title: Organ-specific tropism and adaptation after metastasis of ER+ breast cancers

city: Aurora

first: Peter

last: Kabos

state: CO

address: 12801 E. 17th Avenue

department: Division of Medical Oncology

institute: University of Colorado School of Medicine

summary: Patients diagnosed with estrogen receptor (ER) positive breast cancer have a prolonged risk of distal metastatic recurrence to vital organs. Metastatic disease is incurable at present due to the development of treatment resistant cell populations. Here we used single-cell RNA sequencing to evaluate the transcriptome heterogeneity of ER+ breast cancer patient-derived xenografts (PDX) tropic for three common breast cancer metastatic sites – bone, brain, and liver – compared to primary tumors grown in the mammary fat pad. Metastatic cell populations at each location were phenotypically distinct from primary tumor cells with unique transcriptional programs indicative of signaling programs driven by specific transcription factors. Cells that metastasized to brain and liver tissue adopted gene expression programs indicative of the target organ microenvironments. Discerning the organ-specific phenotypic adaptations of metastatic ER+ breast cancer cells may help tailor appropriate therapies for individual patients and to each metastatic site.

overall_design: Single-cell RNA-seq analysis of human breast cancer patient derived xenografts in mice.

first: Austin

middle: E

last: Gillen

first: Nuria

last: Padilla Just

last: Finlay-Schultz

first: Michael

last: Kriss

first: Kent

last: Riemondy

first: James

last: Costello

first: Mark

last: Buckner

first: Elizabeth

last: Wellberg

first: Diana

last: Cittelly

first: Matthew

last: Burchill

first: Kathryn

middle: B

last: Horwitz

first: Jay

last: Hesselberth

first: Carol

last: Sartorius


title: Heat-induced transgenerational memory of upregulated gene expression

status: Public on May 09 2020

city: shanghai

first: junzhong

last: Liu

state: shanghai

address: 300 Feng Lin Road

department: National Key Laboratory of Plant Molecular Genetics

country: China

institute: Institute of Plant Physiology and Ecology, SIBS, CAS

type: Expression profiling by high throughput sequencing

summary: A histone demethylase-heat shock factor- positive feedback loop transmits heat-induced gene activation transgenerationally

overall_design: Examination of gene expression in wildtype, heat-stressed 1st generation Col-0 plants, and in unstressed 2nd and 3rd generation plants and unstressed sgs3-12 plants .

first: Junzhong

first: Qun

last: Li

first: Zuhua

last: He


title: The long noncoding RNA and mRNA expression profiles of human temporomandibular joint synovial fluid derived mesenchymal stem cell altered by IL-1β

status: Public on May 08 2020

city: guang zhou

first: Yangpeng

last: Sun

state: guang dong

address: 56 Lingyuan West Road, Guangzhou, Guangdong

institute: Guangdong Provincial Key Laboratory of Stomatology, Stomatology Hospital of Sun Yat-sen University

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

summary: Synovial fluid derived mesenchymal stem cells (SFMSC) play an important regulatory role in the physiological balance of the temporomandibular joint. IL-1β, as an important pathogenic factor of temporomandibular joint disorders, can affect the biological behaviors of SFMSC, such as inflammatory activation and chondrogenic differentiation. The functional roles of lncRNA and mRNA expression profiles in SFMSC altered by IL-1β are undefined. The aim of this study is to identify the lncRNA and mRNA expression profiles of SFMSC altered by IL-1β.

overall_design: SFMSC was isolated from synovial fluid samples which was donated by 3 temporomandibular joint osteoarthrosis patients when they accepted arthrocentesis and lavage treatment. Differentially expressed lncRNA and mRNA in SFMSC before and after treatment with IL-1β in vitro were detected using human Arraystar Human LncRNA Microarray V3.0, containing 30,586 lncRNA and 26,109 coding transcripts. Probable function for lncRNAs and mRNAs were predicted according to lncRNA-mRNA network.

first: Yu

last: Yao

first: Jiadong

first: Wenting

last: Liao

first: Lingling

last: Qin

first: Kai

last: Su

first: Yunyang

last: Lu


title: Dysbacteriosis-induced LPS elevation disturbs the development of muscle progenitor cells by interfering with retinoic acid signaling [RNA-seq]

city: Guangzhou

first: Jinhuan

last: Song

state: Guangdong

address: Jinan University, No.601, West Huangpu Avenue

institute: Jinan University

summary: Whether myogenesis is affected by the maternal gut dysbacteriosis still remains ambiguous. In this study, firstly we show elevated level of lipopolysaccharides (LPS) in a gut microbiota dysbiosis mouse model. Secondly, we demonstrate that the diameter of muscle fibres, limb development and somitogenesis were inhibited in both gut microbiota dysbiosis and LPS exposed mice and chicken embryos. These might be due to LPS disturbed the cell survival and the key genes which regulating the somitogenesis and myogenesis. RNA sequencing and subsequent validation experiments verified that retinoic acid (RA) signaling perturbation was mainly responsible for the aberrant somite formation and differentiation. Subsequently, we found that LPS-induced Roxidative stress (ROS generation and antioxidant genes such as Nrf2, AKR) contributed to the above-mentioned interference with RA signaling. These findings highlight that the gut microbiota homeostasis also involved in regulating the development of muscle progenitor cells during pregnancy.

overall_design: The control and LPS-treated HH10 chicken embryos were harvested, and then sequenced and analyzed by Shanghai Majorbio Bio-Pharm Technology Co., Ltd (Shanghai, China).

first: Jin-huan

first: Chao-jie

last: Wang

first: Xuesong

last: Yang


title: RNA-Seq analyses reveal that endothelial activation and fibrosis are induced early and progressively by Besnoitia besnoiti host cell invasion and proliferation

city: Zurich

first: giancarlo

last: russo

state: Schweiz

address: winterthurerstrasse 190

department: Functional Genomics Center Zurich

country: Switzerland

institute: ETH/University of Zurich

summary: The pathogenesis of bovine besnoitiosis and the molecular bases that govern disease progression remain to be elucidated. Thus, we have employed an in vitro model of infection based on primary bovine aortic endothelial cells (BAEC), a target cell culture of acute infection. Next, host-parasite interactions were investigated by RNA-Seq at two post-infection (pi) time points: 12 hpi, when tachyzoites have already invaded host cells, and 32 hpi, when Besnoitia besnoiti tachyzoites have replicated for at least two generations. Additionally, the gene expression profile of B. besnoiti tachyzoites was also studied at both pi time points.

overall_design: Primary bovine endothelial cells from bovine aorta (BAEC) were infected with Besnoitia besnoiti tachyzoites and samples were collected at 12 hours post-infection (hpi) or 32 hpi. Non-infected BAEC cells were included as negative controls. 4 biological replicates were included in the experiment

first: Alejandro

last: Jiménez-Meléndez

first: Chandra

last: Ramakrishnan

first: Adrian

last: Hehl

first: Giancarlo

last: Russo

first: Gema

last: Álvarez-García


title: Expression analysis of inflammatory cytokines in exhaled breath condensates from pediatric patients with sickle cell disease, asthma, sickle cell disease and asthma, and controls

city: Bloomington

first: Patricia

last: Silveyra

email: psilveyr@iu.edu, ptrcslvr@gmail.com

state: Indiana

department: Environmental and Occupational Health

country: USA

institute: Indiana University Bloomington

summary: To analyze expression of inflammatory cytokines in Exhaled Breath Condensates from pediatric patients with sickle cell disease, asthma, sickle cell disease and asthma, and controls

overall_design: 29 samples: 10 controls, 10 sickle cell disease, 5 asthma, and 4 sickle cell disease and asthma

first: Pritish

last: Mondal


title: Recurrent evolution of vertebrate transcription factors via transposase capture [ChIP-Seq]

city: Ithaca

first: Rachel

middle: Leigh

last: Cosby

state: NY

address: 218 Biotechnology Bldg, 526 Campus Rd

department: Molecular Biology and Genetics

institute: Cornell University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: How novel genes and cellular functions evolve is a central question in biology. Exon shuffling represents a potent mechanism to assemble new protein architectures. Here we show that DNA transposons, which are mobile and pervasive in genomes, have provided a recurrent supply of both exons and splice sites to assemble novel protein-coding genes in vertebrates. We find that transposase domains have been captured, primarily via alternative splicing, to form new fusion proteins at least 99 times independently over ~350 million years of tetrapod evolution. Evolution favors fusion of transposase DNA-binding domains to host regulatory domains, especially the Krüppel-associated Box (KRAB), suggesting transposase capture frequently yields new transcriptional repressors. Consistent with this model, we show that four KRAB-transposase fusion proteins born independently in different mammalian lineages repress gene expression in a sequence-specific fashion. Genetic knockout and rescue of the bat-specific KRABINER fusion protein in cell culture demonstrates that it binds its cognate transposons genome wide and controls a network of genes and cis-regulatory elements. Transposase capture is thus a powerful mechanism whereby transcription factors and their associated cis-regulatory networks can evolve by repurposing DNA transposon families, which provide both DNA binding domains and pre-existing genomic binding sites.

overall_design: We assessed genomic binding of myc-tagged KRABINER protein variants in transgenic Myotis velifer embryonic fibroblast cell lines

first: Julius

last: Judd

first: Cédric

last: Feschotte


title: Recurrent evolution of vertebrate transcription factors via transposase capture [PRO-Seq]

overall_design: We sequenced nascent RNAs purified from run-on sequencing reactions (PRO-seq) performed in Myotis velifer embryonic fibroblasts either wild-type or knock-out (KO) for the KRABINER gene, as well as KRABINER KO cells rescued with either wild-type, mutated DNA binding domain (DBD) or mutated KRAB KRABINER transgenes.


title: Program of monkey embryogenesis and germ cell formation in vitro [Bulk-seq]

status: Public on May 07 2020

city: shenzhen

first: CNSA

last: CNGB

address: BGI

institute: BGI

summary: Embryo development of post-implantation and gastrulation is a milestone of embryogenesis. However, the fundamental mechanisms underlying this process remain elusive as technological and ethical limitations. Here, we we improved an in vitro culture system that cynomolgus monkey embryos could develop to 20 days without any maternal tissues, which clearly reveal lineage specification, bi-laminar disc generation, amniotic and yolk sac formation, and primordial germ cell like cells (PGCLC). By applying single cell-omics analysis, unsupervised dimensionality reduction and clustering algorithm data show clear, distinct, stepwise development routes for the epiblast, primitive endoderm, trophectoderm and extra-embryonic mesenchyme lineage. We also found development path of PGCLCs, suggesting origin of PGLCs in amnion instead of EPI. Furthermore, signal pathways analysis showed existence of intimate interactions among lineages. By sequencing (scATAC-seq ) assay for transposase-accessible chromatin, we identify transcription factor grammar specifying of each cell type (EPI, PE and TE) and infer potential master transcriptional regulators. Collectively, the results provide the new insight into understanding molecular and cellular dynamics that underlie monkey post-implantation development, especially beyond E13. Our study provides a basic knowledge about regulation of primate pluripotency in vitro for cell replacement therapy.

