title: Identification of genomic enhancers through spatial integration of single-cell transcriptomics and epigenomics [FluidigmC1_scATACseq]

city: Leuven

first: Carmen

last: Bravo González-Blas

address: Herestraat 49

department: VIB-KU Leuven Center for Brain and Disease Research

country: Belgium

institute: VIB-KU Leuven

summary: Enhancers act as docking stations in the genome to which transcription factors bind, tightly regulating gene expression. Although single-cell technologies allow measuring chromatin accessibility or gene expression in each individual cell, exploiting both layers towards bona fide gene regulatory networks and enhancers is still a challenge. Here, we independently generate comprehensive single-cell transcriptome and epigenome atlases of the Drosophila eye-antennal disc and propose the spatial integration of single-cell RNA-seq and single-cell ATAC-seq data using a virtual latent space that mimics the spatial organization of the 2D tissue. To validate spatially predicted enhancers, we use a large collection of enhancer-reporter lines and identify ~85% of enhancers for which chromatin accessibility and enhancer activity patterns agree; while the remaining ~15% are ubiquitously accessible regions bound by the pioneer transcription factor Grainyhead, for which accessibility and activity do not correlate. Next, we infer linear and non-linear enhancer-to-target gene relationships in the virtual space, and find that genes are mostly regulated by multiple -and in some cases, redundant - enhancers. In addition, using cell-type specific enhancers learned from the scATAC-seq data, we deconvolute the cell-type specific effects of chromatin accessibility QTLs from a panel of 50 bulk ATAC-seq profiles from Drosophila inbred lines. Finally, we identify Prospero as a key transcription factor driving neuronal photoreceptor differentiation through the binding of a GGG recognition motif. In summary, we provide a comprehensive spatial characterization of gene regulation in a 2D tissue, which can be explored via SCope (http://scope.aertslab.org/#/Bravo_et_al_EyeAntennalDisc) and the UCSC Genome browser (http://genome.ucsc.edu/s/cbravo/Bravo_et_al_EyeAntennalDisc).

overall_design: Single-cell ATAC-seq data (Fluidigm C1) of sens-GFP+ cells from the wild type Drosophila third instar larvae eye-antennal disc.

last: González-Blas

first: Stein

last: Aerts


title: Variation of human neural stem cells generating organizer states in vitro before committing to cortical excitatory or inhibitory neuronal fates

status: Public on Apr 15 2020

city: Baltimore

first: Carlo

last: Colantuoni

state: MD

address: 733 N Broadway

department: Neurology

country: USA

institute: Johns Hopkins Univ. School of Medicine

type: Expression 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: Identification of genomic enhancers through spatial integration of single-cell transcriptomics and epigenomics

status: Public on Apr 08 2020

type: Genome binding/occupancy profiling by high throughput sequencing


title: MicroRNA profiling in resistance ovarian cell lines

city: Poznan

first: Marcin

last: Rucinski

address: Swiecicki 6

department: Histology and Embriology

country: Poland

institute: Poznan University of Medical Science

summary:
Although many genes associated with the development of resistance to chemotherapy are known, the mechanisms of their regulation are still poorly understood. One of the ways to regulate gene expression is regulation at mRNA level by small noncoding RNA particles – designated as a micro RNA (miRNA). Changes in miRNA expression were also observed in cell line studyes. Downregulation of miR-31 expression correlated with taxane resistance in ovarian cancer cell lines. In contrast upregulation of miR-98-5p was observed in cisplatin (CIS) -resistant cell lines. Changes in miRNAs expression were also noted in another cancers. miR-195 expression was downregulated in temozolomid-resistant glioma cells  and miR-203 was downregulated in prostate cancer cells resistant to doxorubicin (DOX).
The use of miRNA microarrays to analyse changes in miRNA gene expression is an effective molecular tool for the discovering new miRNA genes involved in drug resistance processes.  The present study shows alterations in the miRNA expression levels in the CIS (W1CR), PAC (W1PR1 and W1PR2), DOX (W1DR), and topotecan (TOP) (W1TR) - resistant variants of W1 sensitive ovarian cancer cell line.

overall_design: The human primary ovarian cancer cell line W1 was established from tumour tissue of untreated 54-year old Caucasian female patient diagnosed for serous ovarian adenocarcinoma (G3, FIGO IIIc). Cells grow as a monolayer, present epithelial morphology and adherent growth model. Sublines resistant to cisplatin (W1CR), doxorubicin (W1DR), topotecan (W1TR) and paclitaxel (W1PR1 and W1PR2) were obtained by exposure of the W1 cell line to stepwise increasing drug concentrations. Final concentration of each drug was twofold greater than the concentration in the plasma 2 hours after intravenous administration. The cells were 8-, 10-, 20-, 641- and 967-folds resistant to their selective drugs, respectively, as determined by Cell Proliferation Kit I (MTT). All cell lines were maintained as monolayer in complete medium [RPMI-1640 medium supplemented with 10% (v/v) fetal bovine serum, 2 pMl-glutamine, penicillin (100 U/ml), streptomycin (100 U/ml) and amphotericin B (25 µg/ml)] at 37˚C in a 5% CO2 atmosphere.

first: Radoslaw

last: Januchowski

first: Dominika

last: Kazmierczak


title: The role of lncRNA Sarrah in human cardiomyocytes

status: Public on Apr 07 2020

city: Frankfurt

first: David

last: John

state: Hessen

address: Theodor-Stern-Kai 7

country: Germany

institute: Institute for Cardiovascular Regeneration

summary: Long non-coding RNAs (lncRNAs) contribute to (patho)physiological processes in the heart. Aging is the major risk factor for cardiovascular disease and cardiomyocyte apoptosis is an underlying cause for age-related cardiac dysfunction. RNA sequencing of cardiomyocytes from young and aged mouse hearts revealed several aging-regulated lncRNAs. An siRNA screen for caspase activity identified the aging-regulated lncRNA Sarrah (ENSMUST00000140003) as anti-apoptotic, which we confirmed in human cells (human SARRAH is annotated as OXCT1-AS1). Importantly, human engineered heart tissue showed impaired contractile force development upon SARRAH knockdown compared with controls. Computational prediction of RNA-DNA triple helix formation showed that SARRAH may directly bind the promoters of genes downregulated after SARRAH silencing, which mainly consist of cell survival genes. Indeed, nuclear magnetic resonance spectroscopy confirmed RNA-DNA triple helix formation and cardiomyocytes lacking the triple helix-forming domain of Sarrah showed an increase in apoptosis. One of the key direct SARRAH targets is NRF2, an anti-oxidant transcription factor. Restoration of NRF2 levels after SARRAH silencing partially rescues the reduction in cell viability. RNA affinity purification mass spectrometry analysis identified CRIP2 as main protein interaction partner. Furthermore, SARRAH associates with acetyltransferase p300 and acetylated histone H3K27. Finally, Sarrah was also profoundly downregulated after acute myocardial infarction (AMI) in mice. Adeno-associated virus-mediated overexpression of Sarrah in mice showed better recovery of cardiac contractile function after AMI compared to control mice, as measured by echocardiography and magnetic resonance imaging, consistent with a decrease in cardiomyocyte cell death and an increase in endothelial cell proliferation. In summary, we identified the anti-apoptotic evolutionary conserved lncRNA Sarrah, which is downregulated by aging, as a pivotal regulator of cardiomyocyte survival. Sarrah overexpression has beneficial effects on AMI recovery highlighting it as a potential therapeutic approach against heart failure.

overall_design: Hearts were harvested from 3 8-week old mice and 3 18-month old mice and cardiomyocytes were separated from non-cardiomyocytes (rest cells) by centrifugation after enzymatic digestion in a Langendorff perfusion setup.

first: Reinier

middle: A

last: Boon

first: D

middle: J

last: Trembinski


title: Identification of genomic enhancers through spatial integration of single-cell transcriptomics and epigenomics [10X_scATACseq]

overall_design: Single-cell ATAC-seq data (10X Genomics, Single-cell ATAC solution) of the wild type Drosophila third instar larvae eye-antennal disc.

middle: B


title: Cell and molecular transitions during efficient dedifferentiation: testing transcription factor mutants

city: London

first: Jonathan

last: Chubb

address: Gower Street

department: MRC Laboratory for Molecular Cell Biology

country: United Kingdom

institute: University College London

summary: Transcriptomic analysis of dedifferentiation in Dictyostelium discoideum: comparing wild type with bzpS-, mybD-, nfyA-, DDB_G0281091-, DDB_G0269374- and DDB_G0272386- mutant cells dedifferentiating in growth medium

overall_design: RNASeq timecourses (0,2,4,6,8,24 h) of dedifferentation in growth media for wild type (AX2), bzpS-, mybD-, nfyA-, DDB_G0281091-, DDB_G0269374-, DDB_G0272386- cells. N = 1

first: John

middle: M

last: Nichols

first: Vlatka

last: Antolovic

first: Jacob

last: Reich

first: Sophie

last: Brameyer

first: Peggy

last: Paschke

middle: R


title: Identification of genomic enhancers through spatial integration of single-cell transcriptomics and epigenomics [Omni-ATACseq]

overall_design: Omni-ATAC-seq data of the Drosophila third instar larvae eye-antennal disc upon TF overexpression with the GMR-GAL4 UAS-TF system.


title: Cell and molecular transitions during efficient dedifferentiation: single cell RNAseq

summary: Transcriptomic analysis of dedifferentiation in Dictyostelium discoideum by single cell RNAseq

overall_design: scRNAseq of cells during the first 6 h of dedifferentiation in liquid growth media. Dedifferentiation cultures with staggered start times were harvested simultaneously at 0, 1, 2, 3, 4, 5 and 6 h of dedifferentiation and pooled together for sequencing using the 10x Chromium platform. Cells from different timepoints were pooled before barcoding. Two biological replicates were collected. In each biological replicate, the input cells were split between two Chromium 10x chip inlets (technical replicates) with data from each technical replicate pooled after mapping for downstream analysis. In biological replicate 1, 967 libraries passed UMI filtering by CellRanger v2.2.0 with median of around 25000 total molecular counts. In biological replicate 2, 2961 libraries passed filtering,with a median of around 18000 total molecular counts.


title: Endogenous itaconate is not required for particulate matter-induced NRF2 expression or inflammatory response

city: Chicago

first: Yan

last: Li

state: IL

address: 900 East 57th St.

department: Center for Research Informatics

institute: The University of Chicago

summary: RNA-sequencing demonstrated Acod1 (Aconitate decarboxylase 1) as one of the top genes induced by air polution particulate matter (PM) in macrophages. We therefore sought to determine the effect of both exogenous itaconate (4-octyl itaconate) and endogenous itaconate on PM-induced inflammation in macrophages through RNA sequencing.

overall_design: Transcriptome of WT and Acod1-/- mouse macrophages in duplicates, using Illumina sequencing.

