title: Single cell RNA sequencing analysis of lnc-HLX-2-7 knock out in medulloblastoma

status: Public on Oct 30 2020

city: St. Petersburg

first: Bongyong

last: Lee

state: Florida

address: 501 6th Ave S

country: USA

institute: The Johns Hopkins University

type: Expression profiling by high throughput sequencing

summary: To gain more insights into the functional significance of lnc-HLX-2-7, gene expression profiles were measured using  D425, D425 lnc-HLX-2-7 KD and their intracranial xenografts by RNA sequencing. Dissociated tumor cells were used for gel bead emulsion (GEM) with chromium controler (10X genomics).

overall_design: Medulloblastoma single cell RNA profiles of D425, D425 lncHLX-2-7 KD and their intracranial xenografts.

first: Keisuke

last: Katsushima

first: Rabi

last: Murad

first: Eric

last: Raabe

first: Charles

middle: G

last: Eberhart

first: Ranjan

middle: J

last: Perera


title: RNA-seq timecourse of p53 activation with Nutlin-3a in IMR90 cells

status: Public on Oct 31 2020

city: Philadelphia

first: Katherine

middle: A

last: Alexander

state: Pennsylvania

address: Smilow Center for Translational Research

institute: University of Pennsylvania

summary: To investigate the dynamics of the p53 response, we treated IMR90 cells with Nutlin-3a, a small molecule that inhibits the interaction between p53 and its inhibitor Mdm2, for 6, 9, or 12 hours.

overall_design: RNA-seq in IMR90 cells treated with Nutlin-3a (inhibitor to Mdm2-p53 interaction) for 6, 9, or 12 hours or treated with a DMSO control.

first: Shelley

middle: L

last: Berger


title: Transcriptome of Drosophila melanogaster third instar larval eye discs expressing GMR-Gal4>UAS-127Q and Wild type reared on normal food or food supplemented with Amalaki Rasayana (AR) or Rasa-Sindoor (RS)

city: Varanasi

first: Subhash

middle: C

last: Lakhotia

state: UP

address: Cytogenetics Lab

department: Zoology

country: India

institute: Banaras Hindu UNiversity

summary:
Purpose: Feeding larvae of fly models of polyQ and other neurodegenerative disorders on AR or RS supplemented food substantially suppressed neurodegeneration. With a view to gain further insight into the suppression of polyQ pathology by AR or RS, we expressed the UAS-127Q transgene using the predominantly eye-specific GMR-GAL4 driver and examined the transcriptomic changes in wild type and 127Q-expressing eye discs following feeding on AR or RS. In order to find out reason underlying the suppression of neurodegeneration by feeding of AR and RS, we checked difference in gene expression between eye discs expressing GMR-GAL4>UAS-127Q and wild type.
Method: Eye disc RNA profiles of wandering late third instar larvae of GMR-GAL4>UAS-127Q and wild type larvae, reared on normal food or food supplemented with AR or RS since after hatching, were generated by sequencing, in triplicate, using Illumina Hiseq2500 platform using 51bp pair-end reads, 12 samples per lane and each sample run across 2 lanes of flowcell (Flowcell ID: C7K52ACXX).This resulted in a sequencing depth of 19-25 million reads. The resulting sequencing fastq files were mapped to the Drosophila genome (dm6) using Tophat with Bowtie. The aligned SAM/BAM file for each was processed for guided transcript assembly using Cufflink 2.1.1 and gene counts were determined. Mapped reads were assembled using Cufflinks. Transcripts from all samples were subjected to merge with Cuffmerge to get final transcriptome assembly across samples. In order to ascertain differential expression of transcripts between different samples, Cuffdiff 2.1.1 was used (Trapnell et al., 2012).
Result: Using an optimized data analysis workflow, we mapped about 19-25 million sequence reads per sample to the Drosophila melanogaster genome (dm6) and identified  15,904 transcripts with cufflink workflow in each genotypes studied. The GMR-GAL4 driven UAS-127Q expression in eye discs reared on AR supplemented food resulted in 259 differential expression, with 147 genes being down-regulated and 112 up-regulated, when compared with those reared on normal food, however, when larvae from same genotype reared on RS supplemented food resulted in  1641 DEGs, with 846 genes being down-regulated and 795 up-regulated compared with larvae reared on normal food. In eye disc of wild type larvae reared on AR supplemented food resulted in 680 DEGs, with 470 genes being down-regulated and 205 up-regulated compared with those reared on normal food. Larvae from wild type reared on RS supplemented food resulted in 427 DEGs, with 264 genes being down-regulated and 163 up-regulated compared with those reared on normal food. Compared to only GMR-GAL4>UAS-127Q and wild type larval eye discs reared on normal food, total of 1691, with 799 gene were up-regulated while 892 were down-regulated.
Conclusion: The present results not only re-inforce earlier findings from our lab that the Ayurvedic Amalaki Rasayana and Rasa-Sindoor are potent suppressors of neurodegeneration but also provide direct evidence that these general health-promoting formulations significantly alter expression of many genes in protein-aggregation-clearance pathways and thus eliminate the cause of proteinopathy so that cell death is inhibited while other normal cellular activities continue. These formulations, which have been used in Ayurvedic practice for thousands of years as health-promoting as well as curative supplements, do not have any side-effects. Therefore, we believe that these Ayurvedic formulations have a good potential to ameliorate the sufferings of polyQ and other neurodegenerative disorders.

overall_design: Total RNA profiling of wandering late third instar larvae of GMR-GAL4>UAS-127Q and wild type third instar larvae, reared on normal food or food supplemented with AR or RS since after hatching, were generated by sequencing, in triplicate, using Illumina Hiseq2500 platform.

first: Yashvant

last: Patel


title: Sphingosine kinase 2 regulates CD4+ T cell responses following LCMV Cl 13 infection

status: Public on Oct 29 2020

city: Columbia

first: Bumsuk

last: Hahm

state: Missouri

address: M331 Medical Science Bldg. One Hospital Drive

department: Surgery/MMI

institute: University of Missouri-Columbia

summary: Viruses often establish persistent infections by interrupting immune cell responses. Sphingosine kinase 2 (SphK2) generates sphingosine 1-phsophate, which is known to regulate versatile cellular processes, including immune responses. However, little is known about the role of SphK2 in the immune response to viral infections. Here, we demonstrate that during lymphocytic choriomeningitis virus (LCMV) clone 13 infection, a virus known to establish a persistent infection in mice, SphK2 functions to limit CD4+ T cell responses, which aids in the establishment of virus-induced immunosuppression and viral persistence. The infection of SphK2-deficient (Sphk2-/-) mice with LCMV resulted in kidney disease and ultimately mortality. Following infection, Sphk2-/- mice were shown to have increased LCMV-specific CD4+ and CD8+ T cell responses. With the use of LCMV epitope-specific TCR transgenic mouse lines in adoptive transfer studies, SphK2 was shown to have intrinsic negative function in CD4+ T cells, but not CD8+ T cells. Furthermore, Sphk2-/- CD4+ T cells were able to promote endogenous, virus-specific CD8+ T cell responses more efficiently than Sphk2+/+ CD4+ T cells. Our results suggest that SphK2 is a novel regulator of the immune response during LCMV clone 13 infection and targeting SphK2 may provide a promising immunotherapeutic strategy for the control of persistent viral infections. This study incorporated the use of RNA sequencing to determine what pathways SphK2 was involved in to affect CD4+ T cell activity and proliferation. Sphk2+/+ or Sphk2-/- LCMV epitope-recognizing tg CD4+ T cells were transferred into C57BL/6 mice and recovered 7 days following LCMV Cl 13 infection. RNA sequencing revealed several pathways upregulated in Sphk2-/- CD4+ T cells relating to cell cycle progression, regulation of transcription, and regulation of nucleic acid binding.

overall_design: 3 replicates of LCMV-specific Sphk2+/+ CD4+ T cells from LCMV Cl 13-infected mice; 3 replicates of LCMV-Sphk2-/- CD4+ T cells from LCMV Cl 13-infected mice

first: Caleb

last: Studstill

first: Curtis

last: Pritzl

first: Young-Jin

last: Seo


title: Comparative Transcriptome Analysis Reveals New Insight into Russeting of the Semi-Russeted ‘Cuiguan’ Pear Variety

city: Yangzhou

first: Jing

last: Zhang

address: 48 Wenhui Road

country: China

institute: Yangzhou university

summary: We carried out the transcriptome analysis to identify the key genes involved in pear fruit semi-russet formation, by comparing the CK (russet) and bagging treated (green) ‘Cuiguan’ pear fruit skin 95 DAFB.

overall_design: Transcriptome profiling of untreated and fruit bagging treated ‘Cuiguan’ pear fruit skin, insights into pear fruit semi-russet formation

first: Chunlei

last: Wang


title: Single cell characterization of arrested B-lymphoid differentiation and leukemic cell states in ETV6-RUNX1-positive pediatric leukemia

city: Kuopio

first: Merja

last: Heinäniemi

address: Yliopistonranta 1 E

department: School of Medicine

country: Finland

institute: University of Eastern Finland

summary: Arrested bone marrow (BM) lymphoid cell differentiation underlies the emergence of the most common childhood cancer, acute lymphoblastic leukemia (ALL). Recurrent genetic lesions often directly involve transcription factors (TFs), such as ETV6 and RUNX1 found in the most common ALL translocation.

overall_design: Here, we studied the effect of ETV6-RUNX1 overexpression in the Nalm-6 cell line model using single cell RNA-seq (scRNA-seq).

first: Juha

last: Mehtonen

first: Susanna

last: Teppo

first: Mari

last: Lahnalampi

first: Aleksi

last: Kokko

first: Riina

last: Kaukonen

first: Laura

last: Oksa

first: Saara

last: Laukkanen

first: Maria

last: Bouvy-Liivrand

first: Tapio

last: Lönnberg

first: Olli

last: Lohi


title: RNA sequencing of Hes5.3+ cells from E5 chick embryonic retinas in control and retinoic acid treated conditions.

city: Geneva

first: Laurent

last: Brodier

state: Geneva

address: 30 Quai Ernest-Ansermet

department: Molecular Biology

country: Switzerland

institute: University of Geneva

summary: Two E5 (HH26) chick embryonic retinas were dissected from two embryos, electroporated with Hes5.3-GFP reporter plasmid, and incubated in 2.5 μM retinoic acid (RA) in culture medium (DMEM, 10% FBS, 1% Penicillin/Streptomycin) for 8 hours. The corresponding opposite retinas from the same embryos were used as controls and incubated in culture medium with DMSO. Cells were dissociated and GFP+ cells were sorted by FACS. RNA was extracted using TRIzol reagent, according to manufacturer's protocol. RNA samples were quantified by Qubit 4 fluorometer (Thermo Fisher), and RNA quality was assessed by BioAnalyzer (Agilent). RNA sequencing was performed. This protocol was done in triplicate for RA and control conditions.

overall_design: Gene expresson by RNA-seq in Hes5.3+ cells from two E5 chick embryonic retinas taken from two different embryos and treated with RA, vs two control retinas from the opposite side of the same embryos, in triplicate.

first: Jean-Marc

last: Matter


title: Transcriptomic analysis of freshly purified human CD226- and CD226+  CD8+ T cell subsets isolated from the peripheral blood of healthy donors.

city: Toulouse

first: ludovic

last: Martinet

address: 2 av Hubert Curien

department: CRCT

country: France

institute: INSERM U1037

summary: We recently found that loss of the activating receptor CD226 (DNAM-1) was a critical mechanism affecting CD8+ T cell responsiveness to TCR stimulation. To better understand the molecular differences between CD226- and CD226+ CD8+ T cells, we decided to perform a global transcriptional analysis of purified naive (Tn, CD62L+CD45RA+), central memory (Tcm, CD62L+CD45RA-)  and terminal effector memory (Temra, CD62L-CD45RA+) CD226+ and CD226- CD8+  T cells using next generation RNA sequencing.

