title: Ectopic Tcf1 expression reprograms exhausted CD8+ T cells to acquire stem cell-like features [RNA-seq]

status: Public on Apr 30 2020

city: Nutley

first: Haihui

last: Xue

state: NJ

address: 123 Metro Boulevard, Bldg. 123, Rm. 5527

department: Center for Discovery and Innovation

country: USA

institute: Hackensack University Medial Center

type: Expression profiling by high throughput sequencing

summary: The goal of this study is to determine the capacity of Tcf1 to reprogram exhausted CD8+ T cells for function restoration. Tex cells elicited by chronic infection contain a CXCR5+Tim3– subset that has stem cell-like self-renewing capacity and expresses an elevated level of Tcf1 (termed Tex-stem), and Tex-stem cells depend on Tcf1 for generation and persistence. We show that ectopic Tcf1 expression profoundly affected the transcriptome of Tex cells.

overall_design: Genome-wide expression profiles of stem cell-like exhauseted CD8+ T cells with or without ectopic Tcf1 expression.

first: Shan

last: Qiang

first: Hu

last: Sheng'en

first: Zang

last: Chongzhi

first: Xue

last: Hai-Hui


title: Gene expression analysis in the zebrafish fractured scale

status: Public on Apr 29 2020

city: Kanazawa

first: Isao

last: Kobayashi

state: Ishikawa

address: Kakumamachi

country: Japan

institute: Kanazawa University

summary: Bone is a connective tissue which undergoes continuous remodeling, including bone resorption and formation by osteoclasts (OCs) and osteoblasts (OBs), respectively. Recently, extracellular vesicles (EVs) are increasingly appreciated as a regulator of intercellular communication between OCs and OBs. The zebrafish scale is a thin membranous bone embedded in the skin and consists of OBs, OCs, and bone matrix, providing an elegant model to visualize OC-OB communication. Here, we developed a double-transgenic zebrafish line, trap:GFP; osterix:mCherry, which expresses GFP and mCherry under the control of the OC-specific trap (tartrate-resistant acid phosphatase) and OB-specific osterix enhancer, respectively. Utilizing this double-transgenic line, in combination with Hoechst 33342 (Hoe) staining, we isolated four distinct fractions from the scale at 1 day post-fracture by flow cytometry, GFP(–) mCh(+) Hoe(high) (OB fraction), GFP(low) mCh(+) Hoe(high) (OC precursor (pOC) fraction), GFP(high) Hoe(high) (mature OC (mOC) fraction), and mCh(+) Hoe(–) (OB-derived extracellular vesicle (EV) fraction). In this study, we have performed RNA-seq analysis using these four fractions to examine the gene expression profile of each  fraction.

overall_design: mRNA profiles of isolated OBs, pOCs,  mOCs, and OB-derived EVs in the zebrafish fractured scales were generated by Quartz-seq using Illumina NextSeq500.

first: Jingjing


title: Ectopic Tcf1 expression reprograms exhausted CD8+ T cells to acquire stem cell-like features [CUT&RUN]

summary: The goal of this study is to determine the capacity of Tcf1 to reprogram exhausted CD8+ T cells for function restoration. Tex cells elicited by chronic infection contain a CXCR5+Tim3– subset that has stem cell-like self-renewing capacity and expresses an elevated level of Tcf1 (termed Tex-stem), and Tex-stem cells depend on Tcf1 for generation and persistence. We show that ectopic Tcf1 expression profoundly affected the transcriptome and chromatin accessibility of Tex cells.

overall_design: Genome-wide mapping of Tcf1 occupancy in f stem cell-like exhauseted CD8+ T cells with ectopic Tcf1 expression.


title: The effects of TBBPA/TBBPS/TCBPA on human hepatic development

city: Beijing

first: Shaojun

last: Liang

address: 18 Shuangqing Road

country: China

institute: Chinese academy of sciences

summary: We evaluated the hepatic developmental toxicity of TBBPA/TBBPS/TCBPA with a human embryonic stem cells (hESC) system. We found that TBBPA/TBBPS/TCBPA might adversely affect human hepatocyte-like cells specification from hESCs via mainly impairing definitive endoderm specifications, suggesting the early stages of embryonic development are susceptible to the three compounds.

overall_design: We studied the toxicity behaviors of TBBPA, TBBPS and TCBPA in definitive endoderm and hepatoblast specification from hESCs by analyzing mRNA profiles with RNA-seq, in duplicate, respectively.

first: Francesco

last: Faiola

first: Shengxian

first: Yuanping

last: Lu

first: Nuoya

last: Yin

first: Hui

last: Zhou


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type, Mst1/2 dKO and Mst1/2; Yap tKO Initial segments of Epididymis Transcriptomes

city: Hong Kong

first: Yin

last: Xia

address: LKIBSB

institute: The Chinese University of Hong Kong

summary: mRNA profiles of 4 week-old contol and Mst1/2 dKO and Mst1/2; Yap tKO Initial segments of Epididymis were generated by deep sequencing, in triplicate, using Illumina HiSeq platform.

first: Chenling

last: Meng


title: Ectopic Tcf1 expression reprograms exhausted CD8+ T cells to acquire stem cell-like features [ATAC-seq]

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The goal of this study is to determine the capacity of Tcf1 to reprogram exhausted CD8+ T cells for function restoration. Tex cells elicited by chronic infection contain a CXCR5+Tim3– subset that has stem cell-like self-renewing capacity and expresses an elevated level of Tcf1 (termed Tex-stem), and Tex-stem cells depend on Tcf1 for generation and persistence. We show that ectopic Tcf1 expression profoundly affected the chromatin accessibility of Tex cells.

overall_design: Genome-wide chromatin accessibility profiles of stem cell-like exhauseted CD8+ T cells with or without ectopic Tcf1 expression.


title: A deep intronic splice mutation of STAT3 underlies hyper IgE syndrome by negative dominance

city: Doha

first: Tanwir

last: Habib

address: Al Luqta Street

country: Qatar

institute: Weill Cornell Medicine Qatar

summary: Heterozygous in-frame mutations in coding regions of human STAT3 underlie the only known autosomal dominant form of hy- per IgE syndrome (AD HIES). About 5% of familial cases remain unexplained. The mutant proteins are loss-of-function and dominant-negative when tested following overproduction in re- cipient cells. However, the production of mutant proteins has not been detected and quantified in the cells of heterozygous pa- tients. We report a deep intronic heterozygous STAT3 mutation, c.1282-89C>T, in 7 relatives with AD HIES. This mutation creates a new exon in the STAT3 complementary DNA, which, when over- expressed, generates a mutant STAT3 protein (D427ins17) that is loss-of-function and dominant-negative in terms of tyrosine phos- phorylation, DNA binding, and transcriptional activity. In immor- talized B cells from these patients, the D427ins17 protein was 2 kDa larger and 4-fold less abundant than wild-type STAT3, on mass spectrometry. The patients’ primary B and T lymphocytes responded poorly to STAT3-dependent cytokines. These findings are reminiscent of the impaired responses of leukocytes from other patients with AD HIES due to typical STAT3 coding muta- tions, providing further evidence for the dominance of the mutant intronic allele. These findings highlight the importance of sequenc- ing STAT3 introns in patients with HIES without candidate variants in coding regions and essential splice sites. They also show that AD HIES-causing STAT3 mutant alleles can be dominant-negative even if the encoded protein is produced in significantly smaller amounts than wild-type STAT3.

overall_design: Examination of gene expression in EBV-B cells from healthy subjects and AD HIES patients stimulated with IL-21, IL-6, IL-23, IL-10, and IFNa

first: Joëlle

last: Khourieh

first: Geetha

last: Rao

first: Danielle

middle: T

last: Avery

first: Alain

last: Lefèvre-Utile

first: Marie-Olivia

last: Chandesris

first: Aziz

last: Belkadi

first: Maya

last: Chrabieh

first: Hanan

last: Alwaseem

first: Virginie

last: Grandin

first: Françoise

last: Sarrot-Reynauld

first: Agathe

last: Sénéchal

first: Olivier

last: Lortholary

first: Xiao-Fei

last: Kong

first: Stéphanie

last: Boisson-Dupuis

first: Capucine

last: Picard

first: Anne

last: Puel

first: Vivien

last: Béziat

first: Qian

last: Zhang

first: Laurent

last: Abel

first: Henrik

last: Molina

first: Nico

last: Marr

first: Stuart

middle: G

last: Tangye

first: Jean-Laurent

last: Casanova

first: Bertrand

last: Boisson


title: Generation of an enteric smooth muscle cell line from pig ileum

city: Blacksburg

first: Honglin

last: Jiang

state: VA

address: 3130 Litton Reaves Hall

department: Animal and Poultry Sciences

institute: Virginia Polytechnic Institute and State University

summary: The goal of this study was to characterize a single-cell clone derived from pig ileum epithelium. Analyses including RNA-seq demonstrated that this clone was derived from an enteric smooth muscle cell. This clone is named PIC7 in the manuscript.

overall_design: Duplicate RNA-seq libraries were prepared and sequenced from the clone originally named PSI.

first: Wen

last: Yao


title: P53 dynamics vary between tissues and are linked with radiation sensitivity

city: Pittsburgh

first: Jacob

last: Stewart-Ornstein

state: PA

address: UPMC Hillman Cancer Center, 5117 Centre Avenue

department: computational and systems biology

institute: University of Pittsburgh, School of Medicine

summary: We used RNAseq to explore the gene expression changes induced by ionizing radiation across multiple tissues

overall_design: Mouse were treated with ionizing radiation (10gy) and sacrificed at different timepoints and tissues extracted and processed for RNA


title: Consequences of decreased TNAP activity during osteogenic differentiation of periodontal ligament cells – a new model for dental defects in hypophosphatasia

city: Würzburg

first: Richa

last: Bharti

state: Bavaria

address: Josef-Schneider-Straße 2 / Bau D15

department: IMIB,Core Unit Systemmedizin

country: Germany

institute: University of Wuerzburg

summary: The effects of TNAP inhibition with levamisole during osteogenic differentiation were analyzed in primary human periodontal ligament cells since patients suffering from hypophosphatasia often display dental symptoms.

overall_design: Analysis of the influence of TNAP inhibition via levamisole in dental stem cells isolated from the periodontal ligament during osteogenic differentiation

first: Stephanie

last: Graser

first: Franz

last: Jakob

first: Hannah

last: Melms


title: Ectopic Tcf1 expression reprograms exhausted CD8+ T cells to acquire stem cell-like features

first: Haihui

last: Xue

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

overall_design: Refer to individual Series


title: Expression profile of muscles from GNE M743T/M743T knock in mice and wild-type

city: Jerusalem

first: Hadar

last: Benyamini

address: Ein Karem

country: Israel

institute: The Hebrew University

summary: Background. Mutations in GNE cause a recessive, adult onset myopathy characterized by slowly progressive distal and proximal muscle weakness. Knock-in mice carrying the most frequent mutation in GNE myopathy patients, GneM743T/M743T, usually die few days after birth from severe renal failure, with no muscle phenotype.  However, a spontaneous  sub-colony remains healthy throughout a normal lifespan without any kidney or muscle pathology.   Objective. We attempted to decipher the molecular mechanisms behind these phenotypic differences and to determine the mechanisms preventing the kidney and muscles from disease.   Methods. We analyzed the transcriptome and proteome of kidneys and muscles of sick and healthy GneM743T/M743T mice.  Results. The sick GneM743T/M743T kidney was characterized by up-regulation of extra-cellular matrix degradation related processes and by down-regulation of oxidative phosphorylation and respiratory electron chain pathway, that was also observed in the asymptomatic muscles. Surprisingly, the healthy kidneys of the GneM743T/M743T mice were characterized by up-regulation of hallmark muscle genes.  In addition he asymptomatic muscles of the sick GneM743T/M743T mice showed upregulation of transcription and translation processes  Conclusions. Overexpression of muscle physiology genes in healthy GneM743T/M743T mice seems to define the protecting mechanism in these mice. Furthermore, the strong involvement of muscle related genes in kidney may bridge the apparent phenotypic gap between GNE myopathy and the knock-in GneM743T/M743T mouse model and provide new directions in the study of GNE function in health and disease.

