title: Epigenetic programming of postnatal spermatogonia

status: Public on Apr 30 2019

city: Ste Anne-de-Bellevue

first: Romain

last: Lambrot

state: QC

address: 21111 Lakeshore road

department: Animal Science

institute: McGill University

summary: The environmental exposures and lifestyle of parents can alter the development of offspring. How this environmental information is coded into heritable messages to be transmitted by gametes remains unknown, but epigenetic mechanisms have been implicated. We recently determined that disruption of histone H3 di-methylation at lysine 4 (H3K4me2) in sperm has transgenerational consequences in the development of offspring. However, little is known about when in spermatogenesis histone methylation is established and whether epimutations induced in developing sperm are permanent. We hypothesize that epigenetic modifications to histones established in spermatogonia persist through spermatogenesis and can be transmitted to offspring via the sperm. Our objective was to determine what genomic regions bearing histone H3K4me2 in spermatogonia are also present in sperm. Methods: Using transgenic mice expressing Oct4-GFP, we isolated an enriched spermatogonia population and performed ChIP-seq for H3K4me2. Results: Our analysis revealed that H3K4me2 is located throughout the genome in spermatogonia and particularly at the transcription start site region (TSS) of more than 16,000 genes. Remarkably 44% of H3K4me2 peaks present in spermatogonia are conserved in sperm. The greatest overlap between spermatogonia and sperm occurred at the TSS with 83% similarity. Finally, we assessed the expression level of genes enriched in H3K4me2 in spermatogonia and sperm. We observed that genes with the highest enrichment in H3K4me2 in sperm are expressed at higher levels in spermatogenesis and during development. Conclusion: These findings suggest that if epimutations are induced in spermatogonia they may persist in sperm and influence the health and development of offspring.

overall_design: Examination of H3K4me2 in postnatal spermatogonia from GOF/deltaPE-Oct4/GFP mice isolated by FACS.

first: Sarah

last: Kimmins


title: Co-transcriptional loading of RNA export factors shapes the human transcriptome

status: Public on May 01 2019

city: Sheffield

first: Ian

last: Sudbery

address: Firth Court, Western Bank

department: Molecular Biology and Biotechnology

country: United Kingdom

institute: University of Sheffield

type: Genome binding/occupancy profiling by high throughput sequencing

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type (WT) and dek41 Transcriptomes

city: Shanghai

first: Chenguang

last: Zhu

address: Nanchen Road 333

country: China

institute: Shanghai University

summary: Analysis of  gene expression level. The hypothesis tested in the present study was that dek41 mutation affects cis-splicing of nad4 intron 3 in mitochondria in mutant kernels. Results provide important information of the gene expression level of  mitochondrial membrane and metabolic process pathway associated genes.

overall_design: Endosperm mRNA profiles of 12 DAP wild type and dek41 mutant were generated by deep sequencing, using Illumina Hiseq 4000 (Zea mays).

first: Xuzhen

last: Feng

first: Guangpu

last: Jin

first: Rentao

last: Song


title: Bronchioalveolar stem cells are a main source for regeneration of distal lung epithelia

status: Public on Apr 24 2019

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

country: Germany

institute: MPI for heart and lung research

summary: Bronchioalveolar stem cells (BASCs) are a potential source for lung regeneration, but direct in vivo evidence is critically missing since specific genetic labeling of BASCs has not been possible. We developed a novel cell tracing approach based on intein-mediated assembly of newly engineered split-effectors, allowing selective targeting of dual-marker expressing BASCs. We found that BASCs generate the majority of distal lung airway cells after bronchioalveolar damage but only moderately contribute to cellular turnover under homeostatic conditions. Importantly, DTA-mediated ablation of BASCs compromised proper regeneration of distal airways. The study defines BASCs as crucial components of the lung repair machinery and provides a paradigmatic example for the detection and manipulation of stem cells that cannot be recognized by a single marker alone.

overall_design: Bulk RNAseq of FACS-isolated lung epithelial cell types (BASC/AT2/Club) in duplicates.

first: Thomas

last: Braun

first: Isabelle

last: Salwig


title: Analysis of the transcriptome of Bacteroides thetaiotaomicron during growth on complex N-glycan as the sole carbon source

status: Public on Apr 26 2019

city: Newcastle

first: John

last: Casement

address: Framlington Place

department: Bioinformatics Support Unit

institute: Newcastle University

summary: The goal of this project was to sequence the transcriptome of wild type Bacteroides thetaiotaomicron VPI-5482 grown in minimal media with either glucose or bovine alpha 1 acid glycoprotein (AAGP) as the sole carbon source. Using these data we could then compare relative gene expression levels under each condition and identify genes specifically upregulated during growth on AAGP. Analysis of the spent media indicated that only the N-glycan component of the AAGP had been used by the cells to support growth.

overall_design: Three replicates of each growth condition were analysed (Glucose and AAGP)

first: David

middle: N

last: Bolam

first: Justina

last: Briliute


title: Molecular signature of asthma-enhanced sensitivity to aerosols of pristine and carboxylated CuO nanoparticles, identified in 3D cell models.

city: Helsinki

first: Harri

last: Alenius

address: Haartmaninkatu 3

department: Human Microbiome Program

country: Finland

institute: University of Helsinki

summary: Via extensive comparative analysis of 3D human bronchial epithelial model (MucilAirTM) exposed to air or CuO-based aerosols, we show that existence of asthma enhances sensitivity of the airways to nanoparticles, possibly as a combined result of a hyperactive airway and inefficient mucociliary clearance mechanisms in asthmatics.

overall_design: The experimental assessment involved exposures to clean, humidified air, low, middle and high concentrations of CuO and CuOCOOH. Cell material for the exposures originated from five asthmatic and three healthy donors. The exposures were split up as one-hour sessions, each consisting of a test block containing three inserts. Parallel exposure sessions were carried out to assess, cytotoxicity, cytokine release and RNA isolation for microarray-based transcriptomics. Each Vitrocell consists of three slots (inserts), thus every time a test block is exposed, the cell material within its three inserts originates from a single donor only. There were in total three healthy and five asthmatic donors, and the cell material of each donor was tested once in each session, once in each test block and once at each CuO/CuOCOOH concentration.

first: Ingeborg

last: Kooter

first: Ilves

last: Marit

first: Mariska

last: Gröllers-Mulderij

first: Evert

last: Duistermaat

first: Peter

middle: C

last: Tromp

first: Frieke

last: Kuper

first: Pia

last: Kinaret

first: Kai

last: Savolainen

first: Dario

last: Greco

first: Piia

last: Karisola

first: Joseph

last: Ndika


title: Next Generation Sequencing of langerhans islets of miR-17-92/106b KO vs control

city: Rehovot

first: Eran

last: Hornstein

address: 234 Herzl St.

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

summary: NGS was used in order to discover novel downstream targets of the miR-17-92/106b clusters.

overall_design: Comperasion of gene expression from miR-17-92/106b KO and control

first: Amitai

middle: D

last: Mandelbaum


title: THZ1-induced transcriptional changes in SMO inhibitor responsive and resistant mouse hedgehog-driven medulloblastoma cells

first: Yujie

last: Tang

address: 280 South Chong-qing Rd

institute: Shanghai Jiao Tong University School of Medicine

summary:
Purpose: To assess THZ1-induced global changes of transcriptome of Hh-driven cancer
Methods: SMB56 or SMB56-shSufu cells were mouse hedgehog-driven medulloblastoma cell lines that are either responsive or resistant to SMO inhibitor (GDC-0449). They were treated with 0.1 uM THZ1 or DMSO for 8 hours. 1 uM GDC-0449 treated SMB56 cells were included as control. Gene expression profiles were generated by RNAseq, in duplicate, using Hiseq3000. The RNAseq reads were mapped to the hg19 reference genome using STAR (v2.5.3a). Expression levels for each sample were quantified to FPKM using Cufflinks (v2.2.1). Differential expression analysis was carried out using R package DESeq2 (v1.20.0)
Results: Compared to GDC-0449 treatment in SMB56 cells, THZ1 induced a robust global transcriptional downregulation in both SMB56 and SMB56-shSufu cells. When we compared the top 2000 significantly downregulated genes between THZ1-treated SMB56 and SMB56-shSufu cells, we found they had ~70% in common. GSEA reveals Hh-target genes are enriched in DMSO treated cells versus THZ1-treated ones.
Conclusions: CDK7 inhibition induced a robust and similar transcriptional downregulation in both SMB56 and SMB56-shSufu cells, with preferential targeting of Hh pathway transcriptional output.

overall_design: RNAseq of SMO inhibitor responsive or resistant hedgehog-driven mouse medulloblastoma cells treated with THZ1, GDC-0449 or DMSO.

first: Liye

last: Zhang


title: iCLIP of components of the TREX complex

first: Ian

last: Sudbery

summary: During gene expression, RNA export factors are mainly known for driving nucleocytoplasmic transport. While early studies suggested that the Exon Junction Complex (EJC) may provide a binding platform for them, subsequent work proposed that they are only recruited by the Cap-Binding Complex (CBC) to the 5’ end of RNAs, as part of the TREX complex. Using iCLIP, we show that the export receptor Nxf1 and two TREX subunits, Alyref and Chtop, are actually recruited to the whole mRNA co-transcriptionally via splicing but before 3’-end processing. Consequently, Alyref can alter splicing decisions and Chtop regulates alternative polyadenylation. Surprisingly, we observe that eIF4A3 stimulates Alyref deposition on single exon or spliced RNAs close to EJC sites. Additional experiments suggest that Alyref is recruited to the 5’-end of RNAs by CBC before binding RNAs near EJCs. Our study reveals mechanical insights into the co-transcriptional recruitment of mRNA export factors and how this shapes the human transcriptome.

