title: ZIKV infection induces robust Th1-like Tfh cell and long-term protective antibody responses in immunocompetent mice

status: Public on May 01 2019

city: Shanghai

first: Jinyi

last: Tang

address: Yueyang road 320

institute: IPS

summary: Induction of long-lived antibody responses during infection or vaccination is often essential for subsequent protection, but the relative contributions of T follicular helper (Tfh) cells and T helper 1 (Th1) cells for induction of antigen specific antibody responses to viruses are unclear. Here, we establish an acute Zika virus (ZIKV) infection model in immunocompetent mice, and show that ZIKV infection elicits robust Th1-like Tfh cell and protective antibody responses. While these Th1-like Tfh cells share phenotypic and transcriptomic profiles with both Tfh and Th1 cells, they also have unique surface markers and gene expression characteristics, and are dependent on T-bet for their development. Th1-like Tfh cells, but not Th1 cells, are essential for class switching of ZIKV-specific IgG2c antibodies and maintenance of long-term neutralizing antibody responses. Our study suggests that specific modulation of the Th1-like Tfh cell response during infection or vaccination may augment the induction of antiviral antibody response to ZIKV and other viruses.

overall_design: IFN-γ-YFP reporter mice were infected by ZIKV with anti-IFNα/β receptor blocking one day before. Spleens and dLNs were harvested 7 dpi to sort. For RNAseq, We have three samples, Tfh(IFN-γ- Tfh), Th1-like Tfh(IFN-γ+ Tfh), Th1 and  2 replicates for each sample.

first: H

last: Wang

first: J


title: Profiling the transcriptome of human thymic epithelial cell subsets

status: Public on May 03 2019

city: Oxford

first: Adam

last: Handel

address: John Radcliffe Hospital

department: Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

type: Expression profiling by high throughput sequencing

summary: RNA-seq libraries were generated on thymic epithelial cell (TEC) subsets from thymic samples (11 days to 3 months of age). Cells were sorted to isolate cortical TEC (cTEC), MHC low medullary TEC (mTEClo) and MHC high medullary TEC (mTEChi). Between 7,575 and 50,000 cells were isolated for each sample. TEC were isolated using CD45 MACS depletion followed by the sorting protocol described in Stoeckler et al. J Vis Exp 2013 (PMID 24084687; doi: 10.3791/50951). The study has been granted ethical approval and is publicly listed (IRAS ID 156910, CPMS 19587).

overall_design: 1 sample for each of cTEC, mTEClo and mTEChi were generated on a total of 3 individuals (~50,000 cells per sample) and 3 replicates for each of cTEC, mTEClo and mTEChi were generated on 1 individual (7,575 cells per sample). Sequencing data were anonymised by aligning, masking mismatches to reference sequence and re-converting to fastq files.

middle: E

first: Georg

last: Hollander

first: Stefano

last: Maio

first: Ioanna

last: Rota

first: Mary

last: Deadman


title: Gene Specific Activation Driven by Small Molecules

status: Public on Apr 30 2019

city: Bethesda

first: Javed

last: Khan

state: MD

address: 37 Convent Dr.

department: Genetics Branch

country: USA

institute: NCI, NIH

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Differing levels of chromatin compaction throughout the genome contribute to cell specificity and function. The importance of studying this complex processes is highlighted by the frequency of chromatin dysregulation in human diseases, which has led to the development of chromatin-based therapies in the clinic. To study this pathway, we designed a novel chemical-based system to redirect specific chromatin modifying machinery in a targeted and reversible manner. We synthesized a new class of bi-functional compounds, Chemical Epigenetic Modifiers (CEM)s, with one warhead arm that engages endogenous chromatin regulators, while the other targeting arm tethers the captured epigenetic regulatory machinery to the gene of interest. By redirecting endogenous chromatin regulatory machinery, we are able to control expression in a gene-specific manner.

overall_design:
Genome-wide profile for BRD4 in 293 HEK cells following a 48 hour treatment with CEM87, a bifunctional molecule that binds and redirects endogenous BRD4 to a specific locus via dCas9-CEM interaction.
RNA-seq in 293 HEK (4 samples)

first: Berkley

last: Gryder

first: Xinyu

last: Wen


title: Single-cell transcriptional and proteomic profiling of tumor-infiltrating lymphocytes

status: Public on May 04 2019

city: Memphis

first: Jeremy

middle: Chase

last: Crawford

state: TN

address: MS 221, 262 Danny Thomas Place

department: Department of Host-Microbe Interactions

institute: St. Jude Children's Research Hospital

summary: To characterize the transcriptional environment of neoepitope-specific TILs, we performed multiplexed quantitative PCR analysis on tetramer-positive and -negative CD8+ T cell populations populations; by using an index sorting approach, we were able to simultaneously assay transcription and cell-surface phenotype at single-cell resolution. The 88 genes we selected for analysis accounted for: transcription factors shown to influence CD8+ T cell differentiation, chemokines and chemokine receptors, cytokines, activating and inhibitory co-receptors, and molecules associated with degranulation and cell survival. We observed a spectrum of dynamic transcriptional changes that take place during antigen-specific CD8+ T cell responses, specifically identifying three clusters with distinct transcriptional signatures across the sorted TIL populations, and these clusters differed in their functional status and in the expression of transcription factors, transcriptional regulators, signaling inhibitors, cytokines, cytotoxic granules, and trafficking molecules.

overall_design: Single-cell gene expression experiments were performed using Fluidigm’s DynamicArray microfluidic chips (Fluidigm) following manufacturer’s instructions (Two-Step Single-cell gene expression using EvaGreen Supermix on Biomark HD System). Single cells were sorted from three Pediatric leukemia patient samples using the Sony SY3200 into individual wells of 96-well plates that had been preloaded with 5 μL consisting of 1.2 μL 5X SuperScript VILO Reaction Mix (Thermo Fisher), 0.3 μL SUPERase-In (20 U/μL; Thermo Fisher), 0.25 μL 10% NP40 (Thermo Fisher), and nuclease free water (Teknova). Each plate contained two empty wells for use as non-template controls (NTC). After successful sorting, the plates were incubated at 65°C for 90 seconds, and chilled on ice for 5 minutes for RNA denaturation. The remaining components of the RT reaction were added to each well, including 0.15 μL 10X SuperScript Enzyme Mix (Thermo Fisher), 0.12 μL T4 Gene 32 Protein (NEB), and nuclease free water (Teknova). Thermal cycling conditions for the reverse transcription of single-cell mRNA into cDNA was 25°C for 5 min, 50°C for 30 min, 55°C for 25 min, 60°C for 5 min, 70°C for 10 min, and then hold at 4°C. After reverse transcription, the cDNA was amplified using 1.5 μL of a pool of the designed primers (STA mix; Fluidigm), 7.5 μL TaqMan PreAmp Master Mix (Thermo Fisher), and 0.075 μL 0.5M EDTA (Thermo Fisher). The thermal cycling conditions were 95°C for 10 min, 20 cycles of 96° for 5 sec and 60°C for 4 min, and then hold at 4°C. Amplified cDNA was then treated with Exonuclease I (NEB) to remove any unincorporated primers by adding 6 μL of 4 U/μL Exonuclease I (20 U/μL Exonuclease I diluted with water and 10X Exonuclease I Reaction buffer). Thermal cycling conditions were 37°C for 30 min, 80°C for 15 min, and then hold at 4°C. The cDNA was then diluted 5-fold for loading onto the chip. The sample mix to be loaded onto the chip included 2.5 μL 2X Sso Fast EvaGreen Supermix with low ROX (Bio-Rad), 0.25 μL 20S DNA Binding Dye Sample Loading Reagent (Fluidigm), and 2.25 μL of the prepared cDNA. The assay mix loaded onto the chip included 2.5 μL 2X Assay Loading Reagent (Fluidigm), 1X DNA Suspension Buffer (Teknova), and 100 μM of each forward and reverse primer mix (Fluidigm). Each chip was primed immediately before loading the 5 μL of each sample mix and 5 μL of each assay mix onto the chip. The chips were then loaded using the IFC Controller HX (Fluidigm) and transferred to the Biomark HD real-time PCR reader to analyze using the GE Fast 96x96 PCR+Melt v2 protocol.

middle: C

first: Anthony

last: Zamora

first: E

middle: K

last: Allen

first: Paul

middle: G

last: Thomas


title: Treatment with antidepressant drugs in a rat model of Traumatic Brain Injury

city: Northbrook

first: Michael

last: Falduto

state: IL

address: 1808 Janke, Unit M

institute: GenUs BioSystems, Inc.

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

summary: Microarray analysis was performed to look at the mRNA and miRNA profiles of several antidepressant drugs in the rat hippocampus after Traumatic Brain Injury to test the hypothesis that antidepressant drugs ameliorate gene and miRNA dysregulation after TBI.

overall_design: Rats received either a Sham injury or TBI injury.  Certain groups of rats that received a TBI were injected one hour after injury with one of the following antidepressent drugs:  Prozac, Zoloft, or Imipramine. Rats were survived for 24 hours and then hippocampus dissected out, stored in RNA later and sent to GenUs Biosystems for miRNA mircoarray analysis.

first: Helen

last: Hellmich

first: Debbie

middle: R

last: Boone

first: Karen

last: Torres

middle: T


title: Activation of neuronal genes via LINE-1 elements upon global DNA demethylation in human neural progenitors

status: Public on May 29 2019

city: Lund

first: Per

last: Brattas

address: Sölvegatan 17

country: Sweden

institute: Lund University

type: Methylation profiling by high throughput sequencing

summary:
DNA methylation is thought to contribute to the maintenance of genomic integrity in somatic cells, in part through the silencing of transposable elements (TEs). In this study, we used CRISPR/Cas9 technology to delete DNMT1, the key maintenance DNA methyltransferase in human neural progenitor cells (hNPCs). Surprisingly, and in contrast to previous findings in mouse somatic cells, inactivation of DNMT1 in hNPCs resulted in viable proliferating cells despite the global loss of DNA CpG-methylation. DNA demethylation led to specific transcriptional activation and chromatin remodeling of evolutionarily young, hominoid-specific LINE-1 elements (L1s), while older L1s and other classes of TEs remained silent. The activated L1s acted as alternative promoters for many protein-coding genes involved in neuronal functions, revealing a hominoidspecific L1-based transcriptional network controlled by DNA methylation that influences neuronal protein-coding genes. Our results give a novel mechanistic insight into the role of DNA methylation in silencing TEs in somatic human cells, as well as further implicating L1s in human
brain development and disease.

overall_design:
CRISPR/Cas9 mediated disruption of DNMT1 in human neural progenitor cells. Guides targeting LacZ as control. Three replicates per condition. 2X125 paired-end RNA-sequencing. 2x150bp WGBS. 1x50bp ChIP-seq.