overall_design: To culture primate embryo in vitro and investigate the molecular determinants of embryonic and extra-embyonic lineage specification

first: Yuyu

last: Niu

first: Ying

last: Lei


title: ADAR1-Dependent RNA Editing Promotes MET and iPSC Reprogramming by Alleviating ER Stress

city: Santiago de Compostela

first: Miguel

last: Fidalgo

state: A Coruña

address: Barcelona Avenue s/n-Campus Vida

department: Physiology

country: Spain

institute: Universidade de Santiago de Compostela

summary: In contrast to chromatin and DNA modifications, whose roles has been widely investigated, the contribution of RNA epitranscriptomics to specification of cellular identity remains largely unexplored. In this study we demonstrated that loss-of-function of ADAR1, an enzyme that catalyzes adenosine deamination in RNA, abrogates epithelial cell fate acquisition during somatic cell reprogramming. Our findings indicate that absence of  A-to-I editing triggers innate immune response and endoplasmic reticulum stress by the cytoplasmic sensor MDA5, resulting in reduced Mesenchymal-to-Epithelial Transition (MET). Additionally, ADAR1 catalytic activity regulates the subcellular distribution of double-strand containing RNAs encoding protein-related membranes. Our study uncovers for the first time the implication of A-to-I RNA editing in cellular plasticity and epithelial specification.

overall_design: RNA profiling  at day 7 of somatic cell reprogramming in Adar Fl/E861A+Veh, AdarFl/E861+4OHT, Adar Fl/Fl +Veh and Adar Fl/Fl+4OHT Mouse Embryonic Fibroblasts.

first: Diana

last: Guallar

last: Fuentes-Iglesias

first: Yara

last: Souto

first: Cristina

last: Ameneiro

first: Oscar

last: Freire-Agulleiro

first: Jose

middle: A

last: Pardavila

first: Adriana

last: Escudero

first: Vera

last: Garcia-Outeiral

first: Tiago

last: Moreira

first: Carmen

last: Saenz

first: Heng

last: Xiong

first: Dongbing

last: Liu

first: Shidi

last: Xiao

first: Yong

last: Hou

first: Kui

last: Wu

first: Daniel

last: Torrecilla

first: Jochen

middle: C

last: Hartner

middle: G

last: Blanco

first: Leo

middle: J

last: Lee

last: López

first: Carl

middle: R

last: Walkley

first: Jianlong


title: Gene expression data from DMD patient hiPSC-derived myoblasts treated with fenofibrate, ginsenoside Rd or DMSO

city: Baltimore

first: Gabsang

state: MD

address: 733 North Broadway

department: School of Medicine

institute: The Johns Hopkins University

summary: Drug development costs a significant amount of time and resources for new pharmaceutical drugs. However, the progress has been limited for orphan diseases such as Duchenne muscular dystrophy (DMD). By using human induced pluripotent stem cells (hiPSCs), here we show an exemplary drug screening campaign and the identification of two potential drugs effective in a DMD mouse model. We developed a DMD-hiPSC screening platform utilizing high-content imaging to identify hit compounds that enhance myogenic fusion abilities of patient-specific myoblasts. Among 1524 compounds (Johns Hopkins Clinical Compound library), two hit compounds restored in vitro fusion defects of DMD patient hiPSC-derived myoblasts. Transcriptional profiling revealed that the function of two hit compounds, ginsenoside Rd (natural product, ginseng extract) and fenofibrate (FDA-approved drug), are associated with FLT3 signaling and TGF-β signaling, respectively. The preclinical tests in mdx mice show that the treatment of the two hit compounds can ameliorate the skeletal muscle and behavioral phenotypes caused by DYSTROPHIN deficiency, suggesting therapeutic potential of these two compounds. Our study demonstrates the feasibility of early-stage drug development for rare diseases using symptom-relevant cells derived from patient-specific hiPSCs.

overall_design: Ginsenoside Rd (5μm),  fenofibrate(8μm) or DMSO(solvent) were used to treat DMD patient (D2325) hiPSC-derived myoblasts for 24 hours in N2 medium without serum. 3 replicates of cells were harvests and processed further.

first: Congshan

last: Sun


title: Immunogenomic identification and characterization of granulocytic myeloid derived suppressor cells in multiple myeloma

city: Cosenza

first: Cirino

last: Botta

address: Via Migliori

department: Hematology Unit

country: Italy

institute: "Annunziata" Hospital of Cosenza

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

overall_design: Refer to individual Series


title: Dysbacteriosis-induced LPS elevation disturbs the development of muscle progenitor cells by interfering with retinoic acid signaling

first: Jinhuan

last: Song

sample_organism:
Gallus gallus
mouse gut metagenome

platform_organism:
Gallus gallus
mouse gut metagenome


title: Program of monkey embryogenesis and germ cell formation in vitro [RNA-seq]

first: CNSA

last: CNGB

first: Yuyu

last: Niu

first: Ying

last: Lei


title: Dysbacteriosis-induced LPS elevation disturbs the development of muscle progenitor cells by interfering with retinoic acid signaling [16S rRNA sequencing]

overall_design: The intestinal flora DNA was extracted from cecum samples of lincomycin hydrochloride or PBS treated pregnant mice using CTAB/SDS method, and then sequenced and analyzed by Novogene.

first: Jin-huan

first: Chao-jie

last: Wang

first: Xuesong

last: Yang


title: RNA-sequencing of primary mouse hematopoietic stem progenitors

city: New York

first: Harold

middle: Kunal

last: Elias

state: New York

address: 417E 68th Street

department: Pathology

institute: Memorial Sloan Kettering Cancer Center

summary: Mechanisms of translational regulation are poorly understood in somatic stem cells. We used polysome profiling, RNA-sequencing, and proteomic approaches to examine translational regulation in hematopoietic stem cell (HSC)-enriched (LSK; Lin-Sca-1+c-Kit+) cells and committed myeloid progenitors (MP). Our studies show that polysomal RNA expression changes more robustly predict changes in protein expression than total RNA and that LSKs preferentially translate transcripts that support HSC maintenance. Collectively, our data reveal that translation is highly regulated during the earliest steps in normal hematopoiesis.

overall_design: Characterizing the translatome in mouse hematopoietic stem and progenitor cells

middle: K

first: Christina

last: Spevak

first: Christopher

middle: Y

last: Park


title: Site-dependent lineage preference of adipose stem cells

city: Morgantown

first: Gangqing

last: Hu

state: West Virginia

address: 64 Medical Center Drive

department: MicroBiology, Immunology, and Cell Biology

institute: West Virginia University

summary: Adult stem cells have unique properties in both proliferation and differentiation preference. However, the molecular mechanisms remain unclear. In this study, we hypothesized that the matrix microenvironment plays a critical role in the fate determination of local stem cells. Four rabbits were used to provide donor-matched adipose stem cells from either subcutaneous adipose tissue (ScAT) or infrapatellar fat pad (IPFP). Proliferation and multi-lineage differentiation were evaluated in adipose stem cells from donor-matched ScAT and IPFP. RNA sequencing (RNA-seq) and proteomics were conducted to uncover potential molecular mechanisms underlying the interaction between adipose stem cells and the local matrix microenvironment. We found that stem cells from ScAT exhibited significantly higher proliferation and adipogenic capacity compared to those from donor-matched IPFP while stem cells from IPFP displayed significantly higher chondrogenic potential compared to those from donor-matched ScAT. Our findings are strongly endorsed by supportive data from transcriptome and proteomics analyses, indicating that a unique extracellular matrix microenvironment is critical in the determination of local stem cell fate.

overall_design: Donor-matched inguinal subcutaneous adipose tissue (ScAT) and infrapatellar fat pad (IPFP) were obtained from four 4-month-old New Zealand white rabbits. The harvested tissues were finely minced and digested using 0.1% collagenase, followed by culture in growth medium. The total RNA samples collected from donor-matched passage 1 IPFP-derived stem cells (IPFSCs) (n=4) and subcutaneous adipose stem cells (ScASCs) (n=4) underwent an initial quality control (QC) check. RNA sequencing was conducted for each.

first: Wang

last: Tingliang

first: Hill

last: Ryan

first: Dzieciatkowska

last: Monika

first: Zhu

last: Lian

first: Infante

last: Aniello

first: Hu

last: Gangqing

first: Hansen

last: Kirk

first: Pei

last: Ming


title: Transcriptomics profiling of the developmental progression of Trypanosoma brucei

city: Mainz

first: Falk

last: Butter

state: Germany

address: Ackermannweg 4

department: Quantitative Proteomics

country: Germany

institute: Institute of Molecular Biology gGmbH

summary: Mitochondrial metabolic remodeling is a hallmark of the Trypanosoma brucei digenetic life cycle since the insect stage utilizes the cost-effective oxidative phosphorylation to generate ATP, while bloodstream cells switch to less energetically efficient aerobic glycolysis. Due to difficulties in acquiring enough parasites from the tsetse fly vector for biochemical analysis, the dynamics of the parasite´s mitochondrial metabolic rewiring in the vector have remained obscure. Here, we took advantage of in vitro-induced differentiation to follow changes at the RNA levels.

overall_design: To determine global changes to the transcriptome across the in vitro induced developmental progression of RBP6OE 123 cells, we applied RNA-seq measurements and analyses

first: Alena

last: Zikova


title: Comparison of Ly6c high splenic monocytes from IL-17A/F-deficient versus control mice

first: Matthias

last: Klein

address: Langenbeckstrasse 1

department: Inst. for Immunology

institute: University Medical Center Mainz

summary: The goal of this study was to compare transcriptional changes, on the single cell level, in splenic monocytes evoked by global IL-17A/F deficiency

overall_design: CD90-CD19-CD11b+Ly6c+(high) monocytes were FACS-sorted from spleens of control and IL-17A/F-deficient mice, single cells were captured and processed using the BD Rhapsody platform, and messenger RNA profiles of 397 genes (BD Rhapsody Immune Response Panel Mm) were generated by deep sequencing using Illumina HiSeq2500

first: Tommy

last: Regen

first: Ari

last: Waisman


title: Human Regulatory T cells from Umbilical Cord Blood Display Increased Repertoire Diversity and Lineage Stability Relative to Adult Peripheral Blood

city: Gainesville

first: M Cecilia

last: Lopez

state: FL

address: 1376 Mowry Road

department: Molecular Genetics and Microbiology

institute: University of Florida

summary: Microarray used to detail bulk transcriptomic differences between sorted CD4+CD25+CD127lo/- Treg and CD4+CD25-CD127+ Tconv from adult peripheral blood (APB) and cord blood (CB) after a 14 day expansion period.

overall_design: CB and APB Tregs and Tconv were FACS sorted as CD4+CD25hiCD127lo and CD4+CD127+, respectively, on a BD FACS Aria III. Both subsets were incubated with anti-CD3 anti-CD28 coated microbeads in the presence of exogenous IL-2 and expanded for 14 days following protocol 1 as described in Seay et al, 2017. 3E5 CB Tregs, CB Tconv, APB Tregs, and APB Tconv were lysed in DNA/RNA lysis buffer (Zymo ResearchR) and stored at -80°C. RNA extraction was achieved using ZR-Duet™ DNA/RNA MiniPrep (Zymo Research, Catalog No. D7001), per the manufacturer’s instructions. Quality assessment of RNA was achieved by Experion™ Automated Electrophoresis System (BIO-RAD) using Experion RNA High Sensitivity Reagents and Experion Standard Sensitivity RNA chips following the manufacturer protocol. Only samples with a minimum RNA concentration of 10 ng/μL and RNA Quality Index (RQI) greater than or equal to 9.4 were used. Briefly, mRNA was reverse transcribed and amplified, and resulting cDNA was fragmented and labeled using Encore Biotin Module (Nugen) and subsequently, hybridized onto GeneChip Human Transcriptome Array 2.0 (Thermo Scientific), following the manufacturer’s procedures.