overall_design: Individual Crosslinkind and ImmunoPrecipitation (iCLIP) was performed in triplicate on HEK293T FlipIn cell lines expressing FLAG tagged copies of one of Alyref, Chtop or Nxf1 or were performed using a cell line expressing the FlipIn FLAG construct only as a control.

first: Nicolas

last: Viphakone

first: Catherine

last: Heath

first: David

last: Sims

first: Stuart

last: Wilson


city: Seropédica

first: Leonardo

middle: Araujo

last: Terra

state: RJ

address: Rodovia BR-465

country: Brazil

institute: Embrapa Agrobiologia

summary:
Background and aims The endophytic diazotrophic strain CBAmC of Nitrospirillum amazonense has been reported as a plant growth promoter of sugarcane variety
RB867515 when grown under field conditions. The present work aimed to assess the influence of apoplast fluid from RB867515 on the transcriptomic and proteomic profiles of CBAmC cultured in vitro.
Methods RNA-Seq in Ion Proton™ and ESI-LC-MS/MS peptide analysis were used to evaluate the transcriptomic and proteomic profiles, respectively, of CBAmC exposed for 2 h to the sugarcane apoplast fluid.
Results The bacterial transcriptomic and proteomic profiles were well correlated. The overall response of CBAmC to the apoplast fluid included overexpression of defense systems against reactive oxygen species (ROS) and osmotic stress, RND efflux pumps for toxic compounds, Sec and Tat secretory systems, and assimilative metabolism of iron. In contrast, active transporters of organic compounds, chemotaxis system and flagellum structure were underexpressed.
Conclusions The bacterial metabolic pathways / functions activated in response to the sugarcane apoplast fluid are most likely related to its adaptation to the peculiar characteristics of the fluid. The activation of some of those functions could be determinant for its adaptation to the sugarcane apoplastic niche, and perhaps be involved in the previously observed effect of promoting plant growth.
SUBMITTER_CITATION: Terra, L.A., de Soares, C.P., Meneses, C.H.S.G. et al. Plant Soil (2019). Transcriptome and proteome profiles of the diazotroph Nitrospirillum amazonense strain CBAmC in response to the sugarcane apoplast fluid.

overall_design: Profiles of mRNA were obtained after two hours of incubation in the presence and absence of sugarcane apoplast fluid. Experiments performed in triplicate.

middle: A

first: Cleiton

last: de P Soares

first: Carlos

middle: H

last: Meneses

first: Michelle

middle: Z

last: Tadra Sfeir

first: Emanuel

middle: M

last: de Souza

first: Vanildo

last: Silveira

first: Márcia

middle: S

last: Vidal

first: José

middle: I

last: Baldani

first: Stefan

last: Schwab


title: In situ vaccination with defined factors overcomes T cell exhaustion in distant tumors [expression data]

status: Public on Apr 19 2019

city: New York

first: Nathan

last: Suek

state: NY

country: USA

institute: Memorial Sloan Kettering Cancer Center

summary:
Mice were given B16F10 (melanoma) tumors on the left and right flank. Anti-CD40 agonist and MPL were given directly into the right tumor along with systemic anti-PD1 administration. Treatment resulted in potent regression of the treated (i.e. right) tumor as well as the distant (i.e. left) tumor.
We used microarray analysis to examine global gene expression changes in response to therapy.

overall_design: Mice bearing tumors were treated with: (1) isotype control (2) anti-PD1 alone and (5) anti-CD40, MPL, and anti-PD1 triple combination (called CMP). From each mouse, the distant tumors were harvested at 1 week after start of treatment.

first: Danny

last: Khalil

first: Jedd

last: Wolchok

first: Taha

last: Merghoub


title: Small molecule targets TMED9, promotes lysosomal degradation to reverse proteinopathy

status: Public on Apr 18 2019

city: Cambridge

first: Moran

last: Dvela Levitt

state: MA

address: 415 Main Street

institute: Broad Institute

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Transcriptomic of MKD (MUC1 kidney disease) patient compares to normal derived kidney epithelial cells

summary: bulk RNAseq of MUC1 kidney disease patient derived kidney epithelial cells compare to normal kidney cells. The goal of this study was to elucidate the biological mechanism underlying MUC1 kidney disease using MUC1 expressing cells derived from either a patient or a healthy individual kidney

overall_design: Bulk RNAseq of immortalized patient compare to normal cell line

last: Levitt

first: Eva

last: Kohnert


title: microRNA expression profile in retina and choroid in oxygen-induced retinopathy model

city: montreal

first: michel

last: desjarlais

state: quebec

address: 5415 Blvd L’Assomption

department: Department of Ophthalmology,

country: Canada

institute: Maisonneuve-Rosemont Hospital Research Center, University of Montréal, Montréal, Québec, Canada.

type: Non-coding RNA profiling by high throughput sequencing

summary: Using Next Generation Sequencing (NGS) we profiled miRNA expression in the retina and choroid during degenerative and NV phases of oxygen-induced retinopathy (OIR).

overall_design: Examination of 12 different samples (6 choroid and 6 retina) to compare the expression of miRNA in the normoxic vs hyperoxic (OIR) condition. Sample are a pool of 5 retina or choroid.

first: Michel

last: Desjarlais

first: Sylvain

last: Chemtob


title: RNAseq of HEK293 cells after Chtop knockdown

first: Ian

last: Sudbery

overall_design: mRNA-seq in triplicate after treatment with either siControl or siChtop

first: Nicolas

last: Viphakone

first: Catherine

last: Heath

first: David

last: Sims

first: Stuart

last: Wilson


title: Quizalofop-p-ethyl induces adipogenesis in 3T3-L1 cells

city: London

first: Robin

last: Mesnage

address: Guy's Hospital, 8th Floor, Tower Wing

institute: Kings College London

summary: We provide here the alterations in gene expression profiles of 3T3-L1 cells, a validated model for adipogenesis, exposed to quizalofop-p-ethyl for 6h, 24h and 12 days.

overall_design: Exposure to endocrine disrupting chemicals is a risk factor for obesity. The most commonly used pesticide active ingredients have never been tested in an adipogenesis assay. We tested for the first time the lipid accumulation induced by glyphosate, 2,4-dichlorophenoxyacetic acid, dicamba, mesotrione, isoxaflutole and quizalofop-p-ethyl (QpE) in 3T3-L1 adipocytes. Only QpE caused triglyceride accumulation from a concentration of 1 µM. We thus conducted an in-depth investigation of molecular mechanisms responsible for the adipogenic effects of quizalopfop-p-ethyl by an RNA-seq analysis.

first: Charles

last: Mein


title: Active and passive mechanisms of 5mC and 5hmC removal in human T lymphocytes

city: Bellinzona

first: Cristina

last: Leoni

state: Ticino

address: Via Vincenzo Vela 6

department: Molecular Immunology

country: Switzerland

institute: Institute For Research in Biomedicine

type: Methylation profiling by high throughput sequencing

summary: In mammals, the 5’-methylcytosine (5mC) modification in the genomic DNA contributes to the dynamic control of gene expression. 5mC erasure is required for the activation of developmental programs and occurs either by passive dilution through DNA replication, or by enzymatic oxidation of the methyl mark to 5-hydroxymethylcytosine (5hmC), followed by passive dilution or further oxidation and active removal. For most biological systems, the relative contribution of active and passive processes of 5mC and 5hmC erasure to the regulation of cell physiology remains poorly defined. Using primary human T lymphocytes as a model of activation-driven cell proliferation and differentiation, we found that DNA demethylation-dependent processes were central in the efficient acquisition of cytokine gene expression by T lymphocytes. As for the underlying mechanism, T cells appeared to rely primarily on the conversion of 5mC into 5hmC, followed by passive, replication-dependent dilution of the 5hmC mark, although active 5hmC removal also occurred during the early stages of activation of naïve, but not memory T lymphocytes. Our data are consistent with a model in which 5hmC is required in quiescent naive T lymphocytes for the establishment and maintenance of regulatory regions poised for rapid response to physiological stimuli. However, cell cycle progression is the primary mechanism to relieve epigenetic constraints in memory T cells.

overall_design: Primary naïve and memory T lymphocytes were obtained from two independent donors and were either left resting or were stimulated for 3 days with anti-CD3 and anti-CD28 antibodies.