Please note that the hEmbryo_PE150.hg38*.txt processed data files are associated with the GSM2940637-GSM2940642 samples.

first: Marie

last: Jönsson

last: Brattås

first: Charlotte

last: Gustafsson

first: Rebecca

last: Petri

first: David

last: Yudovich

first: Shana

last: Verschuere

first: Sofia

last: Madsen

first: Jenny

last: Hansson

first: Jonas

last: Larsson

first: Robert

last: Månsson

first: Alexander

last: Meissner

first: Johan

last: Jakobsson


title: Comparative transcriptomic analyssi of mouse embryonic tissues and mESCs-derived limb bud-organoid tissues

city: Kyoto

first: Mototsugu

last: Eiraku

state: Kyoto

address: 53 Shougoin Kawahara-chou Sakyo-ku

country: Japan

institute: Kyoto University

summary: We established the differentiation method of a limb bud organoid from mouse embryonic stem cells (mESCs) using SFEBq. mESCs-derived limb bud organoid selectively differentiate into forelimb or hindlimb by adjusting the retinoic acids activity. To evaluate a correlation of gene expression between limb bud organoid and embryonic tissues (limb bud, branchial arch, cardiac, and tail bud), we performed comparative transcriptome analysis using RNA-seq.

overall_design: RNA-seq profiling of mouse embryonic limb bud, branchial arch, cardiac, and tail bud and mESCs-derived forelimb and hindlimb bud mesenchyme (Hnad2::GFP positive), in triplicate, using illumina Hi-seq.

first: Shunsuke

last: Mori

first: Mitsutaka

last: Kadota

first: Eiraku

last: Mototsugu


title: The lipid transfer protein OsLTPL159 is involved in cold tolerance at the early seedling stage in rice

status: Public on May 14 2019

city: Beijing

first: Jie

last: Zhao

address: 2 Yuanmingyuan West Road, Haidian District

country: China

institute: China Agricultural University

summary: The genome-wide gene expression differences between the control (ZH17) and OEZ after cold treatment.

overall_design: Total RNA was isolated from the early seedling of the control (ZH17) and the overexpression lines (OEZ) after cold treatment, using Illumina system Hiseq2500.

first: Feng

middle: X

last: Liu


title: Identify signature genes associated with nanoparticle carrying IRF5 mRNA treatment in isolated peritoneal macrophages from ID8 cells-induced ovarian tumor mouse

status: Public on Apr 09 2019

city: Seattle

first: Matthias

last: Stephan

state: WA

address: 1100 Fairview Ave. N., Thomas Research Buildin

institute: Fred Hutchinson Cancer Research Institute

summary: To identify signature genes associated with nanoparticles carrying IRF5 mRNA treatment on peritoneal macrophages, we analyzed 770 genes in 19 different pathways and processes across 7 different myeloid cell types.

overall_design: In the study presented here,  we performed genome analysis on isolated F4/80+, CD11b+ peritoneal macrophage from mice that from three treatment groups (1) two i.p. doses of PBS; (2) two i.p. doses of nanoparticles carrying 30 microgram of mIRF5 mRNA.

first: Fan

last: Zhang


title: Expression data from adult mice pulmonary endothelial cells

status: Public on Apr 14 2019

city: Aurora

first: Kaori

last: Oshima

state: CO

address: 12700 E 19th Ave Research Complex 2 Room 9480A

institute: University of Colorado

summary:
Sepsis patients are at increased risk for hospital-acquired pulmonary infections, potentially due to post-septic immunosuppression known as the compensatory anti-inflammatory response syndrome (CARS).  CARS has been attributed to leukocyte dysfunction, with an unclear role for endothelial cells.  The pulmonary circulation is lined by an endothelial glycocalyx, a heparan sulfate-rich layer essential to pulmonary homeostasis.  Heparan sulfate degradation occurs early in sepsis, leading to lung injury.  Endothelial synthesis of new heparan sulfates subsequently allows for glycocalyx reconstitution and endothelial recovery.  We hypothesized that remodeling of the reconstituted endothelial glycocalyx, mediated by alterations in the endothelial machinery responsible for heparan sulfate synthesis, contributes to CARS. Our experimental animal model of CARS recapitulated post-septic immunosuppression, coincidentally with structural remodeling of endothelial glycocalyx heparan sulfate.
We used microarray to identify which heparan sulfate modifying enzyme is responsible for the remodeling of post-septic reconstituted glycocalyx, characterized with enrichment of heparan sulfate disaccharides sulfated at the 6-O position of glucosamine.

overall_design: Experimental sepsis was induced in adult male mice with cecal ligation and puncture. Sham surgery was performed similarly, albeit without ligation and puncture of the cecum.  The whole lungs were collected from each mouse at 48 hours after the induction of sepsis, immediately prior to the completion of heparan sulfate reconstitution.  Pulmonary endothelial cells were isolated with FAC sorting (CD31+/CD144+), and total RNA was extracted and hybridized on Affymetrix microarrays.

first: Yimu

last: Yang


title: RNA-Seq of sorted Lgr5+ cells with and without infection with Helicobacter pylori

status: Public on Apr 02 2019

city: Berlin

first: Thomas

middle: F

last: Meyer

address: Chariteplatz 1

department: Molecular Biology

country: Germany

institute: Max Planck Institute for Infection Biology

summary: Wnt signaling stimulated by R-spondin (Rspo) via binding to Lgr family members is crucial for stem cell renewal and tissue homeostasis in the gastrointestinal tract. In the stomach, Rspo is secreted by myofibroblasts and controls epithelial gland regeneration by inducing proliferation of Wnt-responsive Axin2+ cells in the isthmus of glands. Infection with Helicobacter pylori results in increased expression of stromal Rspo, leading to an expansion of Axin2+ isthmus stem cells and gland hyperplasia. Basal Lgr5+ cells are exposed to Rspo3 but the effects of this are not well understood. Here we demonstrate that, in the antrum, endogenous Rspo3, apart from its activity as a mitogen, regulates Lgr5+ cells in the gland base and induces their differentiation towards secretory cells.

first: Michael

last: Sigal

last: Rothenberg


title: Bmi1 suppresses adipogenesis in the hematopoietic stem cell niche

status: Public on Apr 12 2019

city: Houston

first: Daisuke

last: Nakada

state: Texas

address: One Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

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

overall_design: Refer to individual Series


title: Differential Contribution of Steady-State RNA and Active Transcription in Chromatin Organization

status: Public on Apr 01 2019

city: Durham

first: Rasim

last: Barutcu

state: NC

address: 6 Davis Drive

institute: ScitoVation

summary: Nuclear RNA and the act of transcription have been implicated in nuclear organization. However, their global contribution to shaping fundamental features of higher-order genome structure such as topologically associated domains (TADs) and genomic compartments remains unclear. To investigate these questions, we perform Hi-C genome-wide chromatin conformation capture in the presence and absence of RNase before and after crosslinking, or a transcriptional inhibitor. TAD boundaries are largely unaffected by RNase treatment, whereas transcriptional inhibition leads to higher inter-TAD interactions. Collectively, our findings demonstrate differences in the relative contribution of RNA and transcription to the formation of TAD boundaries detected by the widely used Hi-C methodology.

overall_design:
Hi-C in RNase treated and transcriptionally inhibited K562 cells
Please note that the processed data was generated from both replicates together and is linked to the corresponding *rep1 sample records.

first: A

first: Benjamin

middle: J

last: Blencowe

first: John

middle: L

last: Rinn


title: Maternal pluripotency factors initiate extensive chromatin remodelling to predefine first response to inductive signals

status: Public on Apr 16 2019

city: London

first: George

middle: E.

last: Gentsch

state: Greater London

address: 1 Midland Road

department: Developmental Biology Laboratory

institute: The Francis Crick Institute

summary: Embryonic development yields many different cell types in response to just a few families of inductive signals. The property of signal-receiving cells that determines how they respond to inductive signals is known as competence, and it differs in different cell types. Here, we explore the ways in which maternal factors modify chromatin to specify initial competence in the frog Xenopus tropicalis. We identify early-engaged regulatory DNA sequences, and infer from them critical activators of the zygotic genome. Of these, we show that the pioneering activity of the maternal pluripotency factors Pou5f3 and Sox3 determines competence for germ layer formation by extensively remodelling compacted chromatin before the onset of inductive signalling. This remodelling includes the opening and marking of thousands of regulatory elements, extensive chromatin looping, and the co-recruitment of signal-mediating transcription factors. Our work identifies significant developmental principles that inform our understanding of how pluripotent stem cells interpret inductive signals.

overall_design: This study generated 202 samples of different applications of high-throughput sequencing inluding ChIP-Seq, DNase-Seq, next-generation capture-C and RNA-Seq.

first: James

last: Smith


title: Bmi1 suppresses adipogenesis in the hematopoietic stem cell niche: RNA-Seq

summary: Bone marrow mesenchymal stromal cells (MSCs) that express high levels of stem cell factor (SCF) and CXC chemokine ligand 12 (CXCL12) are one crucial component of the hematopoietic stem cell (HSC) niche. While the secreted factors produced by MSCs to support HSCs have been well described, little is known regarding the transcriptional regulators controlling the cell fate of MSCs and thus indirectly maintaining HSCs. Bmi1 is a polycomb group protein that regulates HSCs both cell intrinsically and extrinsically, but it is unknown in which cell type and how Bmi1 functions to maintain HSCs extrinsically. Here we show that Bmi1 maintains HSCs by preventing adipogenic differentiation of MSCs. Bmi1 is highly expressed in MSCs but becomes downregulated upon adipogenic differentiation and during aging. Deleting Bmi1 from MSCs increased marrow adipocytes, induced HSC quiescence and depletion, and impaired hematopoiesis. We found that Bmi1 repressed multiple developmental programs in MSCs by safeguarding the repressive epigenetic marks histone H2A ubiquitylation and H3 lysine 27 trimethylation. We identified a novel adipogenic program governed by Pax3, which Bmi1 repressed in MSCs. Our results establish Bmi1 as a critical regulator of MSC cell fate that suppresses marrow adipogenesis to create a supportive niche for HSCs.

overall_design: RNA-Seq of two treatments (Ctrl, KO) with three replications per treatment.

first: Kevin

middle: A

last: Hoegenauer

first: Tianyuan

last: Hu


title: Crosstalk from Non-Cancerous Mitochondria Can Inbibit Tumor Properties of Metastatic Cells by Suppressing Oncogenic Pathways

status: Public on Mar 21 2019

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

summary: Microarray analysis suggested that several oncogenic pathways observed in cybrids with cancer mitochondria are inhibited in cybrids with non-cancerous mitochondria. These results suggest the critical oncogenic regulation by motochondrial-nuclear cross talk and highlights rectifying motochondiral functional properties as a promising target in cancer therapy.

overall_design: MCF10A group and MDA468 group

first: Benny

last: Kaipparettu

first: Yiqun

first: Lee-Jun

last: Wong


title: The AP2/ERF Transcription Factor TINY Modulates Brassinosteroid-Regulated Plant Growth and Drought Response in Arabidopsis

status: Public on Mar 28 2019

city: Ames

first: Yanhai

last: Yin

state: IA

address: 1035D Roy J. Carver Co-Lab

department: Genetic Development and Cell Biology

institute: Iowa State University

summary: The functions of AP2/ERF family transcription factors in stress responses are well documented, but their roles in the brassinosteroid (BR)-regulated growth and stress responses have not been established. Here we show that stress-inducible AP2/ERF family transcription factor TINY inhibits BR-regulated growth while promoting drought response. TINY overexpression plants have stunted growth, increased sensitivity to BR biosynthesis inhibitors and compromised BR-responsive gene expression. In contrast, a tiny tiny2 tiny3 triple mutant has increased BR-regulated growth and BR-responsive gene expression. TINY positively regulates drought response by activating drought responsive genes and promoting abscisic acid-mediated stomatal closure. Global gene expression studies revealed that TINY and BRs oppositely regulate genes involved in plant growth and stress response. TINY interacts with and antagonizes BES1 in the regulation of these genes. The GSK3-like protein kinase BIN2, a negative regulator in the BR pathway, phosphorylates and stabilizes TINY, providing a mechanism for BR-mediated down-regulation of TINY to prevent activation of stress response under optimal growth conditions. Taken together, our results demonstrate that TINY is negatively regulated by BR signaling through BIN2 phosphorylation and positively regulates drought response, as well as inhibits BR-mediated plant growth through TINY-BES1 antagonistic interactions. Our results thus provide insight into the coordination of BR-regulated growth and drought responses.

