title: Gene expression of BAT from GRBATKO mice exposed to cold

status: Public on Aug 26 2019

city: Neuherberg

first: Stephan

last: Herzig

address: Ingolstädter Landstraße 1

institute: Helmholtz Zentrum München

summary:
GRBATKO_BAT_COLDEXPOSURE
Aberrant activity of the glucocorticoid (GC)/glucocorticoid receptor (GR) endocrine system has been linked to obesity-related metabolic dysfunction. Traditionally, the GC/GR axis has been believed to play a crucial role in adipose tissue formation and function in both, white (WAT) and brown adipose tissue (BAT). While recent studies have challenged this notion for WAT, the contribution of GC/GR signaling to BAT-dependent energy homeostasis remained unknown.    Here, we have generated and characterized a BAT-specific GR knockout mouse (GRBATKO), for the first time allowing to genetically interrogate the metabolic impact of BAT GR. The HPA axis in GRBATKO mice was intact, as was the ability of mice to adapt to cold. BAT GR was dispensable for the adaptation to fasting-feeding cycles and the development of diet-induced obesity. In obesity, glucose and lipid metabolism, insulin sensitivity, and food intake remained unchanged, aligning with the absence of changes in thermogenic gene expression.
Together, we demonstrate that the GR in UCP1-positive BAT adipocytes plays a negligible role in systemic metabolism and BAT function, thereby opposing a long-standing paradigm in the field.

overall_design: Gene expression of BAT from GRBATKO mice was compared to Flox control mice. RNA from a selection of brown adipose tissue was purified with RNeasy Minikit columns (Qiagen) and analyzed with RNA 6000 Nano chips and the Agilent 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany). One-hundred nanogram of purified RNA was labeled using the Ambion WT expression kit (Invitrogen) and hybridized to an Affymetrix Mouse Gene 1.1 ST array plate (Affymetrix, Santa Clara, CA). Subsequent hybridization, washing, and scanning were carried out on an Affymetrix GeneTitan platform. Processing and analysis of raw data was performed according to published methods (Lichtenstein L, Mattijssen F, de Wit NJ, Georgiadi A, Hooiveld GJ, van der Meer R, He Y, Qi L, Köster A, Tamsma JT, et al. (2010) Angptl4 protects against severe proinflammatory effects of saturated fat by inhibiting fatty acid uptake into mesenteric lymph node macrophages. Cell Metab 12: 580–592.).

first: Frits

last: Mattijssen


title: Genome-wide maps of double-strand breaks

status: Public on Aug 27 2019

city: Jerusalem

first: Idit

last: Hazan

address: Hadassah Medical School

department: Immunology and Cancer Research

country: Israel

institute: Hebrew University

summary: Mapping physiological double strand breaks (DSBs) in cancer cells uncovers transcription-coupled repair mechanism at oncogenic super-enhancers in which RAD51 of the homologous recombination pathway plays a key role supporting the hyper-transcription of related oncogenes.

overall_design: Examination of changes in DSBs profiles in MCF7 cells upon different treatments and manipulations

first: Rami

last: Aqeilan


title: Endothelial TGFβ signaling drives vascular inflammation and atherosclerosis [scRNA-Seq]

city: New Haven

first: Michael

last: Simons

state: CT

address: 3oo George St, Suite 773

department: Department: Internal Medicine Cardiology

country: USA

institute: Yale University

type: Expression profiling by high throughput sequencing

summary: Endothelial TGFβ signaling is one of the primary drivers of atherosclerosis-associated vascular inflammation.  Inhibition of endothelial TGFβ signaling in hyperlipidemic mice reduces vessel wall inflammation and vascular permeability and leads to arrest of disease progression and regression of established lesions. We performed scRNAseq method to examine endothelial cell gene expression profile using Apoe and EC specific TGFbR1/2 KO in Apoe background mice.

overall_design: Using scRNAseq to compare the gene expression profiles of endothelial cells beteewn ApoE mice and EC specific TGFbR1/2 KO Apoe mice fed with high fat diet

first: Pei-Yu

last: Chen


title: Endothelial TGFb signaling drives vascular inflammation and atherosclerosis [bulk RNA-Seq]

overall_design: Examination of different cell types gene expression in response to TGFb stimulation


title: miRWoods: enhanced precursor detection and stacked random forests for the sensitive detection of microRNAs.

city: Corvallis

first: David

middle: Anthony

last: Hendrix

state: OR

address: 2011 Ag & Life Sciences Bldg

department: Biochemistry and Biophysics/EECS

institute: Oregon State University

type: Non-coding RNA profiling by high throughput sequencing

summary: MicroRNAs are conserved, endogenous small RNAs with critical post-transcriptional regulatory functions throughout eukaryota, including prominent roles in development and disease. Despite much effort, microRNA annotations still contain errors and are incomplete due especially to challenges related to identifying valid miRs that have small numbers of reads, to properly locating hairpin precursors and to balancing precision and recall. Here, we present miRWoods, which solves these challenges using a duplex-focused precursor detection method and stacked random forests with specialized layers to detect mature and precursor microRNAs, and has been tuned to optimize the harmonic mean of precision and recall. We trained and tuned our discovery pipeline on data sets from the well-annotated human genome, and evaluated its performance on data from mouse. Compared to existing approaches, miRWoods better identifies precursor spans, and can balance sensitivity and specificity for an overall greater prediction accuracy, recalling an average of 10% more annotated microRNAs, and correctly predicts substantially more microRNAs with only one read. We apply this method to the under-annotated genomes of Felis catus (domestic cat) and Bos taurus (cow). We identified hundreds of novel microRNAs in small RNA sequencing data sets from muscle and skin from cat, from 10 tissues from cow and also from human and mouse cells. Our novel predictions include a microRNA in an intron of tyrosine kinase 2 (TYK2) that is present in both cat and cow, as well as a family of mirtrons with two instances in the human genome. Our predictions support a more expanded miR-2284 family in the bovine genome, a larger mir-548 family in the human genome, and a larger let-7 family in the feline genome.

sample_organism:
Felis catus
Bos taurus

platform_organism:
Felis catus
Bos taurus

overall_design: small RNA sequenciing from different tissues of Bos taurus and Felis catus

first: Jimmy

last: Bell

first: Christiane

last: Löhr

first: Massimo

last: Bionaz


title: Endothelial TGFb signaling drives vascular inflammation and atherosclerosis

type: Genome binding/occupancy profiling by high throughput sequencing

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: Endothelial TGFb signaling drives vascular inflammation and atherosclerosis [ChIP-Seq]

overall_design: Examination of endothelial cell TGFb signaling downstream transcription factor Smad2/3 in the regulation of inflammatory gene promoters.


title: In vivo epigenetic editing of Sema6a promoter reverses impaired transcallosal connectivity caused by C11orf46/ARL14EP neurodevelopmental risk gene

city: NEW YORK CITY

first: Sergio

last: Espeso-Gil

state: New York

address: 1470 Madison Avenue

institute: Icahn School of Medicine at Mount Sinai

summary: Many neuropsychiatric risk genes contribute to epigenetic regulation of gene expression but very little is known about specific chromatin-associated mechanisms governing the formation and maintenance of neuronal connectivity. Here we show that transcallosal connectivity is critically dependent on C11orf46 (also known as ARL14EP), a small nuclear protein encoded in the chromosome 11p13 Wilms Tumor, Aniridia, Genitourinary Abnormalities, intellectual disability (formerly referred to as Mental Retardation) (WAGR) risk locus. C11orf46 haploinsufficiency in WAGR microdeletion cases was associated with severe hypoplasia of the corpus callosum. In utero short hairpin RNA-mediated C11orf46 knockdown disrupted transcallosal projections of cortical pyramidal neurons, a phenotype that was rescued by wild type C11orf46 but not the C11orf46R236H mutant associated with autosomal recessive intellectual disability. Multiple genes encoding key regulators of axonal growth and differentiation, including Sema6A, were hyperexpressed in C11orf46-knockdown neurons. Importantly, RNA-guided epigenetic editing of Sema6a gene promoters via a Cas9 protein-conjugated SunTag scaffold with multimeric (10x) C11orf46 binding, during early developmental periods, resulted in normalization of expression and rescue of transcallosal dysconnectivity by chromatin-associated mechanisms, including upregulation of repressive histone methylation and interaction with the KAP1-SETDB1 repressor complex. Our study demonstrates that interhemispheric communication is highly sensitive to locus-specific remodeling of neuronal chromatin, revealing the therapeutic potential for shaping the brain’s connectome via gene-targeted designer activators and repressor proteins.

overall_design: WAGR vs. control

first: Cyril

middle: J

last: Peter

first: Atsushi

last: Saito

first: Schahram

last: Akbarian

last: Kamiya

first: Joan

last: Han


title: Genome wide mapping of binding sites of the EMT-inducing transcription factor SNAIL1 in LS174T colorectal cancer cells

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

country: Germany

institute: University clinics Freiburg

summary: At the molecular level, epithelial-to-mesenchymal transition (EMT) necessitates extensive transcriptional reprogramming which is orchestrated by a small group of gene regulatory proteins. The transcription factor SNAIL1 is a zinc-finger DNA-binding protein and well-known master regulator of EMT. However, knowledge of its immediate target genes is incomplete. Here, we performed ChIP-seq to chart genome-wide SNAIL1 chromosomal binding sites and to identify genes directly regulated by SNAIL1. For this we used the colorectal adenocarcinoma cell line LS174T which was engineered to express hemagglutinin epitope-tagged murine SNAIL1 in a doxycycline inducible fashion. In total, 1501 SNAIL1-HA ChIP-seq peaks were mapped which were linked to 1307 genes based on nearest neighbor relationships. The vast majority of SNAIL1-HA binding events occurred within 1 kb upstream of transcriptional start sites (44%), and in intergenic regions and promoter-distal introns (46%). De novo motif deduction showed that nearly all ChIP-seq peak regions harbored at least one sequence element corresponding to the cognate SNAIL1 DNA-recognition motif 5’-CAGGTG-3’. SNAIL1-HA ChIP-seq peaks included previously determined SNAIL1 binding sites at the FOXA1, EPHB3, ITGB4 and CLDN3 genes, thus validating the ChIP-Seq results. When comparing the genomic distribution of SNAIL1-HA to that of the intestinal stem cell (ISC) transcription factors ASCL2 and TCF7L2, we observed a significant overlap. Furthermore, SNAIL1-HA ChIP-seq peaks are associated with a substantial fraction of ISC signature genes. In two colorectal cancer cell lines, we verified that SNAIL1 decreases ISC marker expression. Likewise, SNAIL1-HA  was found to occupy multiple regulatory elements at the proto-oncogene MYB, and the long non-coding RNA (lncRNA) WiNTRLINC1, a recently described regulator of ASCL2. Occupancy of the MYB and WiNTRLINC1 regulatory elements by SNAIL1-HA correlated with the downregulation of the two genes. We propose that SNAIL1-mediated repression of MYB and ISC markers like WiNTRLINC1 contributes to the decrease in proliferation known to be associated with EMT, while simultaneously abrogating stemness features of colorectal cancer cells.

overall_design: SNAIL1 chromosomal binding profiles were obtained by chromatin immunoprecipitation followed by next generation sequencing from LS174T colorectal cancer cells allowing for doxycycline-inducible expression of hemagglutinine epitope-tagged murine SNAIL1. Two biological replicates of uninduced (control) and induced (SNAIL1-HA expressing) cells were analyzed. DNA isolated from chromatin not subjected to immunoprecipitation (Input) was sequenced as reference material.