first: Lucia

last: Vincenzetti

first: Michele

last: Chirichella

first: Silvia

last: Monticelli


title: EML histone readers prevent seed development without fertilization

city: Columbus

first: Jelena

last: Brkljacic

address: 1060 Carmack Rd

institute: The Ohio State University

summary: EML1 and EML3 were previously shown to be histone readers involved in plant-pathogen interactions. To learn more about the developmental function of EML1 and EML3, we generated eml1 eml3 double mutant and showed that it had specific seed developmental phenotypes, including a capability to develop seed without fertilization. Next, we analyzed the mRNA expression of genes in the eml1 eml3 double mutant and compared it to its wild type. Differentially expressed (DE) genes in the mutant were identified and compared with DE of the mutants known to be involved in regulating seed development and in fertilization-independent endosperm development. Our results suggest that some targets are shared between EML histone readers and known regulators of seed development, such as MEA. Auxin response seems to be affected in both types of mutants. However, unlike MEA, EML proteins regulate auxin responsive genes not only in the endosperm, but also in the embryo. This capability makes EML proteins very good candidates for engineering apomictic seeds.

overall_design: 3 eml1,eml3 double mutant samples and 3 WT samples

first: Milica

last: Milutinović

first: Benson

middle: E

last: Lindsey III

first: Asela

last: Wijeratne

first: J

last: Hernandez

first: Nikolas

last: Grotewold

first: Virginia

last: Fernández

first: Erich

last: Brkljačić


title: The nascent RNA binding complex SFiNX licenses piRNA-guided heterochromatin formation

status: Public on Apr 17 2019

city: Vienna

first: Jakob

last: Schnabl

state: Vienna

address: Dr. Bohr-Gasse 3

country: Austria

institute: IMBA - Institute of Molecular Biotechnology

summary: The PIWI-interacting RNA (piRNA) pathway protects animal genome integrity in part through establishing repressive heterochromatin at transposon loci. Silencing requires piRNA- guided targeting of nuclear PIWI proteins to nascent transposon transcripts, yet the subsequent molecular events are not understood. Here, we identify SFiNX (Silencing Factor interacting Nuclear eXport variant), an interdependent protein complex required for Piwi-mediated co-transcriptional silencing in Drosophila. SFiNX consists of Nxf2-Nxt1, a gonad- specific variant of the heterodimeric mRNA export receptor Nxf1-Nxt1, and the Piwi-associated protein Panoramix. SFiNX mutant flies are sterile and exhibit transposon de-repression because piRNA-loaded Piwi is unable to establish heterochromatin. Within SFiNX, Panoramix recruits the cellular heterochromatin machinery, while Nxf2 binds the nascent target RNA and licenses co-transcriptional silencing. Our results reveal an unexpected, RNA-export independent role for Nxf2 in nuclear small RNA biology and suggest that NXF-variants, which have largely unknown function in animals, are functionally linked to the genome-transposon conflict.

overall_design: RNA-Seq analysis of total RNAs (with rRNA depletion or polyA selection) from ovaries and ovarian stem cells (OSCs) of Nxf2, Panx, Piwi mutants.

first: Julia

last: Batki

first: Juncheng

last: Wang

first: Dominik

last: Handler

first: Veselin

last: Andreev

first: Christian

last: Stieger

first: Maria

last: Novatchkova

first: Lisa

last: Lampersberger

first: Kotryna

last: Kauneckaite

first: Wei

last: Xie

first: Karl

last: Mechtler

first: Dinshaw

middle: J

last: Patel

first: Julius

last: Brennecke


title: Evolution of gene expression in one population of the Long-Term Evolution Experiment with Escherichia coli

status: Public on Apr 16 2019

city: La Tronche

first: Thomas

last: Hindré

address: Campus de la Merci

country: France

institute: Université Grenoble Alpes-CNRS

summary: We used microarrays to study the changes in whole-genome expression profiles accompanying the evolution of one bacterial population propagated in glucose minimal medium for 20,000 generations.

overall_design: We sampled two clones from the Ara-1 population of the E. coli Long-Term Evolution Experiment at generations 2,000 (REL1164A) and 20,000 (REL8593A). These 2 clones as well as the ancestral strain (REL606) were grown until mid-exponential phase in the same glucose-limited minimal medium and conditions used in the evolution experiment. Total RNAs were extracted from cell pellets and whole genome expression profiles were obtained by using Affymetrix arrays, with 6 biological replicates for each strain.

first: Dominique

last: Schneider


title: Stabilizing Heterochromatin by DGCR8 Alleviates Senescence and Osteoarthritis (ChIP-seq)

city: Beijing

first: Zunpeng

last: Liu

address: Beichen West Road

department: Institute of Zoology, Chinese Academy of Sciences

institute: State Key Laboratory of Stem Cell and Reproductive Biology

summary: DiGeorge syndrome critical region 8 (DGCR8) is a critical component of the canonical microprocessor complex for microRNA biogenesis. However, the non-canonical functions of DGCR8 have not been studied. Here, we demonstrate that DGCR8 plays an important role in maintaining heterochromatin organization and preventing aging. An N-terminal-truncated version of DGCR8 (DR8dex2) accelerated senescence in human mesenchymal stem cells (hMSCs) independent of its miRNA-processing activity, which is mediated by its C-terminal domain. Further studies revealed that DGCR8 maintained heterochromatin organization by interacting with the nuclear envelope protein Lamin B1, and heterochromatin-associated proteins, KAP1 and HP1g Overexpression of any of these proteins, including DGCR8, reversed premature senescent phenotypes in DR8dex2 hMSCs. Finally, DGCR8 was downregulated in pathological and naturally aged hMSCs, whereas DGCR8 overexpression alleviated hMSC aging and osteoarthritis in mice. Taken together, these analyses uncovered a novel, miRNA-independent role for DGCR8 in maintaining heterochromatin organization and preventing senescence. DGCR8 may therefore represent a new therapeutic target for alleviating human aging-related disorders.

overall_design: H3K9me3 ChIP-seq profiles of DR8dex2 hMSCs transduced with Luc, DR8-WT, or DR8-mtDRBD

first: Guanghui


title: Integrated Metabolomic and Transcriptomic Profiling Reveals Novel Activation Induced Metabolic networks in Human T cells

city: New Delhi

first: Shashank

last: Jatav

state: Delhi

address: 212, C/o Brijendar Pawar, Near Dalip Singh Chowk, Shahpur Jat

country: India

institute: Elucidata

summary: The targeting of metabolic pathways is emerging as an exciting new approach for modulating immune cell function and polarization states. In this study, carbon tracing and systems biology approaches integrating metabolomic and transcriptomic profiling data were used to identify adaptations in human T cell metabolism important for fueling pro-inflammatory T cell function. Results of this study demonstrate that T cell receptor (TCR) stimulation leads to a significant increase in glucose and amino acid metabolism that trigger downstream biosynthetic processes. Specifically, increased expression of several enzymes such as CTPS1, IL4I1, and ASL results in the reprogramming of amino acid metabolism. Additionally, the strength of TCR signaling resulted in different metabolic enzymes utilized by T cells to facilitate similar biochemical endpoints. Furthermore, this study shows that cyclosporine represses the pathways involved in amino acid and glucose metabolism, providing novel insights on the immunosuppressive mechanisms of this drug. To explore the implications of the findings of this study in clinical settings, conventional immunosuppressants were tested in combination with drugs that target metabolic pathways. Results showed that such combinations increased efficacy of conventional immunosuppressants. Overall, the results of this study provide a comprehensive resource for identifying metabolic targets for novel combinatorial regimens in the treatment of intractable immune diseases.

overall_design: Primary human CD4+ T cell isolation, culture, and activation  Blood was collected from healthy human patients in accordance with IRB standards. CD4+ T cells were purified using RosetteSep isolation kit (StemCell) as per manufacturer’s protocol. Cells were cultured in RPMI supplemented with 10% heat inactivated FBS, HEPES, penicillin/streptomycin, non-essential amino acids, glutamax, and sodium pyruvate. Cells were initially activated for 72 hours on plate-bound CD3 (200 ng/mL; OKT3; BioXCell) and CD28 (200 ng/mL; 9.3; BioXCell) on goat-anti-mouse (10 µg/mL; Jackson Immuno Research Labs) pre-coated high- binding plates (Corning Costar). After 72 hours, cells were removed from plate activation and were expanded until Day 8-12, maintained at ~1X106 cells/mL by supplementing with fresh media as required. Cells were then washed with PBS and either rested or re-activated at 0.5-1x106 cells/mL in fresh media with plate-bound CD3/CD28 (100 ng/mL each) or with soluble CD3/CD28 Immunocult (1:100 dilution; StemCell). Cells were treated with Rapamycin (100nM) and/or Cyclosporin A (2µM), or equivalent volume of DMSO during re-activation.    Lentiviral transduction and shRNA knockdown  Lenti-X 293T (Clontech) cells were plated on poly-D-lysine (0.1 mg/mL; Sigma) coated plates at a density of 1.67x105 cells/mL. After 72 hours, cells were transfected with psPAX2 (1.5µg), pCMV-VSV-G (0.5µg), and pZIP-mCMV-ZsGreen-shRNA NT Control or mTOR plasmids (2 µg; Transomic) using the TransIT-LT1 transfection reagent (Mirus) as per manufacturer’s protocol. Virus was collected after an additional 72 hours and CD4+ T cells were spin infected after 48 hours of activation using undiluted virus (~1x108 IFU yielding a MOI of ~70) supplemented with polybrene (10 µg/mL; AmericanBio Inc). After an additional 24 hours of activation, the transduced CD4+ T cells were removed from activation and expanded in the presence of puromycin (1 µg/mL) until Day 8-12, maintained at ~1x106 cells/mL by supplementing with fresh media as required. Cells were then washed and activated as described above.    CRISPR/Cas-9 knockout  Cells were activated on plate-bound CD3/CD28 as described above. Cells were removed from plate activation after 72 hours and were rested overnight at ~1X106 cells/mL. The following day the conditioned media was saved before washing the cells and resuspending in buffer T (Neon Transfection System; ThermoFisher) at 25x106 cells/mL. Guides targeting human mTOR and ZAP70 were designed using the Broad Institute’s online sgRNA designer (https://portals.broadinstitute.org/gpp/public/analysis-tools/sgrna-design)22 (see Sup Table 1). 5 guides per gene were synthesized by IDT and duplexed in a 1:1 ratio with Alt-R-CRISPR-Cas9-tracrRNA (IDT) as per manufacturer’s protocol. Duplexed guides were incubated with Alt-R S.p. Cas9 Nuclease (IDT) before mixing with 2.5x106 cells and electroporating using the Neon Transfection System (ThermoFisher; 100uL tip at 1550V, 10 milliseconds, 3 pulses). Cells were allowed to recover for 1 hour in fresh media before adding back conditioned media in a 1:1 ratio conditioned to fresh media. Cells were expanded in the presence of IL-2 (2 ng/mL; R&D) until Day 8-12, maintained at ~1x106 cells/mL by supplementing with fresh media as required. Cells were then washed and activated as described above.