first: Keshav

last: Motwani

first: Leeana

middle: D

last: Peters

first: William

middle: H

last: Vliegen

first: Ahmed

last: El-sayed

first: Howard

last: Seay

first: M

first: Henry

last: Baker

first: Amanda

middle: L

last: Posgai

first: Maigan

last: Brusko

first: Daniel

last: Perry

first: Rhonda

last: Bacher

first: Michael

last: Haller

first: Todd

middle: M


title: A conserved cytosine-rich sRNA interacting with mycobacterial ribosome and mediate rifampicin phenotypic resistance

city: Shanghai

first: Chuan

last: Wang

address: 131 # Dong An Road

institute: Fudan University

summary: NOT PROVIDED; REQUESTED

overall_design: Tota RNA of Mycobacterium marinum B11-deficient stran (ΔB11) carring either empty plasmid pSMT3 or B11-overexpressed plasmid pSMT3-Phsp60-B11 were compared


title: Genome wide analysis of gene expression changes upon restoration of L-2-hydroxyglutarate dehydrogenase (L2HGDH)

city: Birmingham

first: Sunil

last: Sudarshan

state: AL

address: FOT 1120 -  510 20th Street South

institute: University of Alabama at Birmingham

summary: Renal cancer cells with basal eleavtion of L-2-hydroxyglutarate were transduced with control vector or cDNA encoding L2HGDH

overall_design: Total RNA was extracted from A498 cells expressing control vector (CV) or L2HGDH


title: Expression data in patients with familial (FCS) and multifactorial chylomicronemia (MCM)

city: Montreal

first: Francois

last: Lefebvre

state: QC

address: 845 Sherbrooke St W

department: Human Genetics

country: Canada

institute: McGill University

summary:
FCS and MCM appear highly similar disorders. However, they importantly differ in term of risk and response to treatments. Some sets of genes might be up or down regulated in both disorders and could partly explain those differences.
We used microarrays to explore gene expression patterns in FCS and MCM patients to identify potential targets that can be selected for protein quantification and functional studies.

overall_design: Our study was conducted in a sample of 19 genetically confirmed FCS and 28 MCM patients as well as 15 normolipemic controls. Subjects gave their informed consent and all data were de-identified.

last: Gaudet


title: Recurrent evolution of vertebrate transcription factors via transposase capture

first: Rachel

last: Cosby


title: LKB1 expressed in dendritic cells governs the development and expansion of thymus-derived regulatory T cells

first: Maxim

middle: N.

last: Artyomov

state: MO

address: 660 S. Euclid Avenue, Campus Box 8118

department: Immunology&Pathology

institute: Washington University in St.Louis

summary: Liver Kinase B1 (LKB1) plays a key role in cellular metabolism by controlling AMPK activation. However, its function in dendritic cell (DC) biology has not been addressed. Here, we find that LKB1 functions as a critical brake on DC immunogenicity, and when lost, leads to reduced mitochondrial fitness and increased maturation, migration, and T cell priming of peripheral DCs. Concurrently, loss of LKB1 in DCs enhances their capacity to promote output of regulatory T cells (Tregs) from the thymus, which dominates the outcome of peripheral immune responses, as suggested by increased resistance to asthma and higher susceptibility to cancer in CD11cΔLKB1 mice. Mechanistically, we find that loss of LKB1 specifically primes thymic CD11b+ DCs to facilitate thymic Treg development and expansion, which is independent from AMPK signalling, but dependent on mTOR and enhanced phospholipase C β1-driven CD86 expression. Together, our results identify LKB1 as a critical regulator of DC-driven effector T cell and Treg responses both in the periphery and the thymus.

overall_design: Thymic Dendritic cells subsets (cDC1, cDC2 and pDC) from WT and LKB1 KO mice were isolated from thymi and analyzed.

first: Leonard

last: Pelgrom

first: Alexey

last: Sergushichev

middle: N

first: Bart

last: Everts


title: Mouse Liver Chromatin Circadian ChIP_seq for Bmal1 and Ruvbl2

city: Beijing

first: wang

last: jiawen

address: 7 Science Park Road ZGC Life Science Park

institute: National institute of biological sciences

summary: Mouse livers were collected at 4 hours interval at constant darkness condition after 2 weeks synchronization to ambient light dark cycle, then conducted for the ChIP-seq (Bmal1, Ruvbl2). We found Ruvbl2 rhythmically co-occupancies with Bmal1 binding sites.

overall_design: To evaluate the time course occupancies pattern of Bmal1 and Ruvbl2 in mouse liver.

first: Dapeng

last: Ju

first: Jiawen

first: Eric

middle: E

last: Zhang


title: single-cell mRNA sequencing of human embryonic pancreas

city: Jerusalem

first: Aharon

last: Helman

address: Ein-Kerem

country: Israel

institute: Hebrew university

summary: A drastic transition at birth, from constant maternal nutrient supply in utero to intermittent postnatal feeding, requires changes in the metabolic system. Despite their central role in metabolic homeostasis, little is known about how pancreatic beta cells adjust to the new nutritional program. Our experiments show that after birth beta cells shift from amino acid- to glucose-stimulated insulin secretion that correlates with the nutritional environment of the animal. This metabolic adaptation is mediated by a transition in nutrient sensitivity of the mTORC1 pathway , which leads toresults in intermittent mTORC1 signaling activity. Disrupting nutrient sensitivity of mTORC1 in mature beta cells affects insulin secretion and reverts them to an immature functional state. Finally, manipulating nutrient sensitivity of mTORC1 in stem cell-derived beta cells in vitro strongly enhances their glucose-responsive insulin secretion. These results reveal a mechanism by which nutrient sensing regulates beta cell function, thereby enabling a metabolic adaptation for the newborn.

overall_design:
The goal of this experiment was to compare the transcriptome of embryonic beta cells incubated 4 days in-vitro in different nutrients
comparing medium with high and low amino acid concentration

first: Doug

last: Melton


title: Development and Validation of a DNA Methylation Panel for the Prediction of Outcome in Node-Positive Penile Squamous Cell Carcinoma after Lymphadenectomy

first: Yao

last: Zhu

address: No.270 Dong'an Rd.

department: Urological Oncology

institute: Fudan Universitty Shanghai Cancer Center

type: Methylation profiling by genome tiling array

summary: Genome wide DNA methylation profiling of primary penile squamous cell carcinoma samples with lymphnode metastasis. The Illumina Infinium 450 K Human Methylation was used to obtain DNA methylation profiles in surgical frozen samples. Among the 25 samples, fifteen was infected with HPV, and the others were HPV negative.

overall_design: Bisulphite converted DNA from the 25 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip

first: Weijie

last: Gu


title: Differential expression contributing to memory impairment in AD context

city: Pamplona

first: Ana

last: Garcia Osta

state: Navarra

address: Juslarrocha 10, 3H

department: neuroscience

institute: Cima

summary: Amyloid plaques and neurofibrillary tangles are present in the brains of individuals with intact memory function. The study of these brains can open new avenues to identify new therapeutic targets. This experriment aimed to identified genes contributing to maintain an intact memory in the presence of AD pathology.

overall_design: Comparison of global gene expression profiling in AD mice hippocampi between mice with memory impairment and intact memory

last: García Osta

first: Mar

last: Cuadrado


title: Transcriptome analysis of HEK 293 cells after treatment with Quinolinol B23

city: Singapore

first: Pierre-alexis

last: Goy

state: Singapore

address: 60 Biopolis Street

country: Singapore

institute: Genome Institute of Singapore (GIS-ASTAR)

summary: This work describes the alteration in the expression of genes in response to quinolinol treatment, we noticed an enrichment in the HEK 293 YAP/TAZ signature

overall_design: This dataset contains RNA-seq analysis of DMSO and B23-treated cells, taken as triplicates

first: Ajaybabu

middle: V

last: Pobbati

first: Pierre-Alexis


title: A nutrient sensing transition at birth triggers glucose-stimulated insulin secretion


title: mRNA sequencing of stem cell-derived beta cells before and after transplantation in mice

overall_design: The goal of this experiment was to compare the transcriptome of stage 6 stem cell-derived beta cells in-vitro to transplanted stem cell-derived beta cells


title: Global identification of RNase E sites in Vibrio cholerae

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

institute: ZB MED - Information Centre for Life Sciences

summary: In this study, we employed TIER-seq in V. cholerae to identify cleavage sites of RNase E on a genome-wide scale.

overall_design: V. cholerae wild-type and rneTS (carrying the rne-3071 allele encoding a temperature-sensitive variant of RNase E) were grown in triplicates at 30°C to late exponential phase, divided in half and grown at 30°C or 44°C for 1h before collection of RNA samples. Following RNA-seq, 5'ends profiles were compared to detect RNase E sites (5' ends missing in the rneTS mutant strain at 44°C compared to the wild-type).

first: Mona

last: Hoyos

first: Michaela

last: Huber

middle: U

first: Kai

last: Papenfort


title: Transcriptomic responses to oil, a pathogen, or both in spleen and liver tissues from southern flounder (Paralichthys lethostigma)

status: Public on May 06 2020

city: Ocean Springs

first: Maria

last: Rodgers

state: Mississippi

address: 103 McIlwain Drive

department: Coastal Sciences

institute: University of Southern Mississippi

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

overall_design: P. lethostigma juveniles were exposed to oil, a pathogen (Vibrio anguillarum) or both.  Oil exposure was for 8 days and pathogen exposure was for 1 hour, 24 hours before takedown.  Oil was from the Macondo well from the Deepwater Horizon oil spill and was mixed with sediment, following established procedures.  At the end of the experiments, livers and spleen were taken from organisms, RNA was extracted and sequenced.

first: Robert

last: Griffitt


title: Single-Cell Analyses Reveal Megakaryocyte-Biased Hematopoiesis in Myelofibrosis and Identify Mutant Clone-Specific Targets

city: Oxford

first: Supat

last: Thongjuea

department: The MRC Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

summary: Myelofibrosis is a severe myeloproliferative neoplasm characterised by increased numbers of abnormal bone marrow megakaryocytes that induce fibrosis, destroying the hematopoietic microenvironment.   To determine the cellular and molecular basis for aberrant megakaryopoiesis in myelofibrosis, we performed single-cell transcriptome profiling of 135,929 CD34+Lineage- hematopoietic stem/progenitor cells (HSPCs), single-cell proteomics, genomics and functional assays. We identified a bias towards megakaryocyte differentiation apparent from early multipotent stem cells in myelofibrosis and associated aberrant molecular signatures. A sub-fraction of myelofibrosis megakaryocyte progenitors (MkP) were transcriptionally similar to healthy-donor MkP but the majority were disease-specific, with distinct populations expressing fibrosis- and proliferation-associated genes. Mutant-clone HSPCs showed increased expression of megakaryocyte-associated genes compared to wild-type HSPCs, and we provide early validation of G6B as a potential immunotherapy target. Our study paves the way for selective targeting of the myelofibrosis clone and illustrates the power of single-cell multi-omics to discover tumor-specific therapeutic targets and mediators of tissue fibrosis.