first: Sven

last: Beyes

first: Monika

last: Schrempp

last: Aicher

first: Janna

last: Wenzel

first: Melanie

last: Boerries

first: Andreas

last: Hecht


title: Hsa-miR-139-5p/HNRNPF axis modulates gene-transcripts balance in thyroid cancer cells

city: Madrid

first: Osvaldo

last: Graña

state: Comunidad de Madrid

address: C/ Melchor Fernández Almagro, 3

department: Structural Biology

country: Spain

institute: CNIO

summary: We explored alternative splicing events upon hsa-miR-139-5p/HNRNPF axis regulation in our cell system using the Multivariate Analysis of Transcript Splicing (rMATS) computational tool (https://doi.org/10.1073/pnas.1419161111). Differential analysis of major splicing outcomes (skipped exon, alternative 5’/3’ splice, mutually exclusive exons and retained intron) revealed a total of 174 events significantly activated or repressed (FDR<0.05) upon HNRNPF regulation.

overall_design: CAL62 isogenic cell lines expressing either mature hsa-miR-139-5p or a non-targeting control under a doxycycline inducible promoter were established. Cells were growth with or without doxycycline for 96 hours. The experiment was replicated 3 times and miRNA expression and HNRNPF mRNA/protein abundance quantified. HNRNPF was consistently decreases in doxycycline-treated hsa-miR-139-5p inducible cells.

first: Guillermo

last: Martín-Serrano

last: Graña-Castro

first: Cristina

last: Montero-Conde

first: Mercedes

last: Robledo


title: Arabidopsis TRM5 encodes a nuclear-localised tRNA guanine-N1-methyltransferase and is important for plant growth

status: Public on Aug 25 2019

city: Adelaide

first: Iain

middle: Robert

last: Searle

state: South Australia

address: North Terrace

department: Molecular and Biomedical Science

country: Australia

institute: The University of Adelaide

summary: We show that trm5 plants have less m1G in tRNAs, a slower leaf initiation rate, delayed flowering, and reduced primary root length. Late flowering correlates with reduced transcription of floral activators CO, FT, SOC1 and AP1. We also show that TRM5 methylates tRNA position 37 of several nucleus-encoded tRNA species, trm5 plants have reduced m1G and TRM5 is localized to the nucleus. Our findings highlight the importance of the post-transcriptional tRNA modification m1G37 in plant growth and development.

overall_design: Identification of m1G methylation at position 37 of Arabidopsis thaliana tRNAs and Differential Expression analysis of wild type Col-0 Ecotype and trm5-1 mutant.

middle: R

first: Wenbin

last: Zhou


title: Phosphoethanolamine Accumulation Protects Cancer Cells under Glutamine Starvation through Downregulation of PCYT2

status: Public on Aug 24 2019

city: Tokyo

first: Tsuyoshi

last: Osawa

address: 4-6-1 Komaba, Meguro-ku

department: RCAST

country: Japan

institute: The University of Tokyo

summary: The conditions of the tumor microenvironment, such as nutrient starvation, play critical roles in cancer progression. However, the role of glutamine deprivation in cancer progression is not studied as extensively as that of hypoxia. Here, we show that glutamine starvation triggered down-regulation of PCYT2 by stimulating accumulation of PEtn. Interestingly, glutamine upregulated series of glutamine-responsive genes, not only PCYT2. Furthermore, glutamine-responsive genes were associated with overall survival of cancer patients. Thus, our findings show that glutamine responsive genes such as PCYT2 are key for progression of cancer cells, partly protecting cancer cells to glutamine starvation.

overall_design: Cells were treated for 24 h under each condition. RNA-seq reads were aligned to human transcriptome (UCSC gene) and genome (GRCh37/hg19) references respectively using Burrows-Wheeler Aligner. After transcript coordinate was converted to genomic positions, an optimal mapping result was selected either from transcript or genome mapping by comparing the minimal edit distance to the reference. Local realignment was performed within in-house short reads aligner with smaller k-mer size (k=11). Finally, fragments per kilobase of exon per million fragment mapped (FPKM) values were calculated for each UCSC gene while considering strand-specific information.


title: Gene expression profiles of peptide-primed OT-1 cells with or without corticosteroid

city: Shimotogari, Nagaizumi-cho

first: Akihiro

last: Tokunaga

state: Shizuoka

institute: Kyowa kirin Co., Ltd

summary: We report the gene expression profiles of FACS-sorted OT-I cells stimulated with N4 or Y3 peptide with or without corticosteroids.

overall_design: OT-I cells were stimulated with N4 or Y3 peptide and treated with corticosteroids in vitro for 4 days. mRNA expression was examined with microarray. 1) N4 peptide-primed OT-I cells, 2) N4 peptide-primed OT-I cells treated with corticosteroids, 3) Y3 peptide-primed OT-I cells, 4) Y3 peptide-primed OT-I cells treated with corticosteroids

first: Hiroyoshi

last: Nishikawa


title: Analysis of Drosophila melanogaster Chromosome Topology in Larval Eye and Antennal Discs

city: Baltimore

first: Robert

last: Johnston

state: Maryland

address: 3400 N. Charles St.

department: Biology

institute: Johns Hopkins University

summary: The goal of this study was to examine chromosome topology in Drosophila larval eye and antennal discs by identifying topologically associating domains (TADs) across the genome. TADs were compared between the eye and antennal disc to determine whether they contribute to cell-type-specific homologous pairing and transvection.

overall_design: HiC profiles of Drosophila third-instar larval eye and antennal discs were generated by deep sequencing in triplicate.

first: Kayla

last: Viets

last: Johnston Jr.


title: CytoScan HD array data from Human mammary epithelian cells after Cyclin E overexpression

city: La Jolla

first: SERVANDO

last: GIRALDEZ MACIAS

state: CA

address: 10010 N Torrey Pines Rd

department: REGULATORY BIOLOGY

institute: THE SALK INSTITUTE FOR BIOLOGICAL STUDIES

type: Genome variation profiling by genome tiling array

summary: Cyclin E, a key cell cycle regulatory protein, has been linked to oncogenesis when dysregulated.  We have previously shown that overexpression of cyclin E causes replication stress, leading to failure to complete replication at specific chromosomal loci during S phase of the cell cycle.  This, in turn promotes chromosomal damage during anaphase. Here we show that non-transformed human mammary epithelial cell clones that survive such aberrant mitoses, have a specific and reproducible pattern of chromosomal Copy Number Alterations (CNAs) that we have characterized and termed the cyclin E CNA signature.  Using a number of computational approaches, we show that this signature resembles one specific CNA pattern enriched in differentiated epithelial-like tumors of the breast and ovary. We further show that this CNA signature translates into expected altered patterns of transcription.  In addition, we show that 2 out of 12 clones analyzed were capable of anchorage-independent growth, suggesting acquisition of sufficient oncogenic transformation properties.  Analysis of the CNA profile of these clones provides a potential mechanism for cyclin E-mediated oncogenesis.

overall_design: In order to determine whether cyclin E expression produces a specific genome-wide copy number alteration (CNA) signature, Chromosomal Microarray (CMA) analysis was carried out on DNA from individual clones. CNA call analysis of the CMA data from 12 cyclin E-overexpressing clones and 7 control clones (expressing GFP) was performed to generate a cyclin E-mediated CNA profile.

first: Servando

last: Giraldez

first: Steven

middle: I

last: Reed


title: Small RNA deep sequencing of human thyroid tumors.

summary: Small RNAs of 49 thyroid tissues were extracted and isolated to investigate the correlation of miRNome profiles with specific clinic-pathological and molecular features of the tumors.

overall_design: Forty-six fresh-frozen thyroid tumors representing the histopathological diversity of thyroid cancer and three normal tissues were selected for small RNA deep sequencing.


title: Regulatory interaction between the ZPBP2-ORMDL3/Zpbp2-Ormdl3 region and the circadian clock

city: Montreal

first: Anna

middle: K

last: Naumova

state: QC

address: 1001 Decarie Blvd

department: Obstetrics and Gynecology

country: Canada

institute: McGill University


title: Regulatory interaction between the ZPBP2-ORMDL3/Zpbp2-Ormdl3 region and the circadian clock (RNA-seq at ZT10)

summary:
Purpose: Identifying the biological pathways affected by the deletion of the zona pellucida binding protein 2 in mouse lungs at different time points
Method: RNA profiles of wild type C57BL6/J mice and Zpbp2 homozygous knock-out lungs were generated using next generation sequencing Illumina HiSeq4000 PE100

overall_design: Lung RNA profiles of adult wild type and Zpbp2-/- mice at ZT10

first: Matthew

middle: L

last: Chang

first: Sanny

last: Moussette

first: Enrique

last: Gamero-Estevez

first: Jose

middle: H

last: Galvez

first: Victoria

last: Chiwara

first: Indra

last: Gupta

first: Aimee

last: Ryan


title: Regulatory interaction between the ZPBP2-ORMDL3/Zpbp2-Ormdl3 region and the circadian clock (RNA-seq at ZT7)

summary:
Purpose: Identifying the biological pathways affected by the deletion of the zona pellucida binding protein 2 in mouse lungs at different time points
Method: RNA profiles of wild type C57BL6/J mice and Zpbp2 homozygous knock-out lungs were generated using next generation sequencing Illumina HiSeq2000 SR50

overall_design: Lung RNA profiles of adult wild type and Zpbp2-/- mice at ZT7


title: Expression data of centroblasts (CB) and centrocytes (CC) purified from human tonsils

status: Public on Aug 23 2019

city: RENNES

first: Celine

last: Pangault

address: 2, avenue du Léon Bernard

department: Medical School of Rennes

country: France

institute: Rennes University Hospital

summary: GEP on Affymetrix U133+2.0 microarrays was performed on 6 centroblasts and 6 paired centrocytes from human tonsils in order to explore CB/CC transition and GC-B cell specific signatures

overall_design: 6 different human tonsils were used to purified CB and paired CC by FASCARIA sorting

first: Thierry

last: Fest

first: Fabienne

last: Desmots

first: Karin

last: Tarte


title: Expression data of  human tonsil centroblasts (CB)  cultured w/o CD40L + IL-21

summary: CD40L and IL-21 are major contributors to the transcriptional emergency of PC identify genes in committed B cells. In order to decipher specific CD40L- and IL21-targeted genes, fresly purified human tonsil centroblasts (n=6) were cultured for 3 hours in presence or not of CD40L and IL-21 before transciptome analysis were performed.

overall_design: 6 different human tonsils were used to purified normal centroblast that were cultured for 3 hours with or wihtout CD40L + IL-21


title: Paternal knockout of Slc38a4/SNAT4 causes placental hypoplasia associated with intrauterine growth restriction in mice

city: Tsukuba

first: Shogo

last: Matoba

state: Ibaraki

address: 3-1-1, Koyadai

institute: RIKEN BioResource Research Center

summary: The placenta is critical for mammalian embryonic development because the embryo’s supply of nutrients, including amino acids, depends solely on mother-to-embryo transport through the placenta. However, the molecular mechanisms underlying this amino acid supply are poorly understood. In this study, we focused on the system A amino acid transporters, Slc38a1/SNAT1, Slc38a2/SNAT2, and Slc38a4/SNAT4, which carry neutral, short-side-chain amino acids, to determine their involvement in placental or embryonic development. A triple-target CRISPR screen identified Slc38a4/SNAT4 as the critical amino acid transporter for placental development in mice. We established mouse lines from the CRISPR founders with large deletions in Slc38a4 and found that, consistent with the imprinted paternal expression of Slc38a4/SNAT4 in ther placenta, paternal knockout (KO), but not maternal KO, of Slc38a4/SNAT4 caused placental hypoplasia associated with reduced fetal weight. Immunostaining revealed that SNAT4 was widely expressed in differentiating cytotrophoblasts and maturing trophoblasts at the maternal–fetal interface. A blood metabolome analysis revealed that amino acid concentrations were globally reduced in Slc38a4/SNAT4 mutant embryos. These results indicated that, in mice, SNAT4-mediated amino acid transport plays a major role in both placental and embryonic development. Given that expression of Slc38a4 in placentas is conserved in other species, our Slc38a4/SNAT4 mutant mice could be a promising model for the analysis of placental defects leading to intrauterine growth restriction in mammals.