first: Samantha

last: Hiemer


title: Gene expression analysis of flower buds from BnA9::BnMAGL8.1 and WT

status: Public on Apr 22 2019

city: Wuhan

first: Jie

last: Gao

state: Hubei

address: No.1, Shizishan Street

institute: Huazhong Agricultural University

summary: MAGLs participate lipid mobilization and endocannabinoid signalling in mammal. However, their potential biological function in plants remains elusive. In a survey of BnMAGL molecular function, BnA9::BnMAGL8.1 transgenic plants were outstanding with their male sterile phenotype. To discover the mechanism undering the phenotype, we conducted RNAseq on flower buds in stage 6-9 from BnA9::BnMAGL8.1 transgenic plants with wild type (Col ecotype).

overall_design: 3 biological replicates for BnA9::BnMAGL8.1 transgenic buds and 3 biological replicates for WT buds


title: Exonuclease Requirements for Mammalian Ribosomal RNA Biogenesis and Surveillance

status: Public on Apr 13 2019

city: Boston

first: Aref

last: Ebrahimi

address: 1 Joslin Pl

department: Islet Cell and Regenerative Biology

institute: Harvard Medical School - Joslin

summary: Ribosomal RNAs (rRNAs) biogenesis are multistep processes requiring the activity of several nuclear and cytoplasmic exonucleases. The exact processing steps for mammalian 5.8S rRNA remains obscure. Here, using loss-of-function approaches in mouse embryonic stem cells and deep sequencing of rRNA intermediates, we investigate at nucleotide resolution the requirements of exonucleases known to be involved in 5.8S maturation, and explore the role of the Perlman syndrome-associated 3’-5’ exonuclease Dis3l2 in rRNA processing. We expand the repertoire of Dis3l2 targets to three 5.8S, 5S, and 28S rRNAs. We uncover a novel cytoplasmic intermediate that we name ‘7SB’ rRNA that is generated through sequential processing by distinct exosome complexes. 7SB rRNA can be oligouridylated by TUT4/7 and subsequently processed by Dis3l2 and Eri1. Moreover, exosome depletion triggers Dis3l2-mediated decay (DMD) as a surveillance pathway for rRNAs. Our data identify previously unknown 5.8S rRNA processing steps and provide nucleotide level insight into the exonuclease requirements for mammalian rRNA processing.

overall_design: The 3'-end of indicated ribosomal RNAs (rRNAs) were characterized by MiSeq upon genetic perturbation of Dis3l2, Exosc3, Exosc10, or Eri1 in mouse ESCs. Occasionally, to enrich for Dis3l2 targets, FLAG-tagged mutant Dis3l2 protein was ectopically expressed in Dis3l2 knockout ESCs and Dis3l2-bound rRNAs were co-immunoprecipitated using anti-FLAG antibody, cloned and sequenced. rRNA-specific sequences and adapters were used to extract desired reads from raw data.

first: Mehdi

last: Pirouz

middle: G


title: A subset of type I conventional dendritic cells control cutaneous bacterial infections through VEGFa-mediated recruitment of neutrophils [bulk RNA-seq]

city: Singapore

first: Florent

last: Ginhoux

address: 8A Biomedical Grove, Immunos Building, Level 3

country: Singapore

institute: Singapore Immunology Network (SIgN), A*STAR

summary: Skin conventional dendritic cells (cDC) exist as two distinct subsets, cDC1 and cDC2, which maintain the balance of immunity to pathogens and tolerance to self and microbiota. Here we examined the roles of dermal cDC1 and cDC2 during bacterial infection, notably Propionibacterium acnes (P. acnes). cDC1, but not cDC2, regulated the magnitude of the immune response to P. acnes in the murine dermis by controlling neutrophil recruitment to the inflamed site and survival and function therein. Single-cell mRNA sequencing revealed that this regulation relied on secretion of the cytokine VEGFα by a minor subset of activated EpCAM+CD59+Ly6D+ cDC1. Neutrophil recruitment by dermal cDC1 was also observed during S. aureus, BCG or E. coli infection, as well as in a model of bacterial insult in human skin. Thus, skin cDC1 are essential regulators of the innate response in cutaneous immunity, with roles beyond classical antigen presentation.

overall_design: Examined the effect of cDC1 (CD103+DC) depletion on neutrophils infiltrating the skin during P. acnes infection.

first: Baptiste

last: Janela

first: Amit

first: Mai

last: Lau

first: Chi

last: Goh

first: Rasha

last: Msallam

first: Wan

middle: T

last: Kong

first: Michael

last: Fehlings

first: Sandra

last: Hubert

first: Josephine

last: Lum

first: Yannick

last: Simoni

first: Benoit

last: Malleret

first: Francesca

last: Zolezzi

first: Jinmiao

last: Chen

last: Poidinger

first: Ansuman

last: Satpathy

first: Carlos

last: Briseno

first: Christian

last: Wohn

first: Bernard

last: Malissen

first: Kenneth

last: Murphy

first: Alexander

last: Maini

first: Leen

last: Vanhoutte

first: Martin

last: Guilliams

first: Emmanuel

last: Vial

first: Laurent

last: Hennequin

first: Evan

last: Newell

first: Lai

last: Ng

first: Philippe

last: Musette

first: Simon

last: Yona

first: Feriel

last: Hacini-Rachinel


title: Effect of ER stress on MUC1 kidney disease patient derived cells and and treatment by BRD4780

first: Moran

last: Dvela Levitt

summary: immortalized patient derived kidney epithelial cell were compared to cells exposed to ER stress (thapsigargin) in the absence or present of BRD4780 treatment

overall_design: Patient derived kidney cells were exposed to thapsigargin in the presence and absence of BRD4780 treatment and their transcriptomic was compared

last: Levitt

first: Eva

last: Kohnert


title: RNA sequencing in kidneys of MUC1 Kidney Disease mouse model with and without treatment

summary: MUC1 kidney disease mouse model generated by knock-in of the human mutated MUC1-fs gene. The mice were treated for 7 days, daily with either vehicle control or BRD4780, a compound showed to be beneficial to disease cells in-vitro. The kidneys were then removed and the bulk RNA was sequenced. The goal of this study was to undersand the effect of the compound on the diseased kidneys and to gain insights to its mechanism of action.

overall_design: MUC1 kidney disease mouse models in quatriplate were treated with either vehicle or BRD4780 daily for 7 days, followed by kidney removal, RNA isolation and bulk RNA sequencing


title: Elevated Endothelial Sox2 Causes Lumen Disruption and Cerebral AVMs

status: Public on Apr 12 2019

city: Los Angeles

first: Xiuju

last: Wu

state: CA

address: 650 Charles Young Dr East, CHS A2-237

institute: University of California, Los Angeles

summary: Lumen integrity in vascularization requires fully differentiated endothelial cells (ECs). Here, we report that endothelial-mesenchymal transitions (EndMTs) emerged in ECs of cerebral arteriovenous malformation (AVMs) and caused disruption of the lumen or lumen disorder. We show that excessive Sry-box 2 (Sox2) signaling was responsible for the EndMTs in cerebral AVMs. EC-specific suppression of Sox2 normalized endothelial differentiation and lumen formation, and improved the cerebral AVMs. Epigenetic studies showed that induction of Sox2 altered the cerebral-endothelial transcriptional landscape, and identified jumonji domain-containing protein 5 (JMJD5) as a direct target of Sox2. Sox2 interacted with JMJD5 to induce EndMTs in cerebral ECs. Furthermore, we utilized a high throughput system to identify the beta-adrenergic antagonist pronethalol as an inhibitor of Sox2 expression. Treatment with pronethalol stabilized endothelial differentiation and lumen formation, which limited the cerebral AVMs.

overall_design: Discovery of histone modifications and Sox2 binding in cerebral endothelial cells (ECs) from Mgp knockout and wild type mice.