overall_design: Four male mice up to 3 months, of each state (sick, healthy-mutated or wild-type)

first: Stella

middle: M

last: Rosenbaum


title: Neurons that regulate mouse torpor

city: Boston

first: Sinisa

last: Hrvatin

state: MA

address: 220 Longwood ave, GB405

department: Neurobiology

institute: Harvard Medical School

summary: The advent of endothermy more than a hundred million years ago is thought to have been a defining feature of mammalian and avian evolution, achieved through continuous fine-tuned homeostatic regulation of core body temperature and metabolism. However, when challenged by food deprivation or harsh environmental conditions, many mammalian species initiate adaptive energy-conserving survival strategies, including torpor and hibernation, during which their core body temperature decreases far below its homeostatic setpoint. How homeothermic mammals initiate and regulate these extraordinary hypothermic states remains largely unknown. Here, we discover that entry into mouse torpor, a fasting-induced state with greatly decreased metabolic rate and body temperature as low as 20°C, is regulated by a population of neurons in the preoptic area of the hypothalamus. We show that re-stimulation of neurons activated during a previous bout of torpor is sufficient to initiate torpor, even in animals that are not calorically restricted. We localize these torpor-regulating neurons to the anteroventral medial and lateral preoptic area and molecularly identify a population of glutamatergic Adcyap1+ neurons whose activity accurately determines when calorically-restricted animals naturally initiate and exit torpor, and whose inhibition disrupts the natural process of torpor entry, maintenance and arousal. Taken together, we discover a specific hypothalamic neuronal subpopulation in the mouse brain that serves as a core regulator of torpor. This work forms the basis for future explorations of mechanisms and circuitry regulating extreme hypothermic and hypometabolic states, enabling genetic access to monitor, initiate, manipulate and study these ancient adaptations of homeotherm biology.

overall_design: The anteroventral medial and lateral preoptic area from five animals was processed for single nucleus RNA-sequence.

first: Senmiao

last: Sun

first: Michael

middle: E

last: Greenberg


title: Expression profile of muscle and kidney tissues from GNE M743T/M743T knock in mice and wild-type


title: 4-Methylimidazole (4-MEI) exposure in liver and lung of B6C3F1 mice exposed to four concentrations for 2, 5 and 28 days

city: Research Triangle Park

middle: B.

last: Black

state: North Carolina

address: 100 Capitola Dr., Suite 106

institute: Scitovation, LLC.

summary: 4-Methylimidazole (4-MEI) increased incidence of lung tumors in 2-year studies in both female and male mice. We evaluated changes in gene expression in B6C3F1 mice exposed to 4-MeI for 2, 5 or 28 days using RNA-seq methods and evaluated possible molecular initiating events (MIEs) and modes-of-action (MoAs) for 4-MeI in both a target tissue for tumors (lungs) and a non-target tissue (liver). Although the magnitude of changes in differential expression was small for any one gene, there were relatively large numbers of differentially expressed genes (DEGs) at 2-days in both tissues followed by a decreasing number of DEGs at the two longer exposures. Pathway enrichment of DEGs was determined either by using specific selection criteria based on absolute value of fold-change expression (|FC|) and a false discovery rate (FDR) or with IDEA (Information Dependent Enrichment Analysis). IDEA ranks all genes in order of fold induction, both for upregulated and downregulated genes, and iteratively calculates enrichment for gene lists of different sizes. Enrichment determines whether the DEGs fall into specific biological pathways as defined by standard gene/protein ontologies, e.g. Reactome or MetaCore (GeneGO). While there were significant differences in gene expression in lungs for male and female at 2-days. There also several consistent changes for the sexes, including coordinated regulation of circadian clock genes at 2-days, downregulation of mitochondrial functions at later times, and various effects on G-protein coupled receptor (GPCR) signaling pathways. In liver, in both genders, there was upregulation of mitotic pathways at early times and downregulation of various metabolic pathways and CYPs at later times. Based on (1) structural similarities with histamine, (2) short-term CNS and testicular toxicity, (3) changes in arachidonic metabolism pathways, (4) rapid accommodation to tissue response over several days and (5) alterations in GPCR pathways, we hypothesize that the MIE for 4-MeI likely involves changes in histaminergic GPCR function. Some suggestions are provided for specific short-term studies to follow up on this hypothesis.

overall_design: Time and dose response in liver and lung of both male and female mice. Exposures at 2 days were by gavage, while those at 5 and 28 days used 4-MEI in feed.

middle: B

first: Salil

middle: N

last: Pendse


title: Transcriptomic profiles of gene expression of brain tissue in duck in response to Tembusu virus infection

city: Guangzhou

first: Junqin

last: Zhang

state: Guangdong

address: Baishigang

institute: Institute of Animal Health, Guangdong Academy of Agricultural Sciences

summary: We used high-throughput RNA-sequencing technology to reveal the transcriptome profile of DTMUV-infected duck brain tissue.

overall_design: Twenty-four 10-day-old SPF ducks (Harbin Veterinary Research Institute, Harbin, China) were randomly divided into two groups. The ducks were raised in separated negative-pressure isolators. The challenge group was intramuscularly inoculated with 0.5 ml of 105.5 TCID50/ ml TMUV JM strain. The control group was inoculated with an equal amount of sterile PBS. At 12, 24, and 48 hours post infection (hpi), four ducked were randomly selected from each group for euthanasia. The brain tissues were collected and pooled for NGS sequencing.

first: Minhua

first: Linlin

last: Li


title: RNA-seq analysis of human KMT2A rearranged Molm14 AML cell line treated with DOT1L and/or EZH2 inhibitor

city: Philadelphia

first: Kathrin

last: Bernt

address: 3501 Civic Center Boulevard,

institute: Children's Hospital of philadelphia

summary: The histone methyltransferases DOT1L (H3K79me1,2,3 KMT, "activating" chromatin mark) and EZH2 (H3K27me1,2,3 KMT, "silencing" mark) have both been shown to be required for growth and survival of KMT2A rearranged AML cells. Both KMTs have been shown to modulate expression of HOXA cluster genes, albeit for EZH2 this has not been shown in the context of KMT2A rearranged AML, but in other subtypes of AML. We asked what transcriptional effects dual inhibition of DOT1L and EZH2 has in KMT2A rearranged AML.

overall_design: Molm14  AML cells were exposed to the DOT1L inhibitor EPZ5676 at  0.16 uM, and the EZH2 inhibitor GSK126 at 0.3 uM for 7 days. Fresh media and compound were supplied on day 4. RNA was isolated using RNeasy (Quiagen) and submitted for RNA-Seq

first: Hongbo

last: Xie


title: Regulation of gene expression by ArlRS in Staphylococcus aureus USA300 strain LAC

city: Aurora

first: Alexander

last: Horswill

state: CO

department: Immunology and Microbiology

institute: University of Colorado Anschutz Medical Campus

summary: ArlRS is a two-component regulatory system in Staphylococcus aureus. Here we use RNA-sequencing to compare gene expression in a wild-type USA300 strain and an isogenic arlRS mutant.

sample_organism: Staphylococcus aureus subsp. aureus USA300

overall_design: Illumina RNA-sequencing of S. aureus USA300 LAC and LAC ΔarlRS in triplicate.

first: Heidi

middle: A

last: Crosby

first: Jakub

last: Kwiecinski

middle: R


title: The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments in HuH-7 cells

first: Jian-Hua

last: Yang

address: No. 135, Xingang Xi Road

department: School of Life Sciences

institute: Sun Yat-sen University

summary: To globally analyse the lncRNAs with potential coding ability of HCC cells, we performed Ribo-seq using HuH-7 cells. The cycloheximide (CHX) was added to inhibit the translational elongation of ribosomes of the HuH-7 cells.Furthermore,we identified the candidate ORFs with the selected RPF reads using the RiboCode software.

overall_design: Ribo-seq profiles of HuH-7 cells were generated by deep sequencing, in two independent experiments, using  Xten Illumina sequencing platform. The ribo-seq data of the two biological replicates were integrated.Then,for the analysis of Ribo-seq data, sequenced reads that were trimmed for the adaptor sequence were aligned to the UCSC hg19 reference genome by STAR (version 2.4.2a) with parameters provided by the RiboCode (version 1.2.10) manual.

first: Wen-Li

last: Xu

first: Bing

last: Deng

first: Peng-Hui

last: Lin

first: Chang

last: Liu

first: Bin

first: Qiao-Juan

last: Huang

first: Hui

last: Zhou

first: Liang-Hu

last: Qu


title: Transcriptome analysis of Arabidopsis seedlings between Col-0 and saur41/4071/72

city: Hangzhou

first: Ting

last: Qiu

address: 866 Yuhangtang Road

department: college of life science

institute: Zhejiang University

summary:
Purpose: we used transcriptional profiling to identify differentially expressed genes in Col-0 and saur41/4071/72 seedlings
Methods: Total RNA of 5-day-old Arabidopsis roots and the shoot parts were send to Vazyme BIotech Co., Ltd (Nanjing, China) to carry out library construction, Illumina HiSeq sequencing, and bioinformatical analysis. Each sample generated 4 Gb of clean data and contained three biological replicates.

overall_design: 2 from Col-0 root, 2 from saur41/4071/72 root, 2 from Col-0 shoot part and 2 from saur41/40/71/72 shoot part

first: Mengyuan

last: Qi

first: Xiaohui

last: Ding

first: Yanyan

last: Zheng


title: Hematopoietic Stem Cells response to allergic peritonitis

city: Beer-Sheva

first: Nir

last: Bujanover

address: Ben Gurion 1

department: Immunology

institute: Ben-Gurion University

summary: In our previous work we substantiated the ability of the Fgd5-mCherry mice to tag hematopoietic stem cells (HSCs) during immune response (Bujanover et al., 2018). While most of the research is focused on viral-bacterial models mediated by a Th1 response less has been investigated on Th2 mediated hypersensitivity. Our current experimental model of allergic peritonitis seeks to understand the effect of a Th2 mediated immune response utilizing our transgenic Fgd5-mCherry mice. Our results showed no significant change in quantity of HSCs and their immediate progenitors in the bone-marrow post treatment. Furthermore, transplant experiments showed no significant change in the long term multipotent ability of HSCs vs. control. Examining the cell cycle state of HSCs, quiescence is an essential property for stemness, we find no evidence of proliferation.  We continued to sort and bulk RNAseq HSCs after allergic peritonitis showing relatively small changes in expression profile. Taken together, this data suggests no prominent response of HSCs to our Th2-mediated hypersensitivity model.

overall_design: Fgd5-mCherry mice where treated with a 16 day allergic peritonitis protocol (Zuany-Amorim et al., 1993)  and bulk-RNAseq of bone-marrow Lineage-Sca1+cKit+CD150+Fgd5-mCherry+ cells (HSCs; 100 cells per sample) was performed. HSCs from pIC and PBS treated mice where added as control for activated and non-activated HSCs accordingly.

first: Roi

last: Gazit


title: Exercise Reverses Dysregulated Gene Expression in a Desmoplakin Haplo-insufficient Mouse Model of Arrhythmogenic Cardiomyopathy

city: Houaton

first: Ali

middle: J

last: Marian

state: Texas

address: 6770 Bertner Ave DAC C900a

department: Centre for Cardiovascular Genetics

institute: UTHSC, Houston

summary: Mutations in desmosome genes cause arrhyythmogenic cardiomyopathy (ACM). Using desmoplakin haploinsufficient  mouse model of ACM, we evaluated the effects of treadmill exercise on cardiac myocyte transcritional profile.  Strand specific, ribosome depleted paired end  RNA sequencing of cardiac myocytes from wild type and Myh6-Cre:DspW/F were  generate using  Illumina HiSeq 4000.