overall_design: Global gene expression patterns in the placenta of wildtype (WT) and Slc38a4 mutant mice (MKO, PKO, and Null) were analyzed by one-color Mouse Gene Expression 8x60K microarray. RNA was extracted from E13.5 placentas using an RNeasy Mini Kit (Qiagen). Total RNA (200 ng) was amplified and labeled with a Low Input Quick Amp Gene Expression Labeling Kit (#5190-2305, Agilent Technologies). The labeled cRNA was hybridized to a mouse oligo DNA microarray (8x60K, SurePrint G3 Mouse GE v2; #G4852B, Agilent Technologies). After the scan, the signal intensities on the microarray were processed using the Feature extraction software (Agilent Technologies) and analyzed by GeneSpring 14.5 (Agilent Technologies).

first: Shoko

last: Nakamuta

first: Kento

last: Miura

first: Michiko

last: Hirose

first: Hirosuke

last: Shiura

first: Takashi

last: Kohda

first: Nobuaki

first: Atsuo

last: Ogura


title: Regulation of Drosophila intestinal stem cell proliferation by enterocyte mitochondrial pyruvate metabolism

city: Salt Lake City

first: Carl

last: Thummel

state: UT

address: 15 North 2030 East, Room 5200

department: Human Genetics

institute: University of Utah

summary: Purpose: The goals of this study was to compare differentially expressed transcripts when MPC expression is supressed in the adult intestines or enterocyte. The NCBI gene ID for dMPC1 is 42268.

overall_design: Methods: Intestinal mRNA profiles of 7 days old (WT vs dMPC1 Mutant and control RNAi with MPC RNAi in eneterocytes.

first: Dona

last: Wisidagama

middle: S


title: Control ChIP-seq from mammary epithelial cell (ENCSR000AMN)

status: Public on Aug 30 2019

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

summary:
Control ChIP-seq on human mammary epithelial cell

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Gene expression data from human ovarian cancer cells treated with siRNAs targeting CPNE8 and BHLHE41

city: Hidaka

first: Kazuhiro

last: Ikeda

state: Saitama

address: 1397-1 Yamane

institute: Saitama Medical University

summary: To examine the role of CPNE8 and BHLHE41 in ovarian cancer cells, RMG1 cells were treated with siRNA targeting CPNE8 (siCPNE8 #A and #B) or control siRNA (siControl), and OVCAR3 cells were treated with siRNA targeting BHLHE41 (siBHLHE41 #A and #B) or control siRNA (siControl). Microarray analysis showed that CPNE8 and BHLHE41 are involved in cellular signaling pathways in ovarian cancer.

overall_design: RMG1 cells were treated with siCPNE8 #A, siCPNE8 #B, or siControl. OVCAR3 cells were treated with siBHLHE41 #A, siBHLHE41 #B, or siControl. Total RNAs were extracted from these cells and used for Affymetrix microarrays analysis.

first: Saya

last: Nagasawa

first: Kuniko

last: Horie-Inoue

first: Satoshi

last: Inoue


title: NSD2 overexpression links drives clustered chromatin and transcriptional changes in a subset of insulated domains   of insulated domains

status: Public on Sep 03 2019

city: New York

first: Priscillia

last: Lhoumaud

state: NY

address: 550 first avenue Smilow 307

department: Pathology

institute: NYU Langone Health

summary: We analyzed the impact of NSD2 overexpression on 3D genome reorganization and gene expression in multiple myeloma cell lines

overall_design: RNAseq, ChIP-seq, Hi-C and HiChIP in multiple myeloma cell lines

first: Jane

last: Skok


title: Repurposing an anti-cancer drug for the treatment of hypertrophic heart disease

city: London

first: Eleni

last: Maniati

address: John Vane Science Centre, Charterhouse Square

department: Barts Cancer Institute

country: United Kingdom

institute: Queen Mary University of London

summary: Coronary microvascular dysfunction combined with maladaptive cardiomyocyte morphology and energetics are major contributors towards heart failure advancement. Thus dually enhancing cardiac angiogenesis and targeting cardiomyocyte function to slow, or reverse, the development of heart failure is a logical step towards improved therapy. We present evidence for the potential to repurpose a former anti-cancer Arg-Gly-Asp (RGD)-mimetic pentapeptide, Cilengitide, here used at low doses. Cilengitide targets avb3 integrin and this integrin is upregulated in human dilated and ischemic cardiomyopathies. Treatment of mice after transverse aortic constriction (TAC) surgery with low dose Cilengitide (ldCil) enhances coronary angiogenesis and directly affects cardiomyocyte hypertrophy with a correlating reduction disease severity. At a molecular level ldCil treatment has a direct effect on cardiac endothelial cell transcriptomic profiles with a significant enhancement of proangiogenic signalling pathways, corroborating the enhanced angiogenic phenotype after ldCil treatment.

overall_design: RNASequencing on mouse cardiomyocytes isolated and exposed to angiotensin II (AngII) to mimic the molecular stress of  heart failure. AngII-stimulated cells were also treated with low dose Cilengitide (ldCil).

first: Mathew

last: Dukinfield

first: Jun

last: Wang

first: Kairbaan

last: Hodivala-Dilke


title: Adult mouse skin and lung Treg scRNAseq

status: Public on Aug 22 2019

city: San Francisco

first: Jarish

last: Cohen

address: 513 Parnassus Avenue

department: Dermatology

institute: University of California, San Francisco

summary: Comparison of regulatory T cell transcriptional signatures in adult mouse skin and lung.

overall_design: 1 sample of adult murine back skin, 1 sample of adult murine lung

first: Lokesh

middle: A

last: Kalekar

middle: N


title: Global transcriptomic analyses of the candida albicans response to treatment with a novel inhibitor of filamentation

city: San Antonio

first: Yufeng

state: TX

address: One UTSA Circle

institute: University of Texas at San Antonio

summary: The opportunistic pathogenic fungus Candida albicans can cause devastating infections in severely compromised patients. Its ability to undergo a morphogenetic transition from yeast to filamentous forms allows it to penetrate tissues and cause damage, and the expression of a number of pathogenetic mechanisms are also coordinately regulated with this yeast-to-hyphae conversion. Therefore, it is widely considered that filamentation represents one of the main virulence factors of C. albicans. We have previously identified N-[3-(allyloxy)-phenyl]-4-methoxybenzamide (compound 9029936) as the lead compound in a series of small molecule inhibitors of C. albicans filamentation, and characterized its activity, both in vitro and in vivo, as a promising candidate for the development of alternative anti-virulence strategies for the treatment of C. albicans infections. Here we have performed RNA sequencing analysis of samples obtained from C. albicans cells grown under filament-inducing conditions in the presence or absence of this compound.  Overall treatment with compound 9029936 resulted in 618 up-regulated and 702 down-regulated genes. Not surprisingly some of the top down-regulated genes included well characterized genes associated with filamentation and virulence such as SAP5, ECE1 (candidalysin), and ALS3, as well as genes that impact metal chelation and utilization. Gene ontology analysis revealed an over-representation of cell adhesion, iron transport, filamentation, biofilm formation, and pathogenesis processes among down-regulated genes as result of treatment with this leading compound. Interestingly, the top up-regulated genes pointed to an enhancement of vesicular transport pathways, and in particular SNARE interactions.

overall_design: C. albicans SC5314 strain was grown overnight as described above, washed with PBS and used to inoculate YPD containing 10% fetal bovine serum at a 1:30 dilution and incubated at 37 C for 90 minutes in the presence or absence of compound 9029936 at 5 uM. Total RNA was extracted by using a hot acid phenol protocol. Three biological replicates were obtained for each condition (treated and untreated).

first: Jesus

last: Romo

first: Hao

last: Zhang

first: Cai

last: Hong

first: Jose

last: Lopez-Ribot


title: The effect of insulin on mRNA transcription of human pluripotent stem cells

first: Joshua

last: Knowles

state: California

address: 300 Pasteur Dr.

institute: Stanford University

summary: RNA-seq mRNA transcriptome profiling of human induced pluripotent stem (hiPSCs) cells to identify the effect of insulin on regulation of hiPSC transcriptome

overall_design: 3 hiPSCs lines were each cultured with or without insulin for 1 or 3 days (24 hours and 72 hours, respectively). RNA was extracted and used for RNA Sequencing

first: Josh

last: Knowles.

first: Wenyu

last: Zhou.


title: Transcriptome effects mediated by forced overexpression of BACE1-AS in HAOEC cells

city: Milan

first: Fabio

last: Martelli

address: via morandi 30

country: Italy

institute: IRCCS-Policlinico San Donato

summary: Recently, high-throughput studies identified tens of thousands of sites transcribed to produce transcripts with little protein-coding potential. The function of these transcripts remains largely obscure and their relevance to cardiovascular disease is mostly undefined. Many non-protein-coding transcripts belong to the group of Long non coding RNAs (LncRNAs), which are arbitrarily classified according to their length >200 nt. They control protein targeting to genomic loci, epigenetic silencing and serve as scaffolds for multiple proteins.We measured the expression of 83 diseases-related LncRNAs in biopsies from heart failured patients and in controls. We found 15 lncRNAs modulated in HF samples. To explore the functional relevance of two of them, H19 and BACE1-AS, we investigated the effects of their forced overexpression on transcriptome.

overall_design: BACE1-AS were overexpressed by pREceiver-Lv-105 (GeneCopoeia) lentivirus expressing BACE1-AS human cDNA in human aorta endothelial cells (HAOEC). We measured, by llumina HumanHT-12 v4 BeadChip platform, the transcriptome changes induced by the forced overexpression of the LncRNA compared to a negative control (empty vector).

first: Simona

last: Greco

first: Christine

last: Voellenkle

first: J

middle: M

last: Garcia-Manteiga


title: Gene expression levels after TMAO treatment

city: Boston

first: Sudha

last: Biddinger

state: MA

address: 3 Blackfan Cir

institute: boston children's hospital

summary:
TMAO is gut microbiota dependent metabolite catalyzed by monooxygenase FMO3 from TMA. TMAO is positively assocaited with different metabolic diseases such as diabetes, chronic kidney disease, and atherosclerosis.
We used microarray to analyze the genes regulated by TMAO treatment in primary rat hepatocytes to further understand the mechanistic view of TMAO action.

overall_design: Primary rat hepatocytes were isolated from male rat liver and treated with TMAO (50 μM) for 30 h or left untreated as control. Total RNA was extracted for microarray analysis. Three biological repeats have been performed.

first: Sifan

last: Chen


title: Systematic identification of immunotherapy targets using genome-scale in vivo CRISPR screens in CD8+ cytotoxic T cells [scRNA-Seq]

city: West Haven

first: Ryan

middle: D

last: Chow

address: 850 West Campus Drive

institute: Yale University

summary: CD8+ cytotoxic T cells play essential roles in anti-tumor immune responses. Here, we performed in vivo screens in CD8+ T cells and identified regulators of tumor infiltration and killing, which are directly relevant to cancer immunotherapy. Unlike in vitro screens, the in vivo screen robustly re-identified canonical immunotherapy targets such as PD-1 and Tim-3, along with genes that have not been characterized in T cells. The infiltration and degranulation screens converged on an RNA helicase Dhx37. Dhx37 knockout enhanced the efficacy of antigen-specific CD8+ T cells against cancer in vivo. Immunological characterization in mouse and human CD8+ T cells revealed that DHX37 suppresses effector function, cytokine production, and T cell activation. Transcriptomic profiling and biochemical interrogation revealed a role for DHX37 in modulating the NF-kB pathway. These data demonstrated the power of high-throughput in vivo genetic screens for immunotherapy target discovery, and uncovered DHX37 as a functional regulator of CD8+ T cells.