first: Jiayi

last: Yao


title: Alterations of miRNAs and mRNAs in NIH/3T3 cells overexpressing BPV-13 E6

status: Public on Apr 11 2019

city: Haikou

first: Feng

last: Pang

address: Renmin Road 58

institute: Hainan University

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

overall_design: Refer to individual Series


title: Alterations of miRNAs in NIH/3T3 cells overexpressing BPV-13 E6

summary: To find out differentially expressed miRNAs in NIH/3T3 cells overexpressing BPV-13 E6

overall_design: Three NIH/3T3 samples expressing BPV-13 E6 and three negative controls

first: Fengyang

last: Wang


title: RNA-seq using RNA from KDM4 WT and Knockout haematopoietic stem cells

status: Public on Apr 02 2019

city: Copenhagen

first: Karl

last: Agger

address: Ole Maaloes Vej 5

department: BRIC

country: Denmark

institute: University of Copenhagen

summary: The KDM4/JMJD2 are H3K9- and H3K36- specific demethylases, which are considered promising therapeutic targets for the treatment of acute myeloid leukemia (AML) harboring MLL-translocations. Here, we investigate the long-term effects of depleting KDM4 activity on normal hematopoiesis to probe potential side effects of continuous inhibition of these enzymes. Utilizing conditional Kdm4a/Kdm4b/Kdm4c triple-knockout mice we show that KDM4 activity is required for hematopoietic stem cell (HSC) maintenance in vivo. The knockout of the KDM4 demethylases leads to accumulation of H3K9me3 on transcription start sites and the corresponding downregulation of expression of several genes in hematopoietic stem cells.  We show that two of these genes, Taf1b and Nom1, are essential for the maintenance of hematopoietic cells. Taken together, our results show that the KDM4 demethylases are required for the expression of genes essential for the long-term maintenance of normal hematopoiesis.

overall_design: Haematopoietic stem cells were FACS sorted from WT or KDM4 knockout mice 2 weeks after induction of knockout. Total RNA was prepared and amplified using the Ovation

first: Kristian

last: Helin


title: Expression data from glioma patient

status: Public on Mar 31 2019

city: Shanghai

first: Haizhong

last: Feng

state: Shanghai

address: Pujian Road 160

department: Ren Ji Hospital

institute: Shanghai Jiao Tong University

summary:
Multicentric lesions constitute an increasingly diagnosed subgroup of glioblastoma (GBM) and are more malignant than that of solitary GBM. Understanding their biology is necessary and urgent for glioma patient treatment. However, molecular basis of these lesions are poorly characterized.
We used microarrays to determine the gene expression profiling of three lesions from one multicentric GBM.

overall_design: We sought to obtain expression profile of three lesions from one multicentric GBM patient. Three lesion tissues were selected for RNA extraction and hybridization on Affymetrix microarrays.


title: The KDM4/JMJD2 histone demethylases are required for hematopoietic stem cell maintenance


title: Transcriptomic response of the arcuate nucleus to oral corticosterone treatment

status: Public on Apr 01 2019

city: Manchester

first: Jonathan

last: Wray

address: Oxford Road

institute: University of Manchester

summary: Glucocorticoids (GCs) are widely prescribed to treat inflammatory and autoimmune conditions. However, patients often develop adverse metabolic effects, including hyperphagia, obesity, and hyperglycemia.The arcuate nucleus has an established role in the central control of energy balance. In this study we examined the transcriptomic response of the arcuate nucleus to oral corticosterone treatment. Gene expression changes were measured after 2 days and 4 weeks of Cort treatment in ad libitum fed C57BL6/J mice.

overall_design: Male C57BL6J mice were treated with either vehicle (1% ethanol) or corticosterone (75μg/ml) for 2 days or 4 weeks. Laser capture microsdissection was then used to isolate the hypothalamic arcuate nucleus for RNA-sequencing.

middle: R

first: Erika

last: Harno

first: Anne

last: White


title: Genome-wide maps of H3K9me3 in hematopoietic stem cells from Kdm4a, b, c triple knockout mice

overall_design:
In this study we map the distribution of H3K9me3 in LSK cells before and after the combined knockout of Kdm4a, b and c.
Conditional Kdm4a, b, c knockout mice were injected with tamoxifen to induce knockout. After two weeks LSK cells were sorted from the bone marrow, fixed in formaldehyde and used in ChIPseq experiments.


title: Expression analysis of tomato S. pimpinellifolium accession LA1589 wild type and the Nearly Isogenic Lines lc, fas and lc/fas NILs during floral  development.

city: Athens

first: Esther

last: van der Knaap

state: GA

address: 111 Riverbend Rd

department: Horticulture

institute: University of Georgia

summary: The goal of this study is to decipher the effect of the tomato lc and fas mutation on gene expression during floral development in tomato. The 3'Tag RNA libraries were sequenced on a  Illumina HiSeq2500 at Genomic Resources Core Facility at Weill Cornell Medical College for 100 bp single–end sequencing. Total raw reads for each sample ranged between 5 to 10 million per sample.

overall_design: For each genotype, samples from 5-7 week old seedlings were collected in triplicate in the greenhouse and immediately stored in RNAlater. Using the dissecting microscope, sympodial shoot apical meristem (SYM), the combined floral and inflorescence meristem (F&IM), and floral buds at 2, 4, and 6 days post floral initiation (dpi) were collected and frozen in the -80 C.

first: Yi-Hsuan

last: Chu


title: Expression analysis of S. pimpinellifolium accession LA1589 wild type, lc, fas and lc/fas NILs, SlCLV3 RNAi and SlCLV3-complementation lines during tomato floral development.

summary: The goal of this study is to decipher the effect of the lc and fas mutations on gene expression during floral development in tomato as well as determining the effect of strongly downregulating tomato CLV3 using the RNAi strategy. The strand-specific RNA libraries were sequenced through Illumina HiSeq2000 at Genomic Resources Core Facility at Weill Cornell Medical College for 50 bp single–end sequencing. Total raw reads for each sample ranged between 20-30  millions.

overall_design: Tissues were collected from mature plants grown in the greenhouse of wild type, lc, fas, lc/fas NILs, RNAi-SlCLV3 lines and SlCLV3 complementation lines in the fas mutant background at three developmental stages, each with four replicates. The first stage included inflorescence meristems, floral meristems and 1 to 3 days post floral initiation (dpi) floral buds. The second and third stages included floral buds at 4 and 6 dpi, respectively.


title: RNA SEQ NTHi modA18

city: Gold Coast

first: John

middle: Michael

last: Atack

state: QLD

address: Gold Coast Campus

department: Institute for Glycomics

country: Australia

institute: Griffith University

summary: Comparison of RNA expression profiles from NTHi strain 84P36H1 strains expressing methyltransferase ModA18 (ON) or not (OFF).

overall_design: RNA isolated from triplicate cultures of each strain (modA18 ON and modA18 OFF) grown in sBHI to mid-log; comparison of gene expression profiles by comparing modA18ON vs. modA18 OFF to determine differential gene expression influenced by ModA18 methylation differences.

first: Michael

middle: P

last: Jennings


title: RNA SEQ NTHi modA15

summary: Comparison of RNA expression profiles from NTHi strain 10P129H1 strains expressing methyltransferase ModA15 (ON) or not (OFF).

overall_design: RNA isolated from triplicate cultures of each strain (modA15 ON and modA15 OFF) grown in sBHI to mid-log; comparison of gene expression profiles by comparing modA15ON vs. modA15 OFF to determine differential gene expression influenced by ModA15 methylation differences.


title: Hypericum perforatum LCM-RNAseq

status: Public on Mar 28 2019

city: Legnaro

first: giulio

last: Galla

state: Padova

address: Viale dell'Universita

department: DAFNAE

country: Italy

institute: University of Padova

summary: Hypericum perforatum L. (2n=4x=32) is an attractive model system for the study of aposporous apomixis. The earliest phenotypic features of aposporous apomixis in this species are the mitotic formation of unreduced embryo sacs from a somatic cell of the ovule nucellus and the avoidance of meiosis. In this research we addressed gene expression variation in sexual and apomictic plants, by focusing on the ovule nucellus,  which is the cellular domain primarily involved into the differentiation of meiocyte precursors and aposporous embryo sacs. Gene expression analysis performed by RNAseq identified 396 differentially expressed genes and 1834 transcripts displaying phenotype-specific expression. Overall, our data suggest that phenotypic expression of aposporous apomixis is concomitant with the modulation of key genes involved in cell patterning, RNA splicing and RNA-directed DNA methylation.