first: Kaitlyn

last: Sun

first: Gokhan

last: Mutlu


title: Acquired resistance to combined BET and CDK4/6 inhibition in triple-negative breast cancer  [Exome]

city: Boston

first: Kornelia

last: Polyak

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

type: Genome variation profiling by high throughput sequencing

summary: BET inhibitors are promising therapeutic agents for the treatment of triple-negative breast cancer (TNBC), but the rapid emergence of resistance necessitates investigation of combination therapies and their effects on tumor evolution. Here, we show that palbociclib, a CDK4/6 inhibitor, and paclitaxel, a microtubule inhibitor, synergize with the BET inhibitor JQ1 in TNBC lines. High-complexity DNA barcoding and mathematical modeling indicate a high rate of de novo acquired resistance to these drugs relative to pre-existing resistance. We demonstrate that the combination of JQ1 and palbociclib induces cell division errors, which can increase the chance of developing aneuploidy. Characterizing acquired resistance to combination treatment at single cell level shows heterogeneous mechanisms including activation of G1-S and senescence pathways. Our results establish a rationale for further investigation of combined BET and CDK4/6 inhibition in TNBC and suggest novel mechanisms of action for these drugs, and new vulnerabilities in cells after emergence of resistance.

overall_design: Exome-seq of SUM159 breast cancer cell line treated in vitro with JQ1, palbociclib, paclitaxel, and combinations

first: Jennifer

middle: Y

last: Ge

first: Franziska

last: Michor


title: RNA-Sequencing of nitrogen-stressed spinach tissue

city: Uvalde

first: Vijay

last: Joshi

state: Texas

address: 1619 Garner Field Road

department: Department of Horticultural Sciences

institute: Texas A&M AgriLife Research

summary: Purpose: The goals of this study are to compare differentially expressed transcripts in roots and leaves of spinach plants grown under nitrogen replete and deplete conditions using transcriptome profiling (RNA-seq)

overall_design: Methods: Leaf and root samples for RNA Seq analysis were collected from three independent spinach plants  grown under High N (HNL1, HNL2, HNL3 for leaf samples and HNR1, HNR2, HNR3 for root samples) and Low N (HNL1, HNL2. HNL3 for leaf samples and LNR1, LNR2, LNR3 for root samples) were flash-frozen in liquid nitrogen for further analysis. Results: The clustering of the index-coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the libraries were sequenced on an Illumina Hiseq platform, and 150 bp paired-end reads were generated. Raw reads of fastq format were processed to obtain clean reads by removing the adapter, reads containing ploy-N, and low quality reads from raw data. At the same time, Q20, Q30, and GC content, the clean data were calculated. Reference genome and gene model annotation files were downloaded from SpinachBase (http://spinachbase.org/). Index of the reference genome was built using Bowtie v2.2.3, and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12. : HTSeq v0.6.1 was used to count the reads mapped to each gene. Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated from mapped read by featureCounts. Differential expression analysis of High N and Low N conditions (three biological replicates per tissue per treatment) was performed using the DESeq R package (1.18.0) (Anders and Huber, 2010). Genes with P-value < 0.05 found by DESeq were assigned as differentially expressed. Conclusions: The transcriptomic changes induced by Nitroge ntreatment in leaf tissueand root tissues was used for RNA-Seq analysis. A total of six libraries from leaf and root tissue were sequenced using the Illumina HiSeq platform. On average, 43.8 and 41.2 million raw reads were generated from leaf and root tissues in high N treatment. Across all reads for both control and drought samples, the Q20 and Q30 percentage was more than 98 and 90%, respectively (sequencing error rate was less than 0.02%), and GC content for the libraries was ~45%.  Among all the libraries, the ratio of total mapped reads was above 85%, of which ~82 % reads uniquely mapped to the reference genome . The data generated from all libraries provided a foundation for quality analyses.


title: Identification of genomic enhancers through spatial integration of single-cell transcriptomics and epigenomics [10X_scRNAseq]

first: Carmen

last: Bravo González-Blas

overall_design: Single-cell RNA-seq data (10X Genomics, Single-cell Expression Solution v2) of the wild type Drosophila third instar larvae eye-antennal disc.

last: González-Blas

first: Stein

last: Aerts


title: Identification of genomic enhancers through spatial integration of single-cell transcriptomics and epigenomics [ATACseq]

overall_design: ATAC-seq data of the wild type Drosophila third instar larvae eye-antennal disc across a panel of 29 lines.


title: Acquired resistance to combined BET and CDK4/6 inhibition in triple-negative breast cancer  [scRNA-Seq]

overall_design: RNA-seq of SUM159 breast cancer cell line treated in vitro with JQ1, palbociclib, paclitaxel, and combinations


title: Acquired resistance to combined BET and CDK4/6 inhibition in triple-negative breast cancer  [RNA-Seq]


title: Establishment of macaque trophoblast stem cell lines from cynomolgus monkey blastocysts.

status: Public on Apr 05 2020

city: Tokyo

first: Shoma

last: Matsumoto

address: 1-1-1 Yayoi, Bunkyo-ku

department: Department of Animal Resource Sciences

country: Japan

institute: The University of Tokyo

summary: Analysis of genome wide gene expression of 5 macaque trophoblast progenitor cell lines cultured in proliferative ((A)FHBY), basal (TS) and differentiation (dbcAMP) conditions. Placenta, fibroblast and ESC was used as positive and negative controls.

overall_design: mRNA expression profiles of  5 cynomolgus monkey trophoblastic cell lines in different culture conditions, using Illumina HiSeq 2500.

first: Christopher

last: Porter

first: Naomi

last: Ogasawara

first: Chizuru

last: Iwatani

first: Hideaki

last: Tsuchiya

first: Yasunari

last: Seita

first: Yu-Wei

last: Chang

first: Ikuiro

last: Okamoto

first: Mitinori

last: Saitou

first: Masatsugu

last: Ema

first: Theodore

last: Perkins

first: William

middle: L

last: Stanford

first: Satoshi

last: Tanaka


title: Cell and molecular transitions during efficient dedifferentiation: testing forG- mutant

first: Jonathan

last: Chubb

summary: Transcriptomic analysis of dedifferentiation in Dictyostelium discoideum: comparing wild type and forG- (formin-) mutant cells dedifferentiating in growth medium

overall_design: RNASeq timecourses (0,2,4,6,8,24 h) of dedifferentation in growth media for wild type (AX2) and forG- mutant cells. Two replicates.

first: John

last: Nichols

first: Vlatka

last: Antolovic

first: Jacob

last: Reich

first: Sophie

last: Brameyer

first: Peggy

last: Paschke


title: RNA-seq analysis of mouse normal penile epithelium and penile squamous cell carcinoma

city: Notre Dame

first: Xin

last: Lu

state: IN

address: 100 Mason Center, Building GALVIN Department of Biological Sciences

department: Biological Sciences

institute: University of Notre Dame

summary: We aim to detect differential gene expression using RNA-seq between normal penile epithelial tissue and PB-Cre+ Smad4L/L ApcL/L penile tumors of mice

overall_design: RNA-seq profiling of 3 Smad4/APC mouse penile tumors and 3 wild type penile epithelium tissues using the Illumina pipeline.


title: Acquired resistance to combined BET and CDK4/6 inhibition in triple-negative breast cancer  [Barcode]

first: Kornelia

last: Polyak

overall_design: Barcode-seq of SUM159 breast cancer cell line treated in vivo and in vitro with JQ1, palbociclib, paclitaxel, and combinations

first: Jennifer

last: Ge

first: Franziska

last: Michor


title: Translation and transcription start site profiling of HSV-1 infected cells

city: Würzburg

first: Florian

last: Erhard

address: Versbacher Str. 7

department: Institut für Virologie und Immunbiologie

institute: Julius-Maximilians-Universität Würzburg

sample_organism:
Homo sapiens
Human alphaherpesvirus 1 strain 17

overall_design: Refer to individual Series


title: Homeostatic maintenance and age-related functional decline in the Drosophila ear

status: Public on Apr 03 2020

first: Joerg

last: Albert

address: 332 Grays Inn Rd

department: Ear Institute

summary: Age-related hearing loss (ARHL) is a threat to future human wellbeing. Multiple factors contributing to the terminal auditory decline have been identified; but a unified understanding of ARHL - or the homeostatic maintenance of hearing before its breakdown - is missing. We here present an in-depth analysis of homeostasis and ageing in the antennal ears of the fruit fly Drosophila melanogaster. We show that Drosophila, just like humans, display ARHL. By focusing on the phase of dynamic stability prior to the eventual hearing loss we discovered a set of evolutionarily conserved homeostasis genes. The transcription factors Onecut (closest human orthologues: ONECUT2, ONECUT3), Optix (SIX3, SIX6), Worniu (SNAI2) and Amos (ATOH1, ATOH7, ATOH8, NEUROD1) emerged as key regulators, acting upstream of core components of the fly’s molecular machinery for auditory transduction and amplification. Adult-specific manipulation of homeostatic regulators in the fly’s auditory neurons accelerated - or protected against - ARHL.

overall_design: Inner-ear (second antennal segment) mRNA profiles were generated for virgin male and female Canton-S Drosophila melanogaster flies of different ages (1, 5, 10, 25, and 50 days old, with the exception of day 10 for females), in duplicate (i.e. two replicates per age per sex), using  Illumina NextSeq 500 (paired-end 75 bp-long reads).

first: Alyona

last: Keder

first: Anastasia

last: Filia

first: Marcos

last: Georgiades

first: Camille

last: Tardieu

middle: T


title: Long non-coding RNA GRASLND enhances chondrogenesis via suppression of interferon type II signaling pathway

status: Public on Apr 06 2020

city: St Louis

first: Farshid

last: Guilak

state: Missouri

address: Couch Building, 3rd Floor, #3213

department: Orthopaedics

institute: Washington University in St Louis

type: Non-coding RNA profiling by high throughput sequencing

summary: Long non-coding RNAs (lncRNAs) play critical roles in regulating gene expression and cellular processes; however, their roles in musculoskeletal development, disease, and regeneration remain poorly understood. Here, we identified a novel lncRNA, Glycosaminoglycan Regulatory ASsociated Long Non-coDing RNA (GRASLND), as a regulator of mesenchymal stem cell (MSC) chondrogenesis, and we investigated its basic molecular mechanism and its potential application towards regenerative medicine. GRASLND, a primate-specific lncRNA, is upregulated during MSC chondrogenesis and appears to act directly downstream of SRY-Box 9 (SOX9), but not Transforming Growth Factor Beta 3 (TGF-β3). Utilizing the established model of pellet formation for MSC chondrogenesis, we showed that the silencing of GRASLNDresulted in lower accumulation of cartilage-like extracellular matrix, while GRASLND overexpression, either via transgene ectopic expression or by endogenous activation via CRISPR, significantly enhanced cartilage matrix production. GRASLND acts to inhibit IFN-γ by binding to eukaryotic initiation factor-2 kinase PKR. We further demonstrated that GRASLND exhibited a protective effect in engineered cartilage against interferon type II, and that GRASLND exerted this effect similarly in engineered cartilage across different sources of progenitors. Our results indicate an important role of GRASLND in regulating stem cell chondrogenesis, as well as its therapeutic potential in the treatment of cartilage-related diseases, such as osteoarthritis.

overall_design: High throughput RNA sequencing of day 21 mesenchymal stem cell pellets with shRNAs targeting GRASLND

first: N

middle: P

last: Huynh

first: C

middle: C

last: Gloss

first: J

last: Lorentz

first: R

last: Tang

last: Brunger

first: A

last: McAlinden

first: B

last: Zhang

first: F


title: Genome-wide mapping of 8-oxodG in G0-arrested MCF10A cells

status: Public on Apr 02 2020

city: Naples

first: Stefano

last: Amente

address: via pansini, 5

department: Department of  Molecular Medicine and Medical Biotechnologies

country: Italy

institute: University of Naples "FEDERICO II"

summary: 8-oxo-7,8-dihydro-2’-deoxyguanine (8-oxodG) is one of the major DNA modifications and a potent pre-mutagenic lesion prone to mispair with deoxyadenine (dA). Here, by using OxyDIP-Seq, we report the genome-wide distribution of 8-oxodG in human MCF10A cells arrested in G0.