overall_design: Rag-/- were transplanted with E0771-mCherry-OVA cells. OT-1; Cas9 CD8+ T cells were harvested and transduced with either lenti-Vector or lenti-sgDhx37. Transduced T cells were then adoptively transferred into the tumor-bearing mice. Tumor-infiltrating lymphocytes were subsequently FACS isolated and subject to 10x Genomics single cell RNA-seq.

first: Sidi


title: Nuclear Receptor Corepressor 1 (NCoR1) deletion changed the expression profile in cardiomyocytes

city: DALLAS

first: Zhao

middle: V.

last: Wang

address: 6000 Harry Hines Blvd

institute: UT southwestern medical center

summary: NCoR1 played an important role in regulating the expression of many genes. We were wondering what kinds of genes the NCoR1 would regulate in cardiomyocytes. Therefore we generated the cardiomyocyte-specific  NCoR1 knockout mice (CMNKO). Then we tried to analyze gene expression of left ventricular from littermate control (LC) and CMNKO mice  with an unbiased way.  Therefore the samples from left ventricular were subjected RNA-sequencing.

overall_design: LV samples were collected from littermate control (LC) and cardiomyocyte-specific NCoR1 knockout (CMNKO) mice at the age of 2 months. Then the samples were sent for RNA sequencing.

first: Sheng-Zhong

last: Duan

first: Chao

last: Li


title: Systematic identification of immunotherapy targets using genome-scale in vivo CRISPR screens in CD8+ cytotoxic T cells [RNA-Seq]

overall_design: 4 biological replicates each of mouse OT-1; Cas9 CD8+ T cells, transduced by AAV6 to express either empty vector or sgDhx37


title: RAG-mediated DNA breaks attenuate PU.1 activity in early B cells through activation of a SPIC-BCLAF1 complex [ChIP-Seq]

city: St. Louis

first: Jeffery

last: Bednarski

state: Missouri

address: 660 S. Euclid Ave., Campus Box 8208

department: Department of Pediatrics

institute: Washington University School of Medicine

summary: RAG DSBs trigger ATM-dependent induction of SPIC, an ETS family transcriptional repressor with significant homology to PU.1. RAG DSB-mediated expression of SPIC results in displacement of PU.1 throughout the genome and induction of broad transcriptional changes in pre B cells. SPIC also binds and recruits a unique partner, BCLAF1 to gene regulatory elements that regulate expression of key B cell developmental genes.

overall_design: ChIP was performed using anti-PU.1, anti-HA, and anti-BCLAF1

first: Jeffrey


title: RAG-mediated DNA breaks attenuate PU.1 activity in early B cells through activation of a SPIC-BCLAF1 complex

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

overall_design: Refer to individual Series


title: RAG-mediated DNA breaks attenuate PU.1 activity in early B cells through activation of a SPIC-BCLAF1 complex [RNA-Seq]

overall_design: All cells were treated with imatinib for 48 hours. RNA was extracted using RNeasy Kit. Libraries were prepared using Illumina TruSeq Adpaters and paired-end sequencing was performed using an Illumina HiSeq 3000.


title: Systematic identification of immunotherapy targets using genome-scale in vivo CRISPR screens in CD8+ cytotoxic T cells

state: CT


title: RNA Sequencing  Analysis of macrophage and CD4+T cells from Wild Type and Gsdmd-/- mice

city: Nanjing

first: Yuqing

last: Wu

address: 101 Longmian Road

country: China

institute: Nanjing Medical University

summary: We identified that GSDMD was required for the pathogenesis of EAE, and GSDMD deficiency in peripheral myeloid cells impaired the infiltration of immune cells into the CNS , leading to the suppression of neuroinflammation and demyelination.The purpose of this experiment was to identify how GSDMD induces EAE.

overall_design: Macrophage and CD4+T cells mRNA profiles of wild type (WT) and Gsdmd-/- mice with experimental autoimmune encephalomyelitis were generated by deep sequencing, in triplicate, using BGISEQ-500

first: Shuo

last: Yang

first: Sheng


title: RNAseq of zebrafish (Danio rerio) developmentally exposed to the polychlorinated biphenyl 3,3'-dichlorobiphenyl (PCB-11)

city: Amherst

first: Alicia

last: Timme-Laragy

address: 686 North Pleasant Street, Goessmann Building, Room 149

department: Environmental Health Sciences

institute: UMass Amherst

summary: 3,3’-Dichlorobiphenyl (PCB-11) is a non-legacy PCB congener widely detected in environmental samples and has been detected in human serum, but its toxicity potential is poorly understood. Zebrafish statically exposed to 4,500 µg/L PCB-11 at 24 hours post fertilization (hpf) were collected at 96 hpf for RNA sequencing.

overall_design: At 96 hpf, triplicate pools of 18-20 zebrafish eleutheroembryos exposed to either DMSO or 4,500 µg/L PCB-11 were transferred immediately to FastPrep homogenization tubes containing TRIzol Reagent (Life Technologies) and 0.1 mm RNase free Glass Beads (Next Advance, Inc.). The content was vortexed for 15 seconds, and homogenized in FastPrep-24 5G bead beater (MP Biomedicals) using the following parameters – speed: 6.0 m/sec, time: 30 seconds, and adapter: QuickPrep. The homogenate was spun, and the supernatant was transferred to a sterile tube. Total RNA was purified using the Direct-zol RNA MicroPrep kit with an in-column DNase-I treatment (Zymo Research Corp.), following manufacturer instructions. The quantity of RNA was assayed on Qubit using the RNA BR assay (Life Technologies Corp.), and quality was assessed on an Agilent 2100 Bioanalyzer using RNA 6000 Nano Assay (Agilent Technologies Inc.). The electropherogram results suggest that the total RNA was intact without any sign of RNA degradation, and the RNA Integrity Number (RIN) ranged from 6.9 to 9.2. One microgram of total RNA was used to isolate poly(A) mRNA, convert to cDNA and prepare libraries using the NEBNext Ultra-II Directional RNA Library Prep Kit for Illumina (New England Biolabs), following manufacturer instructions. The quantity of the library was assayed using the Qubit DNA HS assay (Life Technologies Corp), and quality was analyzed on a Bioanalyzer (Agilent Technologies Inc.). The libraries were of good quality as primer dimers or adapter dimers were not detected on the Bioanalyzer electropherogram. Libraries were diluted and normalized for equimolar amount, pooled, denatured and sequenced on an Illumina NextSeq 500 platform using NextSeq 500/550 High Output v2 kit (75 cycles) with 1×75 sequencing parameter. More than 32 million reads were generated per sample. RNA isolation, RNAseq library preparation and sequencing services were performed by the UMass Amherst Genomics Resource Laboratory, which acknowledges funding support from The Massachusetts Life Sciences Center (MLSC).

first: Monika

last: Roy

first: Karilyn

middle: E

last: Sant

first: Olivia

last: Venezia

first: Alix

middle: B

last: Shipman

first: Stephen

last: McCormick

first: Panithi

last: Saktrakulkla

first: Keri

middle: C

last: Hornbuckle


title: Characterization of eQTLs associated with androstenone by RNA sequencing in porcine testis - RNASeq Database

city: Kongens Lyngby

first: Haja

last: Kadarmideen

address: Richard Petersens Plads, Building 324

department: Department of Applied Mathematics and Computer Science

country: Denmark

institute: Technical University of Denmark

summary:
Characterization of genetic variants affecting genome-wide gene expression levels (expression quantitative trait loci or eQTLs) in pig testes may improve our understanding of genetic architecture of boar taint (an animal welfare trait) and helps in genome-assisted or genomic selection programs. The aims of this
study were to identify eQTLs associated with androstenone, to find candidate eQTLs for low androstenone, and to validate the top eQTL by reverse transcriptase quantitative PCR (RT-qPCR). Gene expression profiles were obtained by RNA sequencing in testis from Danish cross-bred pigs and genotype data by 80K single nucleotide polymorphism panel. A total of 262 eQTLs [false discovery rate (FDR) <
0.05] were identified by using two software packages: Matrix eQTL and Krux eQTL. Of these, 149 cis-acting eQTLs were significantly associated with androstenone concentrations and gene expression (FDR < 0.05). The eQTLs were associated with several genes of boar taint relevance including CYP1A2, CYB5D1, and SPHK2. One eQTL gene, AMPH, was differentially expressed (FDR < 0.05) and affected
by chicory. Five candidate eQTLs associated with low androstenone concentrations were discovered, including the top eQTL associated with CYP1A2. RT-qPCR confirmed target gene expression to be significantly (P < 0.05) different based on eQTL genotypes. Furthermore, eQTLs were enriched as QTLs for 15 boar taint related traits from the PigQTLdb. This is the first study to report eQTLs in testes
of commercial crossbred pigs used in pork production and to reveal genetic architecture of boar taint. Potential applications include development of a DNA test and in advanced genomic selection models for boar taint.

overall_design: A total of 32 Danish crossbred Duroc X Landrace/Yorkshire male pigs with divergent androstenone, skatole and indole concentrations were subjected to gene expression profiling in two tissues – liver (n = 24 pigs) and testis (n = 32 pigs). Furthermore, sensoric traits, carcass weights and pedigree data (EBVs) were available for each pig. Finally, a group of pigs received a chicory-additive a number of days before slaughter.

first: Markus

last: Drag

first: Hanne

last: Maribo

first: Lene

last: Meinert

first: Preben

last: Thomsen


title: Expression data from isolated mouse lung endothelial cells

status: Public on Aug 21 2019

city: Uppsala

first: Lena

last: Claesson-Welsh

state: Uppsala

address: Dag Hammarskjölds väg 20

department: Immunology, Genetics and Pathology

country: Sweden

institute: Uppsala University

summary:
Exaggerated signaling by vascular endothelial growth factor (VEGF) A and its receptor, VEGFR2, in pathologies results in poor vessel function. Still, pharmacological suppression of VEGFA/VEGFR2 may aggravate disease. Delineating VEGFR2 signaling in vivo provides strategies for suppression of specific VEGFR2-induced pathways. Three VEGFR2 tyrosine residues (Y949, Y1212, Y1173) induce downstream signaling. Here, we show that knock-in of phenylalanine to create VEGFR2 Y1212F in C57Bl/6 and FVB mouse strains leads to loss of growth factor receptor bound (GRB)2- and phosphoinositide 3´kinase (PI3K)p85-signaling. C57Bl/6 Vegfr2Y1212F/Y1212F show reduced embryonic endothelial cell (EC) proliferation and partial lethality. FVB Vegfr2Y1212F/Y1212F show reduced postnatal EC proliferation. Reduced EC proliferation in Vegfr2Y1212F/Y1212F explants is rescued by c-Myc overexpression. We conclude that VEGFR2 Y1212 signaling induces activation of extracellular-signal regulated kinase (ERK)1/2 and Akt pathways required for c-Myc-dependent gene regulation, endothelial proliferation and vessel stability.
We use microarray to determine the differences in gene expression in endothelial cells between WT or Vegfr2Y1212F/Y1212F mice.

overall_design: Mouse lung ECs were isolated from WT or Vegfr2Y1212F/Y1212F mice (both C57Bl/6 and FVB strains) using MACS lung disassociation kit and CD31 microbeads. The cells from each mouse were starved for 3 hours in MV2 medium with 0.2% FCS and then either left untreated (basal) or treated with VEGFA (50 ng/mL) for 1 or 3 hours. Microarray was performed by using ClariomTM D Assays, mouse (ThermoFisher Scientific) with RNA samples from 5 WT and 5 Vegfr2Y1212F/Y1212F mice for each time point.