overall_design: Sequencing was performed on 3 sexual and 3 apomictic samples. Each sample was originated by by pooling the RNAs purified from the microdissections of 3 plants. SRA Study accession: SRP184423;  BioProject accession: PRJNA521154

first: Giulio

first: Andrea

last: Basso

first: Simone

last: Grisan

first: Michele

last: Bellucci

first: Fulvio

last: Pupilli

first: Gianni

last: Barcaccia


title: Tafazzin Regulates Cell State by Modulating Phosphatidylethanolamine and Phosphatidylserine levels

city: Toronto

first: Ayesh

last: Seneviratne

state: Ontario

address: 610 University Avenue, 7th, PMH, 7-510

institute: University of Toronto

summary: Inhibiting tafazzin a cardiolipin remodeling enzyme reduces stemness of AML by modulating the level of phosphatidylserine

overall_design: Gene expression analysis upon knock-down of TAZ by two independent shRNAs

first: Aaron

last: Schimmer


title: tRNA-derived small non-coding RNAs as novel epigenetic molecules regulating adipogenesis

city: Chengdu

first: Linyuan

last: Shen

state: Sichuan

address: 211# Huiming Road

department: College of Animal Science and Technology

institute: Sichuan Agricultural University

summary: tRNA-derived fragments (tRFs) are a novel class of non-coding RNA that play an vital role in regulating gene expression at post-transcriptional level. To date, it is completely unknown      the regulatory mechanism of tRFs governing fat deposition and adipogenesis. In this study, we used high fat diet successfully induced obese rat model, and used tRFs transcriptome sequencing to select differentially expressed tRFs that response to obesity. We found tRFGluTTC was the highest fold change in the 296 differentially expressed tRFs, which promoted preadipocytes proliferation by increasing the expression of cell cycle regulatory factors. Moreover, tRFGluTTC also suppressed preadipocytes differentiation by reducing lipid accumulation and triglyceride content, and decreasing the expression of genes related to fatty acid synthesis. According to luciferase activity assays, tRFGluTTC directly targeted KLF9, KLF11, and KLF12, and could significantly suppressed the mRNA expression of these target genes. Besides, tRFGluTTC suppressed adipogenesis also accompanied by decreasing the expression of adipogenic transcription factors (AP2, C/EBPα, and PPARγ). Taken together, these results imply that tRFGluTTC may take as a novel epigenetic molecules governing adipogenesis and could be a target for therapeutic intervention in obesity.

overall_design: Adipose small mRNA profiles  (15-40 nt) of high fat diet induced obesity rats and control were generated by deep sequencing, in triplicate, using Illumina Hi-Seq 2500.

first: Zhengdong

last: Tan

first: Mailin

last: Gan

first: Qiang

last: Li

first: Lei

last: Chen

first: Jinyong

last: Wang

first: Xuewei

first: Shunhua

last: Zhang

first: Li

last: Zhu


title: Phenotypic landscape of schizophrenia-associated genes defines candidates and their shared functions

status: Public on Mar 21 2019

city: Cambridge

first: Shristi

last: Pandey

address: 16 Divinity Ave

department: Molecular and Cellular Biology

institute: Harvard University

summary: Znf536 mutant and wild types were profiled to discover cell type landscape modulated by the transcription factor.

overall_design: 10x libraries of single cell transcriptomes


title: Transcriptome profile of breast cancer HS-578T cells overexpressing EP300

status: Public on Mar 19 2019

city: London

first: Ernesto

last: Yague

address: Du Cane Road

department: Division of Cancer

institute: Imperial College London

summary: HS-578T cells overexpressing EP300 show an increase in doxorubicin and paclitaxel resistance, up-regulation of EMT markers together with an increase in motility and invasion, and an increase in the percentage of cancer stem cells and mammosphere formation.

overall_design: Cells were stably transfected with an expression vector (pcDNA 3) carrying EP300 cDNA. Control cells were generated with pcDNA 3 only. Pools of at least 200 clones were selected with G418. For the array experiment, RNA isolated from three independent cultures was used for each condition (control vs. EP300-expressing cells).

first: E

first: Z

last: Mahmud


title: Role of p110a subunit of PI3-kinase in skeletal muscle mitochondria

status: Public on Mar 12 2019

first: Hui

last: Pan

address: 1 Joslin Place

department: Bioinformatics and Biostatistics Core

institute: Joslin Diabetes Center

summary: Skeletal muscle insulin resistance, decreased phosphatidylinositol 3-kinase (PI3K) activation and altered mitochondrial function are hallmarks of type 2 diabetes. We created mice with a muscle-specific knockout of p110α or p110β, the two major catalytic subunits of PI3K. We find that mice with muscle-specific knockout of p110α, but not p110β, display impaired muscle insulin signaling and reduced muscle size due to enhanced proteasomal and autophagic activity. Despite insulin resistance and muscle atrophy, M-p110αKO mice show decreased serum myostatin, increased mitochondrial mass, increased mitochondrial fusion visualized by intravital microscopy, and increased PGC1α expression, especially PCG1α2 and PCG1α3. This leads to enhanced mitochondrial oxidative capacity, striking increases in muscle NADH content, and higher muscle free radical release measured in vivo using pMitoTimer reporter. Thus, p110α is the dominant catalytic isoform of PI3K in muscle in control of insulin sensitivity and muscle mass, and has a unique role in mitochondrial homeostasis in skeletal muscle.

overall_design: All studies were performed in male mice on C57BL/6J background. Muscle-specific p110alpha or p11beta knockout mice were generated by crossing mice carrying the Cre recombinase gene driven by the human alpha-skeletal actin (HSA) promoter (Jackson Laboratories Stock Number: 006149) with mice carrying either floxed p110alpha or p110beta alleles in which exon 1 of p110alpha or exon 2 of p110bet was flanked with loxP sites. Skeletal muscle from 2-3-month-old male mice was harvested and RNA was extracted using Trizol. Gene expression profiling was performed using NEBNext mRNA Sample Prep Master Mix kit (NEB) by BioPolymers Facility at Harvard Medical School. Reads were aligned to the mouse genome (GRCm38) using STAR aligner and counted with Subread featureCounts.

first: Mengyao

first: C

last: Kahn


title: A homeostasis hypothesis of avian influenza resistance in chickens

status: Public on Mar 15 2019

city: Paris

first: Jing

last: An

address: 630 Rue Noetzlin

institute: Universite Paris Saclay

summary: Avian influenza caused significant damages to the poultry industry, efforts have been made to reveal the disease mechanisms as well as mechanisms of disease resistance. Here, by investigating two chicken breeds with distinct responses to avian influenza virus (AIV), Leghorn GB2 and Fayoumi M43, we compared their differences in genome, methylation and transcriptome. Except for MX1 involved direct acting antiviral mechanism, we found that in both methylation and transcriptome levels the more AIV resistant breed Fayoumi showed less variations compared to White Leghorn after AIV challenging. Fayoumi also showed better consistency between the changes in methylation and changes in transcriptome level. Our results suggested a homeostasis hypothesis of avian influenza resistance, with Fayoumi better maintaining homeostasis both in epigenetic and gene expression levels.

overall_design: DNA methylation profiles of two highly inbred chicken lines, Leghorn and Fayoumi, which were generated by deep sequencing, using Illumina GAII.

first: Jinxiu


title: Alterations of mRNAs in NIH/3T3 cells overexpressing BPV-13 E6

first: Feng

last: Pang

summary: To find out differentially expressed mRNAs in NIH/3T3 cells overexpressing BPV-13 E6

first: Fengyang


title: Inhibition of MYC by the SMARCB1 tumor suppressor

city: Nashville

state: TN

address: 2220 Pierce Avenue

institute: Vanderbilt University Medical Center

summary: We report that the protein encoded by the SMARCB1 gene, SNF5, is capable of inhibiting MYC binding in vitro and in a malignant rhabdoid tumor (MRT) cell line. By comparing the effects of reintroduction of SNF5 with genetic inhibition of MYC (OMOMYC) on multiple aspects of chromatin remodeling and transcription in MRT cells, we show that regulation of MYC binding by SNF5 is not connected to the role of SNF5 in chromatin remodeling, but instead is responsible for controlling RNA polymerase pause release during transcription. Our data reveal that SNF5 negatively regulates MYC function and may explain how loss of SNF5 can lead to rapid tumorigenesis.

overall_design: The G401 MRT cell line was transduced with lentiviral vectors expressing tetracycline (TET)-inducible version of EGFP, SNF5, or OMOMYC. Immediately following selection, each group of transduced cells were treated with 1ug/ml doxycycline for 24 hours. All ChIP-seq, ATAC-seq, and PRO-Seq experiments were performed at the 24 hour timepoint.

first: William

last: Tansey

first: April

last: Weissmiller

first: Qi

last: Liu


title: Foxp1 is critical for the maintenance of regulatory T-cell homeostasis and suppressive function

status: Public on Apr 10 2019

first: Jinyi

last: Tang

address: Yueyang road 320

institute: IPS

summary: Regulatory T (Treg) cells play central roles in maintaining immune homeostasis and self-tolerance. However, the molecular mechanisms underlying Treg cell homeostasis and suppressive function are still not fully understood. Here, we report that the deletion of another P subfamily members of the forkhead box (Foxp) subfamily member Foxp1 in Treg cells led to increased numbers of activated Treg (aTreg) cells at the expense of quiescent Treg cells, and also resulted in impaired Treg suppressive function. Mice with Foxp1-deficient Treg cells developed spontaneous inflammatory disease with age; they also had more severe inflammatory disease in colitis and experimental autoimmune encephalomyelitis (EAE) models. Mechanistically, we found that Foxp1 bound to the conserved noncoding sequence 2 (CNS2) element of the Foxp3 locus and helped maintain Treg suppressive function by stabilizing the Foxp3 expression. Furthermore, we found that Foxp1 and Foxp3 coordinated the regulation of cytotoxic T-lymphocyte-associated protein 4 (CTLA-4) expression levels. Taken together, our study demonstrates that Foxp1 plays critical roles in both maintaining Treg cell quiescence during homeostasis and regulating Treg suppressive function.