overall_design: Genome-wide maps of 8-oxodG in G0-arrested MCF10A.

first: Francesca

last: Gorini

first: Giovanni

last: Scala

first: Giacomo

last: Di Palo

first: Gaetano

middle: I

last: Dellino

first: Sergio

last: Cocozza

first: Pier

middle: G

last: Pelicci

first: Luigi

last: Lania

first: Barbara

last: Majello


title: Ribosome profiling of HSV-1 infected cells

first: Florian

last: Erhard

summary: Primary human foreskin fibroblasts (HFF) were infected with wild-type simplex virus 1 (HSV-1) strain 17 at a multiplicity of infection (MOI) of 10. Ribosome profiling was performed at various times during infection with minor modification to the protocol described in Stern-Ginossar N et al., Science 2012. Translation start site profiling was performed by culturing cells in presence of Harringtonin or Lactimidomycin for 30 min prior to cell harvest.

platform_organism:
Homo sapiens
Human alphaherpesvirus 1 strain 17

overall_design: Ribosome profiling was performed a 0, 1, 2, 4, 6 and 8 h post infection. Translation start site profiling was performed using Harringtonin (2µ/ml for for 30 min) or Lactimidomycin (50µM for 30 min) prior to cell lysis. Two biological replicates were analysed.

first: Adam

last: Whisnant

first: Christopher

last: Jürges

first: Andrzej

last: Rutkowski

first: Thomas

last: Hennig

first: Caroline

last: Friedel

first: Lars

last: Dölken


title: Next Generation Sequencing Transcriptome Quantitative Analysis of Placenta of at embryonic day 19

status: Public on Apr 01 2020

city: Cambridge

first: Lucas

last: Pantaleao

address: 11A Glisson Road

institute: University of Cambridge

summary: Obesity during pregnancy is associated with fetal growth restriction in the offspring. We used RNA next generation sequencing analysis (HiSeq2000) to have a snapshot of the placenta transcriptome at embryonic day 19 to examine whether mice exposed to maternal obesity had significant changes in their transcriptome which may lead to growth restriction in the fetus.

overall_design: C57BL/6J mice were fed either a standard control diet, RM1 [7% simple carbohydrates/3% lipids (w/w)] or an energy-rich obesogenic diet [10% simple carbohydrates/20% lipids (w/w)] plus sweetened condensed milk [55% simple carbohydrates, 8% lipids, 8% protein (w/w), Nestle (Nestle, UK), supplemented with mineral and vitamin mix AIN93G]. Female mice were mated, and Pregnant mice were housed individually and maintained on their respective diets until sacrafice.  A subset of the mice on the Obesegenic diet were exercised until E17 of pregnancy. Placenta tissue was collected at embryonic day 19.

first: Susan

middle: E

last: Ozanne

first: Ania

last: Wilczynska


title: A chromosome-scale assembly of the smallest Dothideomycete genome reveals a unique genome compaction mechanism in filamentous fungi

city: Yangling

first: bo

last: wang

state: Shaanxi

address: No. 3 Taicheng Road

country: China

institute: Northwest A&F University

summary: RNA sequencing was applied to compare the transcriptome profiles of mycelium on potato dextrose (PD) for 5days, mycelium on PD for 15days and mycelium on PD + PEG6000 for 15days,

overall_design: For each sample type, independent librarie was generated, sequencing was performed on an Illumina NextSeq 500 platform

first: Bo

last: Wang

first: Guangyu

last: Sun


title: Zeb2 regulates myogenic differentiation in pluripotent stem cells

status: Public on Mar 31 2020

first: Alvaro

last: Cortés Calabuig

address: Herestraat 49 PO box 602

institute: Genomics Core Leuven

summary: Zinc finger E-box-binding homeobox 2 (ZEB2, also known as SMAD interacting protein 1 or Zfhx1b) protein is a transcription factor involved in the transforming growth factor β (TGFβ) and bone morphogenetic proteins (BMPs) signaling pathways. ZEB2 is a two-handed zinc-finger closely related to ZEB1 (ZFHX1a/δEF1) and it is present in many tissues including cardiac and skeletal muscles. Skeletal muscle development and adult myogenesis are regulated by helix-loop-helix proteins, including MyoD, Myf5, myogenin and MRF-4. It has been shown that ZEB1 (ZFHX1a/δEF1) competes with the myogenic regulatory factors for their consensus sequences on some target genes during muscle differentiation, however the role of ZEB2 in myogenesis is still unknown.  In the present study, we evaluated the myogenic potential of Zeb2-null and R26_Zeb2 mouse embryonic stem cells by single-cell RNA-sequencing and tested muscle engraftment capability of the respective myogenic progenitors. Our results support the implication of Zeb2 in promoting myogenesis in pluripotent stem cells and myogenic progenitors by modulating specific genes encoding components of the TGFβ/BMP signaling system.

overall_design: We investigate the role of Zeb2 in skeletal muscle differentiation using genetic tools, transgenic mouse embryonic stem cells together with single-cell RNA-sequencing and in vivo muscle engraftment capability.

first: Ester

middle: S

last: Di Filippo

first: Domiziana

last: Costamagna

first: Giorgia

last: Giacomazzi

last: Cortés-Calabuig

first: Agata

last: Stryjewska

first: Danny

last: Huylebroeck

first: Stefania

last: Fulle

first: Maurilio

last: Sampaolesi


title: Transcription start site profiling of HSV-1 infected cells using cRNA-seq and dRNA-seq

first: Florian

last: Erhard

summary: Primary human foreskin fibroblasts (HFF) were infected with wild-type simplex virus 1 (HSV-1) strain 17 at a multiplicity of infection (MOI) of 10. Sequencing libraries were prepared using the cRNA-seq and dRNA-seq protocol from the indicated time points of infection.

overall_design: HFF were infected with HSV-1 strain 17. Transcription start sites were enriched using the cRNA-seq and dRNA-seq protocol on total cellular RNA. Two independent biological replicates were analysed.

first: Adam

last: Whisnant

first: Christopher

last: Jürges

first: Andrzej

last: Rutkowski

first: Thomas

last: Hennig

last: Friedel


title: H3K4me1 distribution at promoters predicts the poised epigenetic state

city: New Haven

first: Bluma

last: Lesch

state: CT

address: 333 Cedar Street

department: Genetics

institute: Yale University

summary: Post-translational modifications on histone tails are closely correlated to transcriptional states. One such modification is monomethylation on lysine 4 of histone 3(H3K4me1), a mark that has been linked to enhancers. Identifying regions enriched for H3K4me1 and depleted in H3K4me3, or regions enriched for both H3K4me1 and H3K27ac, has proven to be a feasible enhancer discovery method.  At the same time, not all H3K4me1-enriched regions correspond to enhancers. H3K4me1 marks also exist at promoters, which implies that the H3K4me1 modification may have a context-dependent role in regulating transcription. We report distinct patterns of H3K4me1 that predict transcriptional regulatory states at promoters in germ cells and ESCs. We examined ChIP-seq data for H3K4me1, H3K4me3, H3K27me3, and H3K27ac in mouse and human male germ cells, and found that H3K4me1 peak density around the transcription start sites (TSS) exhibits either a broad bimodal profile or a narrower unimodal profile centered at the TSS. We then examined the position of the H3K4me1 marks relative to H3K4me3, and found that unimodal H3K4me1 directly at the TSS predicts a poised (H3K4me1/H3K27me3 bivalent) state of chromatin, while bimodal H3K4me1 flanking the TSS predicts an active state. We conclude that unimodal H3K4me1 centered on the TSS is a characteristic feature of the poised epigenetic state in ESCs and germ cells.  Note: H3K4me1 and H3K27ac data are included in this GEO accession; H3K4me3 and H3K27me3 were released in GSE68507.

overall_design: ChIP-seq for H3K4me1 and H3K27ac in spermatogenic cells (pachytene spermatocytes and round spermatids) from adult mouse and human.

first: Sunhee

last: Bae


title: Gene expression profile of BJAB and CEM cell lines after WNT7A ectopic expression using a lentiviral vector (pLVX)

status: Public on Mar 30 2020

city: Guadalajara

first: Christian

middle: David

last: Barreto Vargas

state: Jalisco

address: Sierra Mojada 800

department: División de Inmunología

country: Mexico

institute: Centro de Investigación Biomédica de Occidente

summary: Analysis of gene expression profile in leukemia derived cell lines after the ectopic expression of WNT7A

overall_design: The ectopic expression of WNT7A was induced in two different leukemia cell lines (BJAB and CEM) using a lentiviral vector. Total RNA was isolated using the Genejet RNA Purification Kit (Thermo Scientific) and converted into cDNA by using cDNA synthesis system (Agilent). The labeling was performed with the Nimblegen One-Color DNA kit. Labeled DNA was hybridized into the Human Expression 12x135K array (Roche) for further scanning with the Nimblegen MS200 microarray scanner.

last: Barreto-Vargas

first: Luis

middle: F

last: Jave-Suarez


title: Acute exposure to graded levels of hypoxia in U87-MG cells: the role of hypoxia in GBM

city: Chongqing

first: bao

last: liu

address: 30 Gaotanyan street

department: Institute of Medicine and Hygienic Equipment for High Altitude Region

institute: 3rd Military Medical University

summary:
Purpose: Hypoxia is a predominant feature in GBM and its microenvironment. It is associated with the tumor growth, progression and resistance to conventional therapy of GBM. We have utilized U87-MG cell line as a human GBM cell model and human brain HEB cell line as non-neoplastic brain cell cultured in different levels of hypoxia for transcriptional profiling to identify the transcriptional signature of U87-MG cells for elucidated the role of hypoxia in GBM phenotype.
Methods: We have utilized U87-MG cell line as a human GBM cell model and human brain HEB cell line as non-neoplastic brain cell cultured in 21%, 5% and 1% O2 for 24h. Then we detected the changes of transcriptional profiling and analyzed the biological process and pathway for the genes with different expression modes in different hypoxia levels.
Results: U87-MG cells present specific transcriptional signature response to different hypoxia levels. The genes associated with organ and system development present an upward trend from normoxia to extreme hypoxia. And the biological process of DNA repair presents a downward trend, indicating that gene mutations of U87-MG cells could derive by hypoxia microenvironment. Otherwise, HEB cells present the canonical response to hypoxia, reducing of the metabolic rate in concert with the degree of hypoxia and extracting more oxygen from the environment.
Conclusion: Hypoxia microenvironment could promote the malignance of GBM through activate of genes involved in organ and system development. Meanwhile it could induce the mutations of genes in GBM, especially extreme hypoxia.

overall_design: Hypoxia is a predominant feature in GBM and its microenvironment. It is associated with the tumor growth, progression and resistance to conventional therapy of GBM. We have utilized U87-MG cell line as a human GBM cell model and human brain HEB cell line as non-neoplastic brain cell cultured in 21%, 5% and 1% O2 for 24h. Then we detected the changes of transcriptional profiling and analyzed the biological process and pathway for the genes with different expression modes in different hypoxia levels to elucidate the role of hypoxia in GBM phenotype.