overall_design: We used 10x genomics platform to profile single-cell transcriptome of CD34+Lineage- hematopoietic stem/progenitor cells (HSPCs) derived from   16 human myelofibrosis tissue samples and 5 healthy donors

first: Bethan

last: Psaila

first: Guanlin

last: Wang

first: Elisabeth

last: Heuston

first: Adam

last: Mead


title: Different mechanisms of hypersynchrony initiation lead to divergent transcriptome changes in the mouse forebrain

city: Storrs

first: Rahul

last: Kanadia

state: CT

address: 75 N. Eagleville Road

department: Physiology and Neurobiology

institute: University of Connecticut

summary: Sodium and potassium channelopathies could lead to seizures and epilepsy through two broad mechanisms: aberrant activity of excitatory neurons, or decrease of GABAergic neuron excitability leading to disinhibition. It is currently unknown whether these two modes of seizure induction lead to similar changes in the brain transcriptome. To address this questions, we performed RNAseq on the cortex and hippocampus of P15 Kcnq2Flx/Flx::Emx1-Cre+ and Scn1aA1783V/+::Slc32a1-Cre+ mice that both have seizures and do no survive past weaning age.

overall_design: RNAseq of cortices and hippocampi of 3 Kcnq2 Flx/Flx::Emx1-Cre+ and 3 littermate control mice. RNAseq of hippocampi of 3 Scn1aA1783V/+::Slc32a1-Cre+ and 3 littermate control mice.

first: Anastasios

last: Tzingounis


title: Peripheral Nerve Single-Cell Analysis Identifies Mesenchymal Ligands that Promote Axonal Growth (scRNAseq data)

city: Toronto

first: Freda

last: Miller

state: ON

address: 686 Bay St

institute: Hospital for Sick Children

summary: Peripheral nerves provide a supportive growth environment for developing and regenerating axons and are essential for maintenance and repair of many non-neural tissues. This capacity has largely been ascribed to paracrine factors secreted by nerve-resident Schwann cells. Here, we used single-cell transcriptional profiling to identify ligands made by different injured rodent nerve cell types and have combined this with cell-surface mass spectrometry to computationally model potential paracrine interactions with peripheral neurons. These analyses show that peripheral nerves make many ligands predicted to act on peripheral and CNS neurons, including known and previously uncharacterized ligands. While Schwann cells are an important ligand source within injured nerves, more than half of the predicted ligands are made by nerve-resident mesenchymal cells, including the endoneurial cells most closely associated with peripheral axons. At least three of these mesenchymal ligands, ANGPT1, CCL11, and VEGFC, promote growth when locally applied on sympathetic axons. These data therefore identify an unexpected paracrine role for nerve mesenchymal cells and suggest that multiple cell types contribute to creating a highly pro-growth environment for peripheral axons.

overall_design: We have applied the high-throughput single-cell mRNA sequencing technique Drop seq to the sciatic nerves of neonatal and adult CD1 mice.

first: Jeremy

middle: S

last: Toma

first: Konstantina

last: Karamboulas

first: Matthew

last: Carr

first: Adelaida

last: Kolaj

first: Scott

middle: A

last: Yuzwa

first: Neemat

last: Mahmud

first: Mekayla

last: Storer

first: David

last: Kaplan


title: Single-cell analysis of human retina identifies evolutionarily conserved and species-specific mechanisms controlling development

first: Yufeng

last: Lu

address: 15 Datun Road, Chaoyang District

institute: Institute of Biophysics, Chinese Academy of Sciences

summary: The development of single-cell RNA-Sequencing (scRNA-Seq) has allowed high resolution analysis of cell type diversity and transcriptional networks controlling cell fate specification. To identify the transcriptional networks governing human retinal development, we performed scRNA-Seq over retinal organoid and in vivo retinal development, across 20 timepoints. Using both pseudotemporal and cross-species analyses, we examined the conservation of gene expression across retinal progenitor maturation and specification of all seven major retinal cell types. Furthermore, we examined gene expression differences between developing macula and periphery and between two distinct populations of horizontal cells. We also identify both shared and species-specific patterns of gene expression during human and mouse retinal development. Finally, we identify an unexpected role for ATOH7 expression in regulation of photoreceptor specification during late retinogenesis. These results provide a roadmap to future studies of human retinal development, and may help guide the design of cell-based therapies for treating retinal dystrophies.

overall_design: More than 45000 single cells from the developing human retina, ranging from gestational weeks (GW)12-27, and postnatal retina on day 8 were analyzed via single cell RNA-sequencing.

first: Wenyang

last: Yi

first: Qian

last: Wu

first: Tian

last: Xue

first: Xiaoqun


title: ChIP_seq for Bmal1 and Ruvbl2 in Mouse Liver and for BMAL1, RUVBL2, CRY1 and CRY2 in Human U2OS Cells

first: wang

last: jiawen

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: ChIP-seq from Human U2OS Cell for BMAL1, CRY1, CRY2 and RUVBL2

summary: To evaluate the chromatin binding of BMAL1, CRY1, CRY2 and RUVBL2 in U2OS cells.

overall_design: To evaluate the chromatin occupancies of BMAL1, CRY1, CRY2 and RUVBL2 in U2OS cells.

first: Dapeng

last: Ju

first: Jiawen

last: Wang

first: Eric

last: Zhang


title: mRNA sequencing of stem cell-derived beta cells

first: Aharon

last: Helman

overall_design:
The goal of this experiment was to compare the transcriptome of stage 6 stem cell-derived beta cells in-vitro in different nutrients
comparing medium with different concentrations of amino acids

first: Doug

last: Melton


title: Differential gene expression in mouse myeloid cells

city: Montpellier Cedex 5

first: Anne

last: Blangy

address: 1919 route de Mende

department: CRBM CNRS UMR 5237

country: France

institute: Montpellier Cell Biology Research Center

summary: Among hematopoietic cells, osteoclasts (Oc) and immature dendritic cells (Dc) are closely related myeloid cells with distinct functions; Oc participate skeleton maintenance while Dc sample the environment for foreign antigens. Such specificities rely on profound modifications of gene and protein expression during Oc and Dc differentiation. We provide global proteomic and transcriptomic analyses of primary mouse Oc and Dc, based on original SILAC and RNAseq data. We established specific signatures for Oc and Dc including genes and proteins of unknown functions. In particular, we showed that Oc and Dc have the same α and β tubulin isotypes repertoire but that Oc express much more β tubulin isotype Tubb6. In both mouse and human Oc, we demonstrate that elevated expression of Tubb6 in Oc is necessary for correct podosomes organization and thus for the structure of the sealing zone, which sustains the bone resorption apparatus. Hence, lowering Tubb6 expression hindered Oc resorption activity. Overall, we highlight here potential new regulators of Oc and Dc biology and illustrate the functional importance of the tubulin isotype repertoire in the biology of differentiated cells.

overall_design: mRNA profiles from OC, Dc and Mo derived from mouse bone marrow were generated by deep sequencing, in quadruplicate, in one lane of an Illumina HiSeq 4000, with 1x 50bp single reads.


title: Peripheral Nerve Single-Cell Analysis Identifies Mesenchymal Ligands that Promote Axonal Growth (sympathetic neuron microarray data)

first: Freda

last: Miller

overall_design: Sympathetic neurons from rat superior cervical ganglion (SCG) neurons were isolated from 4 biological replicates to determine the expression of receptor genes.

first: Jeremy

last: Toma

first: Konstantina

last: Karamboulas

first: Matthew

middle: J

last: Carr

first: Adelaida


title: ChIP-seq from Human U2OS Cell for CRY2 and RUVBL2 with DMSO or Cordycepin Treatment

summary: To evaluate the effects of cordycepin on CRY2 and RUVBL2 binding on the chromatin sites, non-synchronized U2OS cells were treated with cordycepin (100 uM) for 1 h, then performed ChIP-seq. We found that cordycepin relieves CRY2 and RUVBL2 proteins from the chromatin for more than 60-70%.

overall_design: To evaluate the occupancies of RUVBL2 and CRY2, when treated or untreated U2OS cells with cordycepin.


title: Lyve1+ cells expressing BRAFV600E show hepatic vascular cavernomas in developing murine liver.

city: Worcester

first: Chinmay

last: Trivedi

state: MA

address: 368 Plantation St, AS7-1047

department: Medicine

institute: University of Massachusetts Medical School

summary:
Analysis of whole liver samples from BRAFV600E F/+;Lyve1-Cre/+ murine embryos at embryonic day 11.5. Results provide insights into the role of BRAF gain-of-function mutation in hepatic endothelial cells during development.
We used microarray to investigate the gene expression program affected by endothelial BRAFV600E during liver development and identified patterns of differentially-expressed genes and pathways during this process.

overall_design: Murine embryonic livers were dissected from E11.5 embryos and pooled for RNA extraction and hybridization on Affymetrix microarray chips. We utilized three samples for each genotypes.

first: Harish

middle: P

last: Janardhan


title: Single-cell transcriptomics of mouse small intestinal epithelial cells and intraepithelial lymphocytes

city: St. Louis

first: Siyuan

last: Ding

address: 425 S. Euclid Ave., MPRB, Rm 9220

department: Molecular Microbiology

institute: Washington University in St. Louis

summary: The goal of this study is to obtain single-cell based transcription data in different intestinal epithelial cell sub-populations. Specifically, we were interested in determining which intestinal epithelial cell subsets express ACE2, the SARS-CoV-2 receptor, and TMPRSS2, a serine protease that facilitates viral spike protein cleavage and virus entry.

overall_design: mRNA profiles of uninfected 5-day old 129sv wild type (WT) mice were generated by 10x genomics using Illumina HiSeq 4000

first: S

first: H

middle: B

last: Greenberg


title: Peripheral Nerve Single-Cell Analysis Identifies Mesenchymal Ligands that Promote Axonal Growth (injured sciatic nerve microarray data)

overall_design: Distal sciatic nerve fragments from resected rat sciatic nerve were isolated from 4 biological replicates per experimental condition to determine the expression of ligand genes. Experimental conditions include 3 day post injured (dpi) nerve, 7 dpi nerve, and contralateral uninjured control sciatic nerve from animals of both the 3 dpi and 7 dpi conditions. Injuries were performed on 6 week old rats.

last: Kolaj

first: Scott

last: Yuzwa

first: Neemat

last: Mahmud

first: Mekayla

last: Storer

first: David

middle: R

last: Kaplan


title: Identification of microRNAs involved in NOD-dependent induction of pro-inflammatory genes in pulmonary endothelial cells

city: Marburg

first: Wilhelm

last: Bertrams

address: Hans-Meerwein-Str. 2

department: Institute for Lung Research

institute: Philipps University Marburg

summary:
Primary lung endothelial cells were isolated from wildtype mice and stimulated with the NOD1 ligand TD or NOD2 ligand MDP. Unstimulated samples were used as controls. RNA was extracted from these samples, reverse transcribed and microRNA expression was analyzed using TLDA.
350 ng RNA per sample were then reverse transcribed using TaqMan MicroRNA Reverse Transcription Kit and Megaplex RT Primers for rodent Pool A. Reverse transcribed RNA was then loaded on the Taqman Low Density Array (TLDA SetA, v.2.0 rodent, Life Technologies) Cards and run according to manufacturer´s recommendations.