overall_design: Total RNA was extracted using RNeasy Micro kit (QIAGEN) and the sequencing was performed using next generation RNA sequencing

first: Ludovic


title: Acute Kidney Injury Transcriptional Profiles: Single Cell RNA Sequencing reveals Injury induced Renal Developmental program reactivation and Lineage Infidelity in adult kidney

city: Cincinnati

first: Mike

last: Adam

state: Ohio

address: 240 Albert Sabin Way

department: CBDI

institute: Cincinnati Children's Hospital Research Foundation

summary: Acute Kidney Injury (AKI) is a rapid renal function decline associated with pronounced morbidity and mortality. Single Cell RNA Sequencing is a powerful tool allowing for examining transcriptional changes in multiple renal cell populations involved in the injury response. Our study reveals renal developmental gene re-activation and lineage infidelity in response to ischemia/reperfusion induced AKI, along with the novel genes which might serve as markers of acute kidney disease

overall_design: Using droplet RNA sequencing, transcriptomes of single cells from normal and injured mouse kidneys were analyzed

first: Valeria

last: Rudomanova

first: Steve

last: Potter


title: p70 S6 Kinase 1-dependent alterations in cortical mRNA translation in fragile X syndrome mice

city: New York

first: Eric

last: Klann

state: NY

address: 4 Washington Pl

institute: New York University

summary: Fragile X syndrome (FXS) is caused by loss of the fragile X mental retardation protein (FMRP). The mechanism by which FMRP regulates messenger RNA (mRNA) translation remains disputed. We observed reduced ribosome footprint abundance in the majority of differentially translated genes in cortices of FXS mice, which was correlated with an increased rate of ribosome translocation that was normalized by inhibition of p70 S6 Kinase 1 (S6K1). We also show that alterations in translation efficiencies across mRNAs in FXS mouse cortices exhibit a positive to negative gradation with coding sequence length, which is prevented by the genetic reduction of S6K1. Our findings reveal the identity of dysregulated mRNAs and a molecular mechanism by which reduction of S6K1 prevents altered translation in FXS.

overall_design: Examination of genome-wide translational state in wild-type, Fmr1-deficient, Rps6kb1-deficient, and double knockout (Fmr1 and Rps6kb1 deficient) mouse cortices via next-generation sequencing-based profiling of transcription and translation.

first: Sameer

last: Aryal

first: Francesco

last: Longo


title: Next Generation Sequencing Facilitates Quantitative Analysis of basic diet-treated (CON)，lipopolysaccharide-treated(LPS), or lipopolysaccharide+genistein treated broiler chicks (GEN) thymic Transcriptomes

city: nanjing

first: zengpeng

last: lv

address: weigang

institute: nanjing agricultural university

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of biological process. The goals of this study are to characterize the effects of genistein on the thymic transcriptome of chicks, when suffering from lipopolysaccharide challenge using RNA-Seq technology
Methods: Thymic mRNA profiles of 21-day-old chicks with basic diet and lipopolysaccharide-treated, or lipopolysaccharide+genistein treated chick mice were generated by deep sequencing, in triplicate, using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays
Results: Using an optimized data analysis workflow, we mapped about 70 million sequence reads per sample to the chicken genome and identified 25,016 transcripts with TopHat workflow. RNA-seq data confirmed stable expression of 25 known housekeeping genes, and 6 of these were validated with qRT–PCR. RNA-seq data had a linear relationship with qRT–PCR for more than four orders of magnitude and a goodness of fit (R2) of 0.8798. We identified 712 DEGs (367 upregulated and 345 downregulated) between the LPS vs CON group with a |fold change| ＞1 (P ≤0.05, Figure 4 a). There are 1926 DEGs (1014 upregulated and 912 downregulated) in the GEN group compared with the LPS groupAltered expression of 6 genes was confirmed with qRT–PCR, demonstrating the high degree of sensitivity of the RNA-seq method. Hierarchical clustering of differentially expressed genes uncovered several as yet uncharacterized genes that may contribute to retinal function.
Conclusions: Our research has evidenced a novel finding in chicks that dietary genistein could inhibit the increased percentage of CD3+ T lymphocytes, and CD4+/CD8+ T lymphocyte ratio in the peripheral blood induced by lipopolysaccharide injection. Furthermore, dietary genistein exposure altered the mRNA expression profile and AS signatures in the thymus, and regulated the immune response, along with the improvement of thymus index and apoptotic index after lipopolysaccharide challenge. It would help to understand the role of dietary genistein to the regulation of immune function and provide theoretical support for improving healthy production of poultry.

overall_design: Thymic mRNA profiles of 21-day old basic diet-treated, lipopolysaccharide-treated, or lipopolysaccharide+genistein treated chicks

first: Zengpeng

last: Lv


title: TBK1-METTL3 axis facilitates antiviral immunity [RNA-seq: Mock or VSV treated WT and Ythdf1-KO BMDM]

city: beijing

first: fuping

last: you

address: xueyuan street

institute: Peking University Health Science Center

summary: mRNA m6A modification is involved in regulation of immune system. However, its function in antiviral immunity is controversial, and how immune responses regulate m6A modification is unknown. We here found TBK1, a key kinase of antiviral pathways, phosphorylated the core m6A methyltransferase METTL3 at Serine 67. The phosphorylated METTL3 interacted with translational complex and enhanced proteins translation, including IRF3, and facilitated antiviral responses. TBK1 also promoted METTL3 activation and m6A modification, which is required for stabilizing IRF3 mRNA. Type I IFN induction was severely impaired in METTL3 deficient cells. Mettl3flfl-lyz2-Cre mice were significantly more susceptible to IAV-induced lethality than control mice. Consistently, Ythdf1—/— mice cannot control viral infection and showed higher mortality than control mice due to decreased IRF3 expression. Together, we demonstrated that innate signals activated METTL3 via TBK1, and METTL3 and m6A modification secured antiviral immunity by promoting mRNA stability and protein translation.

overall_design: mRNA profiles of wild type (WT)  and Ythdf1 knockout  bone marrow-derived macrophage (BMDM) treated with mock or vesicular stomatitis virus (VSV) for 12 hours

first: Jingxuan

last: Chen

first: Xuemei

last: Wei

first: Xiao

last: Wang

first: Fuping

last: You


title: Effect of over-conditioning on the hepatic global gene expression pattern of dairy cows at the end of pregnancy

city: Merelbeke

first: Osvaldo

last: Bogado Pascottini

state: Flanders

address: Salisburylaan 133

country: Belgium

institute: Ghent University

summary: Over-conditioning is a risk factor for upregulated pre- and postpartum fat mobilization. Therefore, we hypothesized that over-conditioning at the end of pregnancy leads to the accumulation of lipids in the liver and modifications of the hepatic gene expression pattern. The aim of this study was to evaluate the effect of over- versus normal-conditioning on the hepatic transcriptomic profile of dairy cows at the end of pregnancy. Ten dry multiparous Holstein cows were euthanized two weeks before expected calving. Body condition score (BCS) and backfat thickness (BFT) were evaluated, and blood samples for nonesterified fatty acids (NEFA) were taken before euthanasia. After euthanasia, liver biopsy samples were collected for further assessment of total lipids and RNA sequencing. Five cows were classified as normal-conditioned (BCS = 2.5–3.5) and five as over-conditioned (BCS = 3.75–5). Regression models confirmed that normal-conditioned cows had lower BCS [3.17 ± 0.10 (least square mean ± SE)], BFT (1.29 ± 0.29 cm), and serum NEFA (0.16 ± 0.04 mmol/L) in comparison to over-conditioned cows (4.35 ± 0.21, 3.14 ± 0.43 cm, and 0.38 ± 0.07 mmol/L for BCS, BFT, and NEFA, respectively). Total liver lipid percentage tended to be lower in normal- than over-conditioned cows (4.63 ± 0.40% and 6.06 ± 0.44%, respectively). In comparison to the mean liver lipid percentage of the normal and over conditioned cows, one over-conditioned cow had a relatively low (5.21%) and one normal-conditioned cow had a relatively high (6.07%) liver lipid percentage. Differentially expressed genes (DEGs) analysis (edgeR quasi-likelihood method) showed that normal-conditioned presented two upregulated and five downregulated genes in comparison to over-conditioned cows. Linear discriminant analysis effects size revealed 23 DEG between normal- versus over-conditioned cows. Notably, the liver of normal-conditioned cows had upregulated genes associated with liver functionality (albumin, selenoprotein P, and insulin-like growth factor binding protein 1 and 2). On the other hand, over-conditioned cows had upregulated genes associated with the acute phase response (complement C3, hemopexin, and lipopolysaccharide-binding protein). High basal lipolysis in over-conditioned cows at the end of pregnancy increases liver lipid content and alters the hepatic gene expression pattern to a pro-inflammatory state.

overall_design: Evaluation of the liver transcriptome of over- and normal-conditioned dairy cows two weeks before expected parturition

first: O

middle: B

last: Pascottini

first: J

last: De Koster

first: F

last: Van Nieuwerburgh

first: M

last: Van Poucke

first: L

last: Peelman

first: V

last: Fievez

last: Leroy

first: G

last: Opsomer


title: Exploring the involvement of NOX4 in hypoxia adaptation of papillary thyroid cancer

city: Mianyang

first: Hao

last: Dang

state: Sichuan

address: No. 190 The East Jiannan Road, Mianyang, 621000, Sichuan, People’s Republic of China

department: Clinical Laboratory

institute: The Third Hospital of Mianyang(Sichuan mental health center)

summary: Hypoxic stress is a feature of rapidly growing thyroid tumors. Cancer progression is thought to be driven by reactive oxygen species (ROS) induced hypoxia adaptation. NADPH oxidases (NOXs), which produce ROS as their primary and sole function, has become of particular interest in thyroid malignancy. NOX4 was demonstrated to be upregulated in papillary thyroid cancers, functioning as a mitochondrial energetic sensor to modulate ATP levels, mediating overproduction of ROS induced by IL-δ, inversely correlating to thyroid differentiation. In this study, we analyzed hypoxia-treated BCPAP cells transfected with siRNA against NOX4. Results provides insight into the role of NOX4 in hypoxia adaptation.

overall_design: BCPAP cells were transfected with scrambled siRNA or siRNA against NOX4. Subsequently the siRNA-transfected cells were cultured within 1% oxygen incubator. Three independent transfections were performed cells with control siRNA and for cells with siRNA specific to NOX4 where each transfection constitutes biological replicate. Knock-down of NOX4 in all samples was confirmed by quantitative real-time PCR.


title: Molecular Characterization of auditory nerve with Versican deficiency

city: Charleston

first: Jeremy

last: Barth

state: SC

address: 173 Ashley Ave, BSB 627

institute: MUSC

summary: Overall goal of the study is to identify key molecular regulators of auditory nerve development and maintenance

overall_design: Auditory nerve samples from young adult C57BL/6J wildtype and Versican (Vcan) deficient mice were compared. Each group used three independent samples.

first: Hainan

last: Lang

first: Clarisse

last: Paganiban

first: Kenyaria

last: Noble

first: Starr

last: Hazard

first: Gary

last: Hardiman


title: Genome-wide analysis of the JAM-C over-expressed trophoblasts

city: Nanjing

first: Chenrui

last: Cao

address: 321 Zhongshan Road

institute: Drum Tower Hospital

summary: During pregnancy, trophoblasts in the placenta are important in the success of pregnancy. We identify an adhesion molucule, JAM-C, which expresses on membrane of column cytotrophoblasts and regulates the differentiation and migration of trophoblasts. Primary cytotrophoblasts isolated from 1st trimester villi were transfected with JAM-C or control plasmids. RNA-seq analysis was sujected to identify differentially expressed genes and pathways potentially altered.