first: Chiara

last: Testini

first: Ross

middle: O

last: Smith

first: Yi

last: Jin

first: Pernilla

last: Martinsson

first: Ying

last: Sun

first: Marie

last: Hedlund

first: Miguel

last: Sáinz-Jaspeado

first: Masabumi

last: Shibuya

first: Mats

last: Hellström


title: Single-cell RNA-seq reveals the molecular progression of retinal progenitors in human embryonic stem cell models of early retinogenesis

city: los angeles

first: Qin

last: An

state: CALIFORNIA

address: Room 6554 Gonda Building, UCLA

department: Department of Human Genetics

institute: ucla

summary: We used single-cell RNA-sequencing (scRNA-seq) on human embryonic stem cell (hESC)-derived retinal organoid to deconstruct RPC developmental trajectory in the early retinogenesis, which revealed the fate branchpoint in RPC progression.

overall_design: Using single cell RNA-seq to profile the cells isolated from human ESC derived 3D-retinal organoid collected at different culture stages.


title: Analysis of Drosophila melanogaster Third Instar Larval Eye and Antennal Disc Transcriptomes

city: Baltimore

first: Robert

middle: J

last: Johnston Jr.

state: MD

address: 3400 N. Charles Street

department: Department of Biology

institute: Johns Hopkins University

summary: The goal of this study was to examine RNA expression levels in the Drosophila larval eye and antennal discs and determine whether higher levels of transcription were correlated with the ability of transgenes to drive pairing with their homologous endogenous loci between chromosomes. Additionally, RNA expression levels were compared between the eye and antennal discs to determine whether increased insulator protein expression contributed to increased pairing in the eye disc.

overall_design: mRNA profiles of wildtype, non-transgenic Drosophila third-instar larval eye and antennal discs were generated by deep sequencing in triplicate.

first: Kayla

last: Viets


title: Comparison of mammalian reovirus infection from the apical or basolateral membrane of polarized T84 cells

city: Heidelberg

first: Megan

last: Stanifer

address: INF 344

institute: Heidelberg University Hospital

summary: In this study we used Illumina Microarray to compare the induction of immune related genes following enteric virus infection. Results show that infection of T3D mammalian reovirus from the basolateral side lead to a higher induction of all genes compared to apical infection.

overall_design: Mock, Apical, and Basolateral Samples

first: Thomas

last: Hielscher


title: Single-cell atlas of thalamic projection systems

city: Bethesda

first: Anton

last: Schulmann

state: Maryland (MD)

address: 35 Convent Dr

institute: NIH/NIMH

summary: We collected single-cell RNAseq data from neurons of five thalamocortical projection systems (motor, somatosensory, visual, auditory, and prefrontal). Cells of each projection system were retrogradely labeled from their cortical target area, microdissected, and collected individually. By combining single-cell transcriptomics with in situ RNA hybridization, we found heterogeneity not only between thalamic nuclei but also within nuclei, with graded transitions between cell identities.

overall_design: Single-cell transcriptome profiling of 5 thalamocortical projection systems, defined via retrograde labeling

first: James

middle: W

last: Phillips

first: Erina

last: Hara

first: Lihua

last: Wang

first: Andrew

last: Lemire

first: Sacha

last: Nelson

first: Adam

last: Hantman


title: Transcription analysis for the growth of Haloferax volcanii on L-alanine and ammonium chloride

city: Seoul

first: Sungmin

last: Hwang

address: Hwarang-ro 14-gil, Seongbuk-gu

department: Clean Energy Research Center

country: South Korea

institute: Korea Institute of Science and Technology

summary: Identification of global gene expression profiling when Haloferax volcanii H26 strain is grown in minimal medium supplemented with two nitrogen sources, 10 mM L-alanine and 10 mM ammonium chloride.

overall_design: For transcriptome analysis of Haloferax volcanii H26 strain in response to minimal medium supplemented with 10 mM L-alanine or 10 mM ammonium chloride, biological triplicate were adopted in each condition.

first: Amy

last: Schmid

first: Julie

last: Maupin-Furlow


title: Ageing affects DNA methylation and transcriptional cell-to-cell variability in muscle stem cells [scBS-seq]

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

institute: Altos Labs

type: Methylation profiling by high throughput sequencing

summary: Age-related tissue alterations have been associated with a decline in stem cell number and function. Increased cell-to-cell variability in transcription or epigenetic marks has been proposed to be a major hallmark of ageing. Here, using parallel single-cell transcriptome and DNA methylome profiling, we find a global increase of uncoordinated transcriptional heterogeneity and context-dependent alterations of DNA methylation heterogeneity in ageing mouse muscle stem cells. Importantly, promoters with increased methylation heterogeneity are associated with increased transcriptional heterogeneity of the genes they drive. Notably, old cells diverging from young cells revealed alterations in the transcription of multiple extracellular matrix related genes. These findings show linked increases in heterogeneity between the epigenome and the transcriptome, with attendant degradation of coherent transcriptional networks and stem cell functional decline during ageing.

overall_design: 3 young and 3 old mice.

first: Irene

last: Hernando-Herraez

first: Brendan

last: Evano

last: Stubbs

first: Pierre

last: Commere


title: Enhanced hemato-endothelial specification during human embryonic development through developmental cooperation between AF4-MLL and MLL-AF4 fusions

city: Shanghai

first: Xiaonan

address: 227 Chongqing South Road

department: School of Public Health

institute: Shanghai Jiao Tong University School of Medicine

summary: The t(4;11)(q21;q23) translocation is associated with high-risk infant pro-B-cell acute lymphoblastic leukemia (B-ALL) and arises prenatally during embryonic/fetal hematopoiesis. The developmental/pathogenic contribution of the t(4;11)-resulting MLL-AF4 (MA4) and AF4-MLL (A4M) fusions remains enigmatic; MA4 is always expressed in t(4;11)+B-ALL patients, but the reciprocal fusion A4M is expressed in only 50% of patients. Because prenatal leukemogenesis manifests as impaired early hematopoietic differentiation, we took advantage of well-established human embryonic stem cell-based hematopoietic differentiation models to study whether the A4M fusion co-operates with MA4 during early human hematopoietic development. Co-expression of A4M and MA4 strongly promoted the emergence of hemato-endothelial precursors (HEPs), both endothelial-primed and hemogenic-primed. Double fusion-expressing HEPs specified into significantly higher numbers of both hematopoietic and endothelial-committed cells, irrespective of the differentiation protocol used and without hijacking survival/proliferation. Functional analysis of differentially expressed genes and differentially enriched H3K79me3 genomic regions by RNA-seq and H3K79me3 ChIP-seq, respectively, confirmed a hematopoietic/endothelial cell differentiation signature in double fusion-expressing HEPs. Importantly, ChIP-seq analysis revealed a significant enrichment of H3K79 methylated regions specifically associated with HOX-A cluster genes in double fusion expressing differentiating hematopoietic cells. Overall these results establish a functional and molecular cooperation between MA4 and A4M fusions during human hematopoietic development.

overall_design: RNA sequencing of EV or MA4-A4M expressing HEPS cells.

first: Clara

last: Bueno

first: Fernando

last: Calero-Nieto

first: Rafael

last: Valdés-Mas

first: Heleia

last: Roca-Ho

first: Francisco

last: Gutiérrez

first: Veronica

last: Ayllon

first: Pedro

last: Real

first: David

last: Arambilet

first: Antonio

last: Agraz-Doblás

first: Ignacio

last: Varela

first: Lluis

last: Espinosa

first: Anna

last: Bigas

first: Bertie

last: Gottgens

first: Pablo

last: Menendez

first: Rolf

last: Marschalek


title: Transcriptomic atlas of thalamic nuclei

first: Anton

last: Schulmann

summary: We profiled the transcriptome of 22 thalamic nuclei. Nuclei were retrogradely labeled from their forebrain target areas, microdissected and fluorescent cells pooled. Anterograde tracing was used when identification of nuclear boundaries was ambiguous. We found that thalamic nuclei share a common axis of variance closely linked to the mediolateral spatial axis of thalamus. This axis was enriched in functionally relevant genes such as neurotransmitter receptors and ion channels, and was closely linked to functional and morphological properties of the neurons.

overall_design: Transcriptome profiling of 22 thalamic nuclei, defined via projection labeling

first: James

last: Phillips

first: Erina

last: Hara

first: Lihua

last: Wang

first: Andrew

last: Lemire

first: Sacha

last: Nelson

first: Adam

last: Hantman


title: Effect of venetoclax, tedizolid, and combination treatment on gene expression in a venetoclax-resistant AML cell line

status: Public on Aug 20 2019

city: Toronto

first: Steven

last: Chan

state: Ontario

address: 101 College Street, Room 8-354

institute: Princess Margaret Cancer Centre

summary: The goal of this study was to profile the changes in gene expression in an AML cell line with acquired resistance to venetoclax in response to treatment with venetoclax, tedizolid, or combination of the 2 drugs.

overall_design: Venetoclax-resistant MOLM13 cells (designated MOLM13-R2) were treated with DMSO (vehicle control), venetoclax alone (500 nM), tedizolid alone (5 uM), or combination of the two drugs for 4 days. Total RNA was extracted from each sample and subjected to RNA-seq analysis. Two technical replicates for each treatment condition.

last: Sharon


title: A NeuroD1 AAV-Based Gene Therapy For Functional Brain Repair After Ischemic Injury Through In Vivo Astrocyte-To-Neuron Conversion

city: University Park

first: Gong

last: Chen

state: PA

address: Old Main

institute: Penn State University

summary: NeuroD1-mediated in situ astrocyte-to-neuron conversion can regenerate a large number of functional new neurons after ischemic injury. RNA-sequencing was conducted  to confirm neuronal recovery after cell conversion at the  mRNA level.

overall_design: Cortical tissues of healthy mice (n  = 3), ischemic mice at 17 dpi with control or NeuroD1 virus (n = 2 for each) were collected. mRNA samples were extracted and sequenced.

first: Ningxin

last: Ma

first: Yuchen


title: Niche-specific factors dynamically regulate sebaceous gland stem cells during skin homeostasis and aging

city: Ann Arbor

first: Lam

last: Tsoi

state: MI

address: Medical Sciences 1 Bldg. 1301 E. Catherine

institute: University of Michigan

summary: We deleted different Notch pathway components in different sub-compartments of mouse skin, and performed RNA-seq to assess differentially regulated genes, 10 weeks after deletion.

overall_design: Mice were injected with tamoxifen at 8 weeks of age to delete either Rbpj (R) or Notch1 (N) in the skin.  Cre drivers were K14-CreERT (K) and Lrig1-CreERT2 (L).  Dorsal skin in telogen phase was harvested, isolated away from dermis, and extracted for total RNA by Qiagen RNeasy kit, 10 weeks post-tamoxifen.  LR = Lrig1-CreERT2+Rbpj-deletion;  KR = K14-CreERT+Rbpj-deletion;  N = K14-CreERT1+Notch1-deletion.   All 3 mutant strains had matched controls (Cont) from the same batch/litter.  See Veniaminova, Wong et al., 2019

first: Wong

last: Sunny

first: Tsoi

last: Lam


title: Myoepithelial cell perturbations in BRCA mutation carriers and in DCIS (ductal carcinoma in situ)

city: Boston

first: Kornelia

last: Polyak

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: We describe the gene expression profiles and enhancer landscape of normal myoepithelial cells and perturbations of these in BRCA1 and BRCA2 mutation carriers and in DCIS. We identified a myoepithelial transcription regulatory network orchestrated by p63 and TCF7 and defined the genomic targets of these transcription factors by ChIP-seq. While the majority of myoepithelial cells co-express p63 and TCF7 in normal breast of healthy women, the frequency of these cells is significantly lower in BRCA1 mutation carriers and in DCIS. Downregulation of p63 in MCF10DCIS cells leads to loss of myoepithelial cells and invasive tumors, whereas overexpression of TCF7 enhances tumor growth. Our findings suggest that loss of normal myoepithelial cell function facilitates in situ to invasive carcinoma transition and it may also enhance tumor initiation in BRCA mutation carriers.