overall_design: Total RNA Sequencing of cardiac myocytes from wild type and Myh6-Cre:DspW/F mice at 3 months of age  at 6 months of age either with regular activity or 3 months post endurance treadmill exercise (n=5) was performed.

first: Sirisha

last: Cheedipudi

first: Priyatansh

last: Gurha

first: Matthew

last: Robertson

first: Coarfa

last: Cristian


title: Targets of Sf3b4 during neural crest development

city: New York

first: Varshini

last: Vasudevaraja

state: NY

address: 550 1st Avenue

department: Pathology

institute: NYU Langone Health

summary: Mutations in Sf3b4, a component of the spliceosome, have been linked to craniofacial dismorphology known as Nager syndrome. To understand the role Sf3b4 in this condition, we knockdown Sf3b4 in Xenopus laevis embryos, and found that in these embryos the formation of neural crest-derived craniofacial skeletal structures was compromised. We performed RNA-Seq to identify the repertoire of genes affected by Sf3b4 splicing activity.

overall_design: Xenopus laevis embryos were injected at the 2-cell stage with mRNAs encoding noggin and wnt8 to induce neural crest progenitors. A subset of these embryos were co-injected with Sf3b4MO antisense oligonucleotides to interfere with  Sf3b4 fonction during neural crest forrmation. At the blastula stage (stage 8/9), animal cap explants were dissected and cultured for 8 hours in a defined medium. Either two or three biological replicates were performed for each condition.

first: Jean-Pierre

last: Saint-Jeannet

first: Santosh

last: Maharana


title: Molecular comparison of an LSC population and a more differentiated cell population

first: Josephine

last: Wesely

address: 1470 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

summary: We identified 2 phenotyically and functionally distinct populations in our AML-iPSC line upon hematopoieyic differentiation. One population adheres (iLSCs = samples A) and one stays in suspension (iBlasts = samples S). The iLSCs  are phenotyically and functionally leukemia stem cells and the iBlasts are more differentiated cells. We identified the RUNX1 motif as one of the top TF motfs enriched in more accessible peaks in iLSCs compared to iBlasts. Here we perform RUNX1 CHIP-seq on iLSCs (=A) and iBlasts (=S).

overall_design: Samples were prepared in duplicates with IgG controls for each duplicate

first: Eirini

last: Papapetrou


title: A gene locus that controls expression of ACE2 in virus infection

city: Oxford

first: Timothy

last: Hinks

state: United Kingdom

address: John Radcliffe Hospital, Headley Way, Oxford

department: NDM Experimental Medicine - New College

country: United Kingdom

institute: University of  Oxford

summary: The SARS-CoV-2 pandemic has resulted in widespread morbidity and mortality globally, but with widely variable outcomes. The development of severe disease and mortality is higher in older individuals, males and those with other co-morbidities, and may vary across ethnic groups. However, so far, no host genetic factor has been clearly associated with susceptibility and development of severe disease. To understand the impact of host genetics on expression of ACE2 (SARS-CoV-2 receptor) during RNA virus infection we performed a GWAS for ACE2 expression in HCV-infected liver tissue from 195 individuals. We discovered that polymorphisms in the host IFNL region which control expression of IFNL3 and IFNL4 modulate ACE2 expression. ACE2 expression was regulated additionally by age, with a subsidiary effect of co-morbidity. The IFNL locus controlled expression of a gene network incorporating many well-known interferon-stimulated genes which anti-correlated with ACE2 transcript levels. The same anti-correlation was found in the gastrointestinal tract, a site of SARS-CoV-2 replication where inflammation driven interferon-stimulated genes are negatively correlated with ACE2 expression. The interferon dependent regulation of ACE2 was identified in a murine model of SARS-CoV-1 suggesting conserved regulation of ACE2 across species. Polymorphisms in the IFNL region, as well as age, may impact not only on classical antiviral responses but also on ACE2 with potential consequences for clinical outcomes in distinct ethnic groups and with implications for therapeutic interventions.

overall_design:
RNASeq from liver biopsies from HCV infected patients

>>> Raw data are not available due to patient privacy concerns<<<

first: M

last: Ansari

first: Paul

last: Klenerman

first: Emanuele

last: Marchi


title: Single-cell RNA-seq of the intestine sample of ICR mice treated with busulfan and/or Alginate Oligosaccharides

city: Qingdao

first: Yong

last: Zhao

state: Shandong

address: 700 Changcheng Road

department: College of Life Sciences

institute: Qingdao Agricultural University

summary: We profiled a single-cell RNA-seq on ICR mouse intestine treated with busulfan and or Alginate Oligosaccharides (AOS) from 3 weeks of age to 5 weeks of age (for 2 weeks) to study the rescue effect of AOS on the intestine development disrupted by busulfan. We collected single cell from intestine from the four groups AOS 0 (control), B+A 0 (busulfan alone), B+A 10 (busulfan plus AOS 10 mg/kg Body Weight). The the cells were further captured with 10x Genomics based single-cell system. By using single-cell RNA seq, we found busulfan damaged intestinal cells. AOS significantly improved the intestinal cell junction and microvilin formation. Besides, we provide candidate master regulons regulated by AOS. Our data here offers the opportunity for improving  intestine under stress.

overall_design: We totally analyzed ~12,000 single cell transcriptome profile from ICR mouse intestine from the three treatment groups.

first: Wei

last: Ge

first: Pengfei

last: Zhang

last: Shen

first: Hongfu


title: Expression profile of kidney from GNE M743T/M743T knock in mice and wild-type

first: Hadar

last: Benyamini

summary: Background. Mutations in GNE cause a recessive, adult onset myopathy characterized by slowly progressive distal and proximal muscle weakness. Knock-in mice carrying the most frequent mutation in GNE myopathy patients, GneM743T/M743T, usually die few days after birth from severe renal failure, with no muscle phenotype. However, a spontaneous sub-colony remains healthy throughout a normal lifespan without any kidney or muscle pathology. Objective. We attempted to decipher the molecular mechanisms behind these phenotypic differences and to determine the mechanisms preventing the kidney and muscles from disease. Methods. We analyzed the transcriptome and proteome of kidneys and muscles of sick and healthy GneM743T/M743T mice. Results. The sick GneM743T/M743T kidney was characterized by up-regulation of extra-cellular matrix degradation related processes and by down-regulation of oxidative phosphorylation and respiratory electron chain pathway, that was also observed in the asymptomatic muscles. Surprisingly, the healthy kidneys of the GneM743T/M743T mice were characterized by up-regulation of hallmark muscle genes. In addition he asymptomatic muscles of the sick GneM743T/M743T mice showed upregulation of transcription and translation processes Conclusions. Overexpression of muscle physiology genes in healthy GneM743T/M743T mice seems to define the protecting mechanism in these mice. Furthermore, the strong involvement of muscle related genes in kidney may bridge the apparent phenotypic gap between GNE myopathy and the knock-in GneM743T/M743T mouse model and provide new directions in the study of GNE function in health and disease.

first: Stella

last: Mitrani-Rosenbaum


title: High-throughput screening and analysing for circular RNA expression profile in HepG2 cells expressing genotype IV Swine Hepatitis E Virus ORF3

city: shanghai

first: Xie

last: qin

address: Minchi first road, pujiang town, minhang district, Shanghai

institute: LC sciences

type: Non-coding RNA profiling by high throughput sequencing

summary: Swine hepatits E (SHE) is a new type of zoonotic infectious disease caused by swine hepatitis E virus (SHEV). Open reading frame 3 (ORF3) is a key regulatory and virulent protein of SHEV. Circular RNA (circRNA) is a special kind of non-coding RNA molecule, which has a closed ring structure. In this study, to identify the circRNA profile in host cells affected by SHEV ORF3, adenovirus ADV4-ORF3  mediated the overexpression of ORF3 in HepG2 cells, high-throughput sequencing was used to investigate the differentially expressed circRNAs, GO and KEGG were performed to enrich the function of hosting genes, and Targetscan and miRanda softwares were used to analyze the interaction between circRNA and miRNA. In total, 1,105 up-regulation circRNAs and 1,556 down-regulation circRNAs were identified in ADV4-ORF3 infection group compared with the control. GO function enrichment analysis of differentially expressed circRNAs-hosting genes classified three main categories (cellular component, biological process and molecular function). KEGG pathway enrichment analysis scatter plot showed the pathway term of top20. Our findings first screened and analyzed the expression profile of circRNAs in HepG2 cells expressing genotype IV Swine Hepatitis E Virus ORF3, which may facilitate further study to reveal the function of SHEV ORF3 and molecular mechanism of SHEV infection.

overall_design: HepG2 cells were infected adenovirus ADV4-ORF3 and ADV4-NC (MOI=5:1) for 24h, respectively. PBS washed the cell layer three times and added Trizol to fully lyse the cells. The total RNA of six sample (Ad_GFP_1, Ad_GFP_2, Ad_GFP_3, Ad_ORF3_1, Ad_ORF3_2 and Ad_ORF3_3) were extracted for transcriptome sequencing.

first: Hanwei

last: Jiao

first: Zonglin

last: Zheng


title: Transcriptome analysis of Arabidopsis seedlings between Col-0 and OE-SAUR41

first: Ting

last: Qiu

summary:
Purpose: we used transcriptional profiling to identify differentially expressed genes in Col-0 and OE-SAUR41 seedlings
Methods: Total RNA of 5-day-old Arabidopsis roots and the shoot parts were send to Vazyme BIotech Co., Ltd (Nanjing, China) to carry out library construction, Illumina HiSeq sequencing, and bioinformatical analysis. Each sample generated 4 Gb of clean data and contained three biological replicates.

overall_design: 2 from Col-0 root, 2 from OE-SAUR41 root, 2 from Col-0 shoot part and 2 from OE-SAUR41 shoot part

first: Mengyuan

last: Qi

first: Xiaohui

last: Ding

first: Yanyan


title: LncRNA sequencing in dorsal root ganglion cultured with high sugar content

city: Huai'an

first: Jie

state: Jiangsu

address: Huaihai South Road

department: Department of Respiratory Diseases

institute: the Affiliated Huai’an Hospital of Xuzhou Medical University

summary: Primary isolated rat dorsal root ganglion nerve cells (DRGs) were cultured with high glucose in vitro and divided into normal culture group and high glucose culture group


city: Paris

first: Rachel

last: Legendre

address: 28, rue du docteur Roux

department: Research and Resource Center for Scientific Informatics

country: France

institute: Institut Pasteur

summary: Insight on amoebiasis using a 3D model of the human intestine.

sample_organism:
Homo sapiens
Entamoeba histolytica HM-1:IMSS

first: Arturo

last: Aguilar Rojas

first: Silvia

last: Castellanos Castro

first: Mariette

last: Matondo

first: Hugo

last: Varet

first: Odile

last: Sismeiro

first: Julien

last: Fernandes

first: Jean

last: Coppee

middle: C

last: Olivo-Marin

first: Nancy

last: Guillen


title: MYC-associated Factor X, MAX, controls the clock transcriptional network [RNA-Seq]

city: Genoa

first: benedetto

last: grimaldi

address: via Morego 30

department: Molecular Medicine

country: Italy

institute: Fondazione Istituto Italiano di Tecnologia

summary:
Purpose: Quantitative RT-PCR and ChIP analyses identified MAX as a transcriptional repressor of circadian BMAL1 target genes. The goal of this study is to compare the transcriptional effect of a knockdown of either MAX and BMAL1 in a human cell line (MDA-MB-231)
Methods: Polyadenylated mRNA profiles of human breast cancer MDA-MB-231 cells with knocked down MAX or BMAL1 were generated by deep sequencing, in triplicate, using Illumina HiSeq 2000 sequencer. Cells transfected with a non-targeting siRNA sequence were used as a control. RNA sequencing counts were used to determine differentially expressed genes with DeSeq2  package included in the Galaxy web platform (usergalaxy.org). Differentially expressed genes (DEGs) were defined adopting an adjust P < 0.001 as a statistical cut-off value.
Results: Transcript assembly and quantification of RNA-sequencing reads identified 4863 and 4247 differentially expressed genes (DEGs) upon knockdown of BMAL1 or MAX, respectively. The comparison of the two set of genes revealed that 2391 of siBMAL1 DEGs (almost 50%) were also differentially expressed in MAX-silenced cells. Heat map and clustering analysis of this sub-set of genes revealed that more than 90% (2241 out of 2391) were coherently altered in both conditions (i.e. their expression was altered in the same direction). Consistent with our quantitative RT-PCR experiments, genes belonging to the circadian rhythm signalling were altered by both MAX and BMAL1 silencing.
Conclusion: This study indicate that MAX is a  part of the molecular clock transcriptional network.