first: Yixing

last: Gao

first: Bao

last: Liu

first: Erlong

last: Zhang

first: Haibo

last: Wu

first: You-hong

last: Cui

first: Xia

first: Xin-dong

first: Yan

last: Wang

first: Yuqi

first: Xiu-wu

last: Bian


title: Discovery of Frenolicin B as Potential Agrochemical Fungicides for Controlling Fusarium Head Blight on Wheat

city: Harbin

first: Chuanyu

last: Han

state: Heilongjiang

address: Changjiang 600

institute: School of life science

summary: Purpose: To explore the mechanism of Frenolicin B could control the Fusarium Head Blight on Wheat.  Methods: Fusarium graminearum were inoculated into PDB broth and cultivated 36 hours. After that, Frenolicin B was added in the broth of Fusarium graminearum, and the same volumes of methanol were served as the control. Then incubated together 6 hours.

overall_design: mRNA of Fusarium graminearum mycelia incubated together with Frenolicin B (Y1, Y2, Y2) or the same volumes of methanol (ck1, ck2, ck3), three biological replicates, using Illunima NovaSeq 6000.

first: Chongxi


title: Genome-wide maps of HPSH-CTCF binding in prim-5 stage zebrafish embryos

city: Paris

first: Yuvia

middle: Alheli

last: Perez Rico

address: 26 rue d'Ulm

country: France

institute: Institut Curie

summary: CCCTC-binding factor (CTCF) is an architectural protein with context dependent functional outcomes. Although CTCF is conserved throughout Metazoan evolution, its functions have been only evaluated in a limited number of species. Here, we present the first analysis of CTCF binding in the zebrafish genome via chromatin immunoprecipitation followed by sequencing (ChIP-seq). To avoid the need of custom antibodies, we generated a transgenic line with an HA-tagged version of CTCF that enabled the identification of 37,625 CTCF peaks in 24 hours post-fertilization (hpf) embryos. We determined that CTCF peaks generally overlap with histone marks associated to enhancers and active promoters, and identified repeats that are enriched on CTCF binding sites. In addition, we show extended sites of CTCF binding as previously shown in mammals and lamprey, supporting the hypothesis of a CTCF “code” in vertebrates. Our results indicate a positive association between the abundance of CTCF at promoters and gene expression that could be explained by high DNA accessibility. Finally, analysis of chromosome conformation capture data confirms that histone marks associated with active chromatin are enriched at boundaries of topologically associating domains (TADs), but no general enrichment of CTCF peaks nor motifs is observed at these regions. Our zebrafish line and data generated will be important for future studies of genome organization aiming to characterize the roles of CTCF in non-mammalian vertebrates.

overall_design: ChIP-seq screen for CTCF occupancy in 24 hpf zebrafish embryos, in duplicates

last: Pérez-Rico

first: Emmanuel

last: Barillot

first: Alena

last: Shkumatava


title: Blood Biomarkers for Memory: Towards Early Detection of Risk for Alzheimer Disease, Pharmacogenomics, and Repurposed Drugs

city: Indianapolis

first: Dr. Alexander

middle: B.

last: Niculescu

address: 320 W. 15th Street

department: Psychiatry

institute: Indiana University Medical School

summary: Short-memory dysfunction is a key early feature of Alzheimer Disease. Psychiatric patients may be at higher risk for memory dysfunction and subsequent Alzheimer due to the negative effects of stress and depression on the brain. We carried out longitudinal within-subject studies in male and female psychiatric patients to identify blood gene expression biomarkers that track short term memory as measured by the retention measure in the Hopkins Verbal Learning Test. These biomarkers were prioritized with a convergent functional genomics approach using previous evidence in the field  implicating them in Alzheimer Disease. The top candidate biomarkers were tested in an independent cohort for ability to predict state short-term memory, and trait future positive neuropsychological testing for cognitive impairment

overall_design:
Alzheimer disease (AD) is a clear and present danger to older adults, and has a profound socio-economic impact (refs). Existing therapies are limited in efficacy (refs). Early identification of individuals at risk may open the door to preventive approaches.  Short-term memory dysfunction is a key early feature of AD. We proposed to identify blood biomarkers that track a relevant related quantitative phenotype for short-term memory, the retention measure of recall in Hopkins Verbal Learning Test (HVLT) (Figure S1).  Previous work by our group has identified blood gene expression biomarkers that track suicidal ideation using longitudinal within-subject designs, validated them in suicide completers, and tested them in independent cohorts for ability to assess state (suicidal ideation), and ability to predict trait (future hospitalizations for suicidality) (Le-Niculescu et al. Molecular Psychiatry 2013, Niculescu et al. Molecular Psychiatry 2015) (Levey et al. Molecular Psychiatry 2016) (Niculescu et al. Molecular Psychiatry 2017). Those biomarkers were also useful in pharmacogenomic and drug repurposing analyses. We endeavored to use a similar approach to identify biomarkers for short-term memory.  We conducted our longitudinal studies in psychiatric disorder subjects, a population enriched in memory retention abnormalities, and which  may be at increased risk of AD and other aging-related disorders, due to the effects  of stress and depression (Nho et al. 2015, Rangaraju et al. 2016, al refs).  The subjects had blood gene expression data at multiple testing visits, and were phenotyped at each visit, including with HVLT. They also had electronic medical records for long term follow-up of subsequent outcomes, including future neuropsychological testing as part of standard clinical care.

Diagnoses:
SZ - Schizophrenia
SZA - schizoaffective disorder
BP - Bipolar Disorder
MOOD - Mood
PSYCH - Psychotic Disorder NOS
MDD - Major Depressive Disorder
PTSD - Posttraumatic Stress Disorder

first: Alexander

first: Helen

last: Le-Niculescu


title: Metabolic reprogramming promotes neural crest migration via Yap/Tead signaling

city: Ithaca

first: Marcos

last: Simoes-Costa

state: New York

address: 526 Campus Rd

department: Molecular Biology and Genetics

institute: Cornell University

summary: The Warburg effect is one of the metabolic hallmarks of cancer cells, characterized by enhanced glycolysis even under aerobic conditions. While this physiological adaptation is associated with metastatic behavior, we still have a superficial understanding of how it affects cell motility in development and disease. Here we report that the neural crest, a migratory stem cell population in vertebrate embryos, undergoes an extensive metabolic remodeling to engage in aerobic glycolysis prior to delamination. This increase in glycolytic flux promotes Yap/Tead signaling, which directly activates the expression of a set of transcription factors to drive epithelial-to-mesenchymal transition. Our results demonstrate how shifts in carbon metabolism can trigger the gene regulatory circuits that control complex cell behaviors. Our findings also support the hypothesis that the Warburg effect is a tightly regulated developmental mechanism that is anomalously reactivated during tumorigenesis and metastasis.

overall_design: CUT&RUN data for  the active form of the transcriptional regulator YAP1 and modified histone mark H3K27ac in chick neural crest cells at developmental stage HH9+

first: Debadrita

last: Bhattacharya


title: Release of promoter-proximal paused Pol II in response to histone deactylatase inhibition

city: CANBERRA

first: Jiayu

last: Wen

state: ACT

address: 133 Garran Rd

department: Department of Genome Science

country: Australia

institute: John Curtin School of Medical Research, The Australian National University

summary: A correlation between histone acetylation and transcription has been noted for a long time, but little is known about what step(s) in the transcription cycle is influenced by acetylation. Here, we have examined the immediate transcriptional response to histone deacetylase (HDAC) inhibition, and find that release of promoter-proximal paused RNA polymerase II (Pol II) into elongation is stimulated, whereas recruitment to gene promoters is not. Although histone acetylation is elevated globally by HDAC inhibition, less than 100 genes respond within 10 min. These genes are highly paused, are strongly associated with the chromatin regulators NURF and Trithorax, display a greater increase in acetylation of the first nucleosomes than other genes, and become transcriptionally activated by HDAC inhibition. Among these rapidly upregulated genes are HDAC1 (Rpd3) and subunits of HDAC-containing co-repressor complexes, demonstrating feedback regulation upon HDAC inhibition. Our results suggest that histone acetylation stimulates transcription of paused genes, and that increased acetylation is not a consequence of their enhanced expression.

overall_design: Examination of nascent RNA (PRO-seq), 2 different histone modifications (ChIP-seq) and accessible chromatin (ATAC-seq) from Drosophila S2 cells treated with HDAC inhibitor (TSA) for 10 min or 30 min along with DMSO as control drug.

first: Roshan

last: Vaid

first: Mattias

last: Mannervik


title: A Transcriptional Regulatory Network of Rsv3-mediated Extreme Resistance Against Soybean Mosaic Virus

city: Blacksburg

last: Saghai Maroof

state: VA

address: 220 Ag Quad Ln

department: School of Plant and Environmental Sciences

institute: Virginia Tech

summary: Resistance (R) genes are very effective for disease control in plants. Current research shows that R genes predominantly function by inducing a hypersensitive reaction (HR), which results in localized cell death thought to restrict pathogen spread. Some R genes elicit a more atypical response where resistance is not associated with HR or the associated gene expression changes, termed extreme resistance (ER). The molecular regulatory mechanism underlying ER is largely unexplored. One of the few known, naturally occurring, instances of ER is resistance derived from the soybean Rsv3 gene, which confers resistance against the most virulent strains of soybean mosaic virus (SMV). To discern the regulatory mechanism underlying the Rsv3-mediated ER reaction, we generated a gene regulatory network using transcriptomic data from a time course comparison of SMV-G7-infected resistant (L29, Rsv3-genotype) and susceptible (Williams82, rsv3-genotype) soybean cultivars. We identified putative interactions between transcription factors (TFs) regulating gene expression in hormone regulatory pathways, such as abscisic acid (ABA) and jasmonic acid (JA). This is consistent with the demonstrated involvement of these pathways in Rsv3-mediated resistance. We found significant enrichment for the G-box motif (“CACGTG”) among genes implicated in ABA- and JA-related activities. This motif is specifically recognized by MYC2, which is a master regulator of ABA and JA signaling. Our network identified a MYC2 TF encoded by Glyma.07G051500 as a putative transcriptional regulator whose expression was significantly down-regulated in L29. This correlated with the down-regulation of expression of genes involved in ABA and JA processes. Our results suggest an important function for Glyma.07G051500 in ABA and JA derived defense signaling. Additionally, our regulatory network found other putative TFs with differential expression, such as MYBs and ERFs, which may also be involved in regulating ABA and JA signaling for defense. The regulatory network presented here offers new insights into the regulation of the molecular defense mechanism underlying Rsv3-mediated ER against SMV.

overall_design: The soybean cultivars ‘L29’ (Rsv3-genotype; resistant) and ‘Williams82’ (rsv3-genotype; susceptible) were used in this study. The Rsv3-genotype confers ER to the most virulent strains of SMV. Thus the goal of this study was to investigate the regulation of the Rsv3-mediated ER molecular defense mechanism against SMV. Plants were grown in controlled greenhouse conditions and inoculated at first, fully, expanded trifoliolate stage with SMV strain G7 (SMV-G7). Unifoliolate leaves were dusted with carborundum powder and rubbed with SMV-G7 inoculum. The inoculated unifoliolate leaves were collected at 0, 2, 4, 6, and 8 hours post inoculation (hpi) and stored at -80°C until RNA extraction. High-quality total RNA (RNA >7.0) was extracted from frozen samples using RNeasy Plant Mini Kit (QIAGEN, Hilden, Germany) with on-column DNase digestion (QIAGEN, Hilden, Germany). A total of 20 mRNA libraries (= 2 cultivars x 5 time-points x 2 biological replicates) were prepared from duplicate RNA samples of each line at each time point and sequenced as 150PE with Illumina HiSeq4000 (Illumina, San Diego, CA) at Novogene, Sacramento, CA.