overall_design:
RNAseq of CD10+ cells from normal breast and DCIS to compare the expression difference in myoepithelial cells.
RNAseq in cell lines with p63 knockdown or TCF7 overexpression to see the genes and pathways regulated by p63 or TCF7.
ChIPseq for p63 and TCF7 to identify their targets and epigenetic landscaping.
H3K27ac ChIPseq of breast organoids from normal (control) woman and BRCA mutation carriers.

first: Lina

last: Ding

first: Ying

last: Su

first: Xintao

last: Qiu

first: Muhammad

last: Ekram

first: Sung

last: Huh

first: Noga

last: Bloushtain-Qimron

first: Nicholas

last: Harper

first: Bojana

last: Jovanovic

first: William

last: Hines

first: Xiaoyuan

last: Zi

first: Vanessa

middle: F

last: Merino

first: Sibgat

last: Choudhury

first: Gabrielle

last: Ethington

first: Laura

last: Panos

first: Michael

last: Grant

first: Gedge

last: Rosson

first: Jason

last: Clark

last: Herlihy

first: Alfred

last: Au

first: Andrea

last: Richardson

first: Pedram

last: Argani

first: E

last: Hwang

first: Rong

last: Fan

first: D

last: Allred

first: Kristie

last: Bobolis

first: Celina

last: Kleer

first: Joanne

last: Blum

first: Henry

last: Long

first: Saraswati

last: Sukumar

first: So

middle: Y

last: Park

first: Judy

last: Garber

first: Jun

last: Yao

first: Mina

last: Bissell


title: A new strategy for identifying mechanisms of drug-drug interaction using transcriptome analysis: Compound Kushen injection as a proof of principle

city: Adelaide

first: David

middle: L.

last: Adelson

state: South Australia

address: University of Adelaide

department: Molecular and biomedical science

institute: University of Adelaide

summary: Drug-drug interactions (DDIs), especially with herbal medicines, are complex, making it difficult to identify potential molecular mechanisms and targets. We introduce a workflow to carry out DDI research using transcriptome analysis and interactions of a complex herbal mixture, Compound Kushen Injection (CKI), with cancer chemotherapy drugs, as a proof of principle. Using CKI combined with doxorubicin or 5-Fu on cancer cells as a model, we found that CKI enhanced the cytotoxic effects of doxorubicin on A431 cells while protecting MDA-MB-231 cells treated with 5-Fu. We generated and analysed transcriptome data from cells treated with single treatments or combined treatments and our analysis showed that opposite directions of regulation for pathways related to DNA synthesis and metabolism appeared to be the main reason for different effects of CKI when used in combination with chemotherapy drugs . We also found that pathways related to organic biosynthetic and metabolic processes might be potential targets for CKI when interacting with doxorubicin and 5-Fu. Through co-expression analysis correlated with phenotype results, we selected the MYD88 gene as a candidate major regulator for validation as a proof of concept for our approach. Inhibition of MYD88 reduced antagonistic cytotoxic effects between CKI and 5-Fu, indicating that MYD88 is an important gene in the DDI mechanism between CKI and chemotherapy drugs. These findings demonstrate that our pipeline is effective for the application of transcriptome analysis to the study of DDIs in order to identify candidate mechanisms and potential targets.

overall_design: High-depth paired-end RNA-seq from A431 epidermoid carcinoma cell line and MDA-MB 231 adenocarcinoma cell line. Each sample contains 3 biological replicates.

first: Hanyuan

last: Shen


title: Methylation and gene expression data from Dnmt3b+/+, Dnmt3b-/- and Dnmt3bCI/CI embryos harvested at E11.5

status: Public on Aug 19 2019

city: Gainesville

first: Rene

last: Opavsky

state: FL

address: 2033 Mowry rd, CGRC r..265

department: Anatomy and cell biology

institute: University of FLORIDA

summary: Dnmt3b is a DNA methyltransferase, an enzyme which methylates genomic DNA, contributes to genomic stability and transcriptional regulation. Inactivation of Dnmt3b in mice results in embryonic lethality at E13.5. It is however unclear which activities are responsible for this phenomenon. Here, we analyzed methylation and gene expression in Dnmt3b+/+ (WT), Dnmt3b-/- (3bKO) and Dnmt3bCI/CI (3bKI) embryos at E11.5.

overall_design: We performed RRBS and RNA-seq analysis in whole embryos harvested at E11.5. RRBS experiments were performed in biological duplicates, RNA-seq experiments in triplicates. In addition, we performed RRBS in Dnmt3a-/- Dnmt3b-/- lymphoma cell line overexpressing Dnmt3b WT and CI.

first: Pawel

last: Nowialis

first: Katarina

last: Lopusna

first: Jana

last: Opavska

first: Staci

middle: L

last: Haney

first: Ajay

last: Abraham

first: Peike

last: Sheng

first: Alberto

last: Riva

first: Amarnath

last: Natarajan

first: Olga

last: Guryanova

first: Melanie

last: Simpson

first: Ryan

last: Hlady

first: Mingyi

last: Xie


title: microRNA array analysis of differentiated HL60 cells with PfbA

city: Suita

first: Masaya

last: Yamaguchi

state: Osaka

address: 1-8, Yamadaoka

department: Graduate School of Dentistry

institute: Osaka University

summary: Previous studies indicate that host phagocytes are regulated by a complex combination of pattern recognition receptors-signaling and miRNA inductions. We performed microRNA array to determine whether S. pneumoniae PfbA suppresses phagocytosis via miRNA inductions.

overall_design: We performed microRNA array analysis using neutrophil like-differentiated HL60 cells, S. pneumoniae strains and rPfbA. We compared rPfbA-treated and non-treated cells, wild type and ∆pfbA-infected cells, and ∆pfbA with rPfbA-infected and ∆pfbA solely infected cells. In each cell sample, 6 replicates were pooled and microRNA was purified from the pooled cells.


title: PRMT5 methylome profiling uncovers a direct link to splicing regulation in human acute myeloid leukemia

city: New York

first: Kristian

last: Helin

address: 430 East 67 street

institute: MSKCC

summary: Protein arginine methyltransferase 5 (PRMT5) belongs to the class II arginine methyltransferases and catalyzes monomethylation and symmetrical dimethylation of arginines on proteins. It has recently emerged as a promising cancer drug target, and three PRMT5 inhibitors are currently in clinical trials for a range of malignancies. In this study, we aimed to further elucidate the role of PRMT5 in acute myeloid leukemia (AML). Using an enzymatic dead version of PRMT5 as well as a PRMT5-specific inhibitor, we demonstrated the requirement of the catalytic activity of PRMT5 for the survival of AML cells. By using multiplexed quantitative proteomics, we identified PRMT5 substrates and investigated their role in the survival of AML cells. We found that the function of the splicing regulator SRSF1 relies on its methylation by PRMT5. Consistent with this, we found that loss of PRMT5 led to changes in alternative splicing. This analysis revealed multiple affected essential genes, linking PRMT5 activity to its loss of function phenotype. Our results show that PRMT5 regulates binding of SRSF1 to mRNAs and proteins in leukemia and provide potential biomarkers for the treatment response to PRMT5 inhibitors.

overall_design: RNA-sequencing and SRSF1 RIP-sequencing of THP-1 cells with and without PRMT5 knockdown (3 biological replicates, 6 days after transduciton)

first: Aliaksandra

last: Radzisheuskaya


title: Analysis of transcriptome changes following SOX2 knockdown in three different Ewing sarcoma cell lines

first: Thomas

middle: Georg Philipp

last: Grunewald

address: Im Neuenheimer Feld 280

department: Division of Translational Pediatric Sarcoma Research

institute: German Cancer Research Center (DKFZ)

summary: We report that knockdown of SOX2 in Ewing sarcoma cell lines promotes changes in the expression of several genes that are involved a variety of molecular processes.

overall_design: RNA-seq of three Ewing sarcoma cell lines (EW1, RDES, POE), transiently transfected with a non-targeting control siPOOL or two different specific siPOOLs targeting SOX2.

first: Giuseppina

last: Sannino

first: Willian

last: Da Silveira

first: Gary

last: Hardiman

middle: G

last: Grünewald


title: TAIL-seq in cde-1 mutants versus WT C. elegans infected by the Orsay virus

first: Konrad

middle: Ludwig Moritz

last: Rudolph

address: Tennis Court Road

department: Gurdon Institute

institute: University of Cambridge

summary:
Aim: We question non-templated transcript 3ʹ tails in cde-1 mutants versus WT C. elegans (N2 strain) infected by the Orsay virus
Methods: Approximately 200 cde-1 (tm1021) mutants or N2 animals were infected for 48 hours from the L2 stage to the adult stage with 20 µl filtrate of the Orsay virus on 50mm plate seeded with HB101 bacteria, in biological duplicates. Animals were then washed in M9 and resuspended in 1 ml TRIsure (Bioline). Samples were freeze-thaw three times using liquid nitrogen and RNA purification was performed according to Bioline’s guidelines. TAILseq preparation and sequencing was performed as described in Chang, et al. Moll. Cell 2014. Tail-seq libraries were processed using Tailseeker 2 (Chang et al. Moll. Cell 2014). The 5ʹ and 3ʹ libraries were subsequently adapter trimmed using cutadapt 1.10 (Martin. EMBnet.journal 2011) with Illumina small RNA-seq adapters and filtered to a minimum length of 5bp. Trimmed 5’ reads were mapped with STAR 2.5.2a (Dobin, et al. Bioinformatics 2013) against a combined meta-genome consisting of the C. elegans reference genome WBcel235 (Harris, et al. Nucleic Acids Res. 2014) and the Orsay virus genome (Felix, et al. Plos Bio. 2011). Mapping was performed in end-to-end mode allowing no mismatches and a gap opening and extension penalty of 10000. Reads were assigned to genes with bedtools 2.26.0 (Quinlan and Hall. Bioinformatics 2010). Subsequently, 3ʹ reads without poly(A) tail or too many dark cycles were removed from the data. For the subsequent analysis, all C. elegans tags with poly(A) tail length equal to zero were discarded. Average poly(A) tail lengths and uridylation lengths for each sample were calculated as the arithmetic mean weighted by the support for each tag, reported by Tailseeker.

overall_design: Examination of non-templated tails at the 3ʹ end of transcripts in Orsay virus infected animals from two different genetic backgrounds

first: Jérémie

last: Le Pen

first: Marcos

last: Morgan

first: Anton

last: Enright

first: Dónal

last: O’Carroll

first: Eric

middle: A

last: Miska


title: The genome-wide enhancer profiling of breast cancer in the MMTV-PyVT mice [ChIP-seq]

status: Public on Aug 18 2019

city: Wuhan City

first: Qinglan

last: Li

state: Hubei Province

address: Room 5005, Life Science College, Wuhan University

institute: Wuhan University

summary: Activation of transcription enhancers, especially super enhancers, is one of the important epigenetic features of tumorigenesis. However, only very few studies reported how the enhancer landscape evolves during tumorigensis. Here we utilized a proteomics approach and found that H3K27ac and H4K8ac are elevated in the mammary tumor of MMTV-PyVT mouse model, which was then confirmed by IHC results in human BRCA chips. ChIP-seq studies revealed that H4K8ac is highly co-localized with H3K27ac on chromatin, especially on the distal enhancers . We further identified a subgroup of super enhancers which are marked by H3K4me3 peaks in the intergenic regions. These H3K4me3-enriched super enhancers are covered with higher level of H3K27ac and H4K8ac in tumor than normal tissue , and accompanies higher transcription level of the adjacent genes. Combined with global gene expression data, we identified 148 tumor H3K4me3-enriched super enhancer adjacent genes with higher expression in the tumor tissues , which may be critical for breast cancer. We further utilized one inhibitor of p300, C646, to inhibit H3K27ac level, which successfully repressed tumor formation process probably through inhibiting Vegfa and other oncogenes. Taken together, our work identifies novel regulators and provides important resource to the genome-wide enhancer studies in breast cancer, and raises the possibility of cancer treatment through modulating enhancer activity.

