C. lunatus treated with mock N, N-dimethylformamide (DMF); (II) Mycelia of C. lunatus treated with 170 mg/L 11-deoxycortisol 21-acetate (RSA) dissolved in N,N-dimethylformamide. For preparation of RNA samples, germinated young mycelia of C. lunatus after 22-24 pre-culture in liquid potato dextrose broth medium were harvested and transferred into a new 30 ml potassium phosphate buffer supplement with either 170 mg/L RSA dissolved in DMF, or an equal volume of DMF as mock. Additional two-hours cultivation was performed to induction of the P-450lun gene expression. Total RNA for samples were isolated using TRIzol reagent (Invitrogen, Grand Island, USA), then used for high-throughput RNA sequencing. The two 150-nt strand-specific paired-end RNA-seq libraries were generated commercially at Novogene Biotechnology Co. Ltd (Tianjin, China) by using Illumina’s Hiseq X Ten platform (Illumina, San Diego, USA). The clean reads were used to create a  de novo transcriptome assembly using the Trinity pipeline (v2.4.0). The abundance for each of the resulted transcripts was calculated by RSEM (v1.2.0) using the Fragments Per Kilobase per Million (FPKM) method.
Results: A total of 7.1 and 7.9 million 150-bp paired-end clean reads were separately generated from the DMF mock and RSA induced samples,and 23957 transcripts with length more than 600nt were assembled from the pooled reads of both samples using Trinity program. The translated sequences of these transcripts were predicted using TransDecoder, and then used as queries to search against the SWISS-PROT and the Pfam databases for functional annotation. Transcripts DN8493 and DN2353 were separately identified as C.lunatus P-450lun and CPRlun genes.
Conclusions: The 14β-hydroxylase system of C.lunatus was deciphered by transcriptome analysis.

overall_design: mRNA profiles of  C. lunatus treat with DMF mock or steroid RSA were generated by deep sequencing, using Illumina’s Hiseq X Ten platform

first: Jing

last: Chen

first: Jinlei

last: Tang

first: Yongyan

last: Xi

first: Zhubo

last: Dai

first: Changhao

last: Bi

first: Feiyu

last: Fan

first: Xueli


title: RNA-Seq study of Cell lines rendered resistant to idelalisib and ibrutinib

city: Lyon

first: Charles

last: Dumontet

address: 8 avenue Rockefeller

department: Immunology

institute: INSERM

summary: BCR pathway inhibitors idelalisib and ibrutinib are the first small molecule targeted agents for B-cell malignancies. In spite of encouraging response rates in various forms of B cell diseases, patients will eventually develop relapse due to the emergence of resistant cells. To better identify the possible mechanisms of resistance we developed and characterized idelalisib- and ibrutinib-resistant variants of the human non Hodgkin’s lymphoma cell lines DoHH2 and Daudi. These resistant variants displayed a cross-resistance profile limited to PI3K inhibitors, BTK inhibitors and a SYK inhibitor but not to unrelated agents. A number of alterations were observed in the resistant lines, including a strong reduction of the Akt3 protein. Resistant lines tended to express larger amounts of CD38 and CD52 on their cell membrane and were found to display enhanced sensitivity to anti-CD38 antibodies. These results identify potential novel mechanisms of resistance to idelalisib and ibrutinib and raise the possibility that cells resistant to BCR pathway inhibitors might possess enhanced sensitivity to anti-CD38 antibodies.

overall_design: WT cell lines and resistant cell lines have been sequenced with one replicate

first: Eva-Laure

last: Matera

first: Julien

last: Fouret

first: Estelle

last: Baulu

first: Emeline

last: Perrial

first: Zineb

last: Bousfiha

first: Lars

last: Jordheim

first: Chettab

last: Abdelkamel

first: Joel

last: Lachuer

last: dumontet


title: Expression data from dorsal pallium Ctip2+ neuron at E14.5 and E16.5

city: Kyoto

first: Tadashi

last: Sunohara

address: 53 Kawahara-cho, Shogoin, Sakyo-ku,

department: Dept. of clinical application

institute: Center for iPS cell research and application

summary:
Cell-based therapy is a promising treatment for neurodegenerative diseases such as Parkinson’s disease or cardiac disease. Similarly, reconstruction of the corticospinal tract by cell transplantation is expected as a treatment for stroke and degenerative disease.   For efficient cell integration to the corticospinal tract after transplantation, the induction or selection of corticofugal projection neuron (CFuPN) is important. However, no CFuPN specific surface markers for the purification are known. Recently, miRNAs have been reported as alternatives to surface markers; microRNA responsive switch.
In order to separate CFuPN at the axon extension stage, which is optimal for regenerative medicine, by using miRNA switches, we used microarrays to identify miRNAs that are specifically expressed in CFuPN during cerebral cortex V-VI layer formation.