first: Olga

last: Blazevits

first: Benedetto

last: Grimaldi

first: Ottavio

last: Croci


title: MYC-associated factor X, MAX, binds BMAL1 targeted genomic regions with high affinity [ChIP-Seq]

summary:
Purpose: quantitavive RT-PCR and ChIP analyses suggested that the MYC-Associated factor X, MAX, and the essential circadian regulator, BMAL1, might be recruited on the same E-box containing regulatory regions within the promoters of clock target genes. To explore this possibility, we performed ChIP-seq experiments in human cancer MDA-MB-231 cells.
Methods: Chromatin samples from human cancer MDA-MB-231 cells were immunoprecipitated with specific antibodies against BMAL1 and MAX proteins. Immunoprecipitated DNA was sequenced using Illumina HiSeq 2000 sequencer.
Results: ChIP-seq analysis revealed a large number of genomic regions bound by MAX (around 13000 peaks), while BMAL1 binding was limited to about 800 regions. BMAl1 and MAX bound regions comprised both promoters and distal sites. Coherently with the circadian role of BMAL1 and its preference for E-box-containing sites, ontological annotation of BMAL1 bound regions showed a significant enrichment for circadian regulated genes and E-box motifs. The 85% of the BMAL bound sites overlapped with MAX bound regions. MAX enrichment was higher on the genomic regions co-bound by BMAL1 compared with MAX binding loci sites in which BMAL1 was not present, thus indicating that MAX/BMAL1 sites are bound by MAX with high affinity. Strikingly, MAX enrichment was observed on all E-box-containing promoters of the clock core genes.

first: Stefano

last: Campaner


title: Transcriptome Analysis of Drp1-mediated biological pathways under physiological and ischemia conditions in Drp1-knockdown mice

city: Chongqing

first: Chenyang

last: Duan

state: Chongqing

address: Changjiang Road, Yuzhong District

department: Second Department of Research Institute of Surgery, Daping Hospital

institute: Third Military Medical University

summary:
Purpose:to verify Drp1-mediated biological pathways under physiological and ischemia conditions.Methods:C57BL/6 mice and  Drp1 knockdown mice were used for ischemia treatment. Right femoral arteries were catheterized with polyethylene catheters for bleeding 50% of total blood volume (≈7% of weight). The ischemia time started to calculate after the model was established. A laparotomy was then carried out to obtain superior mesenteric artery tissues (SMAs) for transcriptome analysis. Series-Cluster analysis was performed to identify the global trends of mitochondrial DEGs after Drp1 knockdown. Gene ontology (GO) analysis was performed to facilitate elucidating the biological process (BP), molecular function (MF) and cellular component (CC) of unique genes in the significant or representative profiles. Results:In addition to its traditional roles in GTPase regulation and mitochondrial fission, Drp1 may also regulate actin cytoskeleton and the movement of microtubules. Besides, Drp1 may participate in the regulation of morphology and functions of other organelles, including endoplasmic reticulum, peroxisome, phagolysosome, etc. As for general organ functions, Drp1 may regulate vascular constriction and dilation. These consequences indicated the important role of Drp1 in ischemia-induced cellular regulation. Conclusions: Drp1 deficiency proves the important role of Drp1 in ischemia-induced biomedical processes through multiple potential fission-independent manners.
Methods:C57BL/6 mice and  Drp1 knockdown mice were used for ischemia treatment. Right femoral arteries were catheterized with polyethylene catheters for bleeding 50% of total blood volume (≈7% of weight). The ischemia time started to calculate after the model was established. A laparotomy was then carried out to obtain superior mesenteric artery tissues (SMAs) for transcriptome analysis. Series-Cluster analysis was performed to identify the global trends of mitochondrial DEGs after Drp1 knockdown. Gene ontology (GO) analysis was performed to facilitate elucidating the biological process (BP), molecular function (MF) and cellular component (CC) of unique genes in the significant or representative profiles.
Results:In addition to its traditional roles in GTPase regulation and mitochondrial fission, Drp1 may also regulate actin cytoskeleton and the movement of microtubules. Besides, Drp1 may participate in the regulation of morphology and functions of other organelles, including endoplasmic reticulum, peroxisome, phagolysosome, etc. As for general organ functions, Drp1 may regulate vascular constriction and dilation. These consequences indicated the important role of Drp1 in ischemia-induced cellular regulation.
Conclusions: Drp1 deficiency proves the important role of Drp1 in ischemia-induced biomedical processes through multiple potential fission-independent manners.

overall_design: vascular mRNA profiles of 3 C57BL/6 mice for "Normal_Drp1 +/+" and 4 Drp1 knockdown mice for "Normal_Drp1 flox/+" and 3 C57BL/6 mice for "Ischemia_Drp1 +/+" and 4 Drp1 knockdown mice for "Ischemia_Drp1 flox/+".


title: Transcriptome Analysis of rat vascular molecular pathways linked to mitochondria in different phase of ischeia

summary:
Purpose: to determine the molecular pathways linked to mitochondria in different phase of ischemia.
Methods: Rats (220–240 g) were anaesthetized with sodium pentobarbital (initial dosage, 30 mg/kg). Anaesthetized rats were placed on a warmed plate to maintain the body temperature at 37°C. Aseptic techniques were adopted for all surgical procedures. Right femoral arteries were catheterized with polyethylene catheters for bleeding 50% of total blood volume (≈7% of weight). The ischemia time started to calculate after the model was established. At the end of ischemia, rats were killed with a lethal dose of sodium pentobarbital (100 mg/kg, iv). A laparotomy was then carried out to obtain superior mesenteric artery tissues (SMAs).
Results: Base on the Mitochondrial-Genome Microarrays and GSEA database, 1200 DEGs were picked out among the 46095 test probes on the chips. The top 10 mitochondrial-DEGs include Gdap1, Inf2, Pdzd8, Bnip3, Bnip3l, Tomm20, Bik, Lrrk2, Bcl2l1, Ubb. We also find that mitochondrial morphology variation, including mitochondrial fission and fusion, and the interaction between endoplasmic reticulum (ER) and mitochondria were involved in early stage of ischemia, while mitochondrial dysfunctions occurred in late stage of ischemia, including the release of CytC, mitochondrial membrane potential variation and changes in mitochondrial membrane permeability.
Conclusions: variation in mitochondrial morphology and dynamics occurs prior to mitochondrial dysfunctions after ischemic injury.

overall_design: vascular mRNA profiles of 3 SD rats after ischemia 1h and 3 SD rats after ischemia 4h and 3 SD rats for normal control were generated by deep sequencing  using Hiseq Xten


title: Transcriptomic analysis reveals a statin-induced core molecular signature in human iPSC-CMs

city: Stanford

first: Lei

last: Tian

state: CA

address: 1215 Welch Rd

institute: Stanford's Postdoctoral Scholar programs

summary: Statins prevent cardiovascular disease via their salutary function as inhibitors of cholesterol biosynthesis and mediators of pleiotropic effects on the cardiovascular system. The current study focuses on the class effect of statins on the transcriptome of human iPSC-derived cardiomyocytes (iPSC-CMs), applied at serum peak concentrations. We report a comprehensive transcriptomic analysis of iPSC-CMs derived from four healthy donors and different differentiation batches following treatment with fluvastatin, simvastatin, atorvastatin, and lovastatin. Our data display dynamic transcriptional networks and reveal a statin-induced molecular signature in iPSC-CMs independent of genetic background and technical variability. Finally, in-depth pathway enrichment analysis uncovers that all statins affect mainly metabolic properties of iPSC-CMs and particularly the regulation of cholesterol biosynthesis and fatty acid metabolism. Our study provides a global insight into the cardiomyocyte effects of statins revealing novel aspects of their role on cardiomyocyte metabolic regulation, when applied at clinically relevant concentrations.

overall_design: RNA profiling of 20 samples of statin- and vehicle (DMSO)-treated human iPSC-CMs

first: Angelos

last: Oikonomopoulos

first: Joseph

last: Wu


title: MYC-associated factor X, MAX

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

overall_design: Refer to individual Series


title: mSeq of vtRNA1.1 and vtRNA1.3 knockout or control cells in standard and starvation condition

status: Public on Apr 28 2020

city: Bern

first: Norbert

last: Polacek

address: Freiestrasse 3

department: Chemistry and Biochemistry

country: Switzerland

institute: University of Bern

summary: We report on how the loss of vtRNA1.1 reshapes the transcriptome in starved Hela cells. We observe misregulated transcript levels for proteins involved in cellular signaling cascades.

overall_design: Examination of total mRNA isolated after starvation or control condition of Hela cells carrying a vtRNA 1.1 or vtRNA 1.3 knockout or wildtype

first: Lisamaria

last: Bracher

first: Iolanda

last: Ferro

first: Carlos

last: Pulido-Quetglas

first: Rory

last: Johnson

first: Marc-David

last: Ruepp


title: Genome-wide analysis of wild type and prmt5 mutant plants

city: Buenos Aires

first: Marcelo

last: Yanovsky

state: Ciudad Autonoma de Buenos Aires

address: Av. Patricias Argentinas 435

country: Argentina

institute: Fundación Instituto Leloir. IIBBA- CONICET


title: Regulation of gene expression in uveal melanoma cells by ICG-001

city: Houston

first: Nicholas

last: Mitsiades

address: One Baylor Plaza

department: Medicine-Hematology & Oncology

institute: Baylor College of Medicine

summary: We examined the effects of ICG-001 on gene expression in Mel202 uveal melanoma (UM) cells. ICG-001 exerted strong antiproliferative activity against UM cells, leading to cell cycle arrest, apoptosis, and inhibition of migration. Global gene expression profiling revealed strong suppression of genes associated with cell cycle proliferation, DNA replication, and G1/S transition. Gene set enrichment analysis revealed that ICG-001 suppressed Wnt, mTOR, and MAPK signaling. Strikingly, ICG-001 suppressed the expression of genes associated with UM aggressiveness, including CDH1, CITED1, EMP1, EMP3, SDCBP, and SPARC. Notably, the transcriptomic footprint of ICG-001, when applied to a UM patient dataset, was associated with better clinical outcome. Lastly, ICG-001 exerted anticancer activity against a UM tumor xenograft in mice.

overall_design: Mel202 cells were treated with ICG-001 (3 μM) or DMSO control for 24 or 48 hrs

first: Salma

last: Kaochar

first: Cristian

last: Coarfa


title: Genome-wide analysis of wild type and prmt5 mutant plants (Experiment B)

summary: The goal of this study was to compare the transcriptional profile (RNA-seq) of wild type and prmt5 Arabidopsis mutants plants grown under continuous white light at 22 degrees centigrades for 9 days

overall_design: WT (Col accession) and prmt5 mutant plants were grown for nine days under continuous white light at 22 degrees centigrades or exposed for 1 or 24 h to 10ºC on the 9th day, before harvesting. Then the transcriptional profile of these plants was analyzed using RNA-seq.