overall_design: Overall 6 samples: 2 cell types from 3 donors

first: Yali

last: Hu


title: RNAseq analysis of antibacterial mechanism of Cinnamomum camphora essential oil against Escherichia coli

city: Nanchang

first: tian

last: Yu

address: 999 Xuefu Rd.

institute: Human Aging Research Institute and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Human Aging

summary: Transcriptome analysis plays a central role in elucidating the complexity of gene expression regulation in Escherichia coli. By analyzing the transcriptomics of E. coli treated with water, acetone, and Cinnamomum camphora essential oil, the inhibitory mechanism of the essential oil on the human intestinal microbe was studied. The results showed that the inhibitory effect of the essential oil on E. coli increased with an increase in concentration; 1/4 minimum inhibitory concentration was the reaction equilibrium point. RNAseq transcriptomic comparison indicated that the essential oil inhibited the growth of E. coli by inhibiting the metabolism, chemotaxis, and some resistance reactions of them, while E. coli maintained its life activities by enhancing its resistance reactions. These results are of great importance to the study of the medical use of C. camphor essential oil and gene regulation in E. coli under stress conditions.

overall_design: Transcriptome sequencing of RNA under five different treatments in E. coli

first: Yutian

first: Jie

last: Dong

first: Yanlu

last: Wang

first: Xi

last: Gong


title: RNA sequencing analysis of lnc-HLX-2-7 interacting genes and pathways in medulloblastoma

city: St. Petersburg

first: Bongyong

last: Lee

address: 501 6th Ave S

institute: The Johns Hopkins University

summary: To gain more insights into the functional significance of lnc-HLX-2-7, gene expression profiles were measured using  D425, D425 lnc-HLX-2-7 KD and their intracranial xenografts by RNA sequencing.

overall_design: Medulloblastoma mRNA profiles of D425, D425 lncHLX-2-7 KD and their intracranial xenografts.

first: Cuncong

last: Zhong

first: Ben

last: Liu

first: Eric

last: Raabe

first: Charles

last: Eberhart

first: Ranjan

last: Perera


title: RNA-seq Analysis of Wild Type and Mark3-/- mouse primary osteoblasts

city: Charlottesville

middle: R

last: Farber

state: VA

department: Center for Public Health Genomics

institute: University of Virginia

summary: Bone mineral density (BMD) is a highly heritable predictor of osteoporotic fracture.  Genome wide association studies (GWAS) have identified hundreds of loci influencing BMD, but few have been functionally analyzed. In this study, we show that SNPs within a BMD locus on Chromosome 14q32.32 alter splicing and expression of PAR-1a/MARK3, a conserved serine/threonine kinase known to regulate bioenergetics, cell division and polarity.  Mice lacking Mark3 either globally or selectively in osteoblasts have increased bone mass at maturity. RNA profiling from Mark3 deficient osteoblasts suggested changes in the expression of components of the Notch signaling pathway.  Mark3 deficient osteoblasts exhibited greater matrix mineralization compared with controls that was accompanied by reduced Jag1/Hes1 expression and diminished downstream JNK signaling. Overexpression of Jag1 in Mark3 deficient osteoblasts both in vitro and in vivo normalized mineralization capacity and bone mass, respectively.  Together, these findings reveal a mechanism whereby genetically regulated alterations in Mark3 expression perturb cell signaling in osteoblasts to influence bone mass.

overall_design: Primary osteoblast mRNA profiles of control and 24h deletion of Mark3 treatment

first: Thomas

last: Clemens

first: Qian

last: Zhang


title: Transcriptomic analysis of resting or activated human CD226- and CD226+  effector memory CD8+ T cell subsets isolated from the peripheral blood of healthy donors.

first: ludovic

last: Martinet

summary: We recently found that loss of the activating receptor CD226 (DNAM-1) was a critical mechanism affecting CD8+ T cell responsiveness to TCR stimulation. To better understand the molecular differences between CD226- and CD226+ CD8+ T cells, we decided to perform a global transcriptional analysis of purified CD226+ and CD226- CD8+ effector memory T cells before and after TCR activation using next generation RNA sequencing. We report here the total RNA sequencing of healthy donor resting CD226- and CD226+ CD8+ Tem cells (n=6/group) or activated (ACT, n=4/group) by α-CD2/CD3/CD28 for 24 hrs.

first: Ludovic


title: Bulk sequencing of isolated endothelial cells in AD

city: Boston

first: Chengyu

last: Zou

state: MA

address: 240 Longwood Ave

institute: Harvard medical school

summary: We report the application of using next-generation sequencing to quantify gene expression differences in cerebral endothelial cells between APP/PS1 and Ctrl littermates.

overall_design: Cerebral endothelial cells were isolated by FACS (CD31+CD45-). 20000 cells per sample were collected for library preparation and then next-generation sequencing.

first: Junying

last: Yuan


title: Transcriptome analyses indicate changes in seed oil content under drought stress in Brassica napus L.

city: 重庆市

first: Yangyang

last: Li

state: 重庆

address: 中国重庆

institute: 农学与生物科技学院

summary: The libraries of RNA extracted from the seeds on the 30th, 40th and 50th days (30d, 40d, and 50d) after drought treatment were employed for sequencing and analysis. Our results demonstrated the reasons of  the oil content decreased by RNA-seq. These results may help to establish a theoretical foundation for breeding excellent varieties of rapeseed with high oil content in areas with frequent droughts.

overall_design: Seed RNA profiles of 30th, 40th and 50th days after flowering under control and drought treatment

first: Linxue

first: Liezhao


title: Vein and Intervein Drought RNAseq

city: pasco

first: aaron

last: ogden

state: wa

address: 902 battelle boulevard

department: integrative omics

institute: Pacific Northwest National Lab

summary: We report here the RNAseq data generated from a drought experiment using tomato leaves (Solanum lycopersicum), in which three timepoints and two treatments were collected. More specifically, RNAseq was generated from tomato plants prior to drought (T0), during a period of drought (T1) and after a period of recovery from drought (T2). At timepoints 1 and 2 (T1 & T2), a control set of plants that were continuously watered are also included. Furthermore, at each timepoint, each leaf was dissected into two parts, including the vein and intervein. The samples are therefore named as Tissue/Timepoint/Treatment, and include VT0W (vein, T0, watered), VT1W (vein, T1, watered), VT1D (vein, T1, drought), VT2D, VT2W and IVT0W (intervein, T0, Watered), IVT1D, IVT1W, IVT2D, IVT2W. Note that VT2D and IVT2D, while named "drought", were actually recovered from drought.

overall_design: Tomato leaves, before, during, and after recovery from drought (3 timepoints), dissected further into 2 tissues (vein and intervein), all run in biological triplicate. For both T1 and T2 samples, a watered control was included, to which the T1 drought and T2 recovered plants could be compared. There are therefore 30 samples, consisting of 15 vein and 15 intervein tissues. For both vein and intervein tissues, 3 samples correspond to T0 (watered), 6 samples to T1 (3 watered, 3 drought), and 6 samples to T2 (3 watered, 3 recovered from drought).

first: Aaron

last: Ogden

first: Wayne

last: Curtis

first: Jamie

last: Moon

first: Joshua

middle: N

last: Adkins

first: Samwel

middle: M

last: Kariuki

first: Heather

last: Brewer

first: Jishnu

last: Bhatt

first: Jack

last: Kintigh


title: Differential gene expression in a mouse model for pediatric high grade glioma encoding for H3.3-G34R mutation

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

institute: University of Michigan

summary: This experiment was designed to study the effect of the histone H3.3-G34R mutation on the transcriptome of tumor cells and immune-infiltrating cells, in a high grade glioma mouse model.

overall_design: High grade gliomas (HGG) were generated using the Sleeping beauty system and involved these combinations: (i) pSB, pNRAS-G12V, pshATRX and pshp53 (H3.3-WT group), (ii) pSB, pNRAS-G12V, pshATRX, pshp53 and pH3.3-G34R (H3.3-G34R group). There are four groups with 3 or 4 samples each, allowing two independent pairwise comparisons: tumor with overexpression of mutated histone H3.3 G34R (n=3) vs H3.3-WT tumors (n=4), and imune cells isolated from H3.3-G34R tumors (n=3) vs immune cells isolated from H3.3-WT tumors (n=4)

first: Maria

last: Castro

last: Garcia-Fabiani

first: Rebecca

last: Tagett


title: Targeted RNA-seq signature of Breast Cancer Circulating Tumor Cells correlates with occurrence of bone-only metastases

city: Bari

first: Domenica

last: Lovero

state: Bari

address: P.zza Giulio Cesare, 11

department: Department of Biomedical Sciences and Human Oncology

country: Italy

institute: University of study of Bari Aldo Modo

summary: Bone is the most frequent site of metastases from breast cancer (BC), although no biomarkers are yet available to predict the risk of skeletal dissemination. Here, we attempted to identify a gene signature correlated with bone metastasis (BM) onset in circulating tumor cells (CTCs) isolated from 40 metastatic BC patients, grouped according to their metastasis sites at the time of enrollment, namely “BM” (bone-only), “ES” (extra-skeletal) or “BM+ES” (bone and extra-skeletal).   A 134-gene panel, derived from an extensive literature review, was validated on sub-clones of the MDA-MB-231 BC cell line with variable organotropism and then applied to CTC groups for targeted RNA sequencing. No correlation was found between CTC number and clinico-pathologic variables, whereas 31 differentially expressed genes emerged from “BM” and “ES” CTC comparison. The putative prognostic meaning of the “top-10” most deregulated genes was finally explored and pointed out by employing an external BC dataset.

overall_design: Targeted RNA-seq of circulating tumor cells (CTCs) isolated from 40 metastatic BC patients.

first: Stella

last: D'Oronzo

first: Raffaele

last: Palmirotta

first: Paola

last: Cafforio

first: Janet

last: Brown

first: Steven

last: Wood

first: Camillo

last: Porta

first: Robert

last: Coleman

first: Franco

last: Silvestris


title: Transcriptomic profiling of VEXAS syndrome patients

city: Bethesda

first: David

last: Beck

state: MD

address: 9000 Rockville Pike

department: NHGRI

institute: NIH

summary: UBA1 is an E1 enzyme essential for initiating ubiquitylation. We have identified 25 patients with somatic mutations in UBA1 that alter protein isoform expression in myeloid cells. We studied the transcriptional profiles of whole blood, and sorted cell populations from VEXAS patients.

overall_design: RNAseq using the whole blood and isolated cell populations from VEXAS patients

first: Nicholas

last: Balanda

first: Hirotsugu

last: Oda


title: FoxO maintains a genuine quiescent muscle stem-cell state until geriatric age (ATAC-seq)

first: Hong-wei

last: Sun

address: 9000 Rockville Pile

department: Office of Science & Technology

institute: NIAMS

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We identify two quiescent stem-cell states through relative CD34 expression: CD34High, with stemness properties (genuine state), and CD34Low, more committed to myogenic differentiation (primed state). The genuine-quiescent state is preserved into later life succumbing only in extreme old age due to acquisition of primed-state traits. We identified niche-derived IGF1-dependent Akt activation as detrimental to the genuine stem-cell state by imposing primed-state features via FoxO inhibition. Interventions to neutralize Akt and promote FoxO activity drive primed-to-genuine state conversion, while FoxO inactivation deteriorates the genuine state at young age, causing muscle regenerative failure, as in geriatric mice.