overall_design: For RNA sequencing analysis, total RNA was extracted from four-week-old long day grown plants using Zymo DirecZol kit (ZYMO RESEARCH). RNA concentrations and quality were analyzed using AATI Fragment Analyzer with Standard Sensitivity RNA Analysis Kit (DNF-489-0500). Approximately 500ng of RNA was used for library construction via the QuantSeq 3’ mRNA-Seq Library Prep FWD Kit for Illumina and sequenced on an Illumina HiSeq 2500 (50bp single end reads). FASTQ files for each sample were subject to quality control, trimming and mapped to the Arabidopsis TAIR10 genome using the BlueBee A. thaliana (TAIR10) Lexogen QuantSeq 2.2.2 FWD pipeline.


title: Gene expression analysis in the Brainstem of Vglut2:Ndufs4cKO mice

status: Public on Mar 31 2019

city: Bellaterra

first: Elisenda

last: Sanz

state: Barcelona

address: M1/113 Facultat de Medicina

department: Institut de Neurociencies

country: Spain

institute: Universitat Autonoma de Barcelona

summary: Leigh Syndrome is characterized by symmetrical brain lesions and neuroinflammation in select nuclei, predominantly brainstem and/or basal ganglia. Accordingly, Ndufs4-deficient mice present overt lesions in brainstem, olfactory bulb, and basal ganglia. To define the contribution of Ndufs4 deficiency in excitatory neurons to the overall neuroinflammatory phenotype, we performed Gene expression analysis in the brainstem of mice with specific deletion of Ndufs4 in Vglut2-expressing neurons (Vglut2:Ndufs4cKO mice). This analysis allowed us to further define the inflammatory phenotype present in the brainstem of Vglut2:Ndufs4cKO mice.

overall_design: Total RNA extracted from the braistem of Vglut2:Ndufs4KO was compared to total RNA extracted from control (Vglut2:Ndufs4cCT) mice

first: Albert

last: Quintana


title: Mutationally-activated PI3’-kinase-a promotes de-differentiation of lung tumors initiated by the BRAFV600E oncoprotein kinase

status: Public on Mar 19 2019

city: Los Angeles

middle: Edward

last: van Veen

state: CA

address: 610 Charles E young Dr

department: Integrative Biology and Physiology

institute: UCLA

summary: Human lung adenocarcinoma exhibits a propensity for de-differentiation, which complicates diagnosis and treatment, and predicts for poor overall patient survival.  In genetically engineered mouse (GEM) models of lung cancer, expression of the BRAFV600E oncoprotein kinase initiates the growth of benign tumors that retain characteristics of their cell of origin, alveolar type II (ATII) pneumocytes.  Cooperating genetic alterations such as silencing of the PTEN tumor suppressor or expression of mutationally-activated PI3-kinase-a (PIK3CAH1047R) promote malignant progression of such benign tumors to malignant adenocarcinoma, though their effects on differentiation status are unknown.  To address this in vivo, we generated a new conditional BrafCAT allele in which Cre-mediated recombination leads to expression of a bi-cistronic mRNA encoding both BRAFV600E and the tdTomato fluorescent protein.  Using this model, we demonstrate that coincident expression of BRAFV600E and PIK3CAH1047R in ATII pneumocytes leads to rapid and widespread cell de-differentiation.  Surprisingly, the combined effects of BRAFV600E and PIK3CAH1047R on ATII pneumocyte identity occurred without loss of expression of the lung lineage transcription factors NKX2.1, FOXA1, or FOXA2.  Instead, we demonstrate a novel role of PGC1α in maintaining pneumocyte identity, which is lost upon PIK3CAH1047R expression.  These findings provide additional insight into how two of the most commonly mutated growth factor signaling pathways contribute to the pathogenesis of lung adenocarcinoma.

overall_design: BRAFV600E mutant mouse lung adenocarcinoma (n=6) vs BRAFV600E;PIK3CAH1047R mutant lung adenocarcinoma (n= 8), and BRAFV600E;PGC1aHET (n=5) vs BRAFV600E;PGC1aNULL tumors (n=4)

first: J

first: Martin

last: McMahon


title: Single-Cell Transcriptome Analysis Of CD8+ T-cell Memory Inflation

status: Public on Mar 12 2019

first: Timothy

last: Hinks

state: United Kingdom

address: John Radcliffe Hospital, Headley Way, Oxford

department: NDM Experimental Medicine - New College

institute: University of  Oxford

summary: We sought to define the nature of the transcriptional mechanisms underpinning memory inflation at different sites. We used single-cell RNA sequencing of M38-tetramer+-sorted cells from a single MCMV-infected mice, analyzing transcriptional networks in virus-specific populations in the spleen and gut intra-epithelial lymphocytes (IEL).

sample_organism:
Homo sapiens
Mus musculus
other sequences

overall_design: Illumina sequencing of single cells from murine M38 tetramer+ T cells from gut intraepithelium in comparison with murine M38 tetramer+ T cells from spleen.  Lymphocytes were extracted from the spleen and gut intraepithelium by mechanical and enzymatic digestion. CD8+ T-cells were enriched by negative selection using the Miltenyi Biotec GmbH CD8a+ T-cell isolation kit (Bergisch Gladbach, Germany) . After M38-tetramer and surface staining, tetramer+ CD3+ CD8+ single-cells were sorted in two 96-well plates using a SH800S cell sorter (Sony, Tokyo, Japan).  Sequencing libraries were prepared using the TruSeq dual-index sequencing primers (Illumina, San Diego, California) and paired-end sequencing was performed on the Illumina HiSeq4000 platform.

first: Emanuele

last: Marchi

first: Madeleine

last: Zinser

first: Andrew

last: Highton


title: Structure of examined circular RNAs and some of their linear cognate RNAs

status: Public on Mar 20 2019

city: Shanghai

first: Li

last: Yang

address: 131 Dong-An Road

department: Institutes of Biological Sciences

institute: Fudan University

summary: We optimized the SHAPE-MaP (selective 2'-hydroxyl acylation analyzed by primer extension and mutational profiling) assay to analyze structures of paired circular (circSHAPE-MaP) and linear (linearSHAPE-MaP) RNAs.

overall_design: CircSHAPE-MaP and linearSHAPE-MaP for circRNA and linear RNA secondary structure.

first: Ling-Ling

last: Chen

first: Chu-Xiao

last: Liu

first: Xiang

last: Li

first: Fang

first: Wei

last: Xue


title: Zfhx3 is required for the differentiation of late born D1-type medium spiny neurons

status: Public on Mar 08 2019

first: zhuangzhi

last: zhang

address: 138 Yi Xue Yuan Road

summary:
Purpose: The goals of this study are to compare the LGE-derived cells changes gene expression pfofiles between controls and Zfhx3 conditional knockout mice
Methods: Total RNA was isolated and sequenced using an illumina high-seq 2500. Raw data was analyzed using TopHat. Genes were considered significantly changed whicn perform P value <= 0.05
Results: Compared to controls, 1620 genes were significantly down regulated, and 2108 genes were up regulated in the RNA expression level of the mutant LGE.

overall_design: LGE RNA profiles of E16.5 control mouse brain and Zfhx3 conditional knockout mouse brain

first: Zhuangzhi

last: Zhang

first: Zhengang


title: Loss of CBP in newborn neurons interferes with synaptic maturation and SRF-dependent neuronal growth

status: Public on Mar 14 2019

city: Sant Joan d'Alacant

first: Angel

last: Barco

state: Alicante

address: Av. Santiago Ramón y Cajal

institute: Instituto de Neurociencias (UMH-CSIC)

summary: We used genome-wide sequencing methods to study the consequences of eliminating the CREB-binding protein (CBP) in newborn neurons. We found that CBP-deficient newborn neurons show impaired growth and activity-dependent transcription. In particular, genes downstream of the serum response factor (SRF) and related to neuronal growth and activity-dependent plasticity were affected. The expression of a constitutively active SRF protein with the ability to transactivate target genes in a CBP-independent manner reduced the growth and transcriptional defects associated with CBP ablation.

overall_design:
RNA-seq experiment: Crebbpf/f and Nestin-cre mice were crossed to selectively eliminate CBP in the newborn neurons of the central nervous system (CNS). Primary cortical neurons were obtained from E17. Nestin-cKO and cWT embryos are used for RNA-seq analysis and processed separately. The day of plating was considered day in vitro 1 (DIV1). At DIV10, cortical cultures were stimulated with 25 μM bicuculline and 1 mM AP-4 for 2 h and 30 min. The analysed samples represent two variables, effect of selectively eliminate CBP in the newborn neurons after 10 days in culture and effect of selectively eliminate CBP in the newborn neurons after bicuculline stimulation in cultures at DIV10.

ChIP-seq experiment: Primary hippocampal neurons were obtained from E17 embryos. Cultured neurons were infected with syn-VP16-SRF/Syn-GFP viral vector at DIV3. After 7 days post-infection, neurons were collected and genomic DNA from 5x10e6 hippocampal neurons was fragmented by sonication and immunoprecipitated with anti-VP16 antibody (Santa Cruz, sc-7545) as previously described (Scandaglia et al., 2015). Immunoprecipitated DNA was resuspended in 40 μL of water.

first: Beatriz

last: del Blanco

first: M

last: López-Cascales

first: Rafael

middle: M

last: Viana

first: Ángel

last: Barco Guerrero


title: New Insights from Transcriptome Profiling of Bovine Vaginal Epithelial Cell Response to Isolated Lactobacillus

status: Public on Mar 10 2019

city: Hohhot

first: chunyu

last: Niu

address: college of inner mongolia agricultural university ,306 street zhao wu da ,huhhot ,inner mongolia,china

institute: Inner Mongolia Agricultural University

summary:
Purpose: The goals of this study is to investigate host cell responses treated with lactobacillus in various molecular pathways by RNA-Seq and real-time quantitative PCR (RT-qPCR) methods to  and evaluate protocols for optimal high-throughput data analysis.

Methods: mRNA profiles of bovine vaginal epithelial cells treated with lactobacillus and control cells were generated by sequencing, in triplicate, utilizing Illumina HiSeq 4000 platform. The raw RNA-seq data was filtered to remove adaptor contamination, low quality bases, and undetermined bases utilizing Cutadapt software.The filtered reads were aligned and mapped to the reference genome using Hisat 2.0.  RT-qPCR validation was performed using TaqMan and SYBR Green assays.

Results: The transcription profiling results showed that 296 differentially expressed genes (DEGs) were significantly altered, of which 170 were upregulated and 126 downregulated. Gene ontology (GO) enrichment analysis of the DEGs revealed a significant enrichment of 424 GO terms throughout the differentiation process (p< 0.05). Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the DEGs were mainly involved in signal transduction, immune endocrine systems, transport and catabolism, as well as metabolism and genetic information processing. We found a relatively high number of genes enriched in protein processing in the endoplasmic reticulum and IL-17 signaling pathway, as well as antigen processing and presentation. DEGs that enriched into pathways were verified by RT-qPCR. The highest number of DEGs participated in protein processing in pathways involving the endoplasmic reticulum of which might be a major factor causing the adhesion of lactobacillus to cells and pathogenic inhibition.