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: microRNA profiles were used to identify NOD-regulated endothelial cell microRNAs and in silico target genes


title: A coordinated pathway for the synthesis of a novel blood-red pigment in a Mauritian nectar.

city: Duluth

first: Marshall

last: Hampton

state: MN

address: 1117 University Drive

institute: University of Minnesota Duluth

summary: RNA-Seq of a nectary sample of Nesocodon mauritianus

overall_design: Nesocodon mauritianus was curated and maintained by the College of Biological Sciences Conservatory at the University of Minnesota, St. Paul, Minnesota, U.S.A. Plants were grown in the Cloud Forest + Maritime Climate Room with the temperature maintained between 18 and 24 ˚C and 90-100% relative humidity. RNA was isolated from a single nectary that was manually dissected from a flower 24 hours after anthesis (secretory nectary). The RNA was immediately extracted by mechanical disruption with a microcentrifuge pestle and using an RNAqueous® RNA isolation kit (Ambion, Austin, TX) with Plant RNA Isolation Aid (Ambion, Austin, TX). Agarose gel electrophoresis and UV spectrophotometry were used to assess RNA quality for all samples prior to submission to the University of Minnesota Genomics Center for mRNA isolation, barcoded library creation and Illumina HiSeq 2500 sequencing. A single TruSeq RNA v2 library was created and sequenced via 125 bp, paired-end runs on the HiSeq 2500 using Rapid chemistry on a single lane.

first: Clay

last: Carter


title: ChIP-seq from Human U2OS Cell for BMAL1 and CRY1 with DMSO or Cordycepin Treatment

first: wang

last: jiawen

summary: To evaluate the effects of cordycepin on CRY1 and BMAL1 binding on the chromatin sites, non-synchronized U2OS cells were treated with cordycepin (100 uM) for 1 h, then performed ChIP-seq. We found cordycepin relieves CRY1 proteins from the chromatin for more than 60-70%, while unaffects BMAL1 from the chromatin.

overall_design: To evaluate the occupancies of BMAL1 and CRY1, when treated or untreated U2OS cells with cordycepin.

first: Dapeng

last: Ju

first: Jiawen

last: Wang

first: Eric

last: Zhang


title: Peripheral Nerve Single-Cell Analysis Identifies Mesenchymal Ligands that Promote Axonal Growth

first: Freda

last: Miller


title: Single Cell RNAseq on whole muscle one day after injury and uninjured control

city: Durham

first: James

last: White

state: NC

address: 300 N. Duke St.

institute: Duke University

summary: Cellular landscape changes drastically after injury

overall_design: The Tibialis Anterior (TA) muscle was injected with barium chloride and collected 24 hours after.


title: Global RNA stability profiling reveals stabilization of P-body-enriched transcripts in the absence of human Dcp2

city: West Haven

first: Sarah

last: Slavoff

address: 300 Heffernan Dr

department: Chemistry

institute: Yale University

summary: Multiple RNA decapping enzymes coexist in mammalian cells to regulate decay of distinct subsets of cellular transcripts, but their specificity remains incompletely defined to date. Here we present a global profile of RNA stability changes in human Dcp2 knockout cells via TimeLapse-seq. We demonstrate that P-body enrichment is the strongest correlate of Dcp2-dependent RNA decay, and that post-transcriptional modifications such as m6A present additive effect for Dcp2 targeting. Importantly, our data support a model in which P-bodies are sites that sort translationally repressed transcripts for cytoplasmic decay through additional molecular marks.

overall_design: RNA isolated from cells +/- s4U feed was subjected to oxidative-nucleophilic-aromatic-substitution chemistry and sequenced. All sequencing for experimental samples was performed in duplicate per condition assessed, while negative controls were performed as single replicates without s4U treatment.

first: Jeremy

last: Schofield

first: Yang

last: Luo

first: Matthew

last: Simon


title: Kynurenine 3-monooxygenase upregulates pluripotent genes through β-catenin and promotes triple-negative breast cancer progression

city: Taipei

first: Ji-Lin

last: Chen

state: Taiwan

address: No.201, Sec. 2, Shipai Rd.,, Beitou District

country: Taiwan

institute: VGHTPE

summary: We used microarray to indentify KMO-regulated genes.

overall_design: MDA-MB-231 cells transfected with siRNA against control or KMO were individually assayed on Affymetrix GeneChip Human Genome U133 Plus 2.0 Arrays. Expression values were estimated with the Robust Multi-Arry average algorithm, which resulted in log-2 transformed values for each of 54675 probe sets.

first: Chun-Yu

last: Liu

first: Tzu-Ting

last: Huang


title: Gene expression profile of syphilis complicated with diabetes

city: Hengyang

first: Shuangquan

address: Changsheng Road, Xiangxiang District

institute: University of South China

summary: To further investigate the pathogenesis of syphilis with diabetes, we used a gene chip expression profile from a rabbit model of syphilis with diabetes as a discovery platform to identify potential genes. Grouped into normal control group (n=2) and syphilis combined with diabetes group (n=3).

overall_design: Construction of a syphilis and diabetic rabbit model and construction of gene expression profiles. For each experiment, three independent experiments were performed using different donors.

first: Wei

last: Li


title: Differential tissue-specific damage caused by bacterial epididymo-orchitis in the mouse.

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

summary: This study investigated the differential responses of the epididymis and testis to infection with uropathogenic Escherichia coli (UPEC) in adult mice. In contrast to the cauda epididymidis, which exhibited ongoing damage following UPEC-infection, spermatogenic disruption was reversible and the caput epididymidis was largely unaffected. The caput epididymidis is structurally and functionally very different from the cauda, whereas beta-defensins as important epididymal antimicrobial factors are highly expressed in both tissues. The transcriptome of the testis, caput, corpus and cauda epididymidis were analysed in normal, wildtype C57BL/6J mice. Distinct differences in gene signatures were observed between caput and cauda epididymidis, particularly among immune-related genes, whereas corpus and cauda were much more alike. Beta-defensins were found at high levels in both caput and cauda epididymidis, whereas other antimicrobial factors, such as Lipocalin 2 and Lypd8 were found expressed selectively high in the caput epididymidis and hence may play an important role in local protection from bacterial pathogens, including UPEC.

overall_design: Whole transcriptome analysis of testis, caput, corpus and cauda epididymidis of three C57BL/6J mice at 10-12 weeks of age.

first: Britta

last: Klein

first: Sudhanshu

last: Bhushan

first: Ralf

last: Middendorff

first: Kate

last: Loveland

first: Mark

last: Hedger

first: Andreas

last: Meinhardt


title: Peripheral Nerve Single-Cell Analysis Identifies Mesenchymal Ligands that Promote Axonal Growth (sensory neuron microarray data)

first: Freda

last: Miller

overall_design: Sensory neurons from rat dorsal root ganglia (DRG) neurons were isolated from 6 biological replicates to determine the expression of receptor genes.

last: Toma

first: Konstantina

last: Karamboulas

last: Carr

first: Adelaida

last: Kolaj

first: Scott

last: Yuzwa

first: Neemat

last: Mahmud

first: Mekayla

last: Storer

first: David

last: Kaplan


title: Analysis of miRNA expression in young adult mouse colonocyte (YAMC) cells treated with IFNγ

city: Chicago

first: Fangyi

last: Liu

state: IL

address: 2430 N Halsted St

department: Center for Intestinal and Liver inflammation Research

institute: Stanley Manne Children's Research Institute

summary:
Treatment with IFNγ results in alteration of miRNA expression in young adult mouse colonocyte (YAMC) cells.
We used microarrays to examine the effect of  IFNγ on miRNA expression in intestinal epithelial cells.

overall_design: YAMC cells with and without IFNγ treatment were processed for RNA extraction and Affymetrix GeneChip miRNA Array v. 4.0. Data were futher analyzed using Affymetrix Expression Console software.

first: Xiao-Di

last: Tan


title: ARID1A gene status shapes cancer immune phenotype and affects cancer immunotherapy

city: Ann Arbor,

first: Jing

last: Li

state: MI

address: 500 S State St,

department: Surgery

institute: University of Michigan

overall_design: Refer to individual Series


title: RNA-seq in ARID1A WT, KO OVCA429 Cells after IFNγ treatment

summary: Whether cancer driver mutation(s) directly drives cancer immune phenotype and immune tolerance remains a standing question. ARID1A is a core member of the polymorphic BAF chromatin remodeling complex. ARID1A mutations frequently occur in human cancers and drive cancer development. Here, we studied the molecular, cellular, and clinical impact of ARID1A gene status on cancer immunity. We demonstrate that ARID1A mutations, limited expression, and deficiency impair interferon(IFN)-responsive gene chromatin accessibility and expression, resulting in anemic T cell tumor infiltration, weakened tumor immunity, and shortened host survival  in many human cancer histologies as well as in murine cancer models, and are negatively associated with immunotherapy response. Mechanistically, ARID1A interacts with EZH2 via its carboxyl terminal and antagonizes EZH2-mediated IFN responsiveness. Thus, the interaction between ARID1A and EZH2 defines cancer IFN-responsiveness and immune evasion. Our work indicates that cancer epigenetic driver mutations can shape cancer immune phenotype and immunotherapy.

overall_design: OVCA429 WT cells, OVCA429 ARID1A knockout cells, and TOV21G cells with or without IFNγ treatment for 2 hours and 8 hours, duplicates

first: Weichao

last: Wang

first: Marcin

last: Cieślik

first: Yajia

last: Zhang

first: Arul

last: Chinnaiyan

first: Weiping

last: Zou


title: Oncogene regulated release of extracellular vesicles

city: San Francisco

first: Andrei

last: Goga

state: CA

address: 513 Parnassus Ave

department: Cell & Tissue Biology

institute: UCSF

summary: Oncogenes reprogram multiple metabolic phenotypes of cancer cells including the balance between anabolic and catabolic processes, mechanisms of nutrient uptake, and choices in nutrient utilization. Here, we explore how different oncogenes regulate biomass loss via extracellular vesicle release. We use isogenic mammary breast epithelial cells transformed with a panel of oncogenes found commonly mutated, amplified or overexpressed in multiple cancers. We observe an increase in extracellular vesicle (EV) release upon oncogenic transformation, with MYC and AURKB oncogenes eliciting the highest number of EVs produced. Oncogene expression altered the protein composition of released EVs. Likewise, miRNAs were differentially sorted into EVs in an oncogene-specific manner. We performed an integrated pathway analysis of metabolites and gene expression across different oncogene-expressing cells and identified that ceramide-sphingosine metabolism was broadly deregulated, especially in MYC overexpressing cells. Inhibition of neutral sphingomyelinases (N-SMase) resulted in significant decrease in EV production in MYC high cells, while ESCRT-dependent small EV production predominated in AURKB cells.

overall_design: Gene expression analysis using RNA-seq from three different oncogene-expressing (MYC, AURKB, HRas) and control (Puro/Blast) MCF10A cells to identify dysregulated metabolic pathways that are important for extracelluler vesicle biogenesis

first: Seda

last: Kilinc


title: Genomic Alterations in High-risk CLL Frequently Affect Cell Cycle Key Regulators and NOTCH1‑regulated Transcription.