overall_design: Histone modification profile of mammary glands from 12 weeks old FVB wild type mice and mammary tumors from 12 weeks old MMTV-PyVT mice with no treatment, DMSO injection and C646 injection  were generated by deep sequencing, in triplicate, using Illumina X-TEN.

first: Qing-Lan

first: Dan-Ya

last: Wang

first: Lin-Gao

last: Ju

first: Chuan

last: Gao

first: Pin-Ji

last: Lei

first: Lian-Yun

first: Xiao-Lu

last: Zhao

first: Min

last: Wu


title: To characterize bag3 cardiomyopathy model in adult zebrafish through RNA-Seq

status: Public on Aug 15 2019

city: Rochester

first: Xiaolei

last: Xu

state: MN

address: 200 First Street SW

institute: Mayo Clinic

summary: We sequenced mRNA from adult zebrafish heart at 6-month-old bag3 knockout fish and WIK-wildtype controls

overall_design: Examination of differentially exppressed genes between bag3 knockout fish and wildtype controls

first: Yuji

last: Zhang


title: scRNAseq transcriptome analysis of developing regulatory T cells and precursors in the thymus

first: Elham

last: Azizi

state: NY

institute: Memorial Sloan Kettering Cancer Center

summary: We analyzed the individual transcriptomes of thymic Treg cells (CD4+Foxp3+), their immediate precursors (CD25+CD4+Foxp3-) and mature CD4 single positive thymocytes (CD4+Foxp3-CD25-CD62L+CD24-).

overall_design: To gain insight into characteristic features of thymocytes producing IL-2 in situ, single-cell RNA sequencing data was collected from mature CD25-Foxp3-CD4SP, CD25+Foxp3- and Foxp3+ CD4SP thymocytes.

first: Saskia

last: Hemmers

first: Michail

last: Schizas

first: Stanislav

last: Dikiy

first: Yi

last: Zhong

first: Yongqiang

last: Feng

first: Gregoire

last: Altan-Bonnet

first: Alexander

last: Rudensky


title: The expression of circular RNAs in the plasma from five hepatocellular carcinoma patients and five chronic hepatitis B patients

first: Wei-ping

last: Zhou

state: Shanghai

address: 225 Changhai Road, Shanghai

institute: Eastern Hepatobiliary Surgery Hospital

summary: Using CapitalBio Technology Human CircRNA Array v2 (4x180K) microarray, we compared the expression of circular RNAs in the plasma from five hepatitis B virus-related hepatocellular carcinoma patients and five chronic hepatitis B patients.

overall_design: To explore whether plasma circular RNAs (circRNAs) can diagnose hepatitis B virus (HBV)-related hepatocellular carcinoma (HCC), microarray (CapitalBio Technology Human CircRNA Array v2, 4x180K) was used to identify plasma circRNAs that were increased in HBV-related HCC patients compared with chronic hepatitis B patients. All patients were male, aged 43-57.

first: Jian

last: Yu


title: Naa10p Inhibits Beige Adipocyte-mediated Thermogenesis through N-α-acetylation of Pgc1α

status: Public on Aug 16 2019

city: Taipei

first: Li-Jung

last: Juan

address: 128 Academia Road, Section 2, Nankang

department: Genomic Research Center

country: Taiwan

institute: Academia Sinica

summary: We reported that both conventional and adipose-specific Naa10p deletions in mice result in increased energy expenditure, thermogenesis, beige adipocyte differentiation and activation. Mechanistically, Naa10p acetylates the N-terminus of Pgc1α and prevents it from interacting with Ppar𝛾 to activate key genes, such as Ucp1, involved in beige adipocyte function. We used microarrays to profile the gene expression changes by Naa10p KO in inguinal white adipose tissues (iWATs) derived from mice fed with high fat diet for 15 weeks.

overall_design: Complementary DNAs were generated with 3 μg of total RNAs extracted from iWATs of 3 WT and 3 Naa10-KO mice fed with HFD for 15 weeks and exposed to 4°C for 4 hrs, and subsequently hybridized with Gene Chip Mouse Genome 430 2.0 Array.

first: Chen-Cheng

last: Lee


title: RNA sequencing of axillary buds from annual and biennial flowering raspberry

status: Public on Aug 17 2019

city: Palmerston North

first: rubina

last: jibran

address: Tennent Drive

country: New Zealand

institute: Plant and Food Research

summary: We compared gene expression in axillary buds from annual and biennial flowering raspberry to identify differentially expressed genes.

overall_design: Three biological replicates of RNA from each genotype was sequenced using Illumina paried-end sequencing. Differentially expressed genes were identified using DESeq2.

first: Toshi

last: Foster

first: Rubina

last: Jibran


title: Glucagon-receptor signaling regulates energy metabolism via hepatic Farnesoid X Receptor and Fibroblast Growth Factor 21

city: Stanford

first: Mark

middle: Emile

last: Pepin

state: CA

address: 870 Quarry Road

department: Cardiovascular Medicine

institute: Stanford University

summary: Glucagon, an essential regulator of glucose and lipid metabolism, also promotes weight loss, in part through potentiation of fibroblast-growth factor 21 (FGF21) secretion. However, FGF21 is only a partial mediator of metabolic actions ensuing from GcgR-activation, prompting us to search for additional pathways. Intriguingly, chronic GcgR agonism increases plasma bile acid levels. We hypothesized that GcgR agonism regulates energy metabolism, at least in part, through farnesoid X receptor (FXR). To test this hypothesis, we studied whole body and liver-specific FXR knockout (FXR∆liver) mice. Chronic GcgR agonist (IUB288) administration in diet-induced obese (DIO) Gcgr, Fgf21 and Fxr whole body or liver-specific knockout (∆liver) mice failed to reduce body weight (BW) when compared to wildtype (WT) mice. IUB288 increased energy expenditure and respiration in DIO WT mice, but not FXR∆liver mice. GcgR agonism increased [14C]-palmitate oxidation in hepatocytes isolated from WT mice in a dose-dependent manner, an effect blunted in hepatocytes from FXR∆liver mice. Our data clearly demonstrate that control of whole body energy expenditure by GcgR agonism requires intact FXR signaling in the liver. This heretofore-unappreciated aspect of glucagon biology has implications for the use of GcgR agonism in the therapy of metabolic disorders.

overall_design: RNA sequencing analysis of mice given IUB288 or vehicle treatment. Fxr-floxed mice were were used relative to wild-type controls. All mice were vmaintained on a C57Bl/6J background.

first: Teayoun

last: Kim

first: Shelly

last: Nason

first: Cassie

last: Holleman

first: Landon

last: Wilson

first: Taylor

last: Berryhill

first: Adam

middle: R

last: Wende

first: Chad

last: Steele

first: Martin

last: Young

first: Stephen

last: Barnes

first: Daniel

last: Drucker

first: Brian

last: Finan

first: Richard

last: DiMarchi

first: Diego

last: Perez-Tilve

first: Matthias

last: Tschoep

first: Kirk

middle: M

last: Habegger


title: The genome-wide enhancer profiling of breast cancer in the MMTV-PyVT mice

first: Qinglan

last: Li

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

overall_design: Refer to individual Series


title: Naa10p Inhibits Beige Adipocyte-mediated Thermogenesis through N-alpha-acetylation of Pgc1-alpha

first: Li-Jung

last: Juan

department: GRC

summary: We report that both conventional and adipose-specific Naa10p deletions in mice result in increased energy expenditure, thermogenesis, beige adipocyte differentiation and activation. Mechanistically, Naa10p acetylates the N-terminus of Pgc1-alpha and prevents it from interacting with Ppar[gamma] to activate key genes, such as Ucp1, involved in beige adipocyte function.

overall_design: mRNA profiles of 2 biological replicates of each group with or without beige adipocyte induction for 2 and 6 days

first: Chen-Cheng

last: Lee


title: SNAIL1 employs β-Catenin-LEF1 complexes to control colorectal cancer cell invasion and proliferation

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

institute: University of Lübeck

summary: The transcription factor SNAIL1 is a master regulator of epithelial-to-mesenchymal transition, a process entailing massive gene expression changes. To better understand SNAIL1-induced transcriptional reprogramming we performed time-resolved transcriptome analysis upon conditional SNAIL1 expression in colorectal cancer cells. Bioinformatic analyses indicated that SNAIL1 strongly affected Wnt/β-Catenin pathway activity. This correlated with upregulation of LEF1, a nuclear binding partner of β-Catenin. Several tumour entities, including aggressive mesenchymal colorectal cancers, exhibit positively correlated LEF1 and SNAIL1 expression, and elevated LEF1 levels parallel increased colorectal cancer patient mortality. Comparative gene expression profiling suggested that 35% of Snail1-induced transcriptional changes are attributable to LEF1. LEF1 stimulates Wnt/β-Catenin pathway feedback inhibitor expression, causes cell-cycle arrest in vitro, and retards xenograft tumour growth. Conversely, LEF1-deficiency and preventing the β-Catenin-LEF1 interaction impaired the ability of SNAIL1 to alter Wnt/β-catenin target gene expression and to induce cancer cell invasion. Although LEF1 did not autonomously induce epithelial-mesenchymal transition, LEF1 is a critical factor acting downstream of SNAIL1. Apparently, SNAIL1 employs LEF1 as alternative effector to redirect Wnt/β-catenin pathway activity towards anti-proliferative and pro-invasive gene expression.

overall_design: Total RNA was extracted from either SNAI1 or LEF1 overexpression parental LS174T colorectal carcinoma cells at 0,3,6,24,48,72 or 96 hours after induction with Dox.

first: Melanie

last: Boerries

first: Andreas

last: Hecht

first: Kerstin

last: Roensch

first: Viven

last: Freihen


title: The lncRNA locus Handsdown regulates cardiac gene programs and is essential for early mouse development

city: Frankfurt am Main

first: Phillip

last: Grote

state: Hessen

address: Paul-Ehrlich-Str. 42-44

department: Genome Regulation

institute: Georg-Speyer-Haus

summary:
WT and Handsdown mutant ESC were differentatied into the meosdermal cell lineage and harvested at desiganted timepoints für differential expression profiling (n=3). Hearts of E9.5 mouse embryos were harvested and profiled to generate a represantative picture of RNAs (n=1).