overall_design:
Muscles from mice were mechanically disaggregated and dissociated in Ham’s F10 media containing Liberase (0.1mg/g muscle weight) (Roche; 5mg/mL) and Dispase 0.3% at 37 °C for 2 h and then filtered. Cells were then incubated in lysis buffer (BD Pharm Lyse) for 10 min on ice, re-suspended in PBS with 2% goat serum (FACS buffer) and counted. PE-Cy7-conjugated anti-CD45 (Biolegend 103114), anti-Sca-1 (Biolegend 108114) and PE-Cy7-conjugated anti-CD31 (Biolegend 102418) antibodies were used for lineage-negative selection. PE-conjugated anti-α7-integrin (AbLab AB10STMW215) and Alexa Fluor 647-conjugated anti-CD34 (BD Pharmigen 560230) were used for double positive staining of quiescent satellite cells. Satellite cells were sorted using a FACS Aria II (BD) and processed for RNA-seq and ATAC-seq.
This dataset includes the 26 ATAC-Seq samples of this project.

first: Laura

last: García-Prat

first: Eusebio

last: Perdiguero

first: Sonia

last: Alonso-Martín

first: Stefania

last: Dell’Orso

first: Srikanth

last: Ravichandran

first: Stephen

last: Brooks

first: Aster

middle: H

last: Juan

first: Silvia

last: Campanario

first: Kan

last: Jiang

first: Xiaotong

last: Hong

last: Ortet

first: Vanessa

last: Ruiz-Bonilla

first: Marta

last: Flández

first: Elena

last: Rebollo

first: Mercè

last: Jardí

first: Hong

middle: W

first: Antonio

last: Musarò

first: Marco

last: Sandri

last: del Sol

first: Vittorio

last: Sartorelli

first: Pura

last: Muñoz-Cánoves


title: IVIGET (In Vitro Gene Expression Testing)

city: Rome

first: Nicola

last: Cotugno

address: via Montpellier 1

department: Department of Systems Medicine

institute: University of Rome "Tor Vergata"

summary: ABSTRACT: The number of patients affected by chronic diseases with special vaccination needs is burgeoning. In this scenario, predictive markers of immunogenicity, as well as signatures of immune responses are typically missing even though it would especially improve the identification of personalized immunization practices in these populations. We aimed to develop a predictive score of immunogenicity to Influenza Trivalent Inactivated Vaccination (TIV) by applying deep machine learning algorithms using transcriptional data from sort-purified lymphocyte subsets after in vitro stimulation.  Peripheral blood mononuclear cells (PBMCs) collected before TIV from 23 vertically HIV infected children under ART and virally controlled were stimulated in vitro with p09/H1N1 peptides (stim) or left unstimulated (med). A multiplexed-qPCR for 96 genes (Fluidigm, Biomark) was made on fixed numbers of 3 B cell subsets, 3 T cell subsets and total PBMCs. The ability to respond to TIV was assessed through hemagglutination Inhibition Assay (HIV) and ELIspot and patients were classified as Responders (R) and Non Responders (NR). A predictive modeling framework was applied to the data set in order to define genes and conditions with the higher predicted probability able to inform the final score.     Twelve NR and 11 R were analyzed for gene expression differences in all subsets and 3 conditions (med, stim or Δ (stim-med). Differentially expressed genes between R and NR were selected and tested with the Adaptive Boosting Model to build a prediction score. The score obtained from subsets revealed the best prediction score from 46 genes from 5 different subsets and conditions. Calculating a combined score based on these 5 categories, we achieved a model accuracy of 95.6% and only one misclassified patient.     In vitro stimulation, Cell sorting and RNA extraction. PBMC were thawed and cells were counted with Countess Automated Cell counter (Life technology). Cells were resuspended in complete RPMI medium at a concentration of 5 x 106 PBMCs/mL and left at 37°C for 16 hours in the presence or absence of of H1N1 A/California /09 HA peptides in a final concentration 20uL/mL. PMBCs were stained for surface markers, Vivid (Pacific Blue), CD10 (PECy7), CD20 (PE), CD27 (APC), IgD (FITC), CD21 (PECy5) for the B cell panel for 15 minutes and for CD3 (AmCyan), CD4 (PerCP Cy5.5), CD45RO (ECD), CCR7 (Alexa Fluor 700), and CXCR5 (Alexa Fluor 647) and a live/dead marker (ViViD; Molecular Probes) for the T cell panel for 15 minutes. Subsequently, stained PBMCs were washed twice in PBS, finally filtered with a 40 uM mesh and sorted by FACSAriaII (BD Biosciences). The purity of the sorted cell populations were typically >99%. All antibodies were previously titrated. Viable lymphocytes were identified as live dead amine dye negative (ViViD-) cells (Invitrogen).   500 live cells per B and T cell subset were sorted into tubes previously loaded with 9uL of PCR buffer (see also Figure 1 for gating strategy). After sorting, cells were immediately centrifuged (3000RPM for 3 minutes) and kept on ice. Samples were subsequently transferred in PCR tubes and 18 PCR cycles were performed on a C1000 Thermal Cycler (Bio Rad) with the following scheme (50°C for 20’, 95°C for 2’, 95°C 15’’, 60°C for 4’. Last step repeated 18 times). Cells were finally kept at -20 until further analysis. PCR buffer premix for cell sorting contained the following: Cells Direct Reaction mix 5uL, DEPC water 1,4, Superscript III + Taq 1ul, 0.2x diluted assay (96 primer mix) 2,5uL, Superasein 0,1uL.     Multiplexed RT-PCR  Previously amplified samples were loaded on a Fluidigm 96.96 standard chip following manufacturer’s instructions. Briefly, assay pre-mix was prepared 1:1 20X TaqMan Gene Expression Assay (Applied Biosystems) and Assay Loading Reagent (Fluidigm). The sample pre-mix was prepared with TaqMan Universal PCR Master Mix (2X)(Applied Biosystems), 20XGE Sample Loading Reagent (Fluidigm), and cDNA. Full list of the two panels of gene probes (B subsets and T subsets is shown in supplemental table 1 and 2). 5ul of Assay and Sample mix were loaded into the chip according to manufacturers instructions. Genes’ selection has been made according to previous analysis on RNA Sequencing on HIV infected children from a different cohort (data not shown), the literature and online gene banks and biological queries.  Cycle threshold value (Ct) deriving from exported files was corrected according to number of cells sorted if lower than 500. Calculations were made following the expression 67,5 / 500 = Y / X where X is the number of cells sorted and Y is the cells equivalent cDNA of cell sorted. The dilution factor (n) was calculated as n= 67,5/Y, and base 2 log of n was subsequently subtracted to Ct value in order to get Corrected Cycle Threshold (c-Ct). Expression threshold (Et), which was  used for the main analysis was finally obtained with 40-cCT. Once exported and corrected, data were analyzed through Fluidigm SingluaR (SingulaR analysis toolset 3.0) package, loaded on R (software R 3.0.2 GUI 1.62). As previously described (De Armas LR, 2017) gene expression differences between different groups within same subset and condition were used to identify Differentially Expressed Genes (DEGs). Alternatively, paired gene expression differences between stimulated (stim) and unstimulated samples (med) (stim-med) within the same subset were used to define Differentially Induced Genes (DIGs).

overall_design:
Please note that multiple samples in different condition derive from single patients. This is identified by the nomenclature in the sample name.
DN= Double negative (IgD-CD27-CD19+ CD10- B cells); Rem= resting memory (CD19+CD10-CD27+IgD-CD21+ B cells); AM= Activated memory B (CD19+CD10-CD27+IgD-CD21+ B cells); Naive= Naive B cells (CD19+CD10-CD27-IgD+); PBMCs= peripheral blood mononuclear cells; CD4=CD4+ T cells (CD3+CD4+); TfH= T follicula helper cells (CD3+CD4+CCR7+CD45RO+CXCR5+); NT= non T follicular Helper T cells (CD3+CD4+CCR7+CD45RO+CXCR5-)

first: N

first: L

last: De Armas


title: Transcriptome analysis of gene expression in A549 cell by Regulation of HOXC8 expression

city: hefei

first: li

last: yong

state: anhui province

address: 安徽省合肥市经开区九龙路111号安大新区

institute: anhui university

summary: We regulated the gene expression of hoxc8 in a549 to search for emt-related genes by transcriptome sequencing.

overall_design: Overexpression(HOXC8-FLAG) and knockdown(SH4) of HOXC8 were used to identify EMT-related genes in A549 cells. Both PCDH and PLV were empty vectors, which were overexpression and knockdown controls, respectively.

first: Mengqi

last: Yang

first: Dongjia

last: Li

first: Yong


title: RNA-Seq As4.1 cell line and native renin cells isolated from Ren1c-YFP mice

first: Maria

middle: Florencia

last: Martinez

address: 409 Lane Rd. Rm 2006

summary: RNA-seq was performed to compare the transcriptome of three renin cell types: juxtaglomerular cells, cells isolated from chronically recruited mice and in As4.1 cells

overall_design: Evaluate the transcriptome of renin cells

middle: F


title: Chromatin response to hypoxia in MCF7 cells

city: Headington

first: Damien

last: Downes

state: Oxfordshire

address: John Radcliffe Hospital

department: MRC Weatherall Institute of Medicine

country: United Kingdom

institute: The University of Oxford

summary: Oxygen is essential for cell growth, however in tumours quick growth can cause hypoxic conditions. To determine the changes in the chromatin landscape in response to hypoxia in breast cancer we have performed ATAC-seq dugin normoxia and hypoxia.

overall_design: Biological replicates with one or two technical replicates were grown for 48 hours in hypoxic or normoxic conditions before ATAC-seq.

first: Ana

last: Miar

first: Adrian

last: Harris


title: Divergent expression patterns and regulation of the H3.3-encoding genes during normal development and carcinogenesis

first: Michael

last: Tolstorukov

address: 185 Cambridge Street

institute: Massachusetts General Hospital

summary: Minor histone variants replace canonical histones in replication-independent manner, altering chromatin structure and thereby affecting gene expression. This constitutes a distinct mechanism of genome regulation, extending the function of nucleosomes beyond ‘simple’ DNA packaging. In an unusual genomic arrangement, two unique genes (H3F3A and H3F3B), encode the same protein – a developmentally essential histone H3.3. Mutations in each of these genes occur in different cancers, including pediatric brain tumors. To investigate this phenomenon we performed an integrative analysis of the expression, regulatory sequences, and mutability of these genes. We report that H3F3A and H3F3B have distinct expression patterns in human cell types. This difference is maximal between differentiated and stem-like cells, whose expression profile resembles that of cancers. The transcription factors, including Oct4/Sox2 and N-Myc, can differentially regulate these genes, and we demonstrate that Oct4 and Sox2 upregulate H3f3a but not H3f3b in mouse ESCs. Notably, the increased H3F3A contribution to the total H3.3 pool correlates with tumor malignancy. We infer that a similar increase in the H3F3A ‘transcriptional dosage’ in stem-like cells enables the mutations in this gene to impact cell fate determination. Collectively, our findings provide new insights into the interplay between gene expression and DNA mutations in chromatin-associated factors.

overall_design: RNA-seq profiles for Oct4 or Sox2 depleted and wild-type murine samples

first: Jakub

last: Mieczkowski

first: Sihem

last: Cheloufi

first: Aimee

last: Deaton

first: Konrad

last: Hochedlinger

middle: Y


title: Expression data from FITC challenged skin of CLEC4C-DTR mice vs. littermate controls treated with diptheria toxin

status: Public on Oct 28 2020

city: Saint Louis

first: Hannah

middle: Leigh

last: Miller

state: MO

address: 4519 Gibson Ave

department: Pathology and Immunology

institute: Washington University School of Medicine

summary:
CLEC4C-DTR exhibit exacerbated contact hypersensitivty to the FITC hapten.  Here we assess the transcriptional differences in whole skin of FITC challenged CLEC4C-DTR+ mice and DTR- mice treated with diptheria toxin.
Overall, CLEC4C-DTR upregualated 439 genes and downregulated 152 genes compared to transgene negative controls, filtering output on 2 fold expression level difference and FDR<0.05.