overall_design: Spleen and peripheral lymph nodes were harvested in Foxp3-YFP-Cre and Foxp1fl/fl Foxp3-YFP-Cre mice. For RNAseq, We have four samples, WT rTreg, WT aTreg, cKO rTreg, cKO aTreg and  2 replicates for each sample.

first: H

first: J

last: Ren

first: L

last: Han


title: Genes regulated by GSK343 in HepG2 and A549 cells

status: Public on Apr 03 2019

city: New Taipei City

first: Pei-Ming

last: Yang

address: No. 301, Yuantong Rd., Zhonghe Dist.

department: Graduate Institute of Cancer Biology and Drug Discovery

country: Taiwan

institute: Taipei Medical University

summary: Our previous study has found that GSK343 is a potent autophagy inducer. To further investigate the underlying mechanisms, microarray analysis was performed.

overall_design: GSK343-induced gene expression in HepG2 and A549 cells was measured at 6 hours after exposure to 10 uM GSK343.


title: Genome-wide identification of SNAC1-targeted genes involved in drought response in rice

city: Wuhan

first: Yu

last: Chang

address: No.1, Shizishan Street, Hongshan District

department: National Key Laboratory of Crop Genetic Improvement

institute: Huazhong Agricultural University

summary: Drought stress can cause huge crop production losses. Drought resistance consists of complex traits, and is regulated by arrays of unclear networks at the molecular level. A stress-responsive NAC transcription factor gene SNAC1 has been reported for its function in the positive regulation of drought resistance in rice, and several downstream SNAC1 targets have been identified. However, a complete regulatory network mediated by SNAC1 in drought response remains unknown. In this study, we performed Chromatin immunoprecipitation sequencing (ChIP-Seq) and RNA-Seq of SNAC1-overexpression transgenic rice (SNAC1-OE) lines and wild-type under normal and moderate drought stress conditions, to identify all SNAC1 target genes at a genome-wide scale by RNA-Seq analyses. We detected 980 differentially expressed genes (DEGs) in the SNAC1-OE lines compared to the wild-type control under drought stress conditions. By ChIP-Seq analyses, we identified 4,339 SNAC1-binding genes under drought stress conditions (SNAC1BGDs). By combining the DEGs and SNAC1BGDs, we identified 93 SNAC1-targeted genes involved in drought responses (SNAC1TGDs). Most SNAC1TGDs are involved in transcriptional regulation, response to water loss, and other processes related to stress responses. Moreover, the major motifs in the SNAC1BGDs promoters include a NAC recognition sequence (NACRS) and an ABA responsive element (ABRE). SNAC1-OE lines are more sensitive to ABA than wild-type. SNAC1 can bind to the OsbZIP23 promoter, an important ABA signaling regulator, and positively regulate the expression of several ABA signaling genes.

overall_design: 4-leaf-stage SNAC1-overexpressing (SNAC1-OE) and ZH11 wild type (ZH11-WT) seedlings were harvested for RNA-seq and ChIP-seq, in triplicate, using Illumina Hiseq X Ten.

first: Xu

last: Li

first: Lizhong

last: Xiong


title: RNAi Screening for Ubiquitin Ligases that Regulate Myofiber Size Identifies a Key Role for UBR4 in Myofiber Hypertrophy in Drosophila and Mice

status: Public on Mar 01 2019

city: Memphis

first: David

last: Finkelstein

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

summary: Sequencing of RNA isolated from the tibialis anterior muscles of 6 month old C57BL/6J mice that had been injected and electroporated with either a control non-targeting siRNA (NT) or two different UBR4 targeting siRNA sequences (UBR4 siRNA5 and siRNA7) to deplete UBR4. Muscles were harvested 7 days after electroporation and showed significant loss of UBR4 coincident with hypertrophy of type 2A and 2X myofibers.

overall_design: 3 samples each of non targeting control and 2 siRNA UBR4 targeting constructs.

first: Liam

last: Hunt

first: Jared

last: Stover

first: Benard

last: Haugen

first: Timothy

last: Shaw

first: Yuxin

first: Vishwajeeth

last: Pagala

first: Yiping

last: Fan

first: Myriam

last: Labelle

first: Junmin

last: Peng

first: Fabio

last: Demontis


title: Transcriptomic analysis of primary human T cells and murine RAW 264.7 macrophages 3D cultured in different collagen densities

city: Odense

first: Lars

last: Grøntved

address: Campusvej 55

department: Biochemistry and Molecular Biology

institute: University of Southern Denmark

summary: The density of the extracellular matrix has a dramatic impact on the gene expression profile of T cells and macrophages. This may reflect impaired immune response of T cells and macrophages in solid tumors.

overall_design: Quantification of RNA expression in human PBMCs enriched for T cells through the selection of non-adhenernt cells and a murine macrophage cell line (RAW 264.7) cultured in different densities of extracellular matrix (Type I collagen). T cells were isolated from PBMCs

first: Daniel

last: Madsen


title: RNA-seq experiment on five mouse brain regions--hypothalamus, hippocampus, neocortex, cerebellum, and the amygdala --comparing expression in virgin females to primiparous females three weeks after pup weaning.

city: Tallahassee

first: Michelle

last: Arbeitman

state: FL

address: 1115 W Call Street, College of Medicine

department: Biomedical Sciences

institute: FSU

summary: RNA-seq experiment on five mouse brain regions-- --comparing expression in virgin females to primiparous females three weeks after pup weaning. For each brain region there are 8 replicates, though three samples were not used in the final analysis based on inspection of PCA plots (1 sample from the Hippocampus, Cerebellum and Amygdala data sets; see details below).

overall_design: Comparison of gene expression in five brain regions between eight virgin and eight primiparous females three weeks after pup weaning. Pair-wise comparisons were performed using EdgeR transformed data and Limma Voom for statistical analysis.

middle: N


title: Effect of DKK1 on embryo elongation

status: Public on Mar 29 2019

city: Utrecht

first: Maria

middle: Belen

last: Rabaglino

address: Yalelaan 7

department: Population Health Science

country: Netherlands

institute: Utrecht University

summary: We report the effect of DKK1 treatment during culture on the length and transcriptome of embryos on day 15 of development, supporting the notion that changes early in development affect later stages of development.

overall_design: Bovine embryos were produced in vitro and exposed to either 0 or 100 ng/ml DKK1 from day 5 to 7 of culture. Embryos were transferred on day 7 and recovered on day 15 for evaluation of length and transciptome

first: Paula

last: Tribulo

middle: B

first: Martin

last: Bo

first: Luciano

last: Carvalheira

first: Jeanette

middle: V

last: Bishop

first: Thomas

last: Hansen

first: Peter


title: Toxoplasma gondii Infection Promotes NK Cell Conversion into ILC1s and Heterogeneous ILC1 Populations

status: Public on Feb 28 2019

first: Maxim

middle: N.

last: Artyomov

state: MO

address: 660 S. Euclid Avenue, Campus Box 8118

department: Immunology&Pathology

institute: Washington University in St.Louis

summary: Innate lymphoid cells (ILCs) comprise several subsets that were originally classified based on their cytokine production profiles. Natural killer (NK) cells and type 1 ILCs (ILC1s) were initially classified together, but recent data supported their separation into different lineages. Here we describe how infection with the parasite Toxoplasma gondii induces changes to NK1.1+ NKp46+ cells that persist independent of ongoing infection. Notably, there is an expansion of Eomes– CD49a+ cells that superficially resemble ILC1s, but express unique genes, circulate throughout the vasculature, and possess distinct epigenetic marks. Single-cell RNA sequencing confirms T. gondii-induced Eomes– CD49a+ cells are distinct from both conventional NK cells and ILC1s. Furthermore, there is heterogeneity within this population, as both conventional NK cells and ILC1s contribute to their formation. Indeed, downregulation of Eomes within conventional NK cells accounts for most T. gondii-induced Eomes– CD49a+ cells, indicating that NK cells can give rise to cells resembling ILC1s during infection.

overall_design: Droplet-based 3′ end massively parallel single-cell RNA sequencing was performed by encapsulating sorted live CD45+ tumor infiltrating cells into droplets and libraries were prepared using Chromium Single Cell 3′ Reagent Kits v2 according to manufacturer’s protocol (10x Genomics).  The generated scRNAseq libraries were sequenced using an Illumina HiSeq3000.

first: Eugene

last: Park

first: Swapneel

last: Patel

first: Qiuling

last: Wang

first: Prabhakar

last: Andhey

first: Konstantin

last: Zaitsev

first: Sofia

last: Porter

first: Maxwell

middle: L

last: Hershey

first: Michael

middle: D

last: Bern

first: Beatrice

last: Plougastel-Douglas

first: Patrick

last: Collins

first: Marco

last: Colonna

first: Kenneth

last: Murphy

last: Oltz

first: L

last: Sibley

first: Wayne

last: Yokoyama


title: Neonatal T follicular helper cells are lodged in a pre-T follicular helper stage favoring innate over adaptive germinal center responses

status: Public on Feb 21 2019

city: São Paulo

first: Frederico

middle: Moraes

last: Ferreira

state: SP

address: Av. Dr. Arnaldo, 455

department: Clinical Medicine Department

institute: University of São Paulo

summary: Follicular T helper (T FH ) cells have emerged as a critical limiting factor for controlling the magnitude  of neonatal germinal center (GC) reactions and primary vaccine antibody responses. We compared the   functional attributes of neonatal and adult T FH cells at the transcriptomic level and demonstrate that the   T FH cell program is well initiated in neonates although the T FH gene-expression pattern   (i.e. CXCR5, IL-21, Bcl6, TBK1, STAT4, Ascl2 and c-maf) is largely underrepresented as compared   to adult T FH cells. Importantly, we identified a dominant T H2 - bias of neonatal T FH cells, with   preferential differentiation toward short-lived pre-T FH effector cells. Remarkably, adjuvantation with   CpG-ODNs redirect neonatal pre-T FH cells toward committed GC-T FH cells, as illustrated by increased   expression of T FH signature genes and reduced expression of T H2 -related genes.