first: Ariel

last: Chernomoretz


title: Transcriptome analysis of gene expression of strains JNB5-1 and SK68

city: Wuxi

first: Xuewei

last: Pan

address: 1800, Lihu Avenue

institute: Jiangnan University

summary: RNAseq analysis was performed to evaluate gene expression differences between strains JNB5-1 and SK68. S. marcescens JNB5-1 and SK68 cells were grown in LB medium for 4 h before harvesting. The collected cells were then treated with RNAprep pure Kit (TIANGEN) to extract total bacterial RNA and delivered to GENEWIZ in dry ice for transcriptome resequencing analysis. For annotation, the genome of S. marcescens WW4 (NC_020211.1) was used as reference. A total of 32420858 reads matched to the referenced genome in the sample of JNB5-1, and 32993470 reads in the sample of SK68. The significantly differentially expressed genes (DEGs) were determined between strains JNB5-1 and SK68 with the standards of p-value≤ 0.05, fold change |log2Ratio|≥1. Transcriptome data showed that expression of 210 genes were significantly up-regulated while 106 genes were significantly down-regulated by at least 2-fold when comparing the rcsB mutant strain SK68 to its parent strain JNB5-1. Based on the annotation of KEGG_B_class, the up-regulated and down-regulated genes were classified into 18 and 17 major cellular processes, respectively. The transcriptome data indicated that RcsB may regulates a variety of cellular processes in S. marcescens, including prodigiosin synthesis, and cell motility.

overall_design: Gene expression of strains JNB5-1 and SK68 were generated by deep sequencing, in triplicate, using Illumina HiSeq X10

first: Zhiming

last: Rao


title: Generation and molecular characterisation of transient tet1/2/3 zebrafish knockouts

city: darlinghurst

first: Samuel

middle: Ernest

last: Ross

state: NSW

address: 384 victoria st

country: Australia

institute: Garvan Institute of Medical Research

type: Methylation profiling by high throughput sequencing

summary: 5mC is extensively remodelled during vertebrate embryo development where a single cell must give rise to myriad different cell types and tissues with diverse 5mC patterns. 5mC can be remodelled through the catalytic action of Ten-eleven translocation (TET) methylcytosine dioxygenases (TET1, TET2, TET3), which oxidise 5mC resulting in its removal from the genome. In vertebrates, TET enzymes facilitate DNA demethylation of regulatory regions linked to genes involved in important developmental processes. Consequently, TET ablation leads to major morphological defects and developmental arrest. Here we describe a system that can facilitate the study of relationships between TET enzymes, 5mC, and embryo development.

overall_design: Reduced representation bisulfite sequencing (RRBS) of tet1/2/3 KO and wildtype F0 zebrafish at 24hpf in biological replicates.

first: Ozren

last: Bogdanovic


title: Single nuclei RNA-seq of brain of mouse Alzheimer's disease model

city: Jerusalem

first: Naomi

last: Habib

address: Safra Campus

department: Center for brain sciences

institute: Hebrew University of Jerusalem

summary: Here we report single nucleus RNA-seq shows in 5xFAD mouse model of AD and WT,  showing changes in the composition and state of multiple cell types. In particular, we identified a unique population of disease-associated astrocytes (DAAs) in AD. DAAs appeared at early disease stages and increased in abundance with age. Similar cells were found in aged WT mice and human brains, suggesting they are linked to both genetic and age-related factors.

overall_design: Single nuclei RNA-seq of WT and 5xFAD mouse brains, from hippocampus brain region


title: Ileal transcriptome profiles of pigs divergent in feed efficiency

city: Dummerstorf

first: Henry

last: Reyer

address: Wilhelm-Stahl-Allee 2

institute: Leibniz Institute for Farm Animal Biology (FBN)

summary: in vivo microarray study of transcriptional changes of ileum (mucosa) obtained from pigs divergent in feed efficiency

overall_design: ten pigs per experimental group were collected for expression profiling

first: Klaus

last: Wimmers

first: Michael

last: Oster


title: Caecal transcriptome profiles of pigs divergent in feed efficiency

summary: in vivo microarray study of transcriptional changes of caecum (mucosa) obtained from pigs divergent in feed efficiency


title: Caecal and Ileal transcriptome profiles of pigs divergent in feed efficiency


title: Single cell RNA sequencing of murine liver CD45+ mononuclear cells in HBs-HepR mouse model

city: Hefei

first: Xiaolei

last: Hao

state: Anhui

address: huangshan Road 443

institute: Institute of Immunology, USTC

summary: We used immunocompetent Fah-/- mice as the recipients and adoptively transferred HBsAg+ hepatocytes from HBs-Tg mice to replace the recipient hepatocytes (HBs-HepR). HBs-HepR mice maintained persistent HBsAg expression with chronic hepatitis and spontaneous liver fibrosis, and eventually developed HCC with a prevalence of 100%.

overall_design: HBs-HepR mice reconstruction for 0 week, 12 weeks and 18 weeks was harvested and  liver MNCs were isolated and stained with anti-CD45 and 7-AAD. CD45+7-AAD− cells were sorted using the FACSAria II Cell Sorter. Single-cell barcoded scRNA-seq libraries using Chromium Single Cell 3′ Library V2 (10x Genomics) and sc-RNA-libraries were sequenced on HiSeq X Ten (Illumina).

first: Zhigang

last: Tian


title: Chromatin spreading in 3D through Insulator looping regulates genes through to H3K27me3 micro-domains

city: Toulouse

first: Olivier

last: Cuvier

address: 118 route de Narbonne

department: LBME

institute: CNRS

summary: We used the technology of ChIP-sequencing to analyze changes in H3K27me3 levels in Drosophila Schneider S2 depleted of endogenous Beaf32 and expressing  insulator mutants ('mut-Beaf32' or 'muBeaf') as compared to control cells expressing wild-type Beaf32 (Control; 'CTL')

overall_design: Drosophila Schneider S2 cells either containing endogenous Beaf32 or either transfected by mutated insulator looping mutants (mut-Beaf32 ) have been depleted of endogenous Beaf32. Quantification of H3K27me3 has been done using ChIP-seq on both depleted and wild-type condition.

first: Alexandre

last: Heurteau

first: David

last: Depierre

first: Charlène

last: Perrois

last: Fosseprez

first: Jonathan

last: Humbert

first: Priscillia

last: Lhoumaud

first: Stéphane

last: Schaak


title: Genome-wide analysis of wild type and prmt5 mutant plants (Experiment A)

first: Marcelo

last: Yanovsky

summary: The goal of this study was to compare the transcriptional profile (RNA-seq) of wild type and prmt5 Arabidopsis mutants plants grown under continuous light at 22 degrees centigrades.

overall_design: WT and prmt5 mutant plants were grown for fifteen days under continuous white light at 22 degrees centigrades. Then the transcriptional profile of these plants was analyzed using RNA-seq.

first: Ariel

last: Chernomoretz


title: Mammary transcriptome of rats treated with low-dose environmental chemicals from birth to adulthood

city: New York

first: Kalpana

last: Gopalakrishnan

address: 1428 Madison Avenue, Atran Building 03-02

institute: Icahn School of Medicine at Mount Sinai

summary:
Exposure to common environmental chemicals, including those found in personal care products has been linked to mammary cancer at high doses in animal models.  Their effects at low doses at levels comparable to human exposure remain poorly understood.  Using a Sprague-Dawley rat model, we investigated the effects of three prevalently used environmental chemicals – diethyl phthalate (DEP), methyl paraben (MPB), triclosan (TCS) – and their mixture (MIX) on the transcriptome of normal developing mammary at levels mimicking human exposure.  Rats were exposed from birth to adulthood in parous and nulliparous settings.
We used affymetrix arrays to assess the influence of diethyl phthalate (DEP), methyl paraben (MPB), triclosan (TCS) and their mixture (MIX) on global gene expression profiles in rat mammary tissues, using doses comparable to human exposure. Exposure was from birth to adulthood (postnatal day 1 – 180) in parous and nulliparous rats.

overall_design: Female Sprague-Dawley rats were treated by oral gavage with low doses of diethyl phthalate (DEP), methyl paraben (MPB), triclosan (TCS) or a mixture (MIX) of the three chemicals.  These low doses were previously determined to produce urinary biomarker concentrations comparable to those reported for the US population (Teitelbaum SL, 2016).  Control animals received the vehicle, olive oil (OIL).  Exposure was from birth to adulthood (postnatal day 1 – 180) in parous and nulliparous rats.  There were 5 animals in each experimental group.

first: Susan

middle: L

last: Teitelbaum

first: Luca

last: Lambertini

first: James

last: Wetmur

first: Fabiana

last: Manservisi

first: Laura

last: Falcioni

first: Luciano

last: Bua

first: Fiorella

last: Belpoggi

first: Jia

last: Chen


title: Expression profiling by high throughput sequencing of THP-1 cells treated with Monensin

city: Muenster

first: Maria

middle: V

last: Yusenko

address: Wilhelm-Klemm-Str. 2

department: Institute of Biochemistry

institute: University of Muenster

summary: Purpose: to reveal gene expression changes induced by Monensin in THP-1 cells

overall_design: THP-1 cells were grown in the presence or absence of 1 µm Monensin for 16 hs. RNA profiling was obtained in triplicate using Illumina NextSeq

first: Karl-Heinz

last: Klempnauer


title: Modulation of the mouse liver epigenome following TCPOBOP exposure

city: Boston

first: David

middle: J.

last: Waxman

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

institute: Boston University

summary: Changes in the activating histone-H3 chromatin marks K4me1, K4me3, and K27ac were assayed in male mouse liver following exposure to TCPOBOP, an agonist ligand of the nuclear receptor CAR (constitutive androstane receptor). This work is part of a larger study, entitled: "Widespread Epigenetic Changes to the Enhancer Landscape of Mouse Liver Induced by a Specific Xenobiotic Agonist Ligand of the Nuclear Receptor CAR" (Tox Sci, 2019).

overall_design: Chromatin immunoprecipitation (ChIP) analysis of histone marks was carried out using sonicated liver chromatin, either prepared by sonication of cross-linked liver nuclei, or by sonication of cross-linked whole liver tissue. A set of 6 individual liver chromatin samples (3 vehicle-treated, 3 TCPO-treated) was used for ChIP analysis of all three chromatin marks at 3 h; and a set of 7 other individual liver chromatin samples (3 vehicle-treated, 4 TCPOBOP-treated) was used for ChIP analysis of all three chromatin marks at 27 h, namely, H3K4me1, H3K4me3, and H3K27ac.

first: Nicholas

last: Lodato

first: Aram

last: Shin

first: Andy

last: Rampersaud


title: METTL5, an 18S rRNA-specific m6A methyltransferase, modulates expression of stress response genes

first: Yang

last: Shi

state: Massachusetts

address: 320 LONGWOOD AVE

department: NEWBORN MEDICINE

institute: BOSTON CHILDREN'S HOSPITAL

summary: Input mRNAs and ribosome protected fragments (RPFs) from wildtype and Mettl5 knockout (KO) B16 cells were analyzed by TruSeq Ribo Profile (Illumina) library preparation and high throughput sequencing

overall_design: Mouse melanoma B16 cells were grown in standard conditions (DMEM + 10% FBS + Pen/Strep (100U / mL)). Input mRNAs and RPFs were isolated, ribosomal RNAs were depleted and cDNA libraries were prepared according to the TruSeq Ribo Profile pipeline (Illumina)

first: Hao

first: Qi

last: Liu


title: SFPQ depletion is synthetically lethal with BRAFV600E in colorectal cancer cells

status: Public on Apr 27 2020

city: Berlin

first: Bertram

last: Klinger

address: Chariteplatz 1

institute: Charite Universitätsmedizin


title: SFPQ depletion is synthetically lethal with BRAFV600E in colorectal cancer cells II

summary: Oncoproteins such as the BRAFV600E kinase entrust cancer cells with malignant properties, but they also create unique vulnerabilies. Therapeutic targeting of the BRAFV600E-driven cytoplasmic signaling network has proven ineffective, since patients regularly relapse with reactivation of the targeted signaling pathways. Here, we identified the nuclear protein SFPQ to be synthetically lethal with BRAFV600E in a loss-of-function shRNA screen. SFPQ depletion decreased proliferation and induced apoptosis in BRAFV600E-driven colorectal and melanoma cells, and reduced tumor growth in xenografts. Mechanistically, SFPQ loss in BRAF-mutant cancer cells triggered the Chk1-dependent replication checkpoint, resulting in replication stress in the absence of overt DNA damage. Affected cells stalled in S-Phase with hallmark signs of impaired replication factories. Induction of BRAFV600E and concomitant loss of SFPQ sensitized cells to a combination of DNA replication checkpoint inhibitors and chemically induced replication stress, pointing towards future therapeutic approaches exploiting nuclear vulnerabilities induced by BRAFV600E.