Conclusions:Our study provides new insights on the interaction between lactobacillus and host cells, emphasizing the importance of novel candidate pathways involving the protein processing in endoplasmic reticulum and analyzing the possible anti-pathogenic mechanisms of the SQ0048 strain that inhibit pathogenic colonization.

first: Chunyu


title: miR-15/16 restrain cell cycle and memory T cell accumulation

status: Public on Mar 07 2019

city: San Francisco

first: John

middle: D

last: Gagnon

address: 513 Parnasus Ave.

department: Microbiology & Immunology

institute: UCSF

summary: Coordinate control of T cell proliferation, survival, and differentiation are essential for host protection from pathogens and cancer. Long-lived memory cells, whose precursors are formed during the initial immunological insult, provide protection in future encounters and their generation is the goal of many vaccination strategies. microRNAs are key nodes in regulatory networks that shape effective T cell responses through the fine-tuning of thousands of genes. Here, using new compound conditional mutant mice to eliminate miR-15/16 family miRNAs in T cells, we show that miR-15/16 restrict T cell cycle and memory T cell accumulation. High throughput sequencing of RNA isolated by cross-linking immunoprecipitation of AGO2 combined with gene expression analysis in miR-15/16 deficient T cells indicated that these effects are mediated through direct inhibition of an extensive network of known and novel target genes within pathways critical to cell cycle and memory.

overall_design: Gene expression analysis of miR-15/16 sufficient and miR-15/16 deficient CD4+ T cells stimulated in vitro with anti-CD3 and anti-CD28 for 3 days and rested in the presence of IL-2 (20U/ml).

first: K

last: Ansel


title: DNA methylation profiles of 24 whole cord blood samples from healthy children born via caesarian section with matched FACS counts

status: Public on Mar 05 2019

city: Vancouver

first: Michael

middle: S.

last: Kobor

state: BC

address: 950 West 28th Avenue

department: Medical Genetics

country: Canada

institute: Centre for Molecular Medicine and Therapeutics / University of British Columbia

type: Methylation profiling by genome tiling array

summary: In order to accurately evaluate methods for dealing with inter-individual differences in cord blood cell type in DNA methylation data, matched samples with both DNAm profiles and detailed FACS counts are necessary.

overall_design: The Illumina Infinium HumanMethylation450 Beadchip was used to obtain genome-wide DNA methylation measures in human whole cord blood samples (n=24) for use as validation for deconvolution methods in whole blood. We also performed FACS counts as described in PMID 26366232 and quantified as a combination of CBC and FACS counts as described in preprint https://doi.org/10.1101/399279

first: Meaghan

last: Jones

first: Hamid

last: Razzaghian

first: Olivia

last: de Goede

first: Julia

last: MacIsaac

first: Alexander

last: Morin

first: Wendy

middle: P

last: Robinson

first: Pascal

last: Lavoie

middle: S


title: NCBI GEO Submission of human whole blood transcriptomes in response to a high-fat meal

status: Public on Mar 01 2019

city: DAVIS

first: Danielle

last: Lemay

address: 430 West Health Sciences Dr.

institute: USDA ARS WHNRC

summary: Modern humans spend most of their time having eaten recently. The purpose of the current project is to understand how the blood, which contains immune cells, responds in the hours after eating a meal that is moderately high in fat. We used a sequencing method to observe the expression of all the genes in blood cells in five participants who were each fed a high fat meal on three separate days. The results are reported in the manuscript, “Temporal changes in postprandial blood transcriptomes reveal subject-specific pattern of expression of innate immunity genes after a high-fat meal."

overall_design: We used a sequencing method to observe the expression of all the genes in blood cells in five participants who were each fed a high fat meal on three separate days, resulting in 45 whole blood transcriptomes. For each sample, 3 mL of venous whole blood was drawn into a Tempus Blood RNA tube, shaken vigorously, and then frozen at -80°C until use. Total RNA was purified with the Tempus Spin RNA Isolation Kit with minor modifications to the manufacturer’s protocol. To remove residual genomic DNA, RNA samples were treated on-column with RNase-Free DNase per manufacturer’s instructions. RNA quantity, quality, and integrity were assessed with NanoDrop 1000 and 2100 Bioanalyzer. All isolated RNA had A260/A280 ratios greater than 2 and RNA integrity numbers higher than 7.3. RNA-Seq libraries were constructed at the DNA Technologies and Expression Core at the University of California, Davis, using the Ovation Human Blood RNA-Seq Library System (NuGEN Technologies). Sequencing was performed in a 2x100bp format with 45 samples multiplexed on 3 lanes on an Illumina HiSeq 4000. Analysis of the data is reported in the manuscript, “Temporal changes in postprandial blood transcriptomes reveal subject-specific pattern of expression of innate immunity genes after a high-fat meal.”

first: Shurong

last: Huang

first: Zeynep

last: Alkan

first: Daniel

middle: H

last: Hwang


title: Gene expression profile in Liver of 10mo old MANFHet mice

city: Novato

first: Pedro

last: Sousa-Victor

state: CALIFORNIA

address: 8001 Redwood Blvd.

institute: Buck Institute for Research on Aging

summary: Transcriptome analysis comparing livers of 10 month old MANFHet mice and WT littermates revealed the induction of genes associated with inflammation, apoptosis, collagen deposition, usually observed in association with liver damage, along with alterations in lipid metabolism.

overall_design: RNA was extracted and sequenced for 8 litermates, 4 animals/genotype

first: Joana

last: Neves

first: Heinrich

last: Jasper

first: Ilya

last: Soifer

first: Ganesh

last: Kolumam


title: Gene expression profile in Liver of young and old mice with MANF overexpression

summary: MANF overexpression in old mice had a beneficial effect in the liver and restored expression levels of several metabolic genes.

overall_design: RNA was extracted and sequenced for 4 animals/group


title: Structure and degradation of circular RNAs regulate PKR activation in innate immunity

first: Li

last: Yang

summary: RNase L–mediated rapid degradation of circRNAs is required for PKR activation in innate immune responses and linked to the autoimmune disease systemic lupus erythematosus.

overall_design: Poly(A)+ RNA-seq for gene expression, poly(A)–/Ribo– for circRNA, circSHAPE-MaP and linearSHAPE-MaP for circRNA and linear RNA secondary structure, poly(A)+ RNA-seq for gene expression, poly(A)–/Ribo– for circRNA.

first: Ling-Ling

last: Chen

first: Chu-Xiao

last: Liu

first: Xiang

last: Li

first: Fang


title: Gene expression profile in Liver of old mice after 5 weeks of Heterocronic parabiosis with Yg WT or Yg MANFHet mice

summary: To ask whether MANF contributes to the rejuvenating effects of heterochronic parabiosis, we generated heterochronic pairs in which 20 month old WT mice were combined with either 4 month old MANFHet (O-YgHet) or WT (O-YgWT) littermates, and maintained for 5 weeks before analysis. Control pairs in which old WT mice were combined together (O-O) were used. Livers were collected from each animal in the pair and RNA was sequenced for 5 independent animals/condition.

overall_design: RNA was extracted and sequenced for 5 animals/condition

first: P

middle: B

last: Ventura

first: Saul

last: Villeda


title: Rorc disruption in human FG pancreatic cancer cells

status: Public on Feb 15 2019

city: La Jolla

first: Michael

last: Hamilton

address: 2880 Torrey Pines Scenic Dr.

institute: UCSD

overall_design: RNA-seq comparative analysis of sgControl and sgRorc infected human FG pancreatic cancer cells

first: Nikki

last: Lytle

first: Tannishtha

last: Reya


title: Single-cell analysis of KPC pancreatic tumor cells

overall_design: Evaluate the single-cell transcriptomic landscape in 3 KPf/fC tumors


title: Rorc knockdown in mouse KPC cells

summary: Rorc knockdown in mouse KPC cells

overall_design: RNA-seq comparative analysis of shControl and shRorc infected mouse KPC cells


title: Effect of LXR623, liver X receptor agonist, on glioma cells

status: Public on Feb 05 2019

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

summary: We performed micro array analysis in order to evaluate the effect of LXR623 on gene expression in glioma cancer cells (U87).

overall_design: U87 cells were treated with 20 uM of LXR623 or 0.1 % DMSO for neganitve control. After 24 hrs treatment, total RNA was isolated amd analyzed.

first: Chiaki

last: Ishida

first: Markus

last: Siegelin


title: Next Generation Sequencing of isolated EGFR+ and HLA-G+ first trimester human trophoblasts

status: Public on Feb 14 2019

city: Vienna

first: Jürgen

last: Pollheimer

state: Vienna

address: Waehringer Guertel 18-20, 5Q.09.17

department: Dept. of Obstetrics and Gynaecology

country: Austria

institute: Universitiy of Vienna

summary: The aim of this study was to identify differentially expressed signatures of non-invasive (EGFR+) and invasive (HLA-G+) human trophoblast subtypes. These populations were isolated from single first trimester placentas from 10-12 weeks of gestation.

overall_design: We performed RNAseq to analyze the global expression profile of two different trophoblastic subtypes.

first: Roberta

last: Hannibal

first: Xiaowei

last: Zhu


title: RNA sequencing of wild-type Drosophila melanogaster brains in sated, fasted, or refed nutritional states

city: Ann Arbor

first: Monica

last: Dus

state: MI

address: 1150 N. University Ave.

department: Department of Molecular, Cellular and Developmental Biology

institute: The University of Michigan

summary: We report the application of RNA-sequencing technology for high-throughput profiling of RNA abundance in Drosophila melanogaster brains. By obtaining RNA-sequencing reads, we generated quantitative transcriptome-wide measures in three nutritional states: sated, fasted, refed.

first: Daniel

last: Wilinski


title: Effect of LXR623, liver X receptor agonist, on colon cancer cells

summary: We performed micro array analysis in order to evaluate the effect of LXR623 on gene expression in colon cancer cells (HCT116).

overall_design: HCT116 cells were treated with 20 uM of LXR623 or 0.1 % DMSO for neganitve control. After 24 hrs treatment, total RNA was isolated amd analyzed.


title: Single-cell RNAseq data for pancreatic ductal adenocarcinoma tumor from KPC mice

status: Public on Feb 12 2019

city: Phoenix

first: Wei

last: Lin

state: AZ

address: 445 N. Fifth St.

department: Division of Molecular Medicine

institute: Translational Genomics Research Institute

summary: mPDAC tumors of KPC mice

overall_design: medium and large size tumors

first: Pawan

last: Noel


title: Upregulation of FOXD1 by YAP alleviates senescence and osteoarthritis

status: Public on Feb 17 2019

city: Beijing

first: yuqiong

last: hu

address: No.5 Yiheyuan Road, Haidian District

institute: Peking University

type: Genome variation profiling by high throughput sequencing

summary: Cell senescence is a driver of various aging-associated disorders including osteoarthritis. Here, we identified a critical role for Yes-associated protein (YAP), a major effector of Hippo signaling, in maintaining a younger state of human mesenchymal stem cells (MSCs) and ameliorating osteoarthritis in mice. Targeted knockout of YAP in hMSCs resulted in premature cellular senescence. Mechanistically, YAP interacted with TEA domain transcriptional factor (TEAD) to activate forkhead box D1 (FOXD1) expression. YAP deficiency led to the downregulation of FOXD1, a geroprotective protein. In turn, overexpression of YAP or FOXD1 rejuvenated aged hMSCs. Moreover, intra-articular administration of lentiviral vectors encoding YAP or FOXD1 attenuated the development of osteoarthritis in mice. Collectively, our findings reveal YAP-FOXD1, a novel aging-associated regulatory axis, as a potential therapeutic target for gene therapy to alleviate osteoarthritis.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Here, we generated isogenic YAP knockout and TAZ knockout human embryonic stem cells (hESCs) by CRISPR/Cas9-mediated gene editing. RNA sequencing and copy number variation (CNV) analyses demonstrated YAP-/- and TAZ-/- hESCs had similar transcriptomes with wild-type (WT) hESCs and maintained genomic stability. Three replicates per samples were sequenced for RNA analyses, and WT was the control. One repeat per samples were sequenced for CNV. Through directed differentiation, we then generated YAP-/- and TAZ-/- human mesenchymal stem cells (hMSCs) and performed RNA sequencing. Three replicates per samples were sequenced for RNA analyses, and WT was the control. We identified FOXD1, as a novel target of YAP, mediated the senescent phenotypes. Therefore, we knocked out FOXD1 in hMSCs using a lentivirus mediated CRISPR/Cas9 system. NTC was the control, FOXD1 represents FOXD1 knockout hMSCs. Three replicates per samples were sequenced for RNA analyses. Finally, we injected the lentiviruses encoding luciferase, YAP or FOXD1 into the osteoarthritic joint of mice and examined the transcriptional profiles. Mouse_joint_mControl represents the joints did not undergo surgery; Mouse_joint_mLuc represents the joints received anterior cruciate ligament transection (ACLT) followed by administration of lentivirus expressing luciferse; Mouse_joint_mYAP represents the joints received ACLT followed by administration of lentivirus expressing YAP; Mouse_joint_mFOXD1 represents the joints received ACLT followed by administration of lentivirus expressing FOXD1. Three replicates per samples were sequenced for RNA analyses.