overall_design: Six samples were analyzed, one mouse was used per replicate and each replicate contained 1 FITC treated ear.  Three replicates per group were amplified and hybridized to the Affymetrix Mouse Gene 1.0 ST array.  Raw data was processed by Robust Multi-Array (RMA) method. Volcano plots and differential expression analysis was performed using Multiplot studio and Morpheus with a threshold of 2 fold change and a minimum P value significance threshold of 0.05 (after False Discovery Rate [FDR] correction for the number of tests).

first: Marco

last: Colonna


title: cerebellum and hippocampus - deletor x wt

city: Hershey

first: Nuno

last: Raimundo

state: PA

address: 500 University Dr, College Of Medicine, Room C4769

department: Cellular and Molecular Physiology

institute: Penn State College of Medicine

summary: Progressive mitochondrial respiratory chain (RC) deficiency is associated with a wide spectrum of adult-onset degenerative diseases, as well as with normal aging. We have previously generated the Deletor mice to model late-onset progressive RC defects. Here we report novel tissue-specific pathways contributing to mitochondrial disease pathogenesis, identified by gene expression analysis. We found that RC-deficient muscle fibers secrete the fasting-induced hormone, fibroblast growth factor 21 (FGF21). This response leads to fatty acid recruitment from adipocytes and resistance to high-fat-diet induced obesity in mice, but does not affect glucose or insulin metabolism. FGF21 is also induced in the muscle of mitochondrial myopathy patients and in other RC-deficient mice. These data show that skeletal muscle is an endocrine organ, which signals its energy deficiency through FGF21. Furthermore, RC deficiency in single muscle fibers initiates a global starvation response. These data have important implications for conditions with primary or secondary RC deficiency.

overall_design: Mice overexpressing mutant Twinkle (C10ORF2) protein are the first animal model for Progressive External Ophtalmoplegia (PEO). Using PEO-model and wt-mice,  cerebellum and hippocampus were analyzed for gene expression profile.

first: Anu

last: Wartiovaara

first: Henna

last: Tyynismaa


title: miRNA in BEAS-2B lung epithelial cells  response to PRMT1 in vitro

city: Yangling

first: ZHAI

middle: Wei

last: Qi

state: Shaanxi

address: No.3 Taicheng Road

institute: Northwest A&F University

type: Non-coding RNA profiling by high throughput sequencing

summary: Our previous studies proved that both epithelial inflammation and sub-epithelial remodeling were linked to deregulated PRMT1 expression in asthma patients. This sncRNA-seq data from the BEAS-2B cell line after over-expressed PRMT1 for 24h.

overall_design: miRNA profiles of BEAS-2B cell lines were generated by deep sequencing using BGI-500. Sequencing reads filtering and bioinformatic analysis was also performed by BGI

first: WeiQi

last: Zhai

first: QingZhu

last: Sun


title: Do Copper enhance antibiotic resistance (AR) in resistant bacteria and/or induce AR in sensitive bacteria?

city: Adelaide

first: James

last: Breen

state: SA

address: 108 North Terrace (Ground Floor)

department: John Curtin School of Medical Research

country: Australia

institute: Australian National University

type: Genome variation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Network-based integration of multi-omics data identifies the determinants of miR-491-5p effects

city: Paris

first: Loredana

last: Martignetti

address: 26, rue d'Ulm

institute: Insitut Curie/ INSERM U900 / Mines Paris Tech

type:
Expression profiling by array
Other


title: Identification of RNAs bound in cellulo to miR-491-5p

summary: We purified all RNAs in direct interaction with biotinylated versions of miR-491-5p or a control miRNA in the cytoplasmic compartment (see protocol) of IGROV1-R10 chemoresistant human ovarian cancer cell line. Input and purified RNA were deep-sequenced in order to calculate an enrichment score able to identify which transcripts were bound in cellulo by miR-491-5p

overall_design: transcript enrichment was calculated as follow after normalization: (biotin-miR-491-5p Pull-Down/biotin-cel-miR-65 Pull-Down) / (biotin miR 491-5p Input/biotin-cel-miR-Input). This method of enrichment calculation is aimed to normalize for the decrease in miR-491-5p-targeted RNAs levels in biotin-miR-491-5p transfected samples relative to biotin-cel-miR-65. The Pull-Down experiment was run 3 times independently. The RNA from the 3 experiments was pulled together to constitute the samples submitted to NGS.

first: Christophe

last: Denoyelle

first: Matthieu

last: Meryet-Figuiere

first: Mamy

last: Andrianteranagna


title: Do Copper enhance antibiotic resistance (AR) in resistant bacteria and/or induce AR in sensitive bacteria? [RNA-seq]

summary: The aim of this experiment was to determine if the development of resistance to antibiotics can be driven by the concentration and speciation of Cu.   Experimental setup was designed to investigate two hypotheses for which two strains of Gram- bacteria have been selected:  - Do TE enhance AR in resistant bacteria? Resistant strain: Bioluminescent Pseudomonas aeruginosa PAO1 (Xen41, Tetracycline resistant)  - Do TE induce AR in sensitive bacteria? Sensitive strain: Pseudomonas aeruginosa PAO1 (Wild Type)

overall_design: A 72h exposure hydroponic experiment has been carried out. The growth media was selected to provide optimum free Cu2+ concentration in solution by limiting the complexation of Cu2+ by the constituents in the medium. This media was spiked with three Cu concentrations: Cu=0 (control) Cu=MIC/10 and Cu=MIC (MIC= minimal inhibitory concentration). Samples (bacteria + solution) have been collected after 0, 24, 48 and 72 hours.

first: Emmanuel

last: Doelsch

first: David

last: Ogunniyi

first: Jimmy


title: Single-cell RNAseq of CD45+ cells in murine gastric cancer.

city: Osaka

first: Koji

last: Nagaoka

address: 377-2 Ohno-Higashi, Osaka-Sayama

department: Department of Immunology

country: Japan

institute: Kindai University Faculty of Medicine

summary: YTN2 and YTN16 were chemically induced gastric cancer cell lines. When inoculated subcutaneously, YTN2 spontaneously regresses while YTN16 grows progressively. By single-cell RNA-Seq and flow cytometry, we found more IL-17 producing cells in YTN16 than YTN2. Blockade of IL-17 signaling in YTN16 tumor-bearing mice suppressed tumor growth. To investigate tumor-infiltrating cells after IL-17 blockade, we performed single-cell RNA-Seq of CD45+ cells in YTN16 tumors.

overall_design: Mice were inoculated with 5 ×106 YTN16 cells on day 0. Anti-IL-17 antibody (clone 17F3) was injected on days 0, 3, 6, and 9. On day 10, CD45+ cells were sorted from tumor tissues and processed by 10x controller with Single Cell 3' Reagent Kits v2.

first: Kazuhiro

last: Maejima

first: Masashi

last: Fujita

first: Hidewaki

last: Nakagawa

last: Kakimi


title: Do Copper enhance antibiotic resistance (AR) in resistant bacteria and/or induce AR in sensitive bacteria? [DNA-seq]


title: Ribo-depleted RNA-Seq Libraries From Huntington's Disease Brain

first: Adam

last: Labadorf

address: 72 East Concord Street E301

department: Neurology

institute: Boston University Medical School

summary: Transcriptional dysregulation is well documented in Huntington’s disease (HD) post-mortem brain. We previously identified gene expression profiles from both symptomatic and asymptomatic HD prefrontal cortex which characterize the effects of degeneration in disease versus normal brains. Transcriptional dysregulation in HD brain is well documented by these studies and others, but the extent and causes of this dysregulation remain unknown. Here, we present a large ribo-depleted RNA sequencing (rdRNA-Seq) dataset and novel bioinformatic methodology to further characterize transcriptional dysregulation in HD brain as it relates to disease variables, including CAG repeat size, age of symptom onset, and rate of neurodegeneration.

overall_design: rdRNA-Seq was performed in 98 post-mortem HD prefrontal cortex samples previously characterized for CAG repeat size and extent of striatal and cortical involvement. rdRNA-Seq data, in contrast to poly-A selected RNA-Seq, allows the assessment of transcribed non-coding genomic regions that may correspond to large-scale regulatory mechanisms as well as individual genes. Unlike traditional RNA-Seq analysis, which focuses almost exclusively on annotated regions of the genome, we developed a novel bioinformatic method that divides the genome into bins and identifies genomic loci of arbitrary length associated with variables of interest.

first: Diego

last: Crespo

first: Filisia

last: Agus

first: Joli

last: Bregu

first: Richard

last: Myers


title: Tissue-specific transcription footprinting using RNA PolII DamID (RAPID) in C. elegans

city: Bern

first: Peter

last: Meister

state: Schweiz

address: Baltzerstrasse 4

department: Institute of Cell Biology

institute: University of Bern


title: Expression profiles of murine gastric cancer cell lines

summary: YTN2 and YTN16 cell lines are subclones established from chemically induced gastric cancer (Yamamoto M et al. Cancer Science 2018). When inoculated to normal C57BL/6 mice, YTN2 spontaneously regresses , while YTN16 grows progressively. To compare expression profiles of these cell lines, we examined microarray analysis.

overall_design: RNA was extracted from YTN2 and YTN16 and was hybridized on Agilent microarrays.


title: Unique small RNA modifications in Alzheimer's disease

city: Riverside

first: Junchao

last: Shi

state: CA

address: 900 University Ave

department: Division of Biomedical Sciences, School of Medicine

institute: University of California, Riverside

summary: Human post-mortem brain samples from Alzheimer’s disease (AD) and control individuals were processed for small RNA-sequencing followed by comparative analyses

overall_design: Small RNA sequencing (15-45 nt) were performed for human post-mortem brain samples (prefrontal cortex) from AD patient and control individuals.

first: Patrick

last: Kehoe

first: Tong

last: Zhou

first: Yumei

last: Earley


title: TRAP experiment to determine gene expression changes in absence of AMPK activity in the VMN

city: Lausanne

first: Sylvain

last: Pradervand

address: Genopode

department: CIG

institute: UNI Lausanne

summary: The ventromedial hypothalamus (VMN) is implicated in the regulation of many aspects of energy homeostasis, including the counterregulatory response to hypoglycemia. Neurons of the VMN that are activated by hypoglycemia (glucose inhibited neurons (GI)) have been assumed to play a critical, although untested role in this response. Here, we used that expression of a dominant negative form of AMP-activated protein kinase (AMPK) in Sf1 neurons of the VMN which selectively suppressed GI neurons activity.  We then performed Translating Ribosome Affinity Purification (TRAP Seq) to evaluate the transcriptional changes induced specifically in that cell population.

overall_design: Pools of six animals dissected hypothalamus were used for each sample, and an input control was generated.  Immunoprecipitated material constitutes the outputs samples.  In total, six samples were generated in control conditions (dnw_1_i,  dnw_1_o, dnw_2_i, dnw_2_o, dnw_3_i, dnw_3_o) and six in dominant negative conditions (dn1_i,  dn1_o, dn2_i, dn2_o, dn3_i, dn3_o).

first: Simon

last: Quenneville

first: Gwenaël

last: Labouèbe

first: Davide

last: Basco

first: Salima

last: Metref

first: Benoit

last: Viollet

first: Marc

last: Foretz

first: Bernard

last: Thorens


title: Targeted single cell RNA sequencing of T cells infiltrated in mouse gastric cancer.

first: Koji

last: Nagaoka

summary: YTN2 and YTN16 cells are chemically induced gastric cancer cell lines. YTN2 is spontaneously regressed in C57BL/6 mice in CD8+ T cell-dependent manner, while YTN16 grows progressively.  To investigate tumor infiltrating T cells, we performed single-cell RNA-Seq of CD4+ and CD8+ T cells in YTN2 and YTN16 gastric tumor-bearing mice for 44 T cell-related genes (Supplementary Table 1).