first: Lindsay

last: DeMers

first: M

middle: A


title: Differential gene expression in murine olfactory epithelium: effect of aging and loss of APP, APLP2 and PSEN2.

city: Bydgoszcz

first: Katarzyna

last: Bilińska

address: M.Skłodowskiej-Curie 9

institute: Nicolaus Copernicus University

summary:
RNAseq differential gene expression profiling of olfactory mucosa in young wild type, aged wild type, APP deficient, APLP2 deficient and PSEN2 deficient mice.    Purpose: Next-generation gene expression profiling has revolutionized analysis of molecular pathways. The goals of this study were to compare NGS-derived olfactory mucosa transcriptome profiles (RNAseq) of aged wild-type mice, APP knockout mice, APLP2 knockout mice and PSEN2 knockout mice with young wild-type controls. Selected genes and pathways will be analyze further by low-throughput techniques such as real-time RT-PCR.    Methods: Olfactory mucosa mRNA profiles of 2 months old wild-type (WT), 2 years old wild-type, APP knockout, APLP2 knockout and PSEN2 knockout mice were generated by deep sequencing, in triplicate, using Illumina NovaSeq6000 . For inspecting the quality of RNA-Seq data, the 100 most abundant genes are taken from all the samples and heatmaps were generated to observe the relation between samples/conditions. The sequence reads that passed the quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks.     Results: Using our data analysis workflow, we mapped at least 30 million sequence reads per sample to the mouse genome (build mm10) and identified approximately 25,867 transcripts in the olfactory epithelium of WT and genetically modified mice with TopHat workflow. RNAseq data confirmed stable expression of 20 known housekeeping genes, and 3 of them were validated with qRT-PCR. Approximately 20% of transcripts showed differential expression between WT and aged samples and 0.1-1.0 % showed differential expression between WT and genetically modified lines (fold change >1.5; p value < 0.05). Altered expression of 20 genes for aged samples and 10 genes for PS-deficient samples was confirmed by qRT-PCR, demonstrating the high degree of sensitivity of RNAseq approach.    Conlusion: Our study represent the first detailed analysis of differential gene expression by RNAseq technology in murine olfactory mucosa in aged animals.  It is also the first study examining effects of gene knockout for APP, APLP2 and PSEN2 on gene expression profile in murine olfactory mucosa. We conclude that these data would help future studies in olfactory mucosa cells aimed to reveal molecular mechanisms associated with aging and biological function of APP, APLP2 and PSEN2 genes.  RNAseq differential gene expression profiling of olfactory mucosa in young wild type, aged wild type, APP deficient, APLP2 deficient and PSEN2 deficient mice.    Purpose: Next-generation gene expression profiling has revolutionized analysis of molecular pathways. The goals of this study were to compare NGS-derived olfactory mucosa transcriptome profiles (RNAseq) of aged wild-type mice, APP knockout mice, APLP2 knockout mice and PSEN2 knockout mice with young wild-type controls. Selected genes and pathways will be analyze further by low-throughput techniques such as real-time RT-PCR.    Methods: Olfactory mucosa mRNA profiles of 2 months old wild-type (WT), 2 years old wild-type, APP knockout, APLP2 knockout and PSEN2 knockout mice were generated by deep sequencing, in triplicate, using Illumina NovaSeq6000 . For inspecting the quality of RNA-Seq data, the 100 most abundant genes are taken from all the samples and heatmaps were generated to observe the relation between samples/conditions. The sequence reads that passed the quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks.     Results: Using our data analysis workflow, we mapped at least 30 million sequence reads per sample to the mouse genome (build mm10) and identified approximately 24,000 transcripts in the olfactory epithelium of WT and genetically modified mice with TopHat workflow. RNAseq data confirmed stable expression of 20 known housekeeping genes, and 3 of them were validated with qRT-PCR. Approximately 20% of transcripts showed differential expression between WT and aged samples and 0.1-1.0 % showed differential expression between WT and genetically modified lines (fold change >1.5; p value < 0.05). Altered expression of 20 genes for aged samples and 10 genes for PS-deficient samples was confirmed by qRT-PCR, demonstrating the high degree of sensitivity of RNAseq approach.    Conlusion: Our study represent the first detailed analysis of differential gene expression by RNAseq technology in murine olfactory mucosa in aged animals.  It is also the first study examining effects of gene knockout for APP, APLP2 and PSEN2 on gene expression profile in murine olfactory mucosa. We conclude that these data would help future studies in olfactory mucosa cells aimed to reveal molecular mechanisms associated with aging and biological function of APP, APLP2 and PSEN2 genes.
This RNAseq project has been supported by a grant of Polish National Science Centre (UMO-2013/09/NZ3/02359).

overall_design:
In this study 15 samples were analyzed. Analysis of 3 biological replicates for each experimental condition was performed. All mice used had C57BL/6J genetic background and were males.

Please note that each processed data was generated from either all replicates or across different groups, and is linked to the corresponding rep1 sample records.

first: Rafal

last: Butowt

first: Patrycja

last: Jakubowska


title: Synthetic lethal and resistance interactions with BET bromodomain inhibitors [CRISPR screen]

city: Boston

first: Kornelia

last: Polyak

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

summary: BET bromodomain inhibitors (BBDI) are promising therapeutic agents in triple-negative breast cancer (TNBC). However, not all tumors respond and acquired resistance emerges rapidly even in the responders. Using CRISPR and small molecule inhibitor screens combined with comprehensive molecular profiling of BBDI response and resistance in TNBC cell lines, we identified numerous synthetic lethal interactions with BBDIs as well as genes that when deleted confer resistance. The most prominent and consistent synergy was observed with CDK4/6 inhibitors and paclitaxel. We also uncovered functional similarities and differences between BBD proteins BRD2, BRD4, and BRD7, whereas deletion of BRD2 and BRD4 enhances sensitivity to BBDIs, BRD7 loss leads to resistance. Lastly, single cell RNA-seq and cellular barcoding analysis of BBDI responses in sensitive and resistant cell lines highlight heterogeneity among samples and demonstrate that BBDI resistance can be both pre-existing and acquired.

overall_design: CRISPR screen of parental and JQ1 resistant breast cancer cell lines

first: Shaokun

last: Shu

first: Hua-Jun

last: Wu

first: Franziska

last: Michor


title: HDAC1 modulates OGG1-initiated oxidative DNA damage repair, brain aging, and Alzheimer’s disease pathology

first: Li-Huei

last: Tsai

state: Massachusetts

department: Picower Institute for Learning and Memory

institute: MIT

summary: Unrepaired DNA damage contributes to brain aging and neurodegenerative diseases. However, the factors stimulating DNA repair activity to stave off age-associated functional decline remain obscure. Here, we show that histone deacetylase 1 (HDAC1) modulates DNA repair in the aging brain via targeting OGG1 of the base excision repair pathway. Mice deficient in HDAC1 display age-associated accumulation of DNA damage in the brain and cognitive impairment. HDAC1 interacts with and positively stimulates OGG1, a DNA glycosylase that primarily acts on 8-oxoguanine (8-oxoG), a type of oxidative DNA damage associated with transcriptional repression. Loss of HDAC1 leads to impaired OGG1 activity, 8-oxoG accumulation at the promoters of a subset of genes critical for brain function, and transcriptional repression. Moreover, we observe elevated 8-oxoG lesions along with reduced HDAC1 activity and downregulation of a similar set genes in the 5XFAD mouse model of Alzheimer’s disease (AD). Notably, pharmacological activation of HDAC1 confers protection against the deleterious effects of 8-oxoG lesions in the brains of aged wild-type and 5XFAD mice. Our work uncovers an important role for HDAC1 in the repair of 8-oxoG lesions and highlights HDAC1 activation as a novel therapeutic strategy to counter functional decline during brain aging and neurodegeneration.

overall_design: ChIP-Seq and RNA-Seq of mouse hippocampus, and RNA-Seq of GFAP+ nuclei were isolated from mouse cortex

first: Ping-Chieh

last: Pao

first: Fan

last: Gao

first: Hugh

last: Cam


title: Genome-wide identification of WblC (WhiB7) binding sites and Transcriptome profiles of Streptomyces coelicolor A3(2) wild type and wblC (whiB7) mutant treated with tetracycline

status: Public on Mar 28 2020

city: Seoul

first: Jung-Hye

last: Roe

address: 1 Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

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

overall_design: Refer to individual Series


title: Robust landscapes of ribosome dwell times and aminoacyl-tRNAs in response to nutrient stress in liver

status: Public on Mar 26 2020

city: St Lucia

first: Frédéric

last: Gachon

state: QLD

address: 306 Carmody Road

department: Institute for Molecular Bioscience

institute: University Of Queensland


title: Modeling ribosome dwell times and relationship with tRNA loading and codon usage in mammals (Ribosome Profiling)

summary: Protein translation depends on mRNA-specific initiation, elongation, and termination rates. While the regulation of ribosome elongation is well studied in bacteria and yeast, less is known in higher eukaryotes. Here, we combined ribosome and tRNA profiling to investigate the relations between ribosome elongation rates, (aminoacyl-) tRNA levels and codon usage in mammals. We modeled codon-specific ribosome dwell times and translation fluxes from ribosome profiling, considering pair-interactions between ribosome sites.  In mouse liver, the model revealed site and codon specific dwell times, as well as codon pair-interactions clustering by amino acids. While translation fluxes varied significantly across diurnal time and feeding regimen, codon dwell times were highly stable, and conserved in human.  Fasting had no effect on codon dwell times in mouse liver.  Profiling of total and aminoacylated tRNAs revealed highly heterogeneous levels with specific isoacceptor patterns and a correlation with codon usage.  tRNAs for isoleucine, asparagine, aspartate and arginine were lowly loaded and conserved in fasted mice. Finally, codons with low levels of charged tRNAs and high codon usage relative to tRNA abundance exhibited long dwell times. Together, these analyses pave the way towards understanding the complex relation between tRNA loading, codon usage and ribosome dwell times in mammals.

overall_design: Ribosome profiling of liver harvested from mice fed Ad libitum or fasted

first: Gobet

last: Cédric

first: Weger

last: Benjamin

first: Marquis

last: Julien

first: Martin

last: Eva

first: Gachon

last: Frederic

first: Naef

last: Felix


title: A targeted multi-omic analysis approach measures protein expression and low abundance transcripts on the single cell level

city: Seattle

last: Prlic

state: WA

address: 1100 Fairview Ave, Mail stop E5-110

institute: Fred Hutch

summary:
High throughput single-cell RNA sequencing (sc-RNAseq) has become a frequently used tool to assess immune cell function and heterogeneity. Recently, the combined measurement of RNA and protein expression by sequencing was developed, which is commonly known as CITE-Seq. Acquisition of protein expression data along with transcriptome data resolves some of the limitations inherent to only assessing transcript, but also nearly doubles the sequencing read depth required per single cell. Furthermore, there is still a paucity of analysis tools to visualize combined transcript-protein datasets.
Here, we describe a novel targeted transcriptomics approach that combines analysis of over 400 genes with simultaneous measurement of over 40 proteins on more than 25,000 cells. This targeted approach requires only about 1/10 of the read depth compared to a whole transcriptome approach while retaining high sensitivity for low abundance transcripts. To analyze these multi-omic transcript-protein datasets, we adapted One-SENSE for intuitive visualization of the relationship of proteins and transcripts on a single-cell level.