city: London

first: Jennifer

last: Edelmann

address: Charterhouse Square

department: Centre for Haemato-/Oncology

institute: Barts Cancer Institute

summary: To identify genomic alterations contributing to the pathogenesis of high‑risk chronic lymphocytic leukemia (CLL) beyond the well‑established role of TP53 aberrations, we comprehensively analyzed 146 high‑risk CLL cases by single‑nucleotide polymorphism (SNP)‑arrays and targeted next‑generation sequencing including 75 relapsed/refractory and 71 treatment‑naïve high‑risk cases from prospective clinical trials. Increased genomic complexity was a hallmark of relapsed/refractory and treatment‑naïve high‑risk CLL, and was associated with TP53 and ATM dysfunction. In relapsed/refractory cases previously exposed to the selective pressure of chemo(immuno)therapy, gain(8)(q24.21) and del(9)(p21.3) were found particularly enriched. Both of these copy number alterations (CNAs) affected key regulators of cell cycle progression, namely c‑MYC and CDKN2A/B. Gains in 8q24.21 were either focal gains in a c‑MYC enhancer region or larger gains directly affecting the c‑MYC locus, but only the latter type was highly enriched in relapsed/refractory CLL (17%). Loss of CDKN2A/B was found frequently to co‑occur with gain of c‑MYC and in this combination it was likely associated with Richter transformation. In addition to a high frequency of NOTCH1 mutations (23%), we found recurrent genetic alterations in SPEN (4% mutated), RBPJ (8% deleted) and SNW1 (8% deleted), all affecting a protein complex that represses transcription of NOTCH1 target genes. We investigated the functional impact of these alterations on HES1, DTX1 and c‑MYC gene transcription and found de‑repression of these NOTCH1 target genes particularly with SPEN mutations. In summary, we provide new insights into the pathogenesis of high‑risk CLL by defining novel recurrent CNAs and identifying alterations that likely contribute to disease refractoriness.

overall_design:
Affymetrix SNP arrays were performed according to the manufacturer's protocol on DNA extracted from cryopreserved diagnostic peripheral blood samples.
Copy number analysis of Affymetrix® 6.0 arrays was performed for 146 CLL samples. There are also 91 samples from mononuclear cells negative for CD19 which were taken at treatment-initiation and used as references for copy number inference.

first: Stephan

last: Stilgenbauer


title: Lateral transfer of mRNA by migrasomes modifies the recipient cell

city: Beijing

first: Xuerui

last: Yang

address: Haidian District

department: School of Life Sciences

institute: Tsinghua University

summary: we report the discovery of migrasomal RNA.  High-throughput deep sequencing was used to identifiy and quantify the RNAs in migrasome and cytosol

overall_design: mRNA profiles of purified migrasome and cytosol were generated by deep sequencing

first: Mingli

last: Zhu

first: Qin

first: Rongyao

last: Huang

first: Xudong

last: Xing

first: Jianhuo

last: Fang


title: Profiling of Naïve (CD45RA+CD28+), EM (CD45RA-CD28-) and TEMRA (CD45RA+CD28-) CD8+ T cells

city: Nantes

first: Richard

last: Danger

address: 30 Boulevard Jean Monnet

institute: CHU Nantes - INSERM- Nantes Universite

summary: RNAseq of 3 CD8 subsets (NAIVE, TEMRA and EM) from 8 paired Healthy Volunteers

overall_design: Naïve (CD45RA+CD28+), EM (CD45RA-CD28-) and TEMRA (CD45RA+CD28-) CD3+CD8+ were FACS-sorted from freshly isolated human PBMCs obtained from 8 healthy donors.

first: Lola

last: Jacquemont

first: Gaëlle

last: Tilly

first: Nicolas

last: Degauque


title: "Blind-Killing" of male and female Drosophila embryos by a natural variant of the endosymbiotic bacterium Spiroplasma poulsonii

city: Lausanne

first: Sandra

last: Calderon

address: Génopode Building

department: Center for Integrative Genomics

institute: University of Lausanne

summary: “Blind-Killing” of male and female Drosophila embryos by a natural variant of the endosymbiotic bacterium Spiroplasma poulsonii

overall_design: RNA was extracted from (i) the hemolymph of 30 1-week-old infected flies pelleted by 30 min of centrifugation at 16,000 x g by the TRIzol method following the manufacturer’s instructions. Three independent replicates were prepared for each condition.

first: Florent

last: Masson

last: Calderon Copete

first: Fanny

last: Schüpfer

first: Aurélien

last: Vigneron

first: Samuel

last: Rommelaere

first: Mario

last: Gonzalo Garcia-Arraez

first: Juan

last: Camilo Paredes

first: Bruno

last: Lemaitre


title: RNA-Seq of flowering progress in pitaya

city: Haikou

first: rui

last: xiong

address: Renmin Street

institute: Hainan University

summary: To further explore the molecular mechanisms of flowering regulation in pitaya, we used de novo RNA sequencing-based transcriptomic analysis for four stages of pitaya subjected to light induction. We assembled 68113 unigenes in total, of which 29782 unigenes with functional annotations in the Nr database, 20716 annotations in SwissProt, 18088 annotations in KOG, and 11059 annotations in Kegg

overall_design: The plant material is 'Jindu No.1' red meat pitaya, which is located in Enhong Agricultural Technology company of Dongfang city, Hainan province. The pitaya plants at one year growth status were selected to supplementary light in night. The lighting period was from January 1st to March 31. We divided the experiment into four stages, including NL represents no light, L0 represents no flowering after light treatment, L1 represents flower bud stage after light treatment, L2 represents flowering about a week stage after light treatment.

first: Rui

last: Xiong

first: Liu

last: Chengli

first: Min

last: Xu

first: Wei

last: Shuangshuang

first: Hua

last: Tang


title: Transcriptome characterization of chronic myeloid leukemia by RNA sequencing

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

summary: To determine differentially expressed and spliced transcripts in chronic myeloid leukemia, a high throughput RNA-sequencing (RNA-seq) analysis of ten CML specimens and five normal peripheral blood samples was performed. Thousands of differentially expressed genes between CML and normal control were detected, including genes involved in ribosome and signaling pathway. Splicing alterations analysis performed by an independently developed algorithm reveals that intron retention was the most frequent alternative splicing (AS) events in all the samples. Functional groups of differentially spliced genes most highly correlated with disease phase was (blast crisis relative to chronic phase) included spliceosome and nucleotide excision repair (NER), suggesting that genes involved in these processes may have a major contribution to CML progression by affecting splicing  factors and DNA damage and repair as a consequence of mis-splicing.

overall_design: mRNA profiles of peripheral blood mononuclear cells from five patients in chronic phase(CP), five in blast crisis(BC) of chronic myeloid leukemia and five healthy volunteers were generated by deep sequencing using Illumina NextSeq 500.

first: Shu-Qi

last: Li

first: Xiao-zhong

last: Wang


title: Gene Expression profile of Cetuximab response in Colorectal Cancer Derived Xenograft

city: Candiolo

first: Enzo

last: Medico

state: TO

address: Strada Prov. 142, km 3,95

department: Oncology

institute: Candiolo Cancer Institute, University of Torino

summary: EGFR blockade by the monoclonal antibodies cetuximab or panitumumab causes objective tumor regressions in selected patients with metastatic colorectal cancer (mCRC). However, residual disease reservoirs almost invariably remain even after maximal response to therapy, leading to treatment failure and tumor relapse. Using mCRC patient-derived xenografts (PDXs), we observed that residual cancer cells surviving EGFR inhibition exhibited gene expression patterns reminiscent of a quiescent subpopulation of normal intestinal secretory precursors with Paneth-cell traits. These drug-tolerant cells had reduced expression of EGFR-activating ligands, consistent with lower EGFR dependence, and displayed higher HER2/HER3 pathway activity and persistent PI3K signaling. Mechanistically, cell fate reprogramming towards the Paneth cell-like phenotype was mediated by inactivation of YAP – a master regulator of intestinal epithelium recovery after injury – following cetuximab-induced neutralization of the MAPK cascade. Clinically, tumors from patients in whom cetuximab was not effective were enriched for markers of secretory commitment/Paneth-cell differentiation. In PDX therapeutic experiments, Pan-HER antibodies minimized residual disease burden and induced long-term tumor control after treatment discontinuation. We propose that tolerance to EGFR inhibition in CRC is typified by the adaptive disengagement of an in-built lineage program that jointly drives intestinal regenerative signaling and tumorigenesis. Further, our findings motivate therapeutic strategies to pre-emptively target residual disease before acquisition of irreversible resistance.

overall_design: 120 samples including treated and untreated CRC PDX in ex-vivo setting

first: Andrea

last: Bertotti

first: Livio

last: Trusolino

first: Barbara

last: Lupo

first: Claudio

last: Isella


title: Zebrafish mpeg+ cells

status: Public on May 05 2020

city: Rotterdam

first: Laura

middle: Esmee

last: Kuil

address: Wytemaweg 30

country: Netherlands

institute: Erasmus MC

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


title: Zebrafish juvenile mpeg+ macrophages

summary: We used zebrafish lacking functional csf1r or il34 to unravel how and when csf1r is necessary for macrophages. Transcriptomic analysis of mpeg+ macrophages isolated from juvenile fish revealed that csf1r deficient macrophages show a gross macrophage transcriptome, but reduced expression of engulfment related genes and increased expression of genes typical for metaphocytes.

overall_design: Bulk RNA sequencing of juvenile macrophages obtained from wildtype control, il34-/- and csf1rDM zebrafish (triplicates)

first: L

first: T

last: van Ham


title: Zebrafish embryonic mpeg+ macrophages

summary: We used zebrafish lacking functional csf1r to unravel how and when csf1r is necessary for the development of early tissue macrophages from embryonic macrophages. Transcriptomic analysis of mpeg+ macrophages revealed that csf1r deficient macrophages show a macrophage transcriptome, but reduced expression of cell cycle and RNA/DNA metabolism related genes. Transcriptional changes over time were similar between wildtype controls als csf1r deficient embryonic macrophages.

overall_design: Bulk RNA sequencing of embyonic macrophages obtained from wildtype control and csf1rDM zebrafish embryos at 28 hpf and 50 hpf in triplicates


title: Zebrafish adult skin mpeg+ cells

summary: We compared hematopoietic and non-hematopoietic mpeg1.1+ cells from the skin of wild-type fish with non-hematopoietic cells from the skin of zebrafish lacking functional csf1r. We reval that non-hematopoietic mpeg1.1 cells from wild-type and csf1rDM fish show no major differences and likely represent metaphocytes, a newly characterized ectoderm-derived cell population in the skin. Both non-hematopoietic mpeg1.1+ cell populations from wild-type and csf1r mutatns show a major downregulations in canonical macrophages signature genes as compared to hematopoietic mpeg1.1 cells from wild-type fish.