first: Guanghui

last: Liu


title: H3K27-ac ChIP-seq with rorc knockdown in mouse KPC cells

overall_design: H3K27-acetyl ChIP-seq comparative analysis of shControl and shRorc infected mouse KPC cells


title: Expression data from adult mouse brain astrocytes

status: Public on Feb 04 2019

city: Salamanca

first: Juan P

last: Bolanos

state: SALAMANCA

address: C/Zacarías Gonzalez, 2

institute: University of Salamanca

summary:
We aimed to investigate whether reduction of mitochondrial reactive oxygen species (mROS) in adult astrocytes altered the transcriptional profile in vivo. To do so, we used a genetic approach expressing a version of the catalase enzyme within the mitochondria of astrocytes. Astrocytes were acutely isolated from the brains of adult GFAP-mCAT and control mice by the immunomagnetic approach and subjected to a whole-genome transcriptomics array analysis.
We used microarrays to detail the whole genome changes modulated by mROS levels in astrocytes.

overall_design: Study gene expression differences modulated by the modulation of mitochondrial reactive oxygen species in astrocytes compartment. To achieve this objective, we purified astrocytes derived from adult male mice (14 months-old control or GFAP-mCAT male mice) with a commercial immunomagnetic approach used to acutely separate astrocytes (ACSA-2+ cells) from other neural cells (ACSA-2-) from the adult GFAP-mCAT or control mice brain.

first: Juan

first: Carlos

last: Vicente-Gutierrez


title: Mapping polymerase usage by tracking ribonucleotide incorporation (HydEn-seq) during DNA replication

status: Public on Jan 30 2019

city: Durham

first: Zhi-Xiong

last: Zhou

address: 111 TW Alexander Dr.

institute: National Institute of Envinromental Health Sciences

summary: We devised and improved on our hydrolytic end sequencing (HydEn-seq) that mapping ribonucleotide incorporation in genome and used this method to track DNA replicative polymerase usage. We uncovered striking exceptions to canonical polymerase division of labor in Saccharomyces cerevisiae and Schizosaccharomyces pombe.

sample_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

overall_design: Examination of location of ribonucleotides in multiple yeast strains bearing different DNA polymerase variants, deficient in rnh201.

first: Adam

last: Burkholder

first: Scott

last: Lujan

first: Thomas

last: Kunkel


title: Effect of landiolol on sex-related transcriptomic changes in myocardium during sepsis

status: Public on Jan 15 2019

city: Marseille

first: Thom

middle: Thi

last: Tran

address: 163, avenue de Luminy

department: Marseille

country: France

institute: INSERM

summary: We compared the myocardial transcriptional profiles in male and female rats after CLP (Cecal ligation and puncture) induction and landiolol administration. This analysis showed major differences between males and females in the biological processes activated during sepsis. In particular, a very significant decrease in processes related to cell organization, contractile function, ionic transport and PI3K-Akt signaling were observed only in males. Regarding the direct regulation of gene expression of the adrenergic pathway, there was no major differences between male and female. Moreover, our results highlighted the large number of signaling pathways dysregulated during sepsis in males that were reversed by landiolol. In particular, the level of expression of the genes encoding the contractile proteins, TUBA8 and MYH7B, the phosphatase PPP2CA, GRK5 and AKAP6 were close to their basal levels in males. In contrast, in females, only few pathways were affected by the action of landiolol. In addition, adrenergic signaling was decreased while genes potentially involved in calcium overload were overexpressed.

overall_design: Transcriptional profile associated with CLP and after landiolol infusion in male and female

first: Tran

last: Thom

first: Mathieu

last: Calypso

first: Torres

last: Magali

first: Loriod

last: Béatrice

first: Lê

last: Thuy

first: Nguyen

last: Catherine

first: Bernard

last: Monique

first: Leone

last: Marc

first: Lalevée

last: Nathalie


title: Method for absolute quantification of microbial communities by using both microarrays and competitive PCR

status: Public on Jan 16 2019

city: Yokohama

first: Naoyuki

last: Togawa

state: Kanagawa

institute: Mitsubishi Chemical Corporation

summary: We investigated an improved method that combines competitive PCR and microarray techniques. This approach allowed us to quantify specific bacterial groups mounted on DNA chips with accuracy close to that of real-time PCR, despite a measurement at the end point of PCR, and also to estimate the bacterial DNA content in sample DNA.

sample_organism:
Treponema denticola
Campylobacter rectus
Helicobacter pylori
Pseudomonas aeruginosa
Acinetobacter baumannii
Neisseria meningitidis
Escherichia coli
Aggregatibacter actinomycetemcomitans
Phocaeicola vulgatus
Porphyromonas gingivalis
Fusobacterium nucleatum
Capnocytophaga gingivalis
Cereibacter sphaeroides
Staphylococcus aureus
Staphylococcus epidermidis
Deinococcus radiodurans
Streptococcus gordonii
Streptococcus mutans
Streptococcus agalactiae
Streptococcus intermedius
Enterococcus faecalis
Bacillus cereus
Clostridium beijerinckii
Lactobacillus gasseri
Schaalia odontolytica
Bifidobacterium adolescentis
Cutibacterium acnes
Homo sapiens
Tannerella forsythia
Prevotella intermedia
Prevotella nigrescens

platform_organism: Fusobacterium nucleatum subsp. nucleatum

overall_design:
Two bacterial genomic DNA mixtures for calibration curve, twelve kinds of bacterial genomic DNA (4 dilution series, duplicate) for specificity test of DNA chip probes were used.
One bacterial genomic DNA mixture and extraction DNA samples from five human dental plaque samples with a sterile toothbrush (triplicate) were measured.

first: Nana

last: Hoashi

first: Ayaka

last: Yazawa


title: Overexpression of IBIN (CG44404) using C564-GAL4 driver enhances a group of Toll pathway target genes and shows effects on metabolism

status: Public on Jan 01 2019

city: TAMPERE

first: Mika

last: Ramet

address: Arvo Ylpön katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

summary: We performed whole transcriptome profiling of adult flies overexpressing IBIN (Induced By INfection, CG44404) construct with the C564-GAL4 driver and control flies (IBIN;w1118) with and without infection with eiher E. cloacae (6h) or M. luteus (24h). Expression of a group of Toll pathway target genes upon M. luteus infection is slightly elevated when IBIN is overexpressed compared to controls. Importantly, cluster analysis of up- and downregulated genes in C564>IBIN flies without infection revealed two major gene clusters, both of which are involved in metabolism. 8/45 upregulated genes upon IBIN overexpression belong to a carbohydrate metabolism/glycoside hydrolase gene cluster, and 6/21 downregulated genes belong to a proteolysis / peptidase S1 gene cluster. Genes that had a normalized read number >10 in the treatment of interest and an expression fold change >2 were included in the cluster analysis performed with DAVID Bioinformatics resources 6.8 (https://david.ncifcrf.gov) online tool.

overall_design: Three biological replicates (A,B&C) containing 5 flies each are analyzed per condition (six conditions: IBIN overexpression 0h, Ecl6h & Mlut 24h; controls without driver [IBIN;w1118] 0h, Ecl6h & Mlut 24h).

first: Susanna

last: Valanne

first: Mirva

last: Järvelä-Stölting

first: Tiina

last: Salminen

first: Laura

last: Vesala

last: Rämet


title: Expression of immune-inducible genes in Drosophila melanogaster whole fly samples upon Micrococcus luteus infection for 24h

summary: Transcriptome profiling of immune-responsive genes in Drosophila melanogaster during Gram-positive bacterial infection was performed. The most highly induced gene by Micrococcus luteus infection was a novel gene CG44404, named Induced by Infection (IBIN). In the Flybase release FB2019_4 (22.8.2019) IBIN is annotated as coding for a short peptide. In the transcriptome analysis, fourteen immune-inducible long non-coding RNA (lncRNA) genes (Fold Change > 3) were also found.

overall_design: Three biological replicates (A,B&C) containing 5 flies each are analyzed per condition (non-infected vs. M.luteus infected for 24h)


title: Gene expression profiles in brown fat tissues of wild type (WT) and Tsku knock out mice

first: QIUYU

last: WANG

address: 210 Washtenaw Ave

institute: Life sciences institute

summary: Mice lacking TSKU exhibited elevated core body temperature and were unable to adequately suppress energy expenditure during starvation, leading to greater body weight loss. Tsku null mice were strongly resistant to diet-induced obesity and its associated metabolic disorders, including insulin resistance and hepatic steatosis. This metabolic phenotype was associated with sympathetic activation and enhanced brown fat thermogenesis. Here we used microarrays to uncover the metabolic pathways relevant to the phenotype induced by Tsku deficiency.

overall_design: BAT mRNA profiles of 4-month-old WT and Tsku KO mice fed with chow diet were generated by microarray, in duplicate

first: Qiuyu

last: Wang

first: Jiandie

last: Lin


title: Human enteroendocrine cell transcriptomic profiling

status: Public on Dec 31 2018

city: Cambridge

first: Brian

middle: Yee Hong

last: Lam

address: Box 289 Addenbookes Hospital, Hills Road

department: Metabolic Research Laboratories

institute: University of Cambridge

summary: We purified two populations of human jejunal enteroendocrine cells (GLP1+ and GLP1-) by FACS and identified transcripts enriched in endocrine cell lineages.

overall_design: Comparative transcriptomic study of 3x cell populations by bulk RNAseq, with 11 biological replicates

first: Geoffrey

last: Roberts

first: Fiona

last: Gribble


title: MEK1/2 inhibitors unlock the constrained interferon response in macrophages through IRF1 signaling

status: Public on Dec 28 2018

city: Singapore

first: LEI

last: YANG

state: Singapore

address: Science Drive 4, S1A, #05-03, National University of Singapore

department: Biological Sciences

country: Singapore

institute: National University of Singapore

summary: Analysis of bone-marrow derived macrophages (BMDMs) stimulated with single or combinatorial TLR agonist and MEK1/2 inhibitor in wild-type and Irf1-/- macrophages. Results provide insights into the versatile but yet uncharacterized roles of IRF1 in TLR-MEK1/2-ERK MAPK signaling.