overall_design: Immune cell characterization utilizing targeted single cell RNA sequencing paired with oligo tagged antibodies using the BD Rhapsody/ AbSeq system

first: Jami

last: Erickson

first: Florian

last: Mair


title: Gene expression analyasis on hippocampal tissue from young Hdac1 cKO and control mice

summary: We performe RNA-sequencing (RNA-seq) and differential gene expression analysis on hippocampal tissues from young (3-month-old) Hdac1 cKO and control mice.

overall_design: RNA-Seq of mouse hippocampus


title: Transcriptomic profiling in fins of Atlantic salmon parasitized with sea lice: Determining the differentially expressed transcripts in fins of lice-infected salmon at 8 days post-infection

city: St. John's

first: Umasuthan

last: Navaneethaiyer

state: NL

address: 1 Marine Lab Road, Dept of Ocean Sciences, Memorial University of Newfoundland

department: Ocean Sciences

country: Canada

institute: Memorial University of NL

summary: Sea lice (e.g., Lepeophtheirus salmonis) are parasites causing costly disease outbreaks in salmon farming globally. Despite the currently available controlling practices, molecular insights into the parasite-induced host immune responses and host-pathogen interaction will provide the basis for improved and innovative treatment strategies. We investigated the early transcriptomic responses in the fins of Atlantic salmon parasitized with sea lice at the chalimus stage (8 days post-infection). Fin tissue collected from non-infected (PRE) control and at (ATT) and adjacent (ADJ) to chalimus-attachment sites from infected fish were used in profiling the global gene expression using a 44K microarray platform. Microarray analyses indicated that global transcriptomic changes resulted in 6,568 differentially expressed probes (DEPs, FDR < 5%) that include 1928 shared DEPs between ATT and ADJ compared to PRE. A direct comparison of ATT vs. ADJ revealed 90 DEPs, all of which were up-regulated in ATT.

overall_design: Atlantic salmon were acclimated for 14 weeks. Prior to infecting them with sea lice copipodids, pelvic fin tip samples were collected from ~5 fish from each tank (duplicate tanks). Fish were then bath-infected with L. salmonis by adding ~50 copepodids per fish to each tank for 2 h. Tissue from pelvic fin tips at (an area of the fin with lice ‘attached’, ATT) and ‘adjacent’ area (with no signs of previous lice attachment, ADJ) from chalimus attachment sites were excised at 8 days post-infection (dpi) and 30 dpi (when most lice were at their chalimus and pre-adult stages, respectively). A universal reference design was used for the microarray experiment. For the test samples, RNA was used from individual fins of fish from the 3 treatment groups. For each treatment group, we used 6 biological replicates (3 fish from each of 2 tanks). All test samples were labeled with Cy5. The common reference was a pool of 18 RNA samples from the fins of fish from all individuals invovled in microarray experiment. The common reference was labeled with Cy3. Each individual test sample was hybridized together with the common reference sample on an array, so the experiment consisted of 18 arrays.

first: Navaneethaiyer

last: Umasuthan

first: Xi

last: Xue

first: Albert

last: Caballero-Solares

first: Surendra

last: Kumar

first: Jillian

middle: D

last: Westcott

first: Zhiyu

last: Chen

first: Mark

last: Fast

first: Stanko

last: Skugor

first: Barbara

last: Nowak

first: Richard

last: Taylor

first: Matthew

last: Rise


title: Endoplasmic reticulum stress regulates immunosuppressive function of myeloid derived suppressor cells in leprosy that can be overcome by IFNg production

city: Los Angeles

first: Kindra

middle: M

last: Kelly-Scumpia

state: CA

address: 615 Charles E Young Dr Rm 246

institute: UCLA

summary: Transcriptome analysis of human HLADR-CD33+ (MDSC) from ENL (n=4), RR (n=5) and healthy donors (n=3).

overall_design: RNA sequencing of for PBMC enriched for HLADR-CD33+(MDSC) from leprosy patients and healthy controls.

first: Robert

last: Modlin


title: RNA-seq profiles of reprogramming cells at Day 3 and Day 6 from MEFs to iPS cells [siNcor1 or siOct4]

status: Public on Mar 27 2020

city: Nijmegen

first: Georgina

last: Peñalosa Ruiz

address: Geert Grooteplein 30

country: Netherlands

institute: Radboud University

summary:
AIM: To detect differences in transcriptional profiles after knocking down Ncor1 or Oct4, compared to a negative control in early reprogramming to pluripotency.
DESCRIPTION: RNA-seq profiles of early reprogramming mouse embryonic fibroblasts (MEFs) transduced with lentivirus containing doxycycline-inducible OSKM factors to induce pluripotency . Before starting reprogramming, OSKM-MEFs were transfected with different siRNAs and then they were reprogrammed for 3 or 6 days.

overall_design: These samples were transfected with either siNcor1 or siOct4. For every knockdown there is a biological replicate.

last: Peñalosa-Ruiz

first: Klaas

last: Mulder

first: Gert

middle: J

last: Veenstra


title: Intracellular Staphylococcus aureus persisters upon antibiotic exposure

status: Public on Mar 25 2020

first: Rachel

last: Legendre

address: 28, rue du docteur Roux

department: Research and Resource Center for Scientific Informatics

institute: Institut Pasteur

summary: Bacterial persister cells are phenotypic variants that exhibit a transient non-growing state and antibiotic tolerance. Here we provide in vitro evidence of Staphylococcus aureus persisters within infected host cells. We show that the bacteria surviving antibiotic treatment within host cells are persisters, displaying biphasic killing and reaching a uniformly non-responsive, non-dividing state when followed at the single-cell level. This phenotype is stable but reversible upon antibiotic removal. Intracellular S. aureus persisters remain metabolically active, but display an altered transcriptomic profile consistent with activation of stress responses, including the stringent response as well as cell-wall stress, SOS and heat-shock responses. These changes are associated with multidrug tolerance after exposure to a single antibiotic. We hypothesize that intracellular S. aureus persisters may constitute a reservoir for relapsing infection, and could contribute to therapeutic failures.

overall_design: 3 Intracellular persister replicates and 3 control replicates

first: Frédéric

last: Peyrusson

first: Hugo

last: Varet

first: Odile

last: Sismeiro

first: Jean-Yves

last: Coppée

first: Christiane

last: Wolz

first: Tanel

last: Tenson

first: Françoise

last: Van Bambeke


title: Transcriptome analysis in a unique cohort of untreated primary tumors collected from diagnostic prostate needle biopsies (PNBX) of localized (M0) and metastatic (M1) cases

city: LA

first: Sungyong

last: You

address: Beverly Blvd 8400

department: Surgery

institute: Cedars-Sinai Medical Center

summary: PNBX were collected from 99 patients treated in the VA Greater Los Angeles (GLA-VA) Healthcare System between 2000-2016

overall_design: 99 prostate cancer cases with archival biopsy tissue available were selected for RNA sequencing (RNAseq) from a total cohort 1927 cases identified within the GLA-VA cancer registry or procedure logs. The selected cases were divided into sub-cohorts based upon tumor burden at diagnosis or recurrence/progression documented in imaging reports, including 99mTc-methylene disphosphonate (99mTc-MDP) planar bone scintigraphy, 18F-NaF positron emission tomography (18F-NaF PET), ultrasounds, magnetic resonance imaging (MRI), computed tomography (CT) scans, and plain radiographs. Cases were designated clinical stage M1 if metastatic lesions were identified on imaging scans performed within 1 year of the diagnostic PNBX. Osteoblastic, osteolytic, and/or sclerotic bone lesions observed on bone scan were confirmed or by the presence of overlapping lesions on plain radiographs, CT or MRI imaging. Oligometastatic “oligo” disease was defined by <5 extrapelvic lymph node and/or bone metastases and no visceral metastases. Polymetastatic “poly” disease was defined as >5 metastases or any visceral involvement. M1 cases were designated M1-oligo or M0-poly based on the aforementioned tumor burden assessment.  Cases that were considered M0 at diagnosis, but demonstrated eventual metastatic progression (M0-M) were designated M0-oligo or M0-poly based on tumor burden on imaging scans at the time of follow-up. Cases were designated as clinical stage M0 non-metastatic (M0-NM) if no metastatic lesions were identified at the time of last follow-up. If imaging scans were not performed, or equivocal results were obtained, the cases were categorized as MX and excluded from analysis. A significant subset of M0 cases from the original 1927 cohort did not have an indication for diagnostic imaging due to diagnosis of low- or intermediate-risk PC according to D’Amico classification

first: Isla

last: Garraway


title: Single-cell RNA sequencing of murine islets shows high cellular complexity at all stages of autoimmune diabetes

city: St. Louis

first: Pavel

last: Zakharov

state: MO

address: 660 S Euclid Ave Box 8118

department: Pathology and Immunology

institute: Wash.Univ in St. Louis

summary: Tissue-specific autoimmune diseases are driven by activation of diverse immune cells in the target organs. However, the molecular signatures of the immune cell populations over time in an autoimmune process remain poorly defined. Using single-cell RNA sequencing, we performed unbiased examination of diverse islet-infiltrating cells during autoimmune diabetes in the non-obese diabetic mouse. The data revealed a landscape of transcriptional heterogeneity across the lymphoid and myeloid compartments. Memory CD4 and cytotoxic CD8 T cells appeared early in islets accompanied by regulatory cells with distinct phenotypes. Surprisingly, we observed a dramatic remodeling in the islet microenvironment, in which the resident macrophages underwent a stepwise activation program. This process resulted in polarization of the macrophage subpopulations into a terminal pro-inflammatory state. This study provides a single-cell atlas defining the staging of autoimmune diabetes and reveals that diabetic autoimmunity is driven by transcriptionally distinct cell populations specialized in divergent biological functions.

overall_design: 10X Single-cell RNASeq

middle: N

first: Hao

last: Hu

first: Xiaoxiao

last: Wan

first: Emil

middle: R

last: Unanue


title: OncoScan CNV array data for PNBX cohort

type: Genome variation profiling by genome tiling array

summary: To identify genomic evidence of chromosomal instability (CIN) in metastatic (M1) cases, we sampled the same tumor regions for DNA extraction that were previously selected to generate transcriptome data in localized (M0) cases.  Since there is limited tissue in PNBX, only 24 cases yielded sufficient quality/quantity of DNA for copy number alteration (CNA) evaluation.

overall_design: Copy number analysis of Affymetrix Oncoscan arrays was performed for 24 prostate needle biopy samples from GLA-VA.

last: Garaway


title: Expression data from HepG2 cells transfected with the Vitamin D Receptor (VDR) and activated by Vitamin D (calcitriol)

city: Valencia

first: RAMIRO

last: JOVER

address: Avenida Fernando Abril Martorell, 106.