overall_design: Two biological replicates were analyzed for each of 6 conditions (three genotypes; two treatments per genotype)

first: Valérie

last: Wittamer

first: Giuliano

last: Ferrero


title: Expression data from hiPS-derived lung organoids

city: Baltimore

first: Shaun

middle: Michael

last: Kunisaki

state: MD

address: 1800 Orleans St, Suite 7353

department: Pediatric Surgery

institute: Johns Hopkins University

summary:
Lung organoids made from pluripotent stem cells have the potential to enhance our understanding of disease mechanisms in pediatric lung disorders. As proof of concept, we have established a reproducible ex vivo model of lung organoid development derived from human induced pluripotent stem cells generated from fetuses and infants with Bockdalek congenital diaphragmatic hernia (CDH), a polygenic disorder associated with fetal lung compression and often lethal pulmonary hypoplasia at birth.
We used microarrays to compare transcriptomes among the different cell types focusing on genes associated with lung development and extracellular matrix. We seek to identity anomalous gene expression during lung development, using lung organoids generated from hiPS of patients with congenital diafragmatic hernia.

overall_design: RNA from dermal fibroblasts, iPS cells, and lung organoids (20, 40 and 60 days in vitro) from normal controls and CDH patients was obtained and hybridized on Affymetrix microarray. Two replicates of each sample (control and CDH) were analyzed and compared to one human fetal lung sample (total 20 samples).

first: Guihua

last: Jiang

first: Juan

middle: C

last: Biancotti

first: Kenneth

middle: K

last: Ho

first: Briana

last: Dye

first: Allen

last: Liu

first: Jason

last: Spence


title: MMS induced expression changes and the effect of sorafenib

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

summary: Despite the high toxicity, alkylating agents are still at the forefront of several clinical protocols used to treat cancers. In this study, we investigated the mechanisms underlying alkylation damage responses, aiming to identify novel strategies to augment alkylating therapy efficacy. In this pursuit, we compared gene expression profiles of evolutionary distant cell types (D. melanogaster Kc167 cells, mouse embryonic fibroblasts and human cancer cells) in response to the alkylating agent methyl-methanesulfonate (MMS). We found that many responses to alkylation damage are conserved across species independent on their tumor/normal phenotypes. Key amongst these observations was the protective role of NRF2-induced GSH production primarily regulating GSH pools essential for MMS detoxification but also controlling activation of unfolded protein response (UPR) needed for mounting survival responses across species. An interesting finding emerged from a non-conserved mammalian-specific induction of mitogen activated protein kinase (MAPK)-dependent inflammatory responses following alkylation, which was not directly related to cell survival but stimulated the production of a pro-inflammatory, invasive and angiogenic secretome in cancer cells. Appropriate blocking of this inflammatory component blocked the invasive phenotype and angiogenesis in vitro and facilitated a controlled tumor killing by alkylation in vivo through inhibition of alkylation-induced angiogenic response, and induction of tumor healing.

overall_design: RNA sequencing of two independent cultures of MDA-MB231 cells (MDA213 and MDA213_2). Cell were plated either with (srfnb at 5 µM) or without sorafenib. Medium was exchanged 24 hours lated for media either without (Ctrl) or with MMS (MMS at 40 µg/mL) treatment, maintaining sorafenib exposure as appropriate. RNA was harvested either 8 or 24 hours (8h or 24h) following initiation of MMS exposure.

first: Alfeu

last: Zanotto-Filho

first: Ravi

last: Dashnamoorthy

first: Pragathi

last: Masamsetti

first: Eva

last: Loranc

first: Subapriya

last: Rajamanickam

first: Ana

last: Chavez-Santoscoy

first: Sonal

last: Tonapi

first: Robert

middle: L

last: Reddick

first: Uthra

last: Suresh

first: Alexander

last: Bishop


title: A-to-I RNA editing enzyme Adar1 is essential for cardiac morphogenesis

city: Copenhagen SV

first: Shizuka

last: Uchida

email: heart.lncrna@gmail.com, suc@dcm.aau.dk

address: Frederikskaj 10B, 2. (building C)

department: Department of Clinical Medicine

country: Denmark

institute: Aalborg University

summary: In recent years, the topic of RNA modifications, epitranscriptomics, has gained momentum in a variety of fields. It is now firmly established that modifications of RNA can affect splicing, RNA stability and turnover, and translation, which ultimately influence the pathophysiology of organisms. Although its importance has been appreciated, epitranscriptomics in the heart has not been investigated extensively. Among over 140 RNA modifications, adenosine-to-inosine (A-to-I) RNA editing is of particular interest in the heart as it is reported to be increased in patients of congenital heart defects and atherosclerosis. However, its function in cardiomyocytes, especially during development, has not been investigated.

overall_design: Hearts from two Adar1 (flox/flox) // Nkx2.5-Cre (WT/WT) E18.5 embryos and two Adar1 (flox/flox) // Nkx2.5-Cre (Cre/WT) E18.5 embryos


title: C. elegans development

city: New York

first: Iestyn

last: Whitehouse

state: New York

address: 1275 York Avenue

department: Molecular Biology

institute: Sloan-Kettering Institute


title: C. elegans development (Gro-Seq)

summary: Despite highly conserved chromatin states and cis-regulatory elements, studies of metazoan genomes reveal that gene organization and the strategies to control mRNA expression can vary widely among animal species.  C. elegans gene regulation is often assumed to be similar to that of other model organisms, yet evidence suggests the existence of distinct molecular mechanisms to pattern the developmental transcriptome, including extensive post-transcriptional RNA control pathways, widespread splice leader (SL) trans-splicing of pre-mRNAs, and the organization of genes into operons.  Here, we performed ChIP-seq for histone modifications in highly synchronized embryos cohorts representing three major developmental stages, with the goal of better characterizing whether the dynamic changes in embryonic mRNA expression are accompanied by changes to the chromatin state.  We were surprised to find that thousands of promoters are persistently marked by active histone modifications, despite a fundamental restructuring of the transcriptome.  We employed global run-on sequencing using a long-read nanopore format to map nascent RNA transcription across embryogenesis, finding that the invariant open chromatin regions are persistently transcribed by Pol II at all stages of embryo development, even though the mature mRNA is not produced.  By annotating our nascent RNA sequencing reads into directional transcription units, we find extensive evidence of polycistronic RNA transcription genome-wide, suggesting that nearby genes in C. elegans are linked by shared transcriptional regulatory mechanisms.  We present data indicating that the sharing of cis-regulatory sequences has constrained C. elegans gene positioning and likely explains the remarkable retention of syntenic gene pairs over long evolutionary timescales.

overall_design: Nascent Pol II transcription was analyzed by sequencing replicate nascent RNA libraries for gastrula stage and late stage C. elegans embryos; high-quality fastq reads from replicate Gro-seq libraries were combined into a single library representing gastrula or late embryo nascent transcriptomes

first: James

middle: M

last: Bellush


title: Genome-wide survey of ribosome collision [eif5A siRNA]

city: Saitama

first: Peixun

last: Han

address: Hirosawa Wako

country: Japan

institute: Riken

summary: In protein synthesis, ribosome movement is not always smooth, rather often impeded by numerous reasons. Although the deceleration of ribosome defines the fates of the mRNAs and the synthesizing proteins, fundamental questions remain to be addressed including where ribosomes pause in mRNAs, what kind of RNA/amino acid context causes the pausing, and how physiologically significant the slowdown of protein synthesis is. Here we surveyed the position of ribosome collisions, caused by ribosome pausing, at a genome-wide level using the modified ribosome profiling in human and zebrafish. The collided ribosomes, i.e. disome, emerge at various sites; the proline-proline-lysine motif, stop codons, and 3′ UTR. The number of ribosomes in a collision is not limited to two, rather four to five, forming a queue of ribosomes. Especially, XBP1, a key modulator of unfolded protein response, shows striking queues of collided ribosomes thus acts as a substrate for ribosome-associated quality control (RQC) to avoid the accumulation of undesired proteins in the absence of stress. Our results provide an insight into the causes and the consequences of ribosome slowdowns by dissecting the specific architecture of ribosomes.

overall_design: Ribosome profiling

first: Tilman

last: Schneider-Poetsch

first: Shintaro

last: Iwasaki


title: Genome-wide survey of ribosome collision

overall_design: Refer to individual Series


title: C. elegans development (ChIP-Seq)

overall_design: Examination of H3K27ac and H3K4me2 chromatin modifications at three distinct developmental stages (6 libraries); read counts have been normalized relative to a reference genome spike-in control from S. pombe (Orlando et al. 2014)


title: Genome-wide survey of ribosome collision [monosome/disome]

first: Mari

last: Mito


title: ATAC-seq in ARID1A WT or KO OVCA429 Cells after interferron treatment

first: Jing

last: Li

summary: Whether cancer driver mutation(s) directly drives cancer immune phenotype and immune tolerance remains a standing question. ARID1A is a core member of the polymorphic BAF chromatin remodeling complex. ARID1A mutations frequently occur in human cancers and drive cancer development. Here, we studied the molecular, cellular, and clinical impact of ARID1A gene status on cancer immunity. We demonstrate that ARID1A mutations, limited expression, and deficiency impair interferon(IFN)-responsive gene chromatin accessibility and expression, resulting in anemic T cell tumor infiltration, weakened tumor immunity, and shortened host survival  in many human cancer histologies as well as in murine cancer models, and are negatively associated with immunotherapy response. Mechanistically, ARID1A interacts with EZH2 via its carboxyl terminal and antagonizes EZH2-mediated IFN responsiveness. Thus, the interaction between ARID1A and EZH2 defines cancer IFN-responsiveness and immune evasion. Our work indicates that cancer epigenetic driver mutations can shape cancer immune phenotype and immunotherapy.

overall_design: OVCA429 WT cells, OVCA429 ARID1A knockout cells were treated with or without IFNγ treatment for 3 hours, duplicates

first: Weichao

last: Wang

first: Marcin

last: Cieślik

first: Yajia

last: Zhang

first: Arul

last: Chinnaiyan

first: Weiping

last: Zou


title: Tankyrase inhibitors target colorectal cancer stem cells via AXIN-dependent downregulation of c-KIT tyrosine kinase

city: 江東区

first: Myungkyu

last: Jang

state: 東京都

department: Chemotherapy

institute: JFCR

summary: Tankyrase, a poly(ADP-ribose) polymerase family member, destabilizes Axin and positively regulates the Wnt/β-catenin signaling. We demonstrated that tankyrase inhibitors can target the colorectal cancer stem-like cells. Tankyrase inhibitors efficiently suppress colorectal cancer stem-like cell proliferation via AXIN-dependent manner. We sorted CD44-positive COLO-320DM cells, which showed a characteristic of CSCs and were targeted by tankyrase inhibitors. We analyzed gene expression profile of CD44-positive cells (CD44-positive 01, 02, 03) and CD44-negative cells (CD44-negative 01, 02, 03).

overall_design: We sorted CD44-positive and -negative COLO-320DM cells and found a tankyrase inhibitors can selectively target the CD44-positive COLO-320DM cells. We compared gene expression between CD44-positive (CD44-positive cells 01, 02, 03) and CD44-negative (CD44-negative 01, 02, 03) cells.

first: Tetsuo

last: Mashima

first: Hiroyuki

last: Seimiya


title: Next Generation Sequencing Analysis of livers from 2-month WT/12-month WT and 2-month HKO/12-month nontumor/12month- tumor.

city: Shanghai

first: Chang

state: Shanghai

address: 320 Yue Yang Rd, Xuhui District

department: Shanghai Institute of Nutrition and Health

institute: Chinese Academy of Sciences

summary: SRSF2 flanked with flox was specifically depleted in the livers by Alb-Cre(HKO),and took the intact ones as contorl(WT).Near 70% of the HKO livers spontaneously developed malignant tumors(took the tumor areas as tumor while the tumor-adjacent as nontumor).Then total RNAs of 2-month WT/HKO and 12-month WT/nontumor/tumor were isolated and performed the next generation sequencing. We profiled the  gene expression regulated  by  Cre-loxp-mediated knockout system.