overall_design: Corticofugal projection neuron at embryo were selected at successive stages of early development for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain homogeneous populations of embryos at each developmental stage in order to increase the temporal resolution of expression profiles. To that end, we made Ctip2-EGFP transgenic mouse then, surgically resect only dorsal pallium of E14.5 and E16.5 mouse embryo. By these methods, only corticofugal projection neuron at axon elongating stage can be purified.

first: Asuka

last: Morizane


title: Molecularly distinct models of zebrafish Myc-induced B cell leukemia

city: Oklahoma City

first: John

middle: Kimble

last: Frazer

state: Oklahoma

address: 941 Stanton L Young Blvd

department: Pediatrics

institute: University of Oklahoma Health Sciences Center

summary: The goal of this study was to compare transcriptomic profiles of two recent B-cell ALL models in zebrafish, expressing either mMyc (GSE108855) or hMYC transgenes. 13 unique hMYC-expressing samples are included.

overall_design: 13 zebrafish ALL from the rag2:hMYC; lck:GFP double-transgeneic background.

first: Chiara

last: Borga

first: Clay

last: Foster


title: Comparing the difference in gene expression between TDAG51 WT vs TDAG51 KO, and TDAG51 KO Tg vs TDAG51 KO

status: Public on Aug 17 2019

city: Daejeon

first: Hyeongseok

last: Yun

address: 99, Daehak-ro, Yuseong-gu

institute: Chungnam national university

summary: Transcriptional profiling of postpartum day 0 mouse brain, comparing TDAG51 wild-type (WT)  vs TDAG51 knockout (KO), and TDAG51 KO transgenic (Tg) vs TDAG51 KO.

overall_design: Two-condition experiment, TDAG51 WT was compared with TDAG51 KO and TDAG51 KO Tg was compared with TDAG51 KO.

first: Jaerang

last: Rho

first: Eui-Soon

last: Park


title: Single nucleotide polymorphism rs13426236 contributes to an increased prostate cancer risk via regulating MLPH splicing variant 4

status: Public on Aug 16 2019

city: Milwaukee

first: Liang

last: Wang

state: Wisconsin

address: 8701 Watertown Plank Rd.

department: Pathology

institute: Medical College of Wisconsin

summary: A prostate cancer risk single nucleotide polymorphism (SNP), rs13426236, is significantly associated with melanophilin (MLPH) expression. To functionally characterize role of the rs13426236 in prostate cancer, we first performed splicing-specific expression Quantitative Trait Loci (eQTL) analysis and refined the significant association of rs13426236 allele G with an increased expression of MLPH splicing variant 4 (V4) (P= 7.61E-5) but not other protein-coding variants (V1-V3) (P>0.05). We then performed an allele-specific reporter assay to determine if SNP-containing sequences functioned as active enhancer. Compared to allele A, allele G of rs13426236 showed significantly higher luciferase activity on the promoter of the splicing transcript V4 (P <0.03) but not on promoter of transcript V1 (P>0.05) in two prostate cancer cell lines (DU145 and 22Rv1). Transfection of MLPH splicing variants showed stronger effect of transcript V4 than V1 on promoting cell proliferation, invasion and anti-apoptotic activities. RNA profiling analysis demonstrated that transcript V4 overexpression caused significant expression changes in glycosylation/glycoprotein and metal-binding gene ontology pathways (FDR<0.01). We also found that both transcripts V4 and V1 were significantly up-regulated in prostate adenocarcinoma (P<2.49E-6) but only transcript V4 up-regulation was associated with poor recurrence free survival (P=0.028, HR=1.63, 95%CI=1.05-2.42) in The Cancer Genome Atlas (TCGA) data. This study provides strong evidence showing that prostate cancer risk SNP rs13426236 up-regulates expression of MLPH transcript V4, which may function as a candidate oncogene in prostate cancer.

overall_design: To determine effect of MLPH on signaling pathways, we transfected 22Rv1 cells with MLPH transcripts V1 or V4 plasmid for 48 h. Total RNA was isolated using total RNA extraction kit (Zymo Research). RNA-seq was performed in each transfected cell line with a technical replicate. Transfection with empty vector was used as control.

first: Wang

last: Liang

first: Xiao

last: Fankai


title: The mRNAs alteration induced by Neat1 knockdown in HT22 cells

city: Chongqing

first: Zhong

last: Jianjun

address: NO.1 Youyi Road, Yuzhong District, Chongqing

department: Neurosurgery Department

institute: The first Affiliated Hospital of Chongqing Medical University

summary: We knocked down the lncRNA-Neat1 by RNA interference in HT22 cells, which were immortalized from the mice hippocampal neurons. Then we measured the mRNA alteration induced by Neat1 knockdown through the next generation sequencing technique (RNA-seq). A total of 18,309 transcripts were detected in the current sequencing study, in which 593 transcripts were selected out according to the criteria: |log2(fold change)| > 1, P < 0.05 (22 up-regulated and 571 down-regulated). To explore whether the mRNA change induced by Neat1 knockdown in a stressed culture condition was different from that in normal condition, the cells were dealt with OGD and followed by RNA-seq. A total of 18,502 transcripts were detected, in which 121 transcripts were significantly up-regulated and 126 transcripts were significantly down-regulated according to the aforementioned filter rules.