overall_design: Mice were inoculated with 5 ×106 YTN2 or YTN16 on day 0.  Tumors were harvested on day 7 and CD4+ and CD8+ T cells were sorted. Single-cell RNA-Seq was performed using vertical flow array chips (Shirai et al, Scientific Reports, 6, srep36014, 2016).

first: Masataka

last: Shirai

first: Kazuhiro

last: Kakimi


title: Tissue-specific transcription footprinting using RNA PolII DamID (RAPID) in C. elegans [Young adult]

summary: Gene expression is a major determinant of cell fate and physiology, yet it is notoriously difficult to characterize for the widely used model system C. elegans. By using a new method based on in vivo covalent modification of DNA by RNA polymerases, we determine genome-wide transcription patterns in single tissues of embryos or young adult animals. We show that the method is able to identify actively transcribed genes in tissues representing down to 0.2% of the somatic cells in adult animals. Additionally, this method can be fully performed in a single laboratory by using third generation sequencing methods (ONT).

overall_design: DamID experiments with Dam fusions to GFP (control) and RPB-6 (RNA polymerases) in whole animals or specific tissues in young adults C. elegans worms, nanopore amplicon sequencing


title: Tissue-specific transcription footprinting using RNA PolII DamID (RAPID) in C. elegans [Blastomeres]

overall_design: DamID experiments with Dam fusions to GFP (control) and RPB-6 (RNA polymerases) in sorted embryonic blastomeres, nanopore amplicon sequencing


title: Early Pathogenesis of Cystic Fibrosis Gallbladder Disease in a Porcine Model

city: Iowa City

first: Keyan

last: Zarei

state: IA

address: 6330 PBDB

department: Internal Medicine

institute: University of Iowa Carver College of Medicine

summary: Hepatobiliary disease causes significant morbidity in people with cystic fibrosis (CF), yet this problem remains understudied. We previously found that newborn CF pigs have microgallbladders with significant luminal obstruction in the absence of infection and inflammation. In this study, we sought to better understand the early pathogenesis of CF pig gallbladder disease. We hypothesized that loss of CFTR would impair gallbladder epithelium anion/liquid secretion and increase mucin production. By single cell RNA sequencing, we identified a single epithelial cell population that co-expressed CFTR, MUC5AC, and MUC5B. By bulk tissue RNA sequencing, there was no significant difference in the epithelial expression of gel-forming mucins between non-CF and CF pig gallbladders. Also, there were minimal transcriptional changes in CF relative to non-CF.

overall_design: Total RNA sequencing of cystic fibrosis (CF) and non-CF pig gallbladders. Single cell RNA sequencing of non-CF pig gallbladder.

first: Andrew

last: Thurman

first: David

last: Stoltz

first: Mallory

last: Stroik

first: Alejandro

last: Pezzulo


title: Classifying polycyclic aromatic hydrocarbons by carcinogenic potency using in vitro biosignatures

city: Corvallis

first: Susan

middle: C.

last: Tilton

state: OR

address: 1007 ALS Bldg

department: AG Envr & Molec Toxicology

institute: Oregon State University

summary: In this study, we compare genomic signature safter treatment ofprimary human  bronchial epithelial cells (HBEC) cultured in 3D with polycyclic aromatic hydrocarbons (PAHs) and identify genesets predictive of cancer risk.

overall_design: Fully differentiated bronchial epithelial cells (n=4 replicates) were treated with 10 and 100 µg/ml benzo[a]pyrene (BAP), 500 ug/ml benzo[a]anthracene (BAN),  100 ug/ml phenanthrene (PHE), 1500 ug/ml coal tar extract, 250 ug/ml simulated air mixture (AM) or acetone vehicle control for 48 hrs and isolated mRNA were sequenced on Illumina HiSeq 3000.


title: Brain RNA-seq in the LXS RI strains: Saline and ethanol treatment

city: Aurora

first: Richard

last: Radcliffe

state: CO

address: 12850 E Montview Blvd., Room V20-3124

department: Pharmaceutical Sciences

institute: University of Colorado Anschutz Medical Campus

summary:
Purpose: To investigate the effect that acute ethanol tretament (5 g/kg) has on the brain transcriptome and relate that to ethanol-related behaviors.
Methods: Male LXS recombinant inbred mice (40 strains; n=2 or 3 per strain) were treated with saline or ethanol (i.p.; 5 g/kg). Paired-end RNA-seq methods were employed to assess mRNA expression in whole brain 8 hours after the treatment.
Results: The expression of thousands of transcripts was altered by the ethanol treatment. Thousands of expression QTLs (eQTLs) were mapped. A large percentage of the eQTLs were unique to the treatment.

overall_design: Poly-A RNA from whole brain (minus cerebellum, and olfactory bulbs) was profiled using Illumina HiSeq 2000 (2x100).  Tissue was generated from 40 LXS recombinant inbred mouse strains; all mice were males. There were two treatment groups per strain: 1) saline (0.01 ml/g, ip) or 2) ethanol in saline (5 g/kg, ip; 20% v/v) with an an of 3 samples per strain/treatment condition (8 of the strain/treatment groups had an n of 2). Each sample consisted of pooled RNA from 3 individual mice. Mice were euthanized for tissue collection at 8 hours post treatment.


title: Role of the RprY Response Regulator in P. gingivalis Community Development and Virulence

city: Louisville

last: Lamont

state: Kentucky

address: 501 S. Preston St

department: Oral Immunology and Infectious Diseases

institute: University of Louisville

summary: Porphyromonas gingivalis expresses a limited number of two-component systems, including RprY, an orphan response regulator that lacks a cognate sensor kinase. In this study, we examimed the regulon controlled by RprY and found that RprY can control the expression of genes encoding the type IX secretion system (T9SS) machinery and virulence factors secreted through the T9SS, including the gingipain proteases and peptidylarginine deiminase (PPAD).

overall_design: Five biological replicates each of WT and ΔrprY mutant P. gingivalis ATCC 33277 strain

first: Daonan

last: Shen

first: John

middle: D

last: Perpich

first: Kendall

middle: S

last: Stocke

first: Lan

last: Yakoumatos

first: Zackary

last: Fitzsimonds

first: Chengcheng

last: Liu

first: Daniel

middle: P

last: Miller


title: The role of NTS/NTSR1 signal in pancreatic cancer progression

city: Wakayama

first: Shogo

last: Ehata

state: Wakayama

address: Kimiidera 811-1

department: School of Medicine

institute: Wakayama Medical University

summary: Pancreatic cancer is one of the uncurable cancers and 5-year survival rate is still under 10 %. Therefore, it is urgent to identify a new molecular target for cure. In this study, the mouse serial transplantations by pancreatic orthotopic inoculation model were utilized for screening of new targets. The gene expression of highly malignant cancer cell lines, established in our previous study, showed increased expression of neurotensin receptor-1 (NTSR1). Re-analysis of clinical databases revealed that its expression was higher in pancreatic cancer dependent upon its stage. Overexpression of NTSR1 in SUIT-2 and Panc-1 cells accelerated tumorigenic and metastatic ability in vivo. RNA-sequence analysis revealed that MAPK and NF-kB signaling pathway were activated with neurotensin (NTS) stimulation in highly malignant cancer cell lines from Panc-1 cells. Moreover, NTS induced not only MMP-9, but also CTGF and other pro-inflammatory cytokines and chemokines. Administration of SR48692, a selective antagonist for NTSR1, suppressed tumorigenicity in vivo. These data suggested that NTSR1 can be a diagnostic marker and a new molecular target for pancreatic cancer treatment.

overall_design: Target genes for NTS in highly malignant Panc-1- cells were identified.

first: Kei

last: Takahashi

first: Kensuke

last: Miyauchi

first: Yasuyuki

last: Morishita

first: Keiji

last: Miyazawa

first: Kohei

last: Miyazono


title: Alterations of rice (Oryza sativa L.) DNA methylation patterns associated with gene expression in response to Rice black-streaked dwarf virus

city: Hangzhou

first: Linying

last: Li

state: Zhejiang

address: 198 Shiqiao Road

institute: Zhejiang Academy of Agricultural Sciences

type: Methylation profiling by high throughput sequencing

summary: High-throughput single-base resolution bisulfite sequencing (BS-Seq) was carried out to analyze the distribution pattern and characteristics of cytosine methylation in RBSDV-infected rice. Widespread differences were identified at CG and non-CG contexts between the RBSDV-infected and RBSDV-free rice. We identified a large number of differentially methylated regions (DMRs) along the genome of RBSDV-infected rice. And meanwhile, the transcriptome sequencing analysis obtained 1119 differentially expressed genes (DEGs). Correlation analysis of DMRs-related genes (DMGs) and DEGs filtered 71 genes with negative relationship between methylation level at promoter regions and gene expression. Many of them were significantly enriched in the KEGG pathways of biosynthesis of amino acids, plant-pathogen interaction and plant hormone signal transduction.

overall_design: Changes in DNA methylation level and gene expression from RBSDV-infected and virus-free rice using single-base resolution bisulfite sequencing (BS-Seq) and RNA sequencing (RNA-Seq)

first: Gaojie

last: Hong


title: Expression profiling of Sk-Hep1 after PAI-1 silencing (RNAi)

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

summary: Methods: To investigate how tumor cell-derived YAP is changing the paracrine communication network between tumor cells and non-tumorous cells in hepatocarcinogenesis, the expression and secretion of cytokines, growth factors and chemokines were analyzed in transgenic mice with liver-specific and inducible expression of constitutively active YAP (YAPS127A). Transcriptomic and proteomic analyses were performed using primary isolated hepatocytes and blood plasma. In vitro, RNAinterference (RNAi), expression profiling, functional analyses and chromatin immunoprecipitation (ChIP) analyses of YAP and the transcription factor TEA domain transcription factor 4 (TEAD4) were performed using immortalized cell lines. Findings were confirmed in cohorts of HCC patients at the transcript and protein levels.   Results: YAP overexpression induced the expression and secretion of many paracrine-acting factors with potential impact on other tumorous or non-tumorous cells (e.g. plasminogen activator inhibitor-1 (PAI-1), C-X-C motif chemokine ligand 13 (CXCL13), CXCL16). Expression analyses of human HCC patients showed an overexpression of PAI-1 in human HCC tissues and a correlation with poor overall survival as well as early cancer recurrence. PAI-1 statistically correlated with genes typically induced by YAP, such as connective tissue growth factor (CTGF) and cysteine rich angiogenic inducer 61 (CYR61) or YAP-dependent gene signatures (CIN4/25). In vitro, YAP inhibition diminished the expression and secretion of PAI-1 in murine and human liver cancer cell lines. PAI-1 affects the expression of genes involved in proliferation as well as cellular senescence and oncogene-induced senescence was confirmed in YAPS127A transgenic mice. Silencing of TEAD4 as well as treatment with the YAP/TEAD interfering substance Verteporfin reduced PAI-1 expression. ChIP analyses confirmed the binding of YAP and TEAD4 to the gene promoter of PAI-1 (SERPINE1).

overall_design: Three nonsense siRNA samples are compared with 3 samples after RNAi-mediated PAI-1 silencing for 48 hours.