overall_design: CaCo2 wt shRen (Control shRNA), CaCo2 wt shSFPQ, CaCo2 BRAFV600E shControl and Caco2 BRAFV600E shSFPQ were treated with doxycycline for 96h to induce an ectopic expression of  the shRNAs and if applicable the BRAF oncogene. The RNA was isolated, depleted of ribosomal RNA and paired-end sequenced (125 bp).

first: Kathleen

last: Klotz-Noack

last: Rivera

first: Natalie

last: Bublitz

first: Florian

last: Uhlitz

first: Pamela

last: Riemer

first: Mareen

last: Lüthen

first: Thomas

last: Sell

first: Katharina

last: Kasack

first: Bastian

last: Gastl

first: Sylvia

middle: S

last: Ispasanie

first: Tincy

last: Simon

first: Nicole

last: Janssen

first: Matthias

last: Schwab

first: Johannes

last: Zuber

last: Horst

first: Nils

last: Blüthgen

first: Reinhold

last: Schäfer

first: Markus

last: Morkel

first: Christine

last: Sers


title: Transcriptomic analysis reveals the gene expression profiles and cellular functions regulated by the RcsB in Yersinia enterocolitica

city: Beijing

first: Jiao

last: Meng

address: 17 Tsinghua East Road

institute: CAU

summary: A total of 132 differentially expressed genes (DEGs) regulated by the RcsB have been identified, of which 114 were up-regulated and 18 were down-regulated. Analyses of the GO annotation and KEGG enrichment led us to focus on the role of RcsB in the inhibition of chemotactic behavior, flagella biosynthesis and bacterial infection in Y. enterocolitica. Overall, the information provided in this study complements our understanding of Rcs phosphorelay in the regulation of Y. enterocolitica pathogenicity, and, simultaneously, provides clues to additional roles of the Rcs system in other members of family Enterobacteriaceae.

overall_design: Gene expression profiles of wild-type and ΔrcsB mutants were compared by RNA-Seq.

first: Jingyu

last: Chen


title: Next generation sequencing facilities quantitative analysis of ASAP2 knockout or wild-type Panc1 and MiaPaCa2 cells

city: Beppu,Oita

first: Atsushi

last: Fujii

address: 4546 Tsurumibaru

department: Department of Surgery

institute: Kyushu University Beppu Hospital

summary: To assess potential gene expression changes by ASAP2 individual knockout in Panc1 and MiaPaCa2 cells, we performed a transcriptomic analysis using high throughput RNA sequencing (RNA-seq).

overall_design: Total RNA extracted from ASAP2 knockout or wild-type Panc1 and MiaPaCa2 cells was subjected to RNA-seq analysis. The sequencing libraries generated from the RNA were analyzed by BGISEQ-500. The sequencing reads were trimmed for adaptor sequence, and low-complexity or low-quality reads were removed. Subsequently, the reads were aligned to the human reference sequence and the gene annotations (UCSC hg19) using Tophat2 v2.0.14. STAR v2.5.2a was used to calculate fragments per kilobase of transcript per million fragments mapped (FPKM) values.

first: Takaaki

last: Masuda

first: Koshi

last: Mimori


title: RNAseq data comparing iKPC PDAC tumors with KRAS* expression (ON) and KRAS extinction (OFF)

city: Newark

first: Pingping

last: Hou

state: New Jersey

address: 205 South Orange Ave

department: Microbiology, Biochemistry and Molecular Genetics

institute: Rutgers University

summary: KRAS* is required for PDAC tumor mantainence. To dissect the molecular mechanisms that regulated by KRAS* in PDAC tumors, we conducted RNA-seq analysis of KRAS*-expressing  iKPC PDAC tumors and iKPC tumors after KRAS* extinction for 24 hours.

overall_design: Four KRAS*-expressing iKPC PDAC tumors and four iKPC PDAC  tumors after KRAS* extinction for 24 hours were used. The iKPC-1 cells were transplanted subcutaneously in nude mice to generate the tumors.

first: Jun

last: Li

first: Jianhua

last: Zhang


title: TGFbeta treatment drives iKPC PDAC cells to bypass KRAS* dependency

summary: TGFbeta promotes the bypass of KRAS* dependency in PDAC. To dissect the molecular mechanisms that regulated by TGFbeta in PDAC cells, we conducted RNA-seq analysis of iKPC PDAC cells with or without TGFbeta treatment.

overall_design: The iKPC PDAC spheriod colonies in three independent wells were collected as biological replicates with or without TGFbeta treatment for five days after KRAS* extinction.


title: RNAseq data comparing HDAC5 eccaper PDAC cells with HDAC5 knockdown and scramble control

summary: HDAC5 drives PDAC cells to bypass KRAS* dependency. To dissect the molecular mechanisms that regulated by overexpressed HDAC5 in escaper cells, we conducted RNA-seq analysis of HDAC5 escaper PDAC cells knocking down of HDAC5 or scramble shRNA control.

overall_design: Five HDAC5 escaper PDAC cell lines were used as biological replicates with knockdown of HDAC5 by 2 shRNAs and shRNA cramble control.


title: RNA sequencing analysis of LN-229-shControl and LN-229-shMOB2 cells

city: Dalian

first: Ke

last: Jiang

state: Liaoning

address: lvshun south road no.9

institute: Dalian Medical University

summary: We performed RNA-seq to determine the impact of MOB2 depletion on global gene expression profile.The results reveal that dysregulated genes were enriched for genes related to pathways in cancer, including PI3K–AKT signaling, cell adhesion molecules (CAMs), focal adhesion and cytokine-cytokine interaction.

overall_design: Invesitigate transcriptomic difference between control and MOB2-depleted cells.

first: Songshu


title: Histone modifications regulated by HDAC5 in PDAC cells

summary: HDAC5 belongs to Class IIa histone deacetylases and forms corepressor complex with HDAC3. To understand the epignetic regulations by HDAC5, we performed ChIP-seq analysis of H3K4me3, H3K27ac and H3K9ac in PDAC cells overexpressing GFP or HDAC5, and in HDAC5 escaper cells with HDAC5 knockdown or scramble control.

overall_design: ChIP-seq of H3K4me3, H3K27ac and H3K9ac were performed in PDAC cells overexpressing GFP or HDAC5, and in HDAC5 escaper cells with HDAC5 knockdown or scramble control.

first: Jiexi


title: Glycolytic body (G body) RIP-sequencing

city: Baltimore

first: John

middle: Biology

last: Kim

state: Maryland

address: 3400 N Charles St

department: Biology Department

institute: Johns Hopkins University

summary: Glycolytic (G) bodies were purified from hypoxic yeast using differential centrifugation and immunoprecipitation by Pfk2-GFP-Flag in order to determine the RNAs that localize to G bodies by determining the enrichment of RNAs copurified with G bodies over both the flow through and total RNA fractions. We find significant overlap between enriched RNAs and RNAs bound by glycolysis enzymes in normoxic conditions. Our study determined that RNA is an integral component of G bodies and is required for G body formation. Specific mRNAs are only slightly enriched in G bodies.

overall_design: Purification of G bodies from two biological replicates and sequencing of total RNA, flow through RNA and RNA copurified with G bodies for each biological replicate

first: Gregory

last: Fuller

middle: K


title: RNAseq data comparing KRAS*-independent HDAC5 eccaper PDAC cells and KRAS*-dependent iKPC PDAC cells

summary: HDAC5 drives PDAC cells to bypass KRAS* dependency. To dissect the molecular mechanisms that regulated by overexpressed HDAC5 in the bypass of KRAS* dependency, we conducted RNA-seq analysis of HDAC5 escaper PDAC cells and KRAS*-expressing iKPC PDAC cells.

overall_design: Four KRAS* expressing iKPC PDAC cell lines and five HDAC5 escaper PDAC cell lines were used.


title: RNA-seq analysis of young swine following cardiac ischemia/reperfusion injury.

city: Cinicnnati

first: Katherine

last: Yutzey

state: OH

address: 240 Albert Sabin Way

department: Divison of Molecular Cardiovascular Biology

institute: Cinicnnati Children's Hospital Medical Center

summary: This study was a part of a larger study assessing the response of young pigs to cardiac ischemia/reperfusion (IR) injury. A mild cardiac injury approach (IR) was used in post-weaned pigs (1-month), to assess regenerative repair in young large mammals after transient ischemic injury. Female and male postnatal day (P)30 pigs were subjected to cardiac ischemia (1-hour) by occlusion of the left anterior descending artery followed by reperfusion (IR), or to sham operation. In pigs subjected to IR, myocardial damage occurred, indicated by increased circulating cardiac troponin I 2-hours post-ischemia. In addition, cardiac ejection fraction (EF) was significantly decreased 2-hours post-ischemia and reduced EF was maintained to the 4-week study end-point. Histology demonstrated evidence of CM cell cycling at 2-months of age in multinucleated CMs in both sham-operated and IR pigs. Following IR, regional scar formation and inflammation in the epicardial region proximal to injury were observed 4-weeks post-IR. Sex differences in cardiac function and collagen deposition were found, highlighting the importance of representing both sexes in cardiac injury studies. Together, our results describe an effective novel cardiac injury model in 1-month old swine, at a time when CM are still cycling. However, pigs subjected to IR show a prolonged decrease in cardiac function, and the formation of a small, regional scar with increased inflammation. Together, these data demonstrate that 1-month old pigs do not regenerate myocardium, but form a scar, after transient IR injury.

overall_design: Total RNA of myocardial tissue from 16 samples underwent RNA-seq analysis. 8 pigs were used in the study (4 sham surgery and 4 ischemia/reperfusion (IR)). Each pig had 2 samples sent for analysis, 1 from the scar zone and 1 from the border zone from the site of injury. Male and female pigs were both represented.