overall_design: We carried out RNA-seq to detect the mRNA change induced by Neat1 knockdown in normal culture condition and stressed condition.

first: Jianjun

last: Zhong

first: Xiaochuan

last: Sun


title: Transcriptomic analyssis following EHMT1/2 inhibition

city: Cleveland

first: Hyunmin

last: Kim

state: Ohio

address: 10900 Euclid Ave.

department: Department of Genetics and Genome Sciences

institute: Case Western Reserve University

summary: RNA was isolated from PEO1 olaparib resistant (PEO1-OR) cells grown in complete growth media or PEO1-OR clone 4 cells grown in complete growth media with 500 nanomolar of UNC0642 for 72 hrs. RNA-sequencing was performed to evaluate UNC0642-dependent transcriptional reprogramming, which contributes to resensitization of PEO1-OR to olaparib. PEO1 line was authenticated prior to sequencing. PEO1 parental were confirmed to be BRCA2-mutated (5139C>G).

overall_design:
PEO1-OR cells grown in complete growth media (four clones) compared to PEO1-OR clone 4 cells grown in complete growth media with 500 nanomolar UNC0642 for 72 hours (A1/A2 and B1/B2). PEO1-OR clone 4 cells with UNC0642 A1 and A2 were sequenced from a single RNA extraction thus these samples were merged into UNC_A.  PEO1-OR clone 4 cells with UNC0642 B1 and B2 were sequenced from a single RNA extraction thus these samples were merged into UNC_B.

Please note that the four PEO1_Clone sample records (GSM4036839-GSM4036842) are duplicated sample records of the previous GSE117765 samples (GSM3308401-GSM3308404) for the convenient retrieval of the complete raw data from SRA.

first: Benjamin

last: Bitler

first: Zachary

middle: L

last: Watson


title: RNA-seq following JunD depletion

city: Philadelphia

first: Austin

middle: Lewis

last: Good

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

summary: RNA-seq performed in Min6 cells during glucolipotoxicity after CRISPR-mediated depletion of JunD

overall_design: RNA-seq performed on Total RNA in triplicate for Min6 cells transduced with gRNA targeting Rosa26 (negative control) or JunD

first: Doris

middle: A

last: Stoffers


title: TRAP-seq following Pdx1 depletion

summary: TRAP performed in GFP-RPL10A Min6 cells transfected with siRNA targeting Pdx1 or a non-targeting (NT) control. IP RNA was isolated by TRAP protocol and input lysate was used to isolate Total RNA. RNA-seq was performed on both IP and Total RNA.

overall_design: RNA-seq performed on IP RNA and Total RNA in triplicate for Min6 cells transfected with NT siRNA or Pdx1 siRNA


title: Behavioural and neurochemical mechanisms underpinning the synergistic feeding-suppressive effect of GLP-1/CCK combinatorial therapy

first: Brian

middle: Yee Hong

last: Lam

address: Box 289 Addenbookes Hospital, Hills Road

department: Metabolic Research Laboratories

country: United Kingdom

institute: University of Cambridge

summary: Combinatorial therapies are under intense investigation for the development of more efficient anti-obesity drugs, however little is known about how they act in brain to produce enhanced satiety and weight loss. Here we used a multidisciplinary strategy to decipher the central mechanisms engaged downstream from the co-administration of GLP-1R and CCK1R agonists, an efficient combination therapy in obese rodents. The nucleus of the solitary tract (NTS) contained one of the few neuronal populations synergistically activated in response to GLP-1R and CCK1R co-agonism. None of the previously categorized NTS neuronal subpopulations relevant to feeding behaviour were synergistically activated. However, using PhosphoTRAP, we obtained the molecular signature of NTS and ARH neurons synergistically regulated by the GLP-1R and CCK1R co-agonism and identified NTS/AP Calcrl+ neurons and ARH Adcyap1r1+ neurons as targets of this treatment. Collectively these studies advance our understanding of the central mechanisms involved in the synergistic appetite- and weight-suppressive effect of a combinatorial therapy.

overall_design: 24 samples were analyzed , 3 for each groups and sample type (total RNA input and ipRNA)

first: Emma

last: Roth

first: Baptiste

last: Quentin

first: Nick

last: Helley

first: Tamana

last: Darwish

first: Yashawi

last: Shrestha

first: Giles

last: Yeo

first: David

last: Baker

first: James

last: Trevaskis

first: Clemence

last: Blouet

first: Marcella

last: Ma