first: Simone

last: Marquard


title: Novel PGK1 determines AR stability dependent on Spk2 and reprograms granular cell glucose metabolism to facilitate ovulation dysfunction

city: Shanghai

first: Xia

address: 910, Hengshan Road, Shanghai

institute: International Peace Maternity and Child Health Hospital

summary: Ovulation disorder is the main characteristic of polycystic ovary syndrome (PCOS), but the concrete molecular mechanism is unclear. Phosphoglycerate kinase 1 (PGK1) plays an important role in the process of glycolytic cycles. Androgen and androgen receptor (AR) are considered as one of the critical factors in the prevalence of hyperandrogenemia and follicular development, and whether PGK1 participates in the metabolic reaction via AR in PCOS remains vague. PGK1 and AR proteins were highly expressed in PCOS luteinized granulosa cells and the PCOS-like mice ovary tissues. PGK1 increased lactate levels and deteriorated PCOS-like mouse metabolic disorder, and importantly, the phenotype of PCOS-like mice was rescued by PTX (paclitaxel) and the PGK1 and AR protein levels also decreased in the ovary. We demonstrated that PGK1 promoted AR translocation into the nuclear, and PGK1 was dependent on the E3 ligase Skp2 to repress the AR ubiquitination to improve the AR stability. In addition, we found that follicular development critical genes MAP2K6, KLF15, LRIG3 and MYOF were regulated by the PGK1-AR axis in the RNA-seq data, and axis also mediated cell proliferation and apoptosis. This study highlights the glycolysis key gene PGK1 to regulate metabolism in granular cell result in etiology of the PCOS. The PGK1-AR axis might provide a new therapy target of PCOS

overall_design: mRNA profiles of nc3+DHT and shPGK1+DHT were generated by deep sequencing, in triplicate

first: Changfa

last: Sun


title: Inducible smooth muscle specific deletion of Yap1/Wwtr1 in mouse

city: Lund

first: Sebastian

last: Albinsson

address: BMC D12

country: Sweden

institute: Lund University

summary: YAP and TAZ are transcriptional co-activators and downstream effectors of the Hippo pathway, which play crucial roles in organ size control and cancer pathogenesis. Genetic deletion of YAP/TAZ has revealed their critical importance for embryonic development of the heart, vasculature and gastrointestinal mesenchyme. The aim of this study was to determine the functional role of YAP/TAZ in adult smooth muscle cell in vivo.

overall_design: Distal colon and urinary bladder from 3 controls (Myh11CreERT2-negative-Yap1/Wwtr1 floxed) and 3 knockout (Myh11CreERT2-positive-Yap1/Wwtr1 floxed) were isolated and snap frozen in liquid nitrogen 7 days after the first (out of 5) tamoxifen injections


title: Integrative omics analyses reveal epigenetic memory in diabetic cells regulating genes associated with kidney dysfunction. [microarray]

city: Pittsburgh

first: Anita

last: Bansal

address: Biomedical Science Tower

department: Immunology

institute: University of Pittsburgh

summary:
We report novel epigenetic mechanisms of epigenetic memory and its role in regulation of transporter genes in diabetic renal proximal tubules. We have generated RNA-seq, ATAC-seq and Infinium EPIC methylation array datasets from human primary proximal tubule epithelial cells from non-diabetic healthy controls and from patients with history of Type II Diabetes.
Analyses of RNA-seq, ATAC-seq and Methylaiton EPIC array data.

overall_design: Bisulphite converted DNA from the 26 samples were hybridised to the Illumina Infinium Infinium 850K Human Methylation Beadchip

first: Rama

last: Natarajan


title: Comparative analysis using different multiplicity of infection ratios from Chlamydia-infected epithelial cells

city: Wurzburg

first: Regan

last: Hayward

address: Josef-Schneider-Straße 2 / D15

institute: Helmholtz Institute for RNA-based Infection Research

summary: Here we examined gene expression from an in-vitro dual-RNA-seq experiment using Chlamydia trachomatis-infected HEp-2 epithelial cells. The experimental design consisted of three different multiplicity of infection ratio's (0.1, 1 and 10) across two different timeframes (1 and 24hrs), in addition to applying two different depletion methods (rRNA and rRNA + PolyA depletion). The aim was to examine and outline which MOI and depletion methods are most suited for bacterial-based infections.

overall_design: Examination of chlamydial infection (Chlamydia trachomatis) on human epithelial cells (HEp2) from two timepoints, three MOI ratios and two depletion methods through RNA-Sequencing

middle: J

first: Mike

last: Humphrys

first: Willa

last: Huston

first: Garry

last: Myers


title: Next Generation Sequencing For Quantitative Analysis Of Hepatic Transcriptomes In Response To Erythrodiol

city: Zaragoza

first: Roubi

middle: Hamid

last: AbuObeid

state: Spain

address: calle de Miguel Servet, 177

department: Biochemistry and Molecular Biology

country: Spain

institute: university of Zaragoza

summary:
Purpose: The goal of this study was to determine erythrodiol effect on hepatic transcriptome by comparing high-throughput data for tested group vs. control group.
Method: Hepatic mRNA profile of two Apoe deficient male mice groups fed over 12 weeks with either western diet or same diet enriched with 10 mg/kg erythrodiol was analysed by Transcriptome sequencing using BGISEQ-500 platform. Sequence reads that passed quality filters were mapped onto reference genome, followed by novel gene prediction, SNP & INDEL calling and gene-splicing detection.
Results: When using optimized Bioinformatics Workflow, mapping ratio for both tested groups was about 74%. There was no significant difference in SNPs between both groups. Splicing patterns _including Skipped Exon (SE), Alternative 5' Splicing Site (A5SS), Alternative 3' Splicing Site (A3SS), Mutually exclusive exons (MXE) and Retained Intron (RI) _allowed the production of a variety of DSGs with a total of 14,920 novel transcripts, 13,439 coding and 1,481 non coding transcripts. Coding genes showed 11,605 previously unknown splicing events for known genes and 1,834 coding transcripts previously unknown. DEGs were 554 in control group vs. 488 in erythrodiol group. Applying a 2-fold change and P value <0.001 led to 68 up regulated genes and 124 down-regulated genes. Gene Ontology Analysis of DEG With the GO annotation and functional enrichment classified DEGs to 3 main classification with  liver-dependent properties. Altered expression of 21 genes was confirmed with RT-qPCR, demonstrating the high degree of sensitivity and accuracy of RNA-seq technique
Conclusions: This study represents the first analysis of hepatic transcriptome in respond to erythrodiol. Result data confirm that RNA-Sequencing is a sensitive and accurate tool that provides a framework for comparative investigations of known and novel DEGs.

overall_design: Testing the influence of 10 mg/kg of erythrodiol on hepatic gene expression in Apoe deficient mice fed Western diet.

last: Abuobeid

first: Luis

middle: V

last: Herrera

first: María

middle: A

last: Navarro

first: Roberto

last: Martínez-Beamonte

first: Joaquín

middle: C

last: Surra

first: Jesus

last: Osada


title: Integrative omics analyses reveal epigenetic memory in diabetic cells regulating genes associated with kidney dysfunction. [sequencing]

summary: We report novel epigenetic mechanisms of epigenetic memory and its role in regulation of transporter genes in diabetic renal proximal tubules. We have generated RNA-seq, ATAC-seq and Infinium EPIC methylation array datasets from human primary proximal tubule epithelial cells from non-diabetic healthy controls and from patients with history of Type II Diabetes.

overall_design: Analyses of RNA-seq, ATAC-seq and Methylation EPIC array data.


title: Integrative omics analyses reveal epigenetic memory in diabetic cells regulating genes associated with kidney dysfunction.

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

overall_design: Refer to individual Series


title: RNA-sequencing of neutrophils derived from OS-RC-2-bearing mice

first: Shogo

last: Ehata

summary: Advanced clear cell renal cell carcinoma (ccRCC) frequently causes systemic inflammation. Here, we identified the functional role and regulatory mechanism of inflammation driven by advanced ccRCC cells. The inflammatory nature of advanced ccRCC was recapitulated in a preclinical model of ccRCC. Amplification of cancer cell-intrinsic inflammation during ccRCC progression triggered neutrophil-dependent lung metastasis. Massive expression of inflammation-related genes was transcriptionally activated by epigenetic remodelling through mechanisms such as DNA demethylation and super-enhancer formation. Bromodomain and extra-terminal motif inhibitor (BETi) synchronously suppressed C–X–C-type chemokines in ccRCC cells and decreased neutrophil-dependent lung metastasis. Overall, our findings shed insight into the nature of inflammatory ccRCC, which triggers metastatic cascades, and suggest a potential therapeutic strategy.

overall_design: RNA-seq analysis was performed with neutrophils in periphery of OS-RC-2 and its derivative-bearing BALB/c nu/nu mice

first: Jun

last: Nishida

first: Yusaku

last: Momoi

first: Yusuke

last: Tamura

first: Kei

last: Takahashi

first: Daizo

last: Koinuma

first: Kohei

last: Miyazono


title: H3K27ac and BRD4-binding regions in a clear cell renal cell carcinoma cell line, OS-RC-2

overall_design: H3K27ac and BRD4 ChIP-seq analysis was performed with clear cell renal cell carcinoma cell lines, OS-RC-2 and its derivatives.


title: Next-generation sequencing of cholinergic interneurons in the nucleus accumbens of cocaine-addicted and non-addicted mice

city: Daegu

first: JA WOOK

last: KOO

address: 61 Cheomdan-ro, Dong-gu

country: South Korea

institute: Korea Brain Research Institute

summary: Cholinergic interneurons (ChINs) in the nucleus accumbens (NAc) play critical roles in processing information related to reward. However, the contribution of ChINs to development of addiction-like behaviors and the underlying mechanisms remain unknown. Here, using mouse models, we assessed drug seeking behaviors under a prolonged progressive ratio schedule of cocaine self-administration to reliably separate mice susceptible or resilient to express addiction-like behaviors based on motivation to earn cocaine. Cell type-specific RNA sequencing in NAc ChINs and the differential expression analysis identified 2,909 differentially expressed genes from susceptible versus resilient mice, which comprise 1,685 upregulated genes and 1,224 downregulated genes. Our cell type-specific transcriptome data will serve as a valuable and widely applicable resource for investigating molecular mechanism of cocaine addiction and in turn facilitate development of novel therapeutic targets to treat addictive disorders.

overall_design: RNA profiles of cholinergic interneurons in the nucleus accumbens of mice which are susceptible or resilient to cocaine addiction.

first: Ja

last: Koo

first: Eric

last: Nestler

first: Jong

middle: K

last: Kim

first: Joo

last: Lee

first: Efrain

last: Ribeiro

first: Joung

first: Jeongseop

first: Yun

last: Jeong

first: Hope

last: Kronman


title: Global transcriptomic changes following elevated carbon dioxide (5%) in the wild-type (WT) and mutant (M2; RNAi-knockdown line of carbonic anhydrase (CA2)) Nannochloropsis oceanica IMET1: Illumina sequencing

city: Haikou

first: Li

last: Wei

state: Hainan

address: No. 99 Longkun South Road, Haikou

department: Colleage of life science

institute: Hainan normal university

summary: In Nannochloropsis oceanica IMET1, transcript knockdown of a cytosolic carbonic anhydrase (CA2; g2018) specifically inhibited by HC resulted in ~45%, ~30% and ~40% elevation of photosynthetic oxygen evolution rate, growth rate and biomass accumulation rate under high CO2 (5% ), respectively. This CA2-knockdown mutant is demonated as M2. To probe mechanistic links underlying the mutant (M2; RNAi-knockdown line of carbonic anhydrase (CA2)) phenotypes, temporal transcriptomic profiles are compared between RNAi-knockdown line of carbonic anhydrase (CA2) and WT, at 12 h and 24h under high CO2 (5%).