first: Emma

last: Agnew

first: Nivedhitha

last: Velayutham

first: Gabriela

last: Ortiz

first: Christina

last: Alfieri

first: Victoria

last: Moore

first: Kyle

middle: W

last: Riggs

first: Richard

last: Baker

first: Aaron

last: Gibson

first: Sithara

last: Ponny

first: Tarek

last: Alsaied

first: Farhan

last: Zafar


title: Long-term exposure of early-transformed human mammary cells to low-doses of Benzo[a]pyrene and/or Bisphenol-A enhances their cancerous phenotype via an AhR/GPR30 interplay

city: Lyon

first: joel

last: lachuer

address: 8 avenue rockefeller

institute: university Lyon1

summary: We report that long term exposure to BPA and B(a)P enhances cancerous phenotype via an Ahr/GPR30 interplay

overall_design: Transcriptomics analysis and comparisons of cells treated or no treated by combination of BPA and  B(a)P

first: Caterina

last: Donini

first: Helou

last: Myriam El

first: Wierinckx

last: Anne

first: Balazs

last: Gyorffy

first: Sophie

last: Aires

first: Aurélie

last: Escande

first: Séverine

last: Croze

first: Philippe

last: Clezardin

first: Joel

last: Lachuer

first: Mona

last: Diab-Assaf

first: Sandra

last: Ghayad

first: Béatrice

last: Fervers

first: Vincent

last: Cavailles

first: Véronique

last: Maguer-Satta

first: Pascale

last: Cohen


title: Partial loss of CFIm25 causes aberrant alternative polyadenylation and learning deficits

city: Houston,

first: Hari Krishna

last: Yalamanchili

state: TX

address: 1250 Moursund St #1125,

institute: Baylor College of Medicine

summary: We previously showed that NUDT21-spanning copy-number variations (CNVs) are associated with intellectual disability (ID), and that NUDT21-encoded CFIm25 regulates the protein levels of at least one dose-sensitive, ID-associated protein: MeCP2 (Gennarino et al., 2015). However, the patients’ CNVs also spanned multiple other genes raising the possibility that loss or gain of these other genes caused their symptoms. To determine if reduced NUDT21 function alone is sufficient to cause disease, we generated Nudt21 heterozygous null mice to mimic the human state of reduced expression. We found that although these mice have 50% reduced Nudt21 mRNA, they only have 30% less of its cognate protein, CFIm25. Despite this partial protein-level compensation, the Nudt21+/- mice have learning deficits and cortical hyperexcitability. Further, to determine the molecular mechanism driving neural dysfunction, we partially inhibited NUDT21 in human embryonic stem cell-derived neurons to reduce CFIm25 by 30%. This reduction in CFIm25 was sufficient to induce misregulated alternative polyadenylation (APA) and protein levels in hundreds of genes, dozens of which are associated with intellectual disability and whose dysregulation is likely contributing to disease symptoms. Altogether, these results indicate that disruption of NUDT21-regulated APA events in the brain can cause intellectual disability.

overall_design: Anti-NUDT21 and scramble shRNA-infected WA09 human embryonic stem-cell derived excitatory neuron mRNA 3' end sequencing profiles generated by deep sequencing, in triplicate, using Illumina Nextseq 550.

first: Callison

last: Alcott

first: Hari

last: Yalamanchil

first: Ping

last: Ji

first: Meike

last: van der Heijden

first: Alexander

last: Saltzman

first: Mei

last: Leng

first: Bhoomi

last: Bhatt

first: Shuang

last: Hao

first: Qi

last: Wang

first: Afaf

last: Saliba

first: Jianrong

last: Tang

first: Anna

last: Malovannaya

first: Eric

last: Wagner

first: Zhandong

last: Liu

first: Huda

middle: Y

last: Zoghbi


title: RNA-sequencing Analysis Reveals Utility and Limitations of iPSC-derived Cardiomyocytes from Congenital Heart Disease Patients

city: Stanford

first: Lei

last: Tian

address: 1215 Welch Rd

institute: Stanford's Postdoctoral Scholar programs

summary: In conclusion, our result suggested that CHD-iPSC-CMs express specific transcriptome profile, but its significance and correlation with the disease pathogenesis remains to be clarified. Therefore, further effort is needed to use patient-specific iPSC-CMs as an effective tool for CHD research.

overall_design: RNA profiling of human iPSC-CMs from 5 healthy, 5 TOF, and 5 SVD individuals

first: Tomoya

last: Kitani

first: Joseph

last: Wu


title: Myocardial RNA Sequence Analyses throughout the Course of Mouse Cardiac Laminopathy Identify Differential Expressions of the Key Genes for Cell Cycle Control and Mitochondrial Function

city: Cleveland

first: Ying

last: Ni

address: 9500 Euclid Ave

department: Quantitative Health Science

institute: Cleveland Clinic

summary: Gene expression profiling in homozygous LMNA-/- mouse model with cardiomyopathy phenotype unraveled novel LMNA-mediated alterations of signaling pathways leading to dilated cardiomyopathy

overall_design: Gene expression profile comparison in LMNA knockout mice vs LMNA wildtype mice at 3 different time points

first: Wilson


title: Kinetics analysis of gene expression in CD4+ Th17 cells activated with cognate antigen

status: Public on Apr 25 2020

city: Charleston

first: Chrystal

last: Paulos

state: SC

address: 86 Jonathan Lucas St

department: Microbiology & Immunology

institute: Medical University of South Carolina

summary: Analysis of genes expressed at various time points after peptide specific TCR activation in vitro. The hypothesis tested was that activation genes would be upregulated at early times points (D2, D4) while differentiation genes would be expressed at late time points (D12, D18)

overall_design: Total RNA obtained from murine TRP-1 transgenic Th17 cells activated with TRP-1 peptide. RNA was collected at several time points (Day 2, 4, 7, 12, 18) after activation and compared to unactivated, naïve CD4+ T cell controls.

first: Jacob

last: Bowers

first: Hannah

last: Knochelmann


title: Transcriptomic changes induced by salinity stress in the green microalga Chromochloris zofingiensis

city: Shenzhen

first: Xuemei

last: Mao

address: Baishi Road

department: IAS

institute: Shenzhen University

summary: Chromochloris zofingiensis has been considered as potential feedstock for biodiesel production with advantages such as high biomass productivity and great oil content. TAG (triacylglycerol) and astaxanthin accumulate in a well-coordinated manner in response to different stresses in C. zofingiensis. The integrated production of lipids with co-products emerges as a new research direction and is proposed to be a promising approach toward offsetting the algal biodiesel production cost. Therefore, it is suggested C. zofingiensis can serve as research models for the integrated production. Salinity stress simultaneously induced TAG and astaxanthin accumulation in C. zofingiensis. To understand the mechanism underlying TAG and astaxanthin accumulation induced by salinity stress, we applied high-throughput mRNA-sequencing in C. zofingiensis.

overall_design: Chromochloris zofingiensis cells in exponential phase were harvested by centrifugation at 5000 rpm for 5 min and washed twice. Then cells (initial cell density at 0.5 g/L) were re-inoculated in Kuhl medium contained 200 mM of NaCl for salinity stress . Cells were collected for RNA isolation at 0 h and 6 h after re-inoculation. Three biological replicates of algal cultures were carried out under each conditions (salinity stress and control). In total, 6 samples were collected for mRNA-seq.

first: Jin


title: A Tudor-domain containing protein, SIMR-1, mediates silencing of piRNA target mRNAs by the Mutator Complex

city: Arlington

first: Alicia

middle: Kathryn

last: Rogers

state: Texas

address: 1225 W Mitchell Street

department: Department of Biology

institute: University of Texas at Arlington

summary: piRNAs play a critical role in the regulation of transposons and other germline genes. In Caenorhabditis elegans, silencing of piRNA target genes is mediated by the Mutator complex, which synthesizes high levels of siRNAs through the activity of an RNA-dependent RNA polymerase. However, how mRNAs recognized by the piRNA pathway are handed off to the Mutator pathway is unclear. Here, we identify the Tudor domain-containing protein, SIMR-1, as a key mediator of this handoff. Interestingly, SIMR-1 also localizes to distinct subcellular foci adjacent to P granules and Mutator foci, two phase-separated condensates that are the sites of piRNA-dependent mRNA recognition and Mutator complex-dependent siRNA amplification, respectively. Thus, our data suggests a role for multiple perinuclear condensates in organizing the piRNA pathway and promoting silencing by the Mutator complex.

overall_design: 10 small-RNA seq libraries in duplicate, 14 single replicate small-RNA seq libraries, and 10 mRNA-seq libraries in triplicate were generated and analyzed.

first: Carolyn

last: Phillips

first: Kevin

last: Manage

first: Celja

last: Uebel

first: Katerina

last: Arca


title: Mitochondrial Pyruvate Carrier 1 (MPC1) enforces T cell homeostasis by enabling pyruvate oxidation in the mitochondria

city: Holl

first: Ryan

last: O'Connell

state: UT

department: Pathology

institute: University of Utah

summary: The transporter which uptakes pyruvate into the mitochondria during pyruvate oxidation, called the Mitochondrial Pyruvate Carrier (MPC), was only recently identified. While the MPC has been studied in a variety of cell types, including cancer cells and stem cells, very little is known about the importance of MPC in immune cells. Here, we delete MPC from hematopoietic cells and measure its impact on T cell gene expression.

overall_design: CD4 and CD8 T cells were FACS sorted from homogenized and RBC lysed spleens of 8 week old Male MPC1fl/fl (WT) and Vav Cre MPC1fl/fl (MPC1 KO).

first: Andrew

middle: G

last: Ramstead

first: Jared

last: Wallace

middle: M


title: HDAC5-ChIP seq data in HDAC5-driven KRASG12D-independent PDAC cells

first: Pingping

last: Hou

summary: HDAC5 belongs to Class IIa histone deacetylases and forms corepressor complex with HDAC3 to suppess gene expression. To identify the target genes of HDAC5, we performed ChIP-seq analysis in FLAG-tagged HDAC5 PDAC escaper cells. HDAC5 binding chromatins were pulled down by HDAC5 antibody and FLAG antibody as replicates.

overall_design: ChIP-seq were performed in FLAG-tagged HDAC5 PDAC escaper cells.

first: Ming

last: Tang


title: Gene expression data from study on the role of  DISC1 607 variants on immune responses against Toxoplasma gondii

city: Birmingham

first: Shinichi

last: Kano

state: AL

address: 1720 7th Ave South

department: Psychiatry

institute: University of Alabama at Birmingham

summary: A major mental illness-related susceptibility factor, Disrupted in schizophrenia (DISC1), is involved in altered host immune responses against Toxoplasma gondii (T. gondii) infection. Specifically, our gene expression studies have revealed that DISC1 Leu607Phe variation, which changes DISC1 interaction with activating transcription factor 4 (ATF4), modifies gene expression patterns upon T. gondii infection.

overall_design: EBV-transformed human lymphoblastoid cells with DISC1 607 Leu/Leu and Phe/Phe genotypes were infected with T. gondii for 48 hours. Cells were harvested and total RNA was isolated by Qiagen RNEasy kit. Genee expression profiling was conducted with Illumina HT-12 v4.0 platform at the Microarray Core Facility at the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University.

first: Akira

last: Sawa


title: Patient-derived xenograft platform for metastatic melanoma: RNA sequencing of 95 melanoma PDX samples

city: Amsterdam

first: Oscar

last: Krijgsman

state: Outside the US or Canada

address: Plesmanlaan 121

department: Molecular Oncology and Immunology

country: Netherlands

institute: Netherlands Cancer Institute

summary: Although high clinical response rates are seen for immune checkpoint blockade (ICB) of metastatic melanoma, both intrinsic and acquired ICB resistance remain formidable challenges. Combination  ICB shows improved clinical benefit, but is associated with severe adverse events and exceedingly high cost. Therefore, there is a dire need to stratify individual patients for their likelihood of responding to either anti-PD-1 or anti-CTLA-4 monotherapy, or the combination. Since it is conceivable that ICB responses are influenced by both tumor cell-intrinsic and stromal factors, we hypothesized that a predictive classifier ought to mirror both of these distinct features. We used a panel of melanoma patient-derived xenografts (PDX), in which human stromal cells upon transplantation are naturally replaced by their murine counterparts, to computationally subtract PDX RNA expression signals from those in patients’ melanomas. We thus derived both “Stromal immune” (SIM) and tumor cell-specific “Tumor-autonomous inflammation” (TAF) signatures. Here we report  that the SIM signature predicts response to anti-CTLA-4 but not anti-PD-1  treatment, whereas the tumor TAF signature predicts response to anti-PD-1 but not anti-CTLA-4. Moreover, when used in conjunction, the signatures accurately predict response in two independent patient cohorts treated with the anti-CTLA-4 + anti-PD-1 combination. These signatures may be clinically exploited for personalized treatment advice based on the predicted benefit from either anti-CTLA-4 or anti-PD-1 monotherapy or their combination.