department: Experimental Hepatology Unit

country: Spain

institute: IIS Hospital La Fe

summary:
In the present study, we aimed to define the role of VDR in the overall lipid metabolism by transcriptomic and metabolomic analyses of human hepatocytes upon VDR activation by vitamin D (VitD)
In this dataset we include the expression data obtained from HepG2 cells transfected with an insertless adenoviral vector or with an adenovirus encoding human VDR. Cells expressing VDR were treated with VitD or vehicle.

overall_design: 9 total samples were analized: 3 control cells with insertless adenovirus Ad-C for 48 h + 4h vehicle; 3 Ad-VDR cells 48 h + 4 h vehicle; and 3 Ad-VDR cells 48 h + 4 h 10 nM VitD (calcitriol). 3 independent experiments.

first: Ramiro

last: Jover


title: Transcriptome profiles of Streptomyces coelicolor A3(2) wild type and wblC (whiB7) mutant treated with tetracycline

first: Jung-Hye

last: Roe

summary: We determined Streptomyces coelicolor genes that are directly regulated by WblC (or WhiB7), an actinobacterial transcription factor that activates expression of intrinsic resistance in response to translation-inhibitory antibiotic stress. Identification of differentially expressed genes in wblC mutant by RNA-seq and WblC binding sites in wild type by ChIP-seq identified more than 300 genes as WblC regulon. This series encompasses the RNA-seq data of our study.

overall_design: Transcriptome profiles of either tetracycline-treated or untreated wild type and wblC mutant strains were obtained using Illumina HiSeq. RNA samples were prepared in biologically independent duplicates.

first: Ji-Sun

last: Yoo

first: Yeonbum

last: Kim

first: Ju-Hyung

last: Lee

first: Eun-Jin


title: Genome-wide identification of WblC (WhiB7) binding sites in Streptomyces coelicolor A3(2) treated with tetracycline

summary: We determined Streptomyces coelicolor genes that are directly regulated by WblC (or WhiB7), an actinobacterial transcription factor that activates expression of intrinsic resistance in response to translation-inhibitory antibiotic stress. Identification of differentially expressed genes in wblC mutant by RNA-seq and WblC binding sites in wild type by ChIP-seq identified more than 300 genes as WblC regulon. This series encompasses the ChIP-seq data of our study.

overall_design: Chromosomal DNA-binding peaks of WblC were determined from tetracycline-treated wild type using Illumina HiSeq. Chromatin immunoprecipitation (ChIP) and input DNA samples were prepared by pooling biologically independent triplicates, respectively.


title: RNA-seq transcriptome profiling of C. elegans mutants defective in IL-17 signaling

city: Cambridge

first: Alastair

last: Crisp

address: Francis Crick Avenue

institute: MRC Laboratory of Molecular Biology

summary: The whole-animal transcriptomes of ilc-17.1, malt-1 and nfki-1 mutants comapared to that of controls reveals a transcriptional fingerprint of C. elegans IL-17 signaling.

overall_design: Whole-animal RNA-Seq profiles of malt-1; npr-1, ilc-17.1; npr-1, and nfki-1; npr-1 double mutants were compared to that of npr-1 controls.

first: Sean

last: Flynn

first: Mario

last: de Bono


title: MBNL1 regulates essential alternative RNA splicing patterns in MLL-rearranged leukemia

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

summary: In this study, we identify MBNL1 as a unique molecular vulnerability across MLL-rearranged leukemias. Through transcriptomic profiling and novel splicing analyses of MLL-rearranged leukemia cell lines following shRNA knockdown of MBNL1, we show that MBNL1 regulates alternative splicing (predominantly intron retention) of genes essential to MLL-rearranged leukemogenesis, such as DOT1L and SETD1A.

overall_design: Identification of MBNL1-dependent alternative splicing in MLL-fusion leukemia by RNAseq of MOLM-13 cells

first: S

last: Itskovich

first: A

last: Gurunathan

first: J

last: Clark

first: M

last: Burwinkel

last: Wunderlich

last: Berger

last: Kulkarni

first: K

last: Chetal

last: Venkatasubramanian

first: N

last: Kumar

first: L

middle: H


title: RNA sequencing of motor neurons derived from induced pluripotent stem cells of ALS patients with the M337V mutation in TARDBP

city: Oxford

first: Kevin

last: Talbot

address: John Radcliffe Hospital, Headley Way

department: Nuffield Department of Clinical Neurosciences

institute: University of Oxford

summary: Sequencing of human iPS-derived motor neurons from fibroblasts of Amyotrophic lateral sclerosis patients with an M337V mutation in TARDBP and comparison with age matched healthy controls identify differences in glutamate receptor and mitochondrial calcium buffering channels.

overall_design: Comparison of transcriptome between iPS-derived motor neurons from an ALS patient carrying an M337V mutation in TARDBP (3 clones) and age matched healthy controls from 3 independent differentiations. Motor neurons were differentiated for 30 days and RNA was extracted, RNA libraries prepared and sequenced.


title: RNA sequencing analysis of ARV825 target genes in senescent cells

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: Although cellular senescence acts primarily as a tumor suppression mechanism, the accumulation of senescent cells in vivo eventually exerts deleterious side effects through inflammatory/tumor-promoting factor secretion.  Thus, the development of new drugs that cause the specific elimination of senescent cells, termed senolysis, is anticipated.  Here, by an unbiased high-throughput screening of chemical compounds and a bio-functional analysis, we identify ARV825 as a promising senolytic drug.  ARV825 treatment eliminates senescent hepatic stellate cells in obese mouse livers, accompanied by the reduction of liver cancer development.  Furthermore, the elimination of chemotherapy-induced senescent cells by ARV825 increases the efficacy of chemotherapy against xenograft tumors in immunocompromised mice.  These results reveal the vulnerability of senescent cells and open up possibilities for its control.

overall_design:
We performed an RNA sequencing (RNA-seq) analysis to identify the genes whose expression is downregulated by the ARV825 treatment in senescent human diploid fibroblasts )HDFs.
Doxorubicin-induced senescent HDFs were treated with or without ARV825 (10 nM) for 4 days and were subjected to the RNAseq analysis.

first: Masahiro

last: Wakita

first: Eiji

last: Hara


title: Leading edge airway epithelial cell responses to in vitro wounding

city: Nedlands

first: Thomas

last: Iosifidis

state: Western Australia

address: 15 Hospital Avenue

institute: Telethon Kids Institute

summary: The airway epithelium of asthmatics is characterized by intrinsically abnormal wound repair that may contribute to disease pathobiology. In this study, we show that in asthma, the airway epithelial cells at the leading edge of a wound display aberrant migration patterns, reduced expression of α5 and β1 integrin subunits at baseline and during wound repair, resulting in dysregulated cell migration and an inability to fully repair. Transcriptional profiling identified the PI3K/Akt signaling pathway as the top upstream transcriptional regulator of integrin α5β1. Significantly, activation of Akt signaling enhanced airway epithelial repair in cultures derived from asthmatic children via upregulation of α5 and β1 integrin subunits. Conversely, inhibition of the PI3K/Akt signaling pathway in airway epithelial cultures from non-asthmatic children attenuated epithelial repair and reduced α5 and β1 integrin expression. Importantly, the FDA-approved drug celecoxib, and its non-COX2 inhibitory analogue dimethyl-celecoxib, also stimulated the PI3K/Akt/integrin α5β1 axis and restored airway epithelial repair in cells from asthmatics. Thus, targeting the PI3K/Akt pathway may represent a novel therapeutic avenue for asthma.

overall_design: Examination of baseline and wound healing response differences in primary airway epithelial cell cultures from 4 non-asthmatic and 6 asthmatic children

first: Robert

last: Hancock

first: Darryl

last: Knight

first: Stephen

last: Stick

first: Anthony

last: Kicic


title: B cell humoral response and differentiation is regulated by non-canonical poly(A) polymerase TENT5C.

status: Public on Mar 19 2020

city: Warsaw

first: Andrzej

last: Dziembowski

address: 4 Ks. Trojdena Street

institute: International Institute Of Molecular And Cell Biology In Warsaw

summary:
Purpose: The goal of this study was to assess changes in the activated B cells transcriptome upon TENT5C knockout in mice
Methods: RNA-Seq data were obtained for LPS-activated primary B cells isolated from either wild-type or TENT5C KO mice
Results: Immunoglobulins transcripts were found to be downregulated in B cells isolated from TENT5C KO mice

overall_design: mRNA profiles from activated B-cells from wild-type or TENT5C KO mice, generated by deep sequencing, in triplicate, using Illumina NextSeq 500.

first: Pawel

last: Krawczyk

first: Aleksandra

last: Bilska

first: Olga

last: Gewartowska

first: Seweryn

last: Mroczek


title: Modeling ribosome dwell times and relationship with tRNA loading and codon usage in mammals (tRNA Profiling)

first: Frédéric

last: Gachon

summary: Protein translation depends on mRNA-specific initiation, elongation, and termination rates. While the regulation of ribosome elongation is well studied in bacteria and yeast, less is known in higher eukaryotes. Here, we combined ribosome and tRNA profiling to investigate the relations between ribosome elongation rates, (aminoacyl-) tRNA levels and codon usage in mammals. We modeled codon-specific ribosome dwell times and translation fluxes from ribosome profiling, considering pair-interactions between ribosome sites.  In mouse liver, the model revealed site and codon specific dwell times, as well as codon pair-interactions clustering by amino acids. While translation fluxes varied significantly across diurnal time and feeding regimen, codon dwell times were highly stable, and conserved in human.  Fasting had no effect on codon dwell times in mouse liver.  Profiling of total and aminoacylated tRNAs revealed highly heterogeneous levels with specific isoacceptor patterns and a correlation with codon usage.  tRNAs for isoleucine, asparagine, aspartate and arginine were lowly loaded and conserved in fasted mice. Finally, codons with low levels of charged tRNAs and high codon usage relative to tRNA abundance exhibited long dwell times. Together, these analyses pave the way towards understanding the complex relation between tRNA loading, codon usage and ribosome dwell times in mammals.

overall_design: Profiling of total and (aminoacyl)-tRNAs in liver of mice fed Ad libitum or fasted

first: Gobet

last: Cédric

first: Weger

last: Benjamin

first: Marquis

last: Julien

first: Martin

last: Eva

first: Gachon

last: Frederic

first: Naef

last: Felix


title: Genetic interactions and transcriptomics implicate fission yeast CTD prolyl isomerase Pin1 as an agent of RNA 3' processing and transcription termination that functions via its effects on CTD phosphatase Ssu72

status: Public on Mar 20 2020

city: New York

first: Angad

last: Garg

department: Molecular Biology

institute: Memorial Sloan Kettering Cancer Center

summary: This RNA-Seq analysis compares gene expression of the peptidyl-prolyl isomerase Pin1 mutant pin1∆ contrasting to the WT in the fission yeast S. pombe

overall_design: 1 test sample (mutant) was analyzed; 1 WT control sample, sequenced at the same time, was previously deposited in GEO dataset GSE131237 (each sample has 3 replicate experiments)

first: Ana

last: Sanchez

first: Beate

last: Schwer

first: Stewart

last: Shuman


title: Thymic B cells promote germinal center-like structures and the expansion of follicular helper T cells in lupus-prone mice

status: Public on Mar 24 2020

city: Santiago

first: Yessia

last: Hidalgo

state: Ñuñoa

address: Las Palmeras 3425

department: Sciences

country: Chile

institute: Universidad de Chile

summary: Systemic lupus erythematosus (SLE) is an autoimmune disease characterized by autoantibody production and immune complex deposition. Previous evidence showed abnormal accumulation of B cells in the thymus of lupus-prone mice, but the role of this population remains undefined. We analyzed the distribution, function, and properties of thymic B cells in the BWF1 murine model of SLE. We found that B cells proliferate and cluster in germinal center-like structures along with autoantibody-secreting cells in the thymus of diseased-BWF1 mice. These thymic B cells induced the differentiation of follicular helper T cells (TFH). Our data suggest that the accumulation of B cells in the thymus of BWF1 mice results in the formation of germinal center-like structures and the expansion of TFH cells, which may favor the differentiation of autoreactive plasma cells. Therefore, the thymus emerges as a niche supporting the maintenance of the pathogenic humoral response in the development of murine SLE.