overall_design:
Nannochloropsis oceanica IMET1 wild-type and M2 (RNAi-knockdown line of carbonic anhydrase (CA2)) cells were grown in liquid cultures under continuous light (approximately 80±5 µmol photons m-2 s-1) at 25℃ and aerated by bubbling with a mixture of 5% CO2 in air. Mid-logarithmic phase algal cells were collected and washed three times with axenic seawater. Equal numbers of cells were re-inoculated in fresh medium and cultured under 5% CO2. Cell aliquots of WT and M2 were collected for RNA isolation after being transferred to the fresh medium conditions for 12h and 24h. Three biological replicates were randomly selected to prepare mRNA-Seq library. In total, 12 samples collected at two time points (12h and 24h) were used for mRNA-Seq library preparation and then submitted to Illumina HiSeq 2000 for sequencing.
Please note that [1] each FPKM.txt processed data file contains 3 data columns (one for each replicate) and is linked to the corresponding 'replicate1' sample records, [2] the M2_WT_*FPKM.txt files contain the merged data of each sample group for the indicated time point and are linked as Series supplementary files.

last: WEI

first: Jian

last: XU


title: Retrieval of inflammation-compromised periodontal ligament stem cells from dysfunction by exosomes derived from P2X7 receptor gene-modified cells

city: Xi'an

first: Xinyue

last: Xu

state: Shannxi

address: Changle west road

institute: The Fourth Military Medical University

summary: Exosomes derived from P2X7 gene modified stem cells could enhance the osteogenic differentiation of periodontal ligament stem cells under inflammatory cultural conditions. In order to identify differentially expressed miRNAs between Exs-Ad-P2X7 and Exs-Ad- control, total RNA from exosomes were extracted by TRIzol™ Reagent (Invitrogen) according to the instructions. Then, miRNA profile of Exs-Ad-P2X7 and Exs-Ad-control form 3 different individuals were sequenced by Agilent miRNA Microarray System and further confirmed by real-time PCR.

overall_design: Three independent experiments were performed using different donors derived PDLSCs for each experiment. Adenoviral vectors transfected PDLSCs were cultured in serum free osteogenic inductive culture medium for 24 h for exosomes isolation. Exosomes were extracted by Total Exosome Isolation Kit from supernatants. The total RNA from exosomes were extracted by TRIzol™ Reagent according to the instructions.


title: Reliable tumor detection using cerebrospinal fluid cell-free DNA methylomes in pediatric medulloblastoma

city: Houston

first: Jia

last: Li

state: Texas

address: 2121 W HOLCOMBE BLVD

department: CEDP

institute: Guangzhou Medical University

summary: Medulloblastoma (MB) is an embryonal tumor of the cerebellum and a highly malignant childhood brain tumor. Cell-free circulating tumor DNA (ctDNA) from the cerebrospinal fluid (CSF) of patients with brain tumors faithfully represent genomic alterations of brain tumors. Distinct epigenetic signatures among subgroups of MB allow us to detect epigenetic alterations in CSF to aid classify and guide therapy of MB tumors. Here, we evaluate DNA methylation and hydroxymethylation of ctDNA derived from small amount of CSF (200 µL) and matched tumor DNA from 3 MB patients. We find highly concordance of DNA methylation and hydroxymethylation between CSF ctDNA and tumor DNA, especially in CpG islands. Importantly, CSF ctDNA can mostly recapitulate the dynamic changes of DNA methylation and hydroxymehtylation in tumor species compared to healthy cerebellums. Those MB tumor signature CpGs’ DNA methylation status are recovered in CSF ctDNA can clearly distinguish MB subgroups by utilizing public large cohort data. We further identified potential diagnostic and prognostic DNA methylation markers in CSF ctDNA. Our results show that CSF ctNDA methylation and hydroxymethylation can be a minimal invasive method to assess epigenetic alterations of MB, which is complementary to current diagnoses of MB tumors.

overall_design: We collected matched CSF and tumors samples from three pediatric MB patients; four Non-MB CSF and two normal cerebellum tissues are as control. We performed WGBS and CMS-IP for these samples

first: Deqiang

last: Sun

last: Huang

first: Xiaonan


title: Fecal microbial infusion from lean donors increases insulin sensitivity in subjects with metabolic syndrome

city: Groningen

first: vincent

last: bloks

department: Pediatrics

country: Netherlands

institute: UMCG

summary:
Alterations in intestinal microbiota and intestinal short chain fatty acids profiles have been associated with the pathophysiology of obesity and insulin resistance. Whether intestinal microbiota dysbiosis is a causative factor in humans remains to be clarified
We examined the effect of fecal microbial infusion from lean donors on the intestinal microbiota composition, glucose metabolism and small intestinal gene expression. Male subjects with metabolic syndrome underwent bowel lavage and were randomised to allogenic (from male lean donors with BMI<23 kg/m2, n=9) or autologous (reinfusion of own feces, n=9) fecal microbial transplant. Insulin sensitivity and fecal short chain fatty acid harvest were measured at baseline and 6 weeks after infusion. Intestinal microbiota composition was determined in fecal samples and jejunal mucosal biopsies were also analyzed for the host transcriptional response.
Insulin sensitivity significantly improved six weeks after allogenic fecal microbial infusion (median Rd: from 26.2 to 45.3 μmol/kg.min, p<0.05). Allogenic fecal microbial infusion increased the overall amount of intestinal butyrate producing microbiota and enhanced fecal harvest of butyrate. Moreover, the transcriptome analysis of jejunal mucosal samples revealed an increased expression of genes involved in a G-protein receptor signalling cascade and subsequently in glucose homeostasis.
Lean donor microbial infusion improves insulin sensitivity and levels of butyrate-producing and other intestinal microbiota in subjects with the metabolic syndrome. We propose a model wherein these bacteria provide an attractive therapeutic target for insulin resistance in humans. (Netherlands Trial Register  NTR1776).

overall_design: 7 autologous and 5 allogenic-patients after 0 and 6 wks treatment, where arrayed in duplex (technical replication), Quantile Normalized and corrected for intra-experimental variation (Combat) generating robust gene-expression profiles (pubmed: 20181233).

first: A

last: Vrieze

first: E

last: van Nood

first: F

last: Holleman

first: J

last: Salojarvi

first: R

last: Kootte

last: Bartelsman

first: G

middle: M

last: Dallinga-Thie

first: M

middle: T

last: Ackermans

last: Serlie

last: Oozeer

last: Derrien

last: Druesne

middle: E

last: van Hylckama Vlieg

first: V

last: Bloks

last: Groen

first: H

middle: G

last: Heilig

last: Zoetendal

last: Stroes

first: W

last: de Vos

middle: B

last: Hoekstra

last: Nieuwdorp


title: RNAsequencing of Ligilactobacillus agilis grown on Inulin and Lactose

status: Public on Oct 27 2020

city: Davis

first: saumya

last: wickramasibnghe

address: One Shields AVE

department: Food Science and Technology

institute: University of California Davis

summary: RNAsequening revolutionized the bacterial gene expression analysis. The objective of this study was to identify the genes involved in metabolism of Inulin in Ligilactobacillus agilis. We have obtained a list of genes upregulated in Ligilactobacillus agilis when it is grown in 1% Inulin

overall_design: Illumina RNAseq was conducted on RNA extracted from five samples of Ligilactobacillus agilis (n=5) grown in 1% Insulin and five samples of Ligilactobacillus agilis grown in 1% glucose. Samples were takin at the mid log phase of the growth curve

first: David

last: Mills

first: Yuanting

last: Zhu

first: Saumya

last: Wickramasinghe


title: Alterations in liver and epididymal white adipose tissue (eWAT) gene expression in mice with a global ablation of the NcoRω splice isoform of the corepressor Ncor1

first: Michael

middle: L

last: Goodson

address: One Shields Ave

summary: A knockin mouse line created that contains a point mutation that elminates the requisite GT in the 5' donor site of each of the NCoRω splice variants, thus preventing splicing at that site and forcing splicing of the reciprocal NcoRδ splice variant.

overall_design: Adult WT & NCoR-omega KO male C57BL/6N mice fed HF (60% Kcal fat) or LF (10%) diet for 10 weeks

first: Martin

last: Privalsky


title: Epigenetic changes in Langerhans islets preceding the onset of diabetes

city: Nuthetal

first: Heike

last: Vogel

state: BRB

address: Arthur-Scheunert-Allee 114-116

department: Department of Experimental Diabetology

institute: German Institute of Human Nutrition Potsdam-Rehbruecke

summary: Diabetes-resistant and diabetes-prone female New Zealand Obese mice were classified based on liver fat content and early blood glucose concentrations at 10 weeks of age before the onset of T2D. By using transcriptome and DNA methylome analysis of Langerhans islets, we identified early epigenetic alteration in mice and humans which could serve as putative epigenetic biomarkers

overall_design: For Bisulfite seq, we used 5 samples per group for diabtes prone (DP) and resistant (DR). RNA-seq was performed with 4 DR and 5 DR. In our study design, DR animals are healthy animals and are considered as control group

first: Meriem

last: Ouni

first: Sophie

last: Saussenthaler

first: Markus

last: Jähnert

first: Lisa

last: Zellner

first: Pascal

last: Gottmann

first: Annette

last: Schürmann


title: The molecular response of two Brassica napus cultivars to submergence

city: Bayreuth

first: Angelika

last: Mustroph

address: Universitaetsstr. 30, NWI

department: Plant Physiology

institute: University Bayreuth

summary: Heavy rainfall causes flooding of natural ecosystems as well as farmland, negatively affecting crop performance and yield. While the response of the wild model organism Arabidopsis thaliana to such stress conditions is well understood, we hardly know anything about the response of its relative, the important oil crop plant Brassica napus. Here, we analyzed the molecular response of leaves of rapeseed seedlings to full submergence under illumination. RNAseq experiments revealed a strong carbon starvation response under submergence, but no indication for a low-oxygen response. We used two cultivars in this study, one Asian flooding-tolerant cultivar and one European hybrid cultivar, but those genotypes did not show strong differences in their responses to submergence.

overall_design: Two Brassica napus cultivars (Avatar, Zhongshuang 9), one timepoint (24 h), two treatments (aeration, submergence), three replicates.


title: Newly established gastrointestinal cancer cell lines retain the genomic and immunophenotypic landscape of their parental cancers

city: Bethesda

first: Daniela

last: Hirsch

address: 50 South Drive

department: National Cancer Institute

institute: National Institutes of Health

type: Genome variation profiling by genome tiling array

summary: To directly compare genomic alterations between patient tumors and derived cell lines, both parental tumors and cell lines were characterized by array-based comparative genomic hybridization.

overall_design: n = 6 patient tumors (includes two biological replicates) and n = 4 cell lines

first: Timo

last: Gaiser


title: RNA-sequencing of a clear cell renal cell carcinoma cell line, OS-RC-2

city: Wakayama

first: Shogo

last: Ehata

address: Kimiidera 811-1

institute: Wakayama Medical University

overall_design: RNA-seq analysis was performed with clear cell renal cell carcinoma cell lines, OS-RC-2 and its derivatives.

first: Jun

last: Nishida

first: Yusaku

last: Momoi

first: Yusuke

last: Tamura

first: Kei

last: Takahashi

first: Daizo

last: Koinuma

first: Kohei

last: Miyazono


title: LncRNA expression profiles in areca nut chewing induced Tongue Squamous Cell Carcinoma (TSCC) and matched paracancerous tissues

city: Changsha

first: Zhaojian

last: Gong

state: Hunan Province

address: 139 Renmin Road

department: Oral and Maxillofacial Surgery

institute: The Second Xiangya Hospital of Central South University

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

summary: Chewing betel nut is an important risk factor for the carcinogenesis of tongue squamous cell carcinoma (TSCC), but the mechanism is still unknown.To screen the lncRNAs associated with betel nut chewing-induced TSCC and identify potential biomarkers for the TSCC, we collected 5 pairs of TSCC and paracancerous tissues and monitored the resultant lncRNA and mRNA expression profiles using an lncRNA microarray. All 5 patients have a history of areca nut chewing.

overall_design: 5 pairs of TSCC and paracancerous tissues were analyzed using Agilent Human lncRNA gene chip.

first: Wei

last: Xiong

first: Zhaoyang

last: Zeng

first: Panchun

last: Li