overall_design: BMDMs from wild-type or Irf1-/- C57BL/6J mice were stimulated with TLR7 agonist R848 alone or in combination with MEK1/2 inhibitor U0126 for six hours. Non-treated samples and DMSO were used as controls for R848 and MEK1/2 inhibitor, respectively. Total RNA were extracted and subjected to Clariom™ D assays (previously known as GeneChip™ Mouse Transcriptome Array 1.0).

first: Lei

last: Yang

first: Jeak

last: Ding


title: MicroRNA expression in human lymphatic endothelial cells (LEC) and blood endothelial cells (BEC)

status: Public on Feb 19 2019

city: Bethesda

first: Hyun Min

last: Jung

state: MD

address: 6 Center Drive

department: Division of Developmental Biology

institute: National Institutes of Health

type: Non-coding RNA profiling by high throughput sequencing

summary: This experiment was aim to identify differentially expressed miRNAs from cultured human LEC and BEC using microRNA-seq.

overall_design: RNA was isolated from cultured human LEC and BEC. Libraries were prepared using the  Illumina TruSeq Small RNA Sample Preparation Kit, then sequenced on a NextSeq 500  Illumina instrument, generating 50 bp single-end reads. Data was analyzed using  PartekFlow analysis software

first: Brant

last: Weinstein


title: DNA damage and genome instability by G-quadruplex ligands are mediated by R-loops in human cancer cells

status: Public on Dec 27 2018

city: Bologna

first: Giovanni

last: Capranico

state: BO

address: Via Selmi 3

department: FABIT

country: Italy

institute: University of Bologna

summary: G-quadruplexes (G4s) and R-loops are non-canonical DNA structures that can play regulatory functions of basic nuclear processes and can trigger DNA damage and genome instability. We here show that specific G4 ligands can stabilize G4s and simultaneously increase R-loop levels in human cancer cells likely by spreading DNA:RNA heteroduplexes to adjacent regions containing G4 structures. DNA cleavage and DNA damage response induced by G4 ligands were rescued by overexpression of exogenous RNaseH1 in cancer cells independently of BRCA2 status. The data thus show that R-loops are involved in the induction of DNA damage by chemical G4 stabilization. In addition, G4 ligands trigger the formation of micronuclei, particularly in BRCA2-silenced cancer cells, in an R-loop dependent manner. Our results uncover the mechanism of genome instability caused by G4 ligands and can open to the development of unexpected anticancer strategies using G4-targeted agents.

overall_design:
Genomic R-loop maps determined by DRIP-seq methodology,in duplicates, in U2OS cells treated with FG and PDS and in untreated control cells.
PDS - pyridostatin
FG - (2E,2'E)-2,2'-((2,8-diphenyldiimidazo[1,2-a:1',2'-c]pyrimidine-3,9-diyl)bis(methanylylidene))bis(hydrazine-1-carboximidamide)

first: Alessio

last: De Magis

first: Stefano

middle: G

last: Manzo

first: Jessica

last: Marinello

first: Marco

last: Russo

first: Olivier

last: Sordet

first: Rita

last: Morigi


status: Public on Dec 25 2018

city: Seoul

first: Yong-Joon

last: Cho

address: 1 Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

summary:
Purpose: Understanding the Mechanism of Action of the Anti-Dandruff Agent Zinc Pyrithione against Malassezia restricta.
Methods: The transcriptome profile of the ZPT-treated M. restricta cells compared to that of untreated cells were generated by RNA-Seq using Illumina HiSeq. Generated raw reads that passed quality filters were mapped to the reference genome. Mapped reads were counted by featureCounts in Subread package v1.4.3 and the relative transcript abundance was TPM-normalized.
Results: A number of genes were differentially expressed in the ZPT-treated cells, which include genes involved in zinc transporter, mitochondirial function, TCA cycle, electron transport chain and lipase.

overall_design: Transcriptome of zinc pyrithione (ZPT)-treated M. restricta cells (5, 10, 20 uM) vs. Transcriptome of nntreated M. restricta cells

first: Won

first: Minji

last: Park


title: Expression Profile of Genes in Trabecular Meshwork Cells Treated with Dexamethasone

status: Public on Dec 20 2018

city: MADISON

first: Donna

last: Peters

state: WI- WISCONSIN

address: 1300 UNIVERSITY AVE

department: Pathology & Laboratory Medicine

institute: UNIVERSITY OF WISCONSIN SCHOOL OF MEDICINE

summary:
Treatment with glucocorticoids is known to cause ocular hypertension in humans which can lead to steriod-induced glaucoma
We used microarrays to determine changes in gene expression in two human trabecular meshwork  (TM) cell isolates (TM-4 and TM-2) from the same donor that could explain the increase in ocular hypertension.

overall_design: RNA was extracted from confluent cultures of trabecular meshwork cells treated with and without dexamethasone (DEX) for 6 days and prepared for hybridization on Affymetrix microarrays


title: Commensal Microbiota Promote Lung Tumorigenesis via γδ T Cells

status: Public on Feb 23 2019

first: A

last: Bhutkar

address: 77 Massachusetts Avenue

institute: MIT

summary: Lung cancer is closely associated with chronic inflammation, but the mechanism underlying such inflammation has not been clearly defined. The lung is a mucosal tissue colonized by a diverse bacterial community at the steady state, and pulmonary infections commonly present in lung cancer patients are linked to clinical outcomes. Here we provide evidence that local microbiota provoke inflammation associated with lung adenocarcinoma by activating lung-resident gamma-delta T cells. Germ-free or antibiotic-treated mice were significantly protected from lung tumor initiation and progression induced by Kras mutation and p53 loss. Mechanistically, commensal bacteria stimulated My88-dependent IL-1beta and IL-23 production from myeloid cells, inducing proliferation and activation of Vγ6+Vδ1+ γδ T cells that produced IL-17 and other effector molecules to promote inflammation and tumor cell proliferation. Our findings provide a clear link between local microbiota-immune crosstalk and lung tumorigenesis, and thereby define key cellular and molecular mediators that may serve as effective targets in lung cancer treatment and prevention.

overall_design: γδT cells were isolated from tumor-bearing lungs or spleens of KP mice. Their transcriptional profiles are compared with RNA-seq.

first: Chengcheng

last: Jin

first: Georgia

last: Lagoudas

first: Chen

last: Zhao

first: Arjun

first: Bo

last: Hu

first: Samuel

last: Ameh

first: Demi

last: Sandel

first: Mark

middle: T

last: Whary

first: Ronald

last: Germain

first: Paul

last: Blainey

first: James

last: Fox

first: Tyler

last: Jacks


title: Single-cell multi-omic profiling of chromatin conformation and DNA methylome

status: Public on Dec 26 2018

city: La Jolla

first: Joseph

middle: R

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

summary: Recent advances in the development of single cell epigenomic assays have facilitated the analysis of the gene regulatory landscapes in complex biological systems. Single-cell variations of methods such as DNA methylation-sequencing and ATAC-seq hold tremendous promise for delineating distinct cell types and identifying their critical cis-regulatory sequences. Emerging evidence in recent years has shown that in addition to cis-regulatory sequences, dynamic regulation of 3D chromatin conformation is a critical mechanism for the modulation of gene expressions during development and disease. While assays for the investigation of single-cell 3D chromatin structure have been developed, cell-type specific chromatin conformation in primary human tissues has not been extensively explored. It remains unclear whether single-cell Chromatin Conformation Capture (3C) or Hi-C profiles are suitable for cell type identification and allow the reconstruction of cell-type specific chromatin conformation maps. To address these challenges, we have developed a multi-omic method single-nucleus methyl-3C sequencing (sn-m3C) to profile chromatin conformation and DNA methylation from the same cell. We have shown that bulk m3C and sn-m3C accurately capture chromatin organization information and robustly separate mouse cell types. We have developed a fluorescent-activated nuclei sorting strategy based on DNA content that eliminates nuclei multiplets caused by crosslinking. The sn-m3C-seq method allows high-resolution cell-type classification using two orthogonal types of epigenomic information and the reconstruction of cell-type specific chromatin conformation maps.

first: Chongyuan

last: Luo

first: Dong-Sung

last: Lee

first: Jingtian

last: Zhou

first: Sahaana

last: Chandran

first: Angeline

last: Rivkin

first: Anna

last: Bartlett

last: Nery

first: Conor

last: Fitzpatrick

first: Carolyn

last: O’Connor

first: Jesse

last: Dixon


title: Repression of Divergent Noncoding Transcription by a Sequence-Specific Transcription Factor

city: London

first: Folkert

last: van Werven

address: 1 Midland Road

institute: Francis Crick Institute

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

overall_design: Refer to individual Series


title: Identification of non-coding transcripts regulated by Rap1 and other transcription factors by RNA-seq analysis

summary: Eukaryotic cells utilize several mechanisms to ensure that expression of aberrant non-coding RNAs is limited. Gene looping, chromatin modification or remodeling, and RNA surveillance contribute to ensure the fidelity of transcription and limit non-coding transcripts. Here we identify that in Saccharomyces cerevisiae, the transcription factor Rap1 is critical for limiting the expression of aberrant RNAs, particularly near the highly expressed ribosomal protein genes, and characterize them in the context of other non-coding RNAs regulated by chromatin and transcription related factors.

overall_design: RNA-seq analysis of Saccharomyces cerevisiae S288C strains. Data include gene deletion strains (spt10Δ, spt21Δ, rlf2Δ), strains transformed with OsTIR1 ligase and auxin-inducible degron (IAA7) tagged proteins (Rap1, Spt6, Spt16), Rap1 auxin-inducible degron strains expressing depletion-insensitive Rap1 mutant proteins, or wild-type control strains. 2 biological replicates for each sample type and condition were analyzed. For each biological replicate, cells were grown overnight in YPD media, diluted, and treated with DMSO or 500 μM 3-indole-acetic acid (3-IAA, auxin). Samples for auxin-inducible degron strains were taken 2 hours after treatment with DMSO or 3-IAA. For wild-type and gene deletion strains, samples were taken in mid-logarithmic growth. RNA was subjected to rRNA depletion to generate TOTAL RNA-seq libraries, respectively.

first: A

last: Wu

first: H

last: Patel

first: M

last: Chia

first: F

last: Moretto

first: D

last: Frith

last: Snijders

middle: J


title: Identification of non-coding transcripts regulated by the transcription factor Rap1 by RNA-Seq analysis

summary: Many active eukaryotic gene promoters exhibit divergent noncoding transcription, but the mechanisms restricting expression of these transcripts are not well understood. Here we demonstrate how a sequence-specific transcription factor represses divergent noncoding transcription at highly expressed genes in yeast. We find that depletion of the transcription factor Rap1 induces noncoding transcription in a large fraction of Rap1 regulated gene promoters. Specifically, Rap1 prevents transcription initiation at cryptic promoters near its binding sites, which is uncoupled from transcription regulation in the protein-coding direction. We further provide evidence that Rap1 acts independently of chromatin-based mechanisms to repress cryptic or divergent transcription. Finally, we show that divergent transcription in the absence of Rap1 is elicited by the RSC chromatin remodeller. We propose that a sequence-specific transcription factor limits access of basal transcription machinery to regulatory elements and adjacent sequences that act as divergent cryptic promoters, thereby providing directionality towards productive transcription.

overall_design: RNA-Seq analysis of Saccharomyces cerevisiae S288C strains transformed with OsTIR1 ligase and auxin-inducible degron (IAA7) tagged Rap1, or wild-type control strains. 3 biological replicates for each sample type and condition are analyzed. For each biological replicate, cells were grown overnight in YPD media, diluted, and treated with DMSO or 500 μM 3-indole-acetic acid (3-IAA, auxin). UNINDUCED samples were taken 30 minutes after treatment, and INDUCED samples were taken 30 minutes or 2 hours after treatment. For WT controls, samples were taken in mid-logarithmic growth. RNA was either subjected to rRNA depletion or polyA RNA purification to generate POLYA and TOTAL RNA-Seq libraries, respectively.