overall_design: Thymic B cells mRNA profiles of lupus-diseased-BWF1 mice (BWF1 mice) and non-lupus-susceptible mice (control mice) were generated by deep sequencing, in triplicate, using MiSeq Reagent Kit v3 150-cycle PE

first: Felipe

last: Flores-Santibañez

first: Jessica

last: Dorner

first: Victor

last: Martinez


title: Transcriptomic changes in Arabidopsis thaliana upon the expression of mutated TFIIS

city: Gainesville

first: Kevin

last: Begcy

state: Florida

address: 1535 Fifield Hall

institute: University of Florida

summary: The expresion of dominant negative version of Arabidopsis TFIIS (TFIISmut) in plants lacking funtional TFIIS leads to severe growth defects. The genome-wide analysis of transcriptomic changes upon TFIISmut expression was performed by RNA-seq to better understand the biological importance of TFIIS. 10DAS seedlings of transgenic lines carring inducible GFP-TFIIS or GFP-TFIISmut transgenes were studied by RNA-seq following plants exposure to 24h b-estradiol or EtOH (mock) induction.

overall_design: Arabidopsis mRNA profiles of 10-day old transgenic plants with inducible expression of GFP-TFIIS or GFP-TFIISmut fusion proteins in tfIIs-1 background were generated by deep sequencing and analysed comparatively with uninduced plants.

first: W

last: Antosz

first: KD

last: Grasser

first: K


title: Identification of non-coding RNA in sweet sorghum under salt stress

city: Jinan

last: Sui

state: Shandong

address: Wenhua East Road

department: College of Life Sciences

institute: Shandong normal university

summary: Salt stress has become one of the main abiotic stress factors restricting agricultural production worldwide. Sweet sorghum is an important salt and drought tolerant feed and energy crop. Its salt tolerance mechanism has not been widely studied. With the development of transcriptome sequencing technology, it is possible to study the molecular mechanism of sweet sorghum salt tolerance. The purpose of this study was to further reveal the potential salt-tolerant molecular mechanisms of sweet sorghum through high-throughput sequencing analysis of the transcriptome. Finally, through high-throughput sequencing, we read approximately 54.4G of raw base and 53.7G of clean base in total, and used FastQC to assign a quality score (Q) to each base in the read using a similar phred algorithm, Analysis shows that the data is highly credible. We conclude that RNA-based transcriptome characterization will accelerate the study of genetics and molecular biology of sweet sorghum salt tolerance mechanisms and provide a framework for this.

overall_design: Transcriptional profile of non-coding RNA in two sweet sorghum strains was examined.

first: Hong

middle: X

last: Zheng

first: Xi

last: Sun


title: Single-cell RNA-seq with spike-in cells enables accurate quantification of cell-specific drug effects in pancreatic islets [Drop-seq]

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

summary: Single-cell RNA-seq (scRNA-seq) is emerging as a powerful tool to dissect cell-specific effects of drug treatment in complex tissues. Here we treated human islet ex vivo with drugs to study the changes in their cellular identity. Artemether treatment upregulated insulin and other beta cell marker genes in a subset of alpha cells.

overall_design: Single-cell RNA sequencing using Dropseq of pancreatic islets from 1 human donor. Islets were treated ex-vivo with drugs that alter islet cell identity for 72 hrs.

first: Brenda

first: Nikolaus

last: Fortelny

first: Matthias

last: Farlik

first: Andhira

last: Vieira

first: Patrick

last: Collombat

first: Stefan

last: Kubicek


title: Single-cell RNA-seq with spike-in cells enables accurate quantification of cell-specific drug effects in pancreatic islets

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

overall_design: Refer to individual Series


title: Loss of the neural-specific BAF subunit ACTL6B relieves repression of early response genes and causes recessive autism

status: Public on Mar 17 2020

city: Stanford

first: Andrey

last: Krokhotin

address: 279 Campus Drive W

institute: HHMI

summary: Synaptic activity in neurons leads to the rapid activation of genes involved in mammalian behavior. ATP-dependent chromatin remodelers such as the BAF complex contribute to these responses and are generally thought to activate transcription. However, the mechanisms keeping such “early activation” genes silent have been a mystery. In the course of investigating Mendelian recessive autism, we identified 6 families with segregating loss of function mutations in the neuronal BAF (nBAF) subunit ACTL6B (originally named BAF53b).  Accordingly, ACTL6B was the most significantly mutated gene in the Simons Recessive Autism Cohort. At least 14 subunits of the nBAF complex are mutated in autism, collectively making it a major contributor to autism spectrum disorder (ASD). Patient mutations destabilized ACTL6B protein in neurons and rerouted dendrites to the wrong glomerulus in the fly olfactory system. Humans and mice lacking ACTL6B showed corpus callosum hypoplasia, indicating a conserved role for ACTL6B in facilitating neural connectivity. Actl6b knockout mice on two genetic backgrounds exhibited ASD-related behaviors, including social and memory impairments, repetitive behaviors, and hyperactivity. Surprisingly, mutation of Actl6b led to the relief of repression of early response genes including AP1 transcription factors (Fos, Fosl2, Fosb, and Junb), increased chromatin accessibility at AP1 binding sites, and transcriptional changes in late response genes associated with early response transcription factor activity. ACTL6B loss is thus an important cause of recessive ASD, with impaired neuron-specific chromatin repression indicated as a potential mechanism.

overall_design: RNA- and ATAC-sequencing on primary cortical neurons from wildtype or Actl6b-/- E16.5 embryos cultured for 7 days in vitro (DIV7). Neurons were collected from n=5 wildtype and n=7 knockout biological replicates.

first: Wendy

last: Wenderski


title: DNA Methylation Regulates Alternative Polyadenylation via CTCF and the Cohesin Complex

status: Public on Mar 18 2020

city: Houston

first: Angela

last: Ting

state: Tx

address: 1881 East Road

department: Epigenetics and Molecular Carcinogenesis

institute: The University of Texas MD Anderson Cancer Center

summary: Alternative cleavage and polyadenylation (APA) is a form of transcriptional regulation via shifts in how frequently multiple polyadenylation (polyA) sites within genes are used across biological conditions. APA can result in transcripts with varying length and information content, and has been linked to gene regulation in both cancer and development. While trans-acting regulatory factors can cause changes in APA, the process of cleavage and polyadenylation is often co-transcriptional. We hypothesized that epigenetic changes, such as DNA methylation, may regulate APA co-transcriptionally. To identify genes where DNA methylation may regulate APA, we performed a genome-wide quantification of polyA site usage using a next generation sequencing technique. By priming the polyA-tails of an RNA library, we mapped cleavage sites and abundances with base-pair resolution across the genomes of two cell lines. The HCT116 cell line is derived from colon cancer, and contains cancer-associated DNA hypermethylation. The DKO cell line is derived from the parental HCT116 line, but has a near-complete depletion of DNA methylation due to mutations in DNA methyltransferase enzymes. Previous studies have used this sytem to detect genes where promoter DNA methylation regulates the gene expression of tumor suppressors. Analogously, detecting APA between HCT116 and DKO reveals candidate genes where DNA methylation may regulate the process of APA. Mechanistic experiments can further interrogate cross-talk between DNA methylation and APA at these loci, and contribute to the understanding of the function of non-promoter differentially methylated regions.

overall_design: Biological quadruplicates of both the HCT116 and DKO cell lines were subjected to polyA-site sequencing.

first: Thomas

last: Sweet

first: Jeffrey

last: Bhasin


title: An engineered CRISPR/Cas9 mouse line for simultaneous readout of lineage histories and gene expression profiles in single cells

city: Boston

first: Duluxan

last: Sritharan

state: MA

address: 240 Longwood Avenue, Bldg. C

institute: Harvard University

summary: Tracing the lineage history of cells is key to answering diverse and fundamental questions in biology. Coupling of cell ancestry information with other molecular readouts represents an important goal in the field. Here, we describe the CARLIN (for CRISPR Array Repair LINeage tracing) mouse line and corresponding analysis tools that can be used to simultaneously interrogate the lineage and transcriptomic information of single cells in vivo. This model exploits CRISPR technology to generate up to 44,000 transcribed barcodes in an inducible fashion at any point during development or adulthood, is compatible with sequential barcoding, and is fully genetically defined. We have used CARLIN to identify intrinsic biases in the activity of fetal liver hematopoietic stem cell (HSC) clones and to uncover a previously unappreciated clonal bottleneck in the response of HSCs to injury. CARLIN also allows the unbiased identification of transcriptional signatures associated with HSC activity without cell sorting.

overall_design: Analysis of CARLIN arrays sequenced from mouse embryonic stem cells and different mouse tissues in presence/absence of Doxycycline. Single-cell transcriptomic sequencing during developmental and adult hematopoiesis.

first: Sarah

last: Bowling

first: Fernando

last: Osorio

first: Maximilian

last: Nguyen

first: Priscilla

last: Cheung

first: Alejo

last: Rodriguez-Fraticelli

first: Sachin

last: Patel

first: Wei-Chien

last: Yuan

first: Yuko

last: Fujiwara

first: Bin

last: Li

first: Stuart

last: Orkin

first: Sahand

last: Hormoz

last: Camargo


title: Single cell RNA-Seq adult mouse skin during homeostasis and wound repair

city: Irvine

first: Daniel

last: Haensel

state: California

address: Medical Sciences D288

institute: UC Irvine

summary: Our knowledge of transcriptional heterogeneities in epithelial stem/progenitor cell compartments is limited. Epidermal basal cells sustain cutaneous tissue maintenance and drive wound healing. Previous studies have probed basal cell heterogeneity in stem/progenitor potential, but a comprehensive dissection of basal cell dynamics during differentiation is lacking. Using single-cell RNA-sequencing coupled with RNAScope and fluorescence lifetime imaging, we identify three non-proliferative and one proliferative basal cell transcriptional states in homeostatic skin that differ in metabolic preference and become spatially partitioned during wound re-epithelialization. Pseudotemporal trajectory and RNA velocity analyses produce a quasi-linear differentiation hierarchy where basal cells progress from Col17a1high/Trp63high state to early response state, proliferate at the juncture of these two states, or become growth arrested before differentiating into spinous cells. Wound healing induces plasticity manifested by dynamic basal-spinous interconversions at multiple basal states. Our study provides a systematic view of epidermal cellular dynamics supporting a revised “hierarchical-lineage” model of homeostasis.

overall_design: Droplet Based Single Cell RNA sequencing libraries were generated for 2 un-wounded and 3 wounded adult moue skin samples using the 10x Genomics Chromium Platform and sequenced on the Illumina HighSeq 4000

first: Xing

last: Dai