overall_design: mRNA profiles of w8-WT80,w8-HKO82,M13-WT44,M13-HKO24,M13-tumor24 liver samples were generated by deep sequencing.


title: Genome-wide survey of ribosome collision [anisomycin]


title: Niche-Specific Re-Programming of Epigenetic Landscapes Drives Myeloid Cell Diversity in NASH

city: La Jolla

first: Christopher

last: Glass

address: 9500 Gilman Drive

department: School of Medicine

institute: University of California, San Diego


title: Mortality risk score in postsurgical patients based on gene expression

city: Valladolid

first: Pedro

last: Martinez-Paz

state: Valladolid

address: C/ Ramón y Cajal 7

institute: Faculty of Medicine

summary: Nowadays, there are different ICU scoring systems to predict the likelihood of mortality, such as Acute Physiology And Chronic Health Condition (APACHE), Sequential Organ Failure Assessment (SOFA), and SAPS (Simplified Acute Physiology Score). Theses risk scores are based on the use of physiologic and other clinical data. However, the use of these score systems depend on the clinical trust in the reliability and predictions by physicians. In this work, we have evaluated the expression profile by microarray analysis from postsurgical patients with the aim of proposing a candidate set genes as a mortality risk score.

overall_design: Microarray analysis was performed to compare the gene expression profiles from patients who will not die and who will die before 90 days from surgery. After, a set of six upregulated genes were evaluated by real time PCR as a validation platform to verify the potential of these genes as score system.

last: Martínez-Paz

first: Eduardo

last: Tamayo

first: Emilio

last: Garcia-Moran


title: Niche-Specific Re-Programming of Epigenetic Landscapes Drives Myeloid Cell Diversity in NASH [ATAC-seq]

summary: Tissue resident macrophages and recruited monocyte-derived macrophages contribute to host defense but also play pathological roles in a diverse range of human diseases. Multiple macrophage phenotypes are often represented in a diseased tissue, but we lack a deep understanding of the mechanisms that control diversification. Here we use a combination of genetic, genomic, and imaging approaches to investigate the origins and epigenetic trajectories of hepatic myeloid cells during a diet-induced model of nonalcoholic steatohepatitis (NASH). We provide evidence that distinct microenvironments within the NASH liver induce strikingly divergent transcriptomes of resident and infiltrating cells. Myeloid cell diversification results from both remodeling open chromatin landscapes of recruited monocytes and altering activities of preexisting enhancers of resident Kupffer cells. These findings provide evidence that niche-specific combinations of disease-associated environmental signals instruct resident and recruited macrophages to acquire distinct programs of gene expression and corresponding phenotypes.

overall_design: RNA-seq, ATAC-seq, H3K27ac ChIP-seq and LXR alpha + beta ChIP-seq on liver and peripheral myeloid cells in healthy and NASH model diet mice.


title: Niche-Specific Re-Programming of Epigenetic Landscapes Drives Myeloid Cell Diversity in NASH [scRNA-seq]

summary: Tissue resident macrophages and recruited monocyte-derived macrophages contribute to host defense but also play pathological roles in a diverse range of human diseases. Multiple macrophage phenotypes are often represented in a diseased tissue, but we lack a deep understanding of the mechanisms that control diversification. Here we use a combination of genetic, genomic, and imaging approaches to investigate the origins and epigenetic trajectories of hepatic myeloid cells during a diet-induced model of nonalcoholic steatohepatitis (NASH). We provide evidence that distinct micro-environments within the NASH liver induce strikingly divergent transcriptomes of resident and infiltrating cells. Myeloid cell diversification results from both remodeling open chromatin landscapes of recruited monocytes and altering activities of pre-existing enhancers of resident Kupffer cells. These findings provide evidence that niche-specific combinations of diseaseassociated environmental signals instruct resident and recruited macrophages to acquire distinct programs of gene expression and corresponding phenotypes.

overall_design: Single-cell RNA-seq of CD45+ CD146- FACS purified liver non-parenchymal cells from control mice or mice on fed the Amylin liver NASH model diet


title: Niche-Specific Re-Programming of Epigenetic Landscapes Drives Myeloid Cell Diversity in NASH [ChIP-seq]


title: The AML-associated K313 mutation enhances C/EBPα activity by increasing translation via release of ribosome stalling

city: Freiburg

first: Mohamed

middle: Tarek

last: Badr

address: Hermann-Herder-Str. 11

department: Institute of Medical Microbiology and Hygiene

institute: University of Freiburg

summary: Mutations in the transcription factor C/EBPα are found in about 10% of all acute myeloid leukaemia (AML) cases but the contribution of these mutations to leukaemogenesis is incompletely understood. We here use a mouse model of granulocyte progenitors expressing conditionally active HoxB8 to assess the cell biological and molecular activity of C/EBPα-mutations associated with human AML.

overall_design: Total RNA was isolated from HoxB8 neutrophil proginitor cells expressing WT or K313-C/EBPα (day 1 of differentiation). Triplicates were used for hybridization on the Affymetrix Mouse Clariom™ S microarray.

first: I

last: Moelter

first: J

last: Schott

first: D

last: Lindner

first: G

last: Stoecklin

first: K

last: Döhner

first: M

last: Lübbert

middle: T

last: Gentle

last: Häcker


title: Tolerogenic transcriptome landscape in CD8+ T lymphocytes after exposure to erythrocyte-targeted antigen

city: Chicago

first: Jeffrey

middle: Alan

last: Hubbell

address: 5640 South Ellis Avenue, ERC 369

department: Institute for Molecular Engineering

institute: University of Chicago

summary: Our group has recently shown induction of antigen-specific T cell tolerance through targeting antigen to erythrocytes in situ, based on the premise that as the erythrocytes age and are cleared eryptotically, their carried antigen payload is processed tolerogenically. The tolerogenic state is characterized by initial proliferation of antigen-specific CD4+ and CD8+ T cells, and subsequent acquisition of deletional, anergic and CD25+FOXP3+ regulatory T cell phenotypes. In this study, we wished to further understand the molecular mechanisms behind induction of tolerance by erythrocyte-targeted antigens. RNA sequencing was performed to determine how genes are regulated in tolerized ovalbumin-specific CD8+ T cells and which pathways are activated after treatment with this technology. High similarity between the gene response reported during self-tolerance, deletional tolerance and tolerance induced by erythrocyte-targeted antigens was observed. Treatment with erythrocyte-targeted antigens led to the upregulation of genes encoding several TCR co-inhibitory receptors such as CTLA4, PD1, LAG3, TIGIT and CD200R1, and lack of upregulation of cytotoxic and pro-inflammatory signaling molecule genes. Modulation in expression of the master transcription factors Egr2/NFatc1, Nur77 family and E2f1 was also observed, all known to be associated with the process of peripheral tolerance. Expression of these genes differed in response to treatment with soluble ovalbumin or free SIINFEKL MHCI peptide, suggesting a specific mechanism of T cell modulation and tolerance induction in response to the erythrocyte-associated forms. Together these results provide novel insights to further understand the mechanisms and potential of erythrocyte-targeted antigens for induction of antigen-specific immune tolerance.

overall_design: Gene response was evaluted in adoptively transfered ovalbumin-specific CD8+ T cells in mice treated with erythrocyte-targeted ovalbumin (N=3), erythrocyte-targeted SIINFEKL (N=3), soluble ovalbumin (N=3), soluble SIINFEKL (N=2) or in naïve mice (N=3). Naïve group is used as control group to determine background gene levels in resting cells.

first: Alizée

last: Grimm

first: Cédric

last: Gobet

first: Giacomo

last: Diaceri

first: Xavier

last: Quaglia-Thermes


title: ChIP-Seq for LXR in the mouse substantia nigra midbrain dopaminergic cell line SN4741 treated with the synthetic LXR ligand GW3965 for 1.5 hours

city: Stockholm

first: Sten

last: Linnarsson

address: Scheeles väg 1

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

summary: We investigated mechanisms by which LXRs regulate midbrain dopaminergic neuron development. Using a systems biology approach, we found that LXR interacts with β-catenin and that LXR activation inhibits the activity of the Wnt/β-catenin pathway

overall_design: Two replicates each of input with or without GW3965, and two replicates each with LXR antibody with or without GW3965

first: Enrique

last: Toledo

first: Ernest

last: Arenas


title: RNA-seq on mouse E11.5 ventral midbrain neurosphere cultures treated with the LXR agonist GW3965 and the GSK3beta inhibitor CT99021

overall_design: Three replicates each of control, GW3965-treated, CT990212 treated, and combined GW3965+CT99021 treated


title: small RNA sequencing of plasma miRNA from sepsis patients

status: Public on May 04 2020

first: Sheng

last: Wang

address: 660 W Redwood Street, Howard Hall 564

department: Anesthesiology

institute: University of Maryland Baltimore

type: Non-coding RNA profiling by high throughput sequencing

summary:
Purpose: The aim of this study is to compare the plasma miRNA profile between healthy control and sepsis patients
Methods: Plasma from healthy control and sepsis patients were used in the study. Total RNA was isolated from equal volume of plasma using Trizol LS. NGS cDNA libraries were prepared using Norgen Biotek Small RNA Library Prep Kit. Library quality was validated prior to sequencing on an Illumina NextSeq 500 platform.

overall_design: Plasma from eight healthy control and ten sepsis patients were used in this study. cDNA librarues were sequenced using Illumina NextSeq 500 platform.

first: Wei

last: Chao


title: Study of mechanisms by which Liver X Receptors regulate mouse midbrain dopaminergic neuron development

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


title: Intersection of ARID1A, EZH2 RNA-seq in OVCA429 cells with IFNγ treatment

city: Ann Arbor,

first: Jing

last: Li

address: 500 S State St,

department: Surgery

institute: University of Michigan

overall_design: OVCA429 WT cells, OVCA429 ARID1A knockout cells were treated with or without IFNγ treatment for 8 hours; OVCA429 WT cells were treated by IFNγ (8 hours) and GSK126 (48hours). Duplicates

first: Weichao

first: Marcin

last: Cieślik

first: Yajia

last: Zhang

first: Arul

last: Chinnaiyan

first: Weiping

last: Zou


title: DNA methylation and gene expression signatures are associated with ataxia-telangiectasia phenotype [gene expression/RNA-seq]

first: Benjamin

middle: D.

last: Singer

state: Illinois

address: 303 E. Superior St., Simpson Querrey 5th floor

institute: Northwestern University Feinberg School of Medicine

summary: People with ataxia-telangiectasia (A-T) display clinical variability, yet molecular profiles associated with distinct A-T phenotypes remain undefined. We report transcriptional and DNA methylation signatures that inform the regulatory networks underlying A-T phenotypes.

overall_design:
Peripheral blood mononuclear cells from 8 participants with ataxia-telangiectasia, 4 control participants

>>>Submitter states: Raw data are not available because our IRB does not allow us to submit the raw sequence files to either GEO or dbGaP<<<

middle: D

first: Sharon

last: McGrath-Marrow