title: Gene expression analysis of subpopulations of mouse embryonic stem cells sorted based on Id1 and Nanog expression

status: Public on Dec 15 2018

city: Edinburgh

first: Sally

last: Lowell

address: SCRM Building, 5 Little France Drive

department: MRC Cente for Regenerative Medicine

institute: The University of Edinburgh

summary: Analysis of gene expression in sorted subpopulations of mouse embryonic stem cells. We set out to investigate whether expression of Id1 in Nanog-low cells affected the expression of pluripotency factors and signalling molecules.

overall_design: Id1-Venus Nanog-tagRFP (IVNR) reporter mouse ES cells cultured in LIF+FCS were sorted into Nanog-tagRFP-high, Id1-Venus-high, or double low subpopulations. Unsorted IVNR cells cultured in LIF+FCS, as well as Id1-Venus (Id1V) reporter ES cells cultured in 2i and in 2i+LIF were included as controls. All samples were collected in duplicate. Total 12 samples.

first: Mattias

last: Malaguti


title: Single cell RNA-Seq reveals Fgf signaling dynamics during sensory hair cell regeneration

status: Public on Dec 03 2018

city: Kansas City

first: Tatjana

last: Piotrowski

state: MO

institute: Stowers Institute

summary: Loss of sensory hair cells leads to deafness and balance deficiencies. In contrast to mammalian hair cells, zebrafish ear and lateral line hair cells regenerate from poorly characterized, proliferating support cells. Equally ill-defined is the gene regulatory network underlying the progression of support cells to cycling hair cell progenitors and differentiated hair cells. We used single-cell RNA-Sequencing (scRNA-Seq) of lateral line sensory organs and uncovered five different support cell types, including quiescent and activated stem cells. In silico ordering of support cells along a developmental trajectory identified cells that self-renew and new groups of genes required for hair cell differentiation. scRNA-Seq analyses of fgf3 mutants, in which hair cell regeneration is increased demonstrates that Fgf and Notch signaling inhibit proliferation of support cells in parallel by inhibiting Wnt signaling. Our scRNA-Seq analyses set the foundation for mechanistic studies of sensory organ regeneration and is crucial for identifying factors to trigger hair cell production in mammals.

overall_design: Single cell RNA sequecing on FACS sorted cells from the zebrafish neuromast in 5df embryos in 3 different samples: wild type, fgf3 mutants, and fgf3 siblings.

first: Daniel

middle: C

last: Diaz

first: Sungmin

last: Baek

first: Helena

last: Boldt

first: Anoja

last: Perera

first: Kate

last: Hall

first: Allison

last: Peak

first: Jeffrey

last: Haug


title: RNA-seq reveals novel PAF1c regulation of transcription in mouse hematopoietic progenitor cells

status: Public on Dec 01 2018

city: Indianapolis

first: James

last: Ropa

state: IN

address: 950 W Walnut St

institute: Indiana University

summary: The Polymerase Associated Factor 1 complex (PAF1c) functions at the interface of epigenetics and gene transcription and plays a role in solid tumors and leukemia. Previous reports demonstrated that the PAF1c is required for MLL-fusion driven acute myeloid leukemia (AML) through the direct regulation of pro-leukemic target genes like Hoxa9 and Meis1. This is due to direct interactions between the PAF1c and wild type MLL or MLL fusion proteins. However, a detailed exploration of the PAF1c in normal hematopoiesis is lacking. Here, we utilize mouse genetic models to interrogate the role of the PAF1c subunit, Cdc73, in the development and maintenance of normal hematopoiesis. Using hematopoietic-specific expression of Cre recombinase, we discovered that Cdc73 is required for both embryonic and adult hematopoiesis. Here, we performed gene expression profiling (RNA-seq) in normal ckit+ HSPCs expressing Cdc73 or lacking Cdc73. Gene expression profiling in normal ckit+ HSPCs revealed differential regulation of Hoxa9 and Meis1 gene programs by CDC73 in normal hematopoietic cells compared to previously reported effects on AML cells.

overall_design: Differential gene expression of genes regulated by Cdc73 in mouse hematopoietic cells. RNA-seq of cKit+ bone marrow from 3 mice with hematopoietic specific deletion of Cdc73 or 3 control mice performed on Illumina HiSeq4000

first: Nirmalya

last: Saha

first: Andrew

last: Muntean


title: Excess light priming in Arabidopsis thaliana genotypes with altered DNA methylomes

status: Public on Nov 27 2018

city: Philadelphia

first: Diep

last: Ganguly

state: PA

address: 433 S University Ave

department: Department of Biology

institute: University of Pennsylvania

summary: Plants must continuously react to the ever-fluctuating nature of their environment. Repeated exposure to stressful conditions can lead to priming, whereby prior encounters heighten a plant’s ability to respond to future events. A clear example of priming is provided by the model plant species Arabidopsis thaliana (Arabidopsis), in which photosynthetic and photoprotective responses are enhanced following recurring light stress. While there are various post-translational mechanisms underpinning photoprotection, an unresolved question is the relative importance of transcriptional changes towards stress priming and, consequently, the potential contribution from DNA methylation – a heritable chemical modification of DNA capable of influencing gene expression. Here, we systematically investigate the potential molecular underpinnings of physiological priming against recurring excess light (EL), specifically DNA methylation and transcriptional regulation: the latter having not been examined with respect to EL priming. The capacity for physiological priming of photosynthetic and photoprotective parameters following a recurring EL treatment was not impaired in Arabidopsis mutants with perturbed establishment, maintenance and removal of DNA methylation, nor was the transmission of this priming into naive tissues developed in the absence of excess light. Importantly, no differences in developmental or basal photoprotective capacity were identified in the mutants that may confound the above result. Little evidence for a causal transcriptional component of physiological priming was identified; in fact, most alterations in primed plants presented as a transcriptional ‘dampening’ in response to an additional EL exposure, likely a consequential of physiological priming. However, a set of transcripts uniquely regulated in primed plants provide preliminary evidence for a novel transcriptional component of recurring EL priming, independent of physiological changes. Thus, we propose that physiological priming of recurring EL in Arabidopsis occurs independently of DNA methylation; and that the majority of the associated transcriptional alterations are a consequence, not cause, of this physiological priming.

overall_design: Experiments were performed using recurring excess-light treatments on Arabidopsis thaliana. MethylC-seq was performed on 3 replicates of unstressed Col-0 and strs2  plants. RNA-seq was performed on 3 replicates of naïve, naïve-triggered, primed, and primed-triggered plants.

first: Bethany

last: Stone

middle: F

last: Bowerman

first: Steven

last: Eichten

first: Barry

last: Pogson


title: RNA-seq of resting and activated CD4+ T cells +-JQ1

status: Public on Nov 21 2018

city: Heidelberg

first: Marina

last: Lusic

address: Im Neuenheimer Feld 400

institute: Heidelberg University Hospital

summary: HIV-1 recurrently targets active genes that are positioned in the outer shell of the nucleus and integrates in the proximity of the nuclear pore compartment. However, the genomic features of these genes and the relevance of their transcriptional activity for HIV-1 integration have so far remained unclear. Here we show that recurrently targeted genes are proximal to super-enhancer genomic elements and that they cluster in specific spatial compartments of the T cell nucleus. We further show that these gene clusters acquire their location at the nuclear periphery during the activation of T cells. The clustering of these genes along with their transcriptional status are the major determinants of HIV-1 integration in T cells. Our results show for the first time the relevance of the spatial compartmentalization of the genome for HIV-1 integration, thus further strengthening the role of nuclear architecture in viral infection.

overall_design: Triplicates of: resting JQ1 treated CD4 T cells, activated JQ1 treated CD4 T cells, resting control CD4 T cells, activated control CD4 T cells

first: Bojana

last: Lucic


title: Effects of Bcl11b-deficiency on gene expression in the main olfactory epithelium of neonatal mice

first: Junji

last: Hirota

address: 4259-B63, Nagatsuta-cho

department: Center for Biological Resources and Informatics

institute: Tokyo Institute of Technology

summary: Each olfactory sensory neuron (OSN) chooses a single odorant receptor (OR) gene from the class I or class II OR repertoire in mice. We have found that the transcription factor Bcl11b, which is coexpressed with class II OR genes both in frog and mouse, determines the class of OR to be expressed in OSNs. Both loss- and gain-of-function analyses demonstrate that Bcl11b is necessary for class II genes expression, by suppressing the class I-specific enhancer. Overall, we identified a unique transcriptional mechanism that serves as a binary switch for the OR class choice that is likely to have contributed to the acquisition of terrestrial-specific class II OR expression.

overall_design: To reveal the downstream genes of Bcl11b in the main olfactory epithelium (MOE), we analyzed the gene expression changes by loss-of-Bcl11b-function using conventional Bcl11b knockout (KO) mice. This dataset is gene expression comparison in the MOE between wild-type and Bcl11b KO mice at postnatal day 0. Total RNA was individually isolated from each whole MOE sample that was dissected from offspring of Bcl11b heterozygous KO female and male mice. There are five replicates for wild-type and six replicates for Bcl11b KO mice (Bcl11b KO contains two female).

first: Takayuki

last: Enomoto

first: Makoto

last: Ohmoto

first: Ichiro

last: Matsumoto


title: ChIP seq of primary CD4+ T cells

status: Public on Nov 22 2018

overall_design: Biological duplicates of H3K27Ac, repeated once as technical duplicates (2 samples sequenced 2 times), duplicates of H3K36me3 and H3K20me1. Triplicates of H3K4me3 and H3K9me2.


title: Mouse duodenal enteroendocrine transcriptome

first: Brian

last: Lam

summary: Using genetically modifed mice to express fluorescent reporter in proglucagon expressing cells (GluVenus) or in all enteroendocrine cells (NeuroD1), we purifed positive and negative cells by FACS from duodenal epithelial cells and identified transcripts enriched in positive populations

overall_design: Comparative transcriptomics between positive and negative cells in two different mice strains, with three replicates (2 for the GluVenus negative population)

first: Pierre

last: Larraufie

first: Frank

last: Riemann

first: Fiona

last: Gribble


title: Transcriptional profiles of murine E13 epidermal cells and P4 epidermal basal cells

status: Public on Oct 05 2018

city: Houston

first: Hoang

last: Nguyen

state: TX

address: 1 Baylor Plaza

department: Center for Cell and Gene Therapy

institute: Baylor College of Medicine

summary: Transcriptional profiling of mouse epidermal cells at embryonic day 13 (E13) compared with epidermal basal cells at postnatal day 4 (P4), both isolated from Krt14-H2BGFP mouse skin. Goal was to identify the genes differentially expresssed in E13 epidermal cells vs P4 epidermal basal cells.

overall_design: Two-condition experiments to compare gene expression profile of E13 epidermal cells vs P4 epidermal basal cells. Biological replicates: 2 replicates.

first: Qi

last: Miao


title: Transcriptional profiles of Sox4 cKO, Sox11 cKO, and Sox4/11 dcKO mouse epidermis at E16

summary: Transcriptional profiling of mouse E16 epidermis deficient of Sox4, Sox11, or both as compared to  gender matched wild type littermate controls. Goal was to identify the genes differentially expresssed in the conditional knockout epidermis vs the wild-type control epidermis.