4C-seq analysis of mESCs, cardiomyocytes and whole hearts from E11.5 mouse embryos

overall_design:
Examination of 2 differnet chromatin states and RNA expression in 2 different Brachyury mutants embryos of in vitro differentiated mouse embryonic stem cells

4C-seq with the promoter region of Handsdown as the viewpoint

first: Nicole

last: Ritter

first: Tamer

last: Ali


title: Global transcriptional response of three highly acid-tolerant field strains of L. monocytogenes to HCl stress

city: Zürich

first: Marc

last: Stevens

address: Winterthurerstrasse 272

department: Vetsuisse

country: Switzerland

institute: University of Zurich

summary: Transcriptional response of 3 Listeria monocytogenes strains against acid stress was determined.

overall_design: Samples without acid treatment were compared to samples with acid treatment. 2 or 3 biological experiments were performed

first: Jule

last: Horlbog

first: Roger

last: Stephan

first: Claudia

last: Guldimann


title: A comparative transcriptome analysis reveals physiological maturation properties of mycelia in Pleurotus tuoliensis

city: beijing

first: fang

last: Du

state: china

address: zhongguancun south street 12

institute: Chinese Academy of Agricultural Sciences

summary: Pleurotus tuoliensis is a precious edible fungus with extremely high nutritive and medicinal value. The cultivation period of P. tuoliensis is longer than those of other Pleurotus species, which is mainly due to a longer mycelium physiological maturation period (30-60 days). Currently, the molecular processes underlying physiological maturation of the mycelium remain unclear. We performed a comparative transcriptomic analysis of immature and mature mycelia using RNA-seq. De novo transcriptome assembly resulted in identification of 17,030 unigenes. 451 differentially expressed genes, including those encoding nucleoside diphosphate kinase (NDPK), glycoside hydrolase family proteins, exopolygalacturonase, and versatile peroxidases, were identified. GO and KEGG analyses revealed that nucleotide synthesis and energy metabolism are highly active during the physiological maturation of mycelia, and genes related to these pathways were significantly up-regulated in mature mycelia. NDPK is predicted to be essential for mycelia maturation. Our findings contribute to a comprehensive understanding of mycelia maturation in a commercially important fungal species. Future efforts will focus on the function of NDPK and the mechanism by which it regulates mycelia maturation.

overall_design: mRNA profiles of 0 day and 35 days Pleurotus tuoliensis mycelia were generated by deep sequencing, in triplicate, based on Illumina HiSeq 2000 platform.

first: Fang

first: Qing

middle: X

last: Hu

first: Ya

last: Zou

first: Dou

last: Ye

first: Hai

last: Zhang


title: Epigenetic changes in the adult brain following exposure to prenatal maternal immune activation and dietary intervention

city: Houston

first: Basil

last: Paul

address: 1515 Holcombe Blvd

institute: MD Anderson Cancer Center

summary: Epigenetic changes such as DNA cytosine methylation modulate gene function across brain and are implicated in the pathophysiology of neurodevelopmental disorders including schizophrenia and autism. Epigenetic changes can be caused by environmental exposures such as inflammation, and may at least partly explain why prenatal exposure to inflammation increase risk of neurodevelopmental disorders. We used an MIA mouse model to investigate the postnatal epigenetic changes associated with exposure to the viral analogue PolyI:C. The effect of dietary supplement with omega-3 polyunsaturated fatty acids (PUFA) on exposed mice was also examined. Methylation was estimated genome-wide across gene regulatory regions. Widespread epigenetic changes were observed following exposure to inflammation during prenatal life. The differentially methylated gene set was enriched for genes involved in nervous system development and function. Omega-3 intervention modified the epigenetic profile, including a number of genes which were affected by MIA. These experiments indicate that environmental and genetic risk factors modulate similar biological pathways that are associated with neurodevelopmental disorders.

overall_design: Adult brain following exposure to prenatal maternal immune activation and dietary intervention

first: Paul

last: Basil

first: Pak

last: Sham


title: Analysis of Roquin targetome during HCMV infection

city: Seoul

first: Jaewon

last: Song

state: Seoul

address: 504-407, School of Biological Sciences, College of Natural Sciences, 1 Gwanak-ro, Gwanak-gu

institute: Seoul National  University

summary: To investigate how Roquin regulates cellular transcripts during Human cytomegalovirus (HCMV) infection, we examined the levels of cellular transcripts in cells treated control or Roquin-targeting siRNA during HCMV replication. Also, we performed Roquin crosslinking and immunoprecipitation followed by high-throughput sequencing (Roquin CLIP-seq) in HCMV-infected cells to identify which transcripts are directly bound by Roquin.

overall_design: Human fibroblasts (HFFs) were treated with control siRNA (siCon) or two different Roquin-targeting siRNAs (siRoq), and RNA-seq was performed in in uninfected cells (NI) or at 6, 24, or 72 hours post-infection (hpi). CLIP-seq was performed in uninfected or infected cells at 24 and 72 hpi using two different antibodies against Roquin.

first: Sanghyun

last: Lee

first: Dongyeon

last: Cho

first: Kwangseog

last: Ahn


title: Gene expression changes with LGR5 knockdown in LoVo colon cancer cells

status: Public on Aug 13 2019

first: Kendra

last: Carmon

state: TX

address: 1825 Pressler St., Rm 530H

department: The Brown Foundation Institute of Molecular Medicine

institute: UT Health Science Center at Houston

summary: The goal of this study was to identify gene expression changes in response to loss of LGR5 in the LoVo colon cancer cell line.

overall_design: Stable knockdown cell lines were established by lentiviral infection using two individual short hairpin RNAs targeting LGR5 (shLGR5-1 and shLGR5-2) or control shRNA pLKO.1 vector (shCTL). Two replicates were included for each cell line.

middle: S


title: DNA Analysis by Restriction Enzyme (DARE) enables concurrent genomic and epigenomic characterization of single cells

status: Public on Aug 14 2019

city: Singapore

first: Lih Feng

last: Cheow

address: 4 Engineering Drive 3

department: Biomedical Engineering

country: Singapore

institute: National University of Singapore

summary: Genome-wide profiling of copy number alterations and DNA methylation in single cells could enable detailed investigation into the genomic and epigenomic heterogeneity of tumor populations. However, current methods to do this require complex sample processing and cleanup steps, lack consistency, or are biased in their genomic representation. Here, we describe a novel single-tube enzymatic method, DNA Analysis by Restriction Enzyme (DARE), to perform deterministic whole genome amplification while preserving DNA methylation information. This method was evaluated on low amounts of DNA and single cells, and provides accurate copy number aberration calling and representative DNA methylation measurement across the whole genome. Single cell DARE is an attractive and scalable approach for concurrent genomic and epigenomic characterization of cells in a heterogeneous population.

overall_design: Analysis of HepG2 and K562 copy number aberrations and methylation status in bulk genomic DNA and single cells. ESC bulk genomic DNA was used to verify the copy number aberration analysis.

first: Lih

first: Ramya

last: Viswanathan

first: Elsie

last: Cheruba


title: Differential gene expression analysis between pre-metamorphic WT control X. laevis tadpoles and tadpoles with thioridazine-induced brain abnormalities.

city: Medford

first: Kelly

last: McLaughlin

state: MA

address: 200 Boston Avenue

department: Biology

country: USA

institute: Tufts University

summary: Differential gene analysis between control and thioridazine brain cDNA libraries revealed 13 differentially expressed genes at stage 45 and 16 at stage 47.

overall_design: We utilized whole-brain tissue samples from tadpoles exposed to thioridazine during neurulation and compared them to wild-type controls, at NF stage 45 and 47.

first: Kaylinnette

last: Pinet


title: Genome-wide analysis of chromatin accessibility in developing thymic Treg cells

city: Shanghai

first: Yi

last: Zhong

address: 227 South Chongqing Rd.

institute: SJTU

summary: We analyzed open chromatin regions in thymic Treg cells, their immediate precursors (CD25+ Foxp3-), and mature and semi-mature CD4 single positive cells. We wished to understand which chromatin regions become accessible in response to TCR-stimulation and then Foxp3 expression as Treg cells develop.

overall_design: Examination of chromatin accessibility in developing CD4SP thymocyte subsets, including Treg cells and immediate precursors

first: Stanislav

last: Dikiy

first: Yongqiang

last: Feng

first: Alexander

last: Rudensky


title: Identifying Novel Roles for Peptidergic Signaling in Mice

city: Farmington

first: Richard

middle: E

last: Mains

state: CT

address: 263 Farmington Ave, Neuroscience Dept., Neuroscience Dept.

department: Neuroscience

institute: University of Connecticut Health Center

summary: PamcKO/cKO mice, with loxp sites flanking exons previously deleted in the global Pam knockout, were created,  viable and equivalent to wildtype mice in every test.  Eliminating Pam expression in excitatory forebrain neurons reduced anxiety-like behavior, increased locomotor responsiveness to cocaine and improved thermoregulation in the cold.  Eliminating Pam expression in cardiomyocytes increased anxiety-like behavior, improved thermoregulation and markedly diminished atrial levels of pro-atrial natriuretic peptide.  RNASeq analysis of atria  revealed a set of PAM-regulated transcripts related to cardiac function.

overall_design: Examination of mRNA profiles in mouse atria expressing basal or reduced levels of PAM, followed by biochemical, behavioral and physiological analyses.

first: Betty

last: Eipper


title: Analysis of murine neonatal Germinal Center (GC) B cells transcriptome (RNA-Seq) following HA/CAF01 immunization in the presence or absence of maternal antibodies

city: Geneva

first: Sylvain

last: LEMEILLE

address: 1 rue Michel-Servet

department: Department of Pathology and Immunology

institute: University of Geneva Medical School

summary:
Purpose: the goals of this study are to characterize GC B cells elicited by neonatal immunization with HA/CAF01 at the transcriptome level (RNA-seq) and study whether and how maternal antibodies affect GC B cell differentiation in early life
Methods: transcriptomic analysis of highly pure GC B cells and the corresponding non-GC B cells isolated from draining lymph nodes of immunized neonatal mice were generated by HiSeq 4000 sequencing, using Illumina Technology. The sequence reads that passed quality filters were analyzed using the package edgeR: the fold-change and the Benjamini-Hochberg corrected p-value thresholds were set to 2 and 0.05 respectively.
Main results:  1) we identified the differentially expressed genes (DEGs) in GC B cells versus non-GC B cells in murine neonates born to naive or influenza-immune mothers and observed that the canonical changes reflecting the acquisition of a GC B cell phenotype and state after neonatal immunization are not affected by high titers of maternal antibodies. 2) 39 DEGs distinguished GC B cells elicited in the presence or absence of MatAbs. GC B cells elicited in presence or absence of MatAbs used different VH  and Vk genes and showed differences in genes associated with B cell differentiation and isotype switching.

overall_design: Transcriptomic analysis of neonatal GC B cells at day 18 post HA/CAF01 immunization in the presence or absence of maternal antibodies were generated by deep sequencing, in triplicate, using Illumina Technologies.

first: Maria

last: Vono

first: Claire-Anne

last: Siegrist


title: The genome-wide enhancer profiling of breast cancer in the MMTV-PyVT mice [RNA-seq]

first: Qinglan

last: Li

address: Room 5005, Life Science College, Wuhan University

institute: Wuhan University

summary: Activation of transcription enhancers, especially super enhancers, is one of the important epigenetic features of tumorigenesis. However, only very few studies reported how the enhancer landscape evolves during tumorigensis. Here we utilized a proteomics approach and found that H3K27ac and H4K8ac are elevated in the mammary tumor of MMTV-PyVT mouse model, which was then confirmed by IHC results in human BRCA chips. ChIP-seq studies revealed that H4K8ac is highly co-localized with H3K27ac on chromatin, especially on the distal enhancers . We further identified a subgroup of super enhancers which are marked by H3K4me3 peaks in the intergenic regions. These H3K4me3-enriched super enhancers are covered with higher level of H3K27ac and H4K8ac in tumor than normal tissue , and accompanies higher transcription level of the adjacent genes. Combined with global gene expression data, we identified 148 tumor H3K4me3-enriched super enhancer adjacent genes with higher expression in the tumor tissues , which may be critical for breast cancer. We further utilized one inhibitor of p300, C646, to inhibit H3K27ac level, which successfully repressed tumor formation process probably through inhibiting Vegfa and other oncogenes. Taken together, our work identifies novel regulators and provides important resource to the genome-wide enhancer studies in breast cancer, and raises the possibility of cancer treatment through modulating enhancer activity.

overall_design: mRNA profiles of mammary glands from 12 weeks old FVB wild type mice and mammary tumors from 12 weeks old MMTV-PyVT mice with no treatment, DMSO injection and C646 injection  were generated by deep sequencing, in triplicate, using Illumina X-TEN.

first: Qing-Lan

first: Dan-Ya

last: Wang

first: Lin-Gao

last: Ju

first: Chuan

last: Gao

first: Pin-Ji

last: Lei

first: Lian-Yun

first: Xiao-Lu

last: Zhao

first: Min

last: Wu