overall_design: A total of 12 samples: 4 groups with 3 biological replicates each.

first: Beatris

last: Mastelic-Gavillet

first: Maria

last: Vono

first: Patrícia

last: Gonzalez-Dias

middle: M


title: Single cell expression profiling of the mouse Sox17-null endocardium at E8.5

status: Public on Feb 12 2019

city: Kyoto

first: Rie

last: Saba

state: Kyoto

address: Kajii-cho 465, Kawaramachi-dori, Kamigyo-ku

department: Dapartment of Radiology

country: Japan

institute: Kyoto Prefectural University of Medicine

summary: To understand the function of Sox17 in the precursor cells of the mouse endocardium and the effect in the develoiping heart tube, single cell expression profiling of the Sox17-null endocardium and myocardium were performed.

overall_design: 4 samples, each for Sox17 wild type and mesoderm-specific knockout endocardium cells. Each array represents a single cell.

first: Lucille

last: Rainbow

first: John

last: Kenny

first: Kenta

last: Yashiro


title: Single cell expression profiling of the mouse Sox17-null myocardium at E8.5

summary: To understand the function of Sox17 in the precursor cells of the mouse endocardium amd the effect in the develoiping heart tube, single cell expression profiling of the Sox17-null endocardium and myocardium were performed.

overall_design: 4 samples, each for Sox17 wild type and mesoderm-specific knockout myocardial cells.  Each array represents a single cell.


title: Saturation mutagenesis of disease-associated regulatory elements

status: Public on Feb 15 2019

city: Luebeck

first: Martin

last: Kircher

state: SH

address: Ratzeburger Allee 160

department: Humangenetics

country: Germany

institute: University of Luebeck

summary: The majority of common variants associated with common diseases, as well as an unknown proportion of causal mutations for rare diseases, fall in noncoding regions of the genome. Although catalogs of noncoding regulatory elements are steadily improving, we have a limited understanding of the functional effects of mutations within them. Here, we performed saturation mutagenesis in conjunction with massively parallel reporter assays on 20 disease-associated gene promoters and enhancers, generating functional measurements for over 30,000 single nucleotide substitution and deletion mutations. We find that the density of putative transcription factor binding sites varies widely between regulatory elements, as does the extent to which evolutionary conservation or various integrative scores predict functional effects. These data provide a powerful resource for interpreting the pathogenicity of clinically observed mutations in these disease-associated regulatory elements, and also comprise a gold-standard dataset for the further development of algorithms that aim to predict the regulatory effects of noncoding mutations.

overall_design: We set out to generate variant-specific activity maps for 20 disease-associated regulatory elements, including ten promoters (of TERT, LDLR, HBB, HBG, HNF4A, MSMB, PKLR, F9, FOXE1 and GP1BB) and ten enhancers (of SORT1, ZRS, BCL11A, IRF4, IRF6, MYC (2x), RET, TCF7L2 and ZFAND3), together with one ultraconserved enhancer (UC88). Specifically, we used massively parallel reporter assays (MPRAs) to perform saturation mutagenesis on each of these regulatory elements. Altogether, we empirically measured the functional effects of over 30,000 SNVs or single nucleotide deletions. We focused primarily on regulatory sequences in which specific mutations are known to cause disease, both for their clinical relevance and to provide for positive control variants. Selected elements were limited to 600 base pairs (bp) for technical reasons related to the mapping of variants to barcodes by subassembly. In addition, we selected only sequences where cell line-based reporter assays were previously established. For each of the 21 regulatory elements, we used error-prone PCR to introduce sequence variation at a frequency of less than 1 change per 100 bp. While error-prone PCR is known to be biased in the types of mutations that are generated (e.g. a preference for transitions and T/A transversions), high library complexities (50k-2M constructs per target) allowed us to capture nearly all possible SNVs as well as many single base pair deletions with multiple independent constructs per variant. To distinguish the individual amplification products, we incorporated 15 or 20 bp random sequence tags 3' of the target region using overhanging primers during the error-prone PCR. We cloned promoter libraries and all but two enhancer libraries (RET in pGL3, ZRS in pGL4Z) into the backbones of slightly modified pGL4.11 (Promega, promoter) or pGL4.23 (Promega, enhancer) vectors. For each MPRA experiment, around 5 million cells were plated and incubated for 24 hours before transfection with the libraries. In each experiment, three independent cultures (replicates) were transfected with the same library. In addition, for LDLR and SORT1, independent MPRA libraries were created, as outlined above, and cells were transfected from a different culture and on a different day. In one case (TERT), the same MPRA library was used for experiments in two different cell-types (HEK293T and a glioblastoma cell line). The relative abundance of reporter gene transcripts driven by each promoter or enhancer variant was measured by counting associated 3’ UTR tags in amplicons derived from RNA (obtained by targeted RT-PCR), and normalized to its relative abundance in plasmid DNA (obtained by targeted PCR). For all experiments, we excluded tags not matching the assignment and determined the frequency of a tag in RNA or DNA from high-throughput sequencing experiments based on the number of unique molecular identifiers. We only considered tag sequences observed in both RNA and DNA.

first: Nadav

last: Ahituv

first: Jay

last: Shendure


title: Parallel analysis of RNA ends (PARE) sequencing of Barley CI 16151 and fast-neutron-derived, immune-compromised mutants infected with the powdery mildew fungus (Blumeria graminis f. sp. hordei; isolate 5874)

status: Public on Feb 08 2019

city: Ames

first: Roger

last: Wise

state: IA

address: Department of Plant Pathology, Entomology, and Microbiology, Iowa State University, 1344 Advanced Teaching & Research Bldg., 2213 Pammel Dr.

department: CICGRU

institute: USDA/ARS

summary: The powdery mildew fungus, Blumeria graminis, is an obligate biotrophic pathogen of cereals and has significant impact on food security (Dean et al., 2012. Molecular Plant Pathology 13 (4): 414-430. DOI: 10.1111/j.1364-3703.2011.00783.x). Blumeria graminis f. sp. hordei (Bgh) is the causal agent of powdery mildew on barley (Hordeum vulgare L.). We sought to identify small RNA-derived transcript cleavage sites from both barley and Bgh that regulate gene expression at the post-transcriptional level both within species and cross-kingdom.

sample_organism:
Hordeum vulgare
Blumeria hordei

platform_organism:
Hordeum vulgare
Blumeria hordei

overall_design:
6 timepoints (0, 16, 20 24, 32, and 48 hours after inoculation with Bgh 5874) pooled for each of 5 genotypes.

This experiment used the identical split-plot design, tissue, and source RNA as GEO submission GSE101304.

first: Matthew

last: Hunt

first: Gregory

last: Fuerst


title: Characterization of Transcriptomic Profile in Early Zebrafish PGCs by Single Cell Sequencing

status: Public on Feb 01 2019

city: Shanghai

first: XiaoYuan

last: Zhang

address: 320 Yueyang road

country: China

institute: Shanghai Institute of Biochemistry and Cell Biology,CAS

summary: In this study, single cell sequencing technique was utilized to explore the transcriptomes of zebrafish PGCs in three time points: 6hpf (shield stage), 11hpf (3-somite stage) and 24hpf (prim-5 stage).

overall_design: Studying the dynamic gene expression of PGCs during early zebrafish development.

first: Xiaoyuan


title: Single cell expression profiling of the mouse Sox17-null endocardium and myocardium at E8.5

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

overall_design: Refer to individual Series


title: Arundo donax L. transcriptome under salt stress

city: Catania

first: Angela Roberta

last: Lo Piero

state: CT

address: Via S. Sofia 98

institute: University of Catania

summary: Arundo donax L. is one of the most promising bioenergy crop due to its high biomass yield and low irrigation requirement. The resistance to biotic and abiotic stress causes the high invasiveness of this plant which can grow with very low management input (e.g., pesticides, fertilization, irrigation) even in marginal lands or in fields irrigated with waste or salty water. Despite its economic importance, the A. donax genomic resources are still limited. In particular, no information on its transcriptional response to salt stress is available.We report the leaf transcriptome sequencing, de novo assembly and annotation of a giant reed genotype under two levels of salt stress. The study will be useful for providing insight into the molecular mechanism underlying its extreme adaptability also offering a platform for directing future efforts towards the genetic improvement of this species.

overall_design: Examination of A. donax genotype (namely, G2) under two levels of NaCl concentration (250 mM and 420 mM). The control samples is the genotype under 0 mM NaCl concentration. All the