overall_design: Two-condition experiments to compare gene expression profile of Sox4 cKO, Sox11 cKO, or Sox4/11 dcKO vs wild-type epidermis at E16. Biological replicates: 2 replicates for each comparison with color-swapping


title: Expression data of human primary placenta trophoblast cells, at different time points following seeding

status: Public on Oct 01 2018

city: Rehovot

first: Valery

last: Krizhanovsky

address: Herzel 234

department: Molecular Cell Biology

country: Israel

institute: Weizmann Institute of Science

summary:
Cellular senescence is a permanent state of cell cycle arrest that protects the organism from tumorigenesis and regulates tissue integrity upon damage. Recently, several studies have shown that senescence plays a role in embryonic and placental development. Molecular markers of senescence are expressed in human syncytiotrophoblast, but the molecular mechanisms that govern senescence in these cells are not yet understood. To unravel the molecular mechanisms that mediate the impact of senescence on the placenta, we studied human syncytiotrophoblast in culture.
We isolated cytotrophoblast cells from human term placentas. In culture, cytotrophoblast cells spontaneously differentiate into syncytium, creating the large multinucleated syncytiotrophoblast structure that can be monitored and studied for its molecular and cellular characteristics (Kliman et al., 1986; Li and Schust, 2015). We performed mRNA profiling on two human term placenta trophoblast cultures, at 1.5, 2, 3 and 5 days after seeding.

overall_design: To gain an insight into the molecular mechanisms activated during fusion of the placental syncytiotrophoblast, we performed mRNA profiling, using affymetrix PrimeView, on primary trophoblasts obtained independently from two human term placentas, at 1.5, 2, 3 and 5 days after seeding.

first: Hilah

last: Gal


title: Transcriptional profile of SOX11-induced mouse epidermis

summary: Transcriptional profiling of SOX11-expressing mouse epidermis (K14-rtTA;TRE-Sox11-FLAG) compared to control (K14-rtTA) epidermis at postnatal day 4 (P4). The littermate pairs were injected with Dox for 12 h before their epidermis was harvested. Goal was to identify the gene expression profile of postnatal epidermis changed by SOX11 induced expression.

overall_design: Two-condition experiments to compare gene expression profile of SOX11-overexpressing versus littermate control mouse epidermis at P4.5 where endogeneous Sox11 expression is not detectable. Biological replicates: 2 replicates.


title: H3K4me3 ChIP-seq from B6CASTF1-PRDM9 Humanized/CAST testes

status: Public on Sep 28 2018

city: Berkeley

first: Nicolas

last: Altemose

state: CA

address: 327 Stanley Hall

department: Bioengineering

institute: University of California, Berkeley

summary: We report testis H3K4me3 enrichment in an F1 male from a C57BL/6J (B6) x CAST/Eij (CAST) cross (B6 mother, CAST father). This mouse is heterozygous at PRDM9 for a humanized allele (Davies et al. Nature 2016) and the CAST allele. After filtering of promoter H3K4me3 regions, these data serve as a measure of PRDM9 binding enrichment on each homologue. We found that both crossovers and non-crossovers (observed by sequencing F2/F4/F5 genomic DNA) are depleted at "asymmetric" Double-Strand Break hotspots where PRDM9 primarily binds only one of the two homologues. This proves that PRDM9 plays an important role in promoting inter-homologue interactions and can explain why increasing PRDM9 binding asymmetry predicts hybrid infertility. See Li, Bitoun, Altemose et al. 2018 (pending) for a complete summary.

overall_design: Two replicates of anti-H3K4me3 ChIP-seq, one per testis, plus an input chromatin control, from a male B6CAST-F1-PRDM9 Humanized/CAST mouse

first: Simon

last: Myers


title: The Genetic Landscape of Diamond-Blackfan Anemia

status: Public on Sep 14 2018

first: Vijay

last: Sankaran

address: 7 Cambridge Center

institute: Broad Institute

summary: Diamond-Blackfan anemia (DBA) is a rare bone marrow failure disorder that affects 7 out of 1,000,000 live births and has been associated with mutations in components of the ribosome. In order to characterize the genetic landscape of this heterogeneous disorder, we recruited a cohort of 472 individuals with a clinical diagnosis of DBA and performed whole exome sequencing (WES). We identified rare and predicted damaging mutations in likely causal genes for 78% of individuals. The majority of mutations were singletons, absent from population databases, predicted to cause loss of function, and in one of 19 previously reported ribosomal protein (RP) encoding genes. Using exon coverage estimates, we identified and validated 31 deletions in RP genes. We also observed an enrichment for extended splice site mutations and validated their diverse effects using RNA sequencing in individual-derived cell lines. Leveraging the size of our cohort, we observed robust genotype-phenotype associations with congenital abnormalities and treatment outcomes. We further identified rare mutations in 7 previously unreported RP genes that may cause DBA, as well as several distinct disorders that appear to phenocopy DBA, including 9 individuals with biallelic CECR1 mutations that result in deficiency of ADA2. However, no new genes were identified at exome-wide significance, suggesting that there are no unidentified genes containing mutations readily identified by WES that explain > 5% of DBA cases. Overall, this report should not only inform clinical practice for DBA individuals, but also the design and analysis of rare variant studies for heterogeneous Mendelian disorders.

overall_design: 9 individuals with DBA with putative splice mutations and 5 control individuals were processed for RNA-seq.

first: Jacob

last: Ulirsch

first: Jeffrey

last: Verboon


title: TSS identification of Rap1-regulated transcripts by 5' end RNA sequencing

first: Folkert

last: van Werven

summary: Eukaryotic cells utilize several mechanisms to ensure that expression of aberrant non-coding RNAs is limited. Gene looping, chromatin modification or remodeling, and RNA surveillance contribute to ensure the fidelity of transcription and limit non-coding transcripts. We have identified that the transcription factor Rap1 is critical for limiting the expression of aberrant RNAs, particularly near the highly expressed ribosomal protein genes. Here we utilize a 5’ end RNA sequencing protocol to identify transcript TSSs at single nucleotide resolution in wild-type and Rap1 auxin-inducible degron strains of Saccharomyces cerevisiae.

overall_design: 5’ end RNA sequencing analysis of Saccharomyces cerevisiae S288C strains transformed with Os TIR1 ligase and auxin-inducible degron (IAA7) tagged Rap1, or wild-type control strains. 3 biological replicates of each condition are analysed. For each biological replicate, cells were grown overnight in YPD medium, diluted, and treated with 500 μM 3-indole-acetid acid (3-IAA, auxin) for RAP1_AID_IAA samples or left untreated for WT samples. RAP1_AID_IAA samples were taken 2 hours after treatment, and for WT control samples were taken in mid-logarithmic growth. Details for library preparation are described below.

first: A

last: Wu

first: H

last: Patel

first: M

last: Chia

first: F

last: Moretto

first: D

last: Frith

last: Snijders


title: Identification of StdE and StdF binding targets in the Salmonella enterica genome

city: Seville

first: Lucía

last: García

address: Avda. Reina Mercedes

institute: Universidad de Sevilla

summary: ChIP-seq analysis in a Salmonella enterica Serovar Typhimurium SL 1344 strain that constitutively expresses stdEF::3xflag.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

overall_design: 4 ChIP-seq assays were used to determine chromosome-wide DNA binding profiles of StdE and StdF in Salmonella enterica.

last: García-Pastor

first: Elena

last: Puerta-Fernández

first: Maria

middle: A

last: Sánchez Romero

first: Gabriel

last: Gutierrez

first: Josep

last: Casadesús


title: Gene expression signatures in FAM46C (TENT5C)-deleted multiple myeloma (MM) cell lines

status: Public on Sep 05 2018

city: Nagoya

first: Akinobu

last: Ota

state: Aichi

address: 1-1 Yazakokarimata

department: Food and Nutritional Environment

institute: Kinjo Gakuin University

summary: To investigate the effect of FAM46C disruption on gene expression, we generated FAM46C-knockout (FAM46C-KO) cell clones using CRISPR/Cas9 system with MM cell lines OCI-My5, KMS-11, and ANBL-6. Using the generated cell clones, we have employed whole genome microarray expression profiling as a discovery platform to identify genes that are associated with FAM46C expression in MM cell lines. OCI-My5, KMS-11, and ANBL-6 cell clones were cultured for 48 h in vitro.

overall_design: OCI-My5 and KMS-11 cells were maintained in RPMI 1640 supplemented with 10% FBS, while the IL-6-dependent ANBL-6 cells were maintained in RPMI1640 medium supplemented with 10% FBS in the presence of recombinant human IL-6 (10 ng/mL; R&D systems, Minneapolis, MN, USA) at 37 °C in 5% CO2 humidified atmosphere.

first: Ichiro

last: Hanamura

first: Jo

last: Kanasugi


title: Small RNA analysis of epidermis uncovered miRNAs involved in cuticle biosynthesis in Brassica napus

status: Public on Nov 30 2018

city: WUHAN

first: Tingting

last: Liu

address: Shizishan Street

department: College of Plant Science and Technology

institute: Huazhong Agricultural University

summary: To investigate the function of small RNAs in cuticle biosynthesis in B. napus, we constructed four small RNA libraries from stem epidermis of wax-deficient and wild-type materials for sequencing. Subsequently, a total of 43,840,451 clean reads were generated and 24nt sequences represented the dominant percentage. Totally, 300 unique conserved miRNAs were identified and 8 of them showed differentially expressed. In addition, the expression of six novel miRNAs were also changed. After target prediction and function annotation, three miRNAs (aly-miR165a-5p, aly-miR408-5p, and novel-mir2) might influence cuticle morphogenesis not only by repressing the biosynthesis of cuticular substrates and components, but also blocking the transmembrane transport processes. The expression level of aly-miR408-5p and aly-miR165a-5p were increased in glossy materials examined by stem-loop qRT-PCR, while their predicted target genes (BnaC04g29170D, BnaA01g25630D, BnaA06g40560D) were down-regulated. These results suggested that miRNAs might influence cuticle biosynthesis by repressing cuticle-related genes expression in B. napus. Both the biosynthesis and secretion processes of cuticlular components might be influenced by miRNAs. These results will promote the study of post-transcriptional regulation mechanisms of cuticle biosynthesis in B. napus and provide new direction for further research.

overall_design: Four small RNA libraries were constructed for glossy mutant and wildtype materials of rapeseed.

first: Jingquan

last: Tang


title: Hi-C contact map of the Jurkat T cell genome

city: Barcelona

first: Guillaume

last: Filion

address: Dr. Aiguader 88

department: GRSCC

institute: CRG

summary: We performed Hi-C on untreated Jurkat T cells growing in culture. We obtained contact maps with a final resolution of 5 kb where Topologically Associated Domains (TADs) are clearly visible. We identified 3D sub-compartments, characterized by enriched Hi-C contacts within themselves compared to contacts with other compartments. Our results suggest that the A compartment, associated with ongoing transcription, consists of two distinct sub-compartments called A1 and A2; and that the B compartment, associated with lack of transcription, consists of three sub-compartments called B1, B2 and B3. Genes in the A1 and A2 compartments are typically expressed at the same level, but chromatin marks associated with transcription, such as H3K4me2 or H3K27ac, are typically more abundant in A1 than in A2. The B1, B2 and B3 sub-compartments correspond to Polycomb, HP1 and lamina-associated chromatin, which were previously identified types of silent chromatin. Overall, these results suggest that spatial neighborhoods of the Jurkat nucleus correspond to homogeneous chromatin types, and that transcriptionally active regions are in fact two distinct types.

overall_design: Two Hi-C libraries were prepared from independent Jurkat T cell cultures.

first: Heng-Chang

last: Chen

first: Eduard

last: Zorita

first: Ralph

last: Stadhouders