overall_design: RNA sequencing of 95 melanoma PDX samples.

first: Kristel

last: Kemper

first: Daniel

last: Peeper


title: Genetic screening for single-cell variability modulators driving therapy resistance

city: Philadelphia

first: Eduardo

last: Torre

state: PA

department: Bioengineering

institute: University of Pennsylvania

summary: We present the transcriptome of WM989 melanona cells without or without inhibition of DOT1L. Different samples represent either the bulk population of melanoma cells, or subpopulations that express high or low levels of the drug resistance markers EGFR and NGFR

overall_design: RNA-seq of WM989 melanona cells without or without inhibition of DOT1L.

first: Eri

last: Arai

first: Sareh

last: Bayatpour

first: Connie

last: Jiang

first: Lauren

middle: E

last: Beck

first: Benjamin

last: Emert

first: Sydney

last: Shaffer

first: Ian

last: Mellis

first: Krista

last: Budinich

first: Filipe

last: Almeida

first: Mitchell

last: Fane

first: Ashani

last: Weeraratna

first: Junwei

last: Shi

first: Arjun

last: Raj


title: RNA-seq analysis of Eubacterium limosum KIST612 across different carbon/energy/electron sources and growth phases.

city: Seoul

first: kucsbl

last: submitter

state: Seoul

address: Anamdong 5-ga, Seongbuk-gu

department: Department of Biotechnology

country: South Korea

institute: Korea University

summary: To understand transcriptional regulation of Eubacterium limosum KIST612 across different carbon/energy/electron sources, RNAseq analysis was carried out over different substrate conditions (glucose, CO, H2/CO2).

overall_design: Comparison of three different substrate conditions (glucose, CO, H2/CO2) at two different growth phases (mid-log phase, early-stationary phase) by differentially expressed genes.

first: Jiyeong

last: Jeong

first: Byeonghyeok

last: Park

first: In-Geol

last: Choi

first: In-Seop

last: Chang


title: Pheno-RNA, a method to identify genes linked to a specific phenotype: application to cellular transformation

city: Boston

first: Rabih

last: Darwiche

state: MA

address: 240 longwwod ave

department: BCMP

institute: Harvard Medical School

summary: Cellular transformation is associated with dramatic changes in gene expression, but it is difficult to determine which regulated genes are oncogenically relevant. Here, we describe Pheno-RNA, a general approach to identify candidate genes associated with a specific phenotype. Specifically, we generate a “phenotypic series” by treating a non-transformed breast cell line with a wide variety of molecules that induce cellular transformation to various extents. By performing transcriptional profiling across this phenotypic series, the expression profile of every gene can be correlated with the transformed phenotype. We identify ~200 genes whose expression profiles are very highly correlated with the transformation phenotype, strongly suggesting their importance in transformation. Within biological categories linked to cancer, some genes show high correlations with the transformed phenotype, but others do not. Many genes whose expression profiles are highly correlated with transformation have never been linked to cancer, suggesting the involvement of heretofore unknown genes in cancer .

overall_design: Performing whole-genome, transcriptional profiling experiments (RNA seq) under 17 transformation conditions, to identify genes whose expression profiles are highly correlated (or negatively correlated) with the degree of transformation.

first: Kevin

last: Struhl


title: The circadian clock gene Bmal1 facilitates cisplatin-induced renal injury and hepatization

status: Public on Apr 24 2020

city: Nanjing

first: Jiangyi

last: Yu

address: No. 155, Hanzhong Rd

institute: Affiliated Hospital of Nanjing University of Chinese Medicine

summary: Cisplatin is one of the most potent chemotherapy drugs to treat cancers, but its clinical application remains limited due to severe nephrotoxicity. Several approaches have been developed to minimize such side effects, notably including chronotherapy, a well-known strategy based on the circadian clock. However, the component of the circadian clock machinery that particularly responses to the cisplatin stimulation remains unknown, including its functions in cisplatin-induced renal injury. In our present study, we demonstrated that Bmal1, as a key clock gene, was induced by the cisplatin stimulation in the mouse kidney and cultured human HK-2 renal cells. Gain- and loss-of-function studies indicated that Bmal1 facilitated cisplatin-induced renal injury both in vivo and in vitro, by aggravating the cell apoptotic process. More importantly, RNA-seq analysis revealed that Bmal1 triggered the expression of hallmark genes involved in renal hepatization, a critical event accompanied by the injury. At the molecular level, Bmal1 activated the transcription of hepatization-associated genes through direct recruitment to the E-box motifs of their promoters. Our findings suggest that Bmal1, a pivotal mediator induced renal injury in response to cisplatin treatment, and the therapeutic intervention targeting Bmal1 in the kidney may be a promising strategy to minimize the toxic side-effects of cisplatin in its clinical applications.

overall_design: Total RNA were isolated from HK-2 cells which were infected with adenovirus expressing either Bmal1 CDS domain or GFP and seqenced using Illumina HiSeq 3000

first: Min

last: Zha

first: Ting

last: Tian

first: Weilong

last: Xu

first: Su

last: Liu

first: Jia

last: Jia

first: Lijuan

last: Wang

first: Qianhua

last: Yan

last: Li


title: Next Generation Sequencing Facilitates Quantitative Analysis of MV4-11 cell line Transcriptomes

city: Chengdu

first: Fangfang

address: Guoxuexiang NO.37

institute: West China Hospital, Sichuan University

summary:
Purpose:  The goals of this study are to compare side population and main population cells transcriptome profiling (RNA-seq) .
Methods: We sorted side population and main population cells by staining Hoechst 33342 and using Flow Cytometer (Beckman Coulter, Moflo XDP). 200,000 cells per sample were analysed in RNA-Seq experiments.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

overall_design: 4 samples: CTR-SP,CTR-MP,A+H-SP,A+H-MP.A+H:AC220+HHT treated MV4-11 for 24h.

first: Yong

last: Guo


title: Transcriptome analysis of C. albicans response to mucin from porcine stomach

city: Wuerzburg

first: Marie-Therese

last: Eckstein

state: Bavaria

department: Molecular Infection Biology

institute: University Clinic Wuerzburg

summary: An RNA-Seq study was undertaken to compare the global response of the fungus C. albicans to intestinal mucin (compared to control medium and medium containing glucose).

overall_design: C. albicans wild type strain was cultured in yeast nitrogen base (YNB) medium (Becton and Dickinson) alone or supplemented with either glucose or mucin from porcine stomach (Sigma). Cultures were incubated at 37°C for 24 h under anaerobic conditions. Cells were collected by centrifugation and RNA was extracted with the RiboPure™ RNA Purification Kit for yeast (Thermo Fisher Scientific) following the manufacturer’s instructions. Illumina library preparation and paired-end sequencing were carried out by Novogene (Cambridge, UK) following standard operating procedures.

first: J

last: Pérez


title: Human villous cytotrophoblast: Rosiglitazone treated (RT-VCT) vs. Control (VCT)

city: PARIS

first: Severine

middle: Aude

last: Degrelle

address: 4 avenue de l'Observatoire

institute: INSERM UMRS-1139

summary: Trophoblasts, as the main part of placenta, undergo cell differentiation including invasion, migration, and fusion. Abnormalities in these processes can lead to a series of gestational diseases whose underlying mechanisms are still unclear. The peroxisome proliferator-activated receptor γ (PPARγ), expressed in the nuclei of extravillous trophoblasts (EVCTs) at the first trimester and villous cytotrophoblasts (VCTs) throughout the pregnancy, is proved to be essential in placentation. We aimed to explore the genome-wide effects of PPARγ on EVCTs and VCTs by the treatment of PPARγ agonist rosiglitazone. EVCTs and CTs were purified from human chorionic villi, followed by primary culture and rosiglitazone treatment. Transcriptomes of EVCTs and VCTs were performed by microarray experiments (Affymetrix and Axon). Owing to the different platforms, threshold for differentially expressed genes (DEGs) detection was performed based on 1.5-fold change and 5% FDR for EVCTs gene expression while 1% FDR was set for VCTs gene expression. Gene ontology (GO) annotation and pathways analysis of DEGs were conducted with ClueGO. PPARγ and DEGs protein interactions predicted by online tool STRING, while PPARγ and DEGs promoters binding sites prediction was conducted by iRegulon. GO and pathway terms were compared between EVCTs and VCTs through ClusterProfiler. Visualization was achieved and modified by Cytoscape. Our microarray data showed that 139 DEGs were detected in rosiglitazone-treated EVCTs (RT-EVCTs) and 197 DEGs in rosiglitazone-treated VCTs (RT-VCTs). Downstream annotation analysis showed the commons and differences between RT-EVCTs and RT-VCTs, including biological process, molecular function, cellular component, KEGG pathway and protein-protein-interaction and transcription factor – target gene binding site prediction. To sum up, our results provide a sight of view to PPARγ-activated trophoblasts performances by giving transcriptomic signatures of the RT-EVCTs and RT-VCTs and make it feasible to acquire more information for further research and find out possible drug-targeted genes or pathways in human placenta.

overall_design: One microgram of total RNA from each sample preparation was amplified using the MessageAmp RNA kit  (Ambion), and 3 µg of amplified RNA  (aRNA) was Cy-dye labeled using the CyScribe first-strand cDNA labeling kit  (Amersham Biosciences). To compare the gene expression pattern obtained from each 24h rosiglitazone-treated cells (RT-VCT) with the  corresponding not treated control cells (VCT), amplified RNA from RT-VCT was labeled with Cy5, while the aRNA from VCT was labeled with Cy3. A total of five (RT-VCT vs VCT) individual cDNA microarrays were performed in this condition.

first: Fulin

first: Christine

last: Rouault

first: Karine

last: Clément

first: Marie-Aline

last: Charles

first: Barbara

last: Heude

first: Séverine

middle: A

first: Thierry

last: Fournier*


title: RNA-sequencing analysis of transcriptional changes in DLD-1 KRAS MUT and WT isogenic cells following IL-22 or IL-6 stimulation

city: Oxford

first: Fiona

last: Powrie

address: Roosevelt Drive

department: Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences

institute: University of Oxford

summary: The cytokine IL-22 promotes tumor progression in murine models of colorectal cancer (CRC). However, the clinical significance of IL-22 in human CRC remained unclear. Using a rigorous discovery/verification analysis of tumor gene expression from over 1,000 patients, we discovered that among CRC patients with high expression of either or both subunits of the heterodimeric IL-22 receptor, KRAS mutation confers poor prognosis. Analysis of human CRC cell lines and primary tumor organoids, including a DLD-1 isogenic cell line pair that differed only in KRAS mutation status, showed that IL-22 and mutant KRAS cooperatively enhance cancer cell proliferation. The purpose of this study was to identify unique mechanisms of interaction between IL-22 signaling and mutant KRAS. Taking advantage of the DLD-1 isogenic pair with match IL-22 receptor expression, differing only in the presence or absence of mutant KRAS global transcriptomic changes were explored in an unbiased manner following IL-22 stimulation. RNA-sequencing was performed on DLD-1 isogenic cells stimulated with 10ng/mL IL-22 for 2h to identify early transcriptional changes and after 24h to explore late changes. Given that IL-6 receptor expression does not interact with mutant KRAS in a prognostically significant manner, nor did it enhance proliferation in KRAS mutant versus WT cells, DLD-1 isogenic cells were also stimulated with 10ng/mL IL-6 for 2 and 24h to identify pathways uniquely regulated by IL-22 and not IL-6.

overall_design: RNA-sequencing of 2 cell lines (DLD-1 KRAS MUT (parental) or WT (KRAS +/-) cells), 3 treatment conditions (untreated, 10ng/mL IL-22, 10ng/mL IL-6), 2 time points (2h, 24h), 3 independent experiments with cell lines at passages 6-8.

first: Nick

last: Ilott

first: Sarah

last: McCuaig

first: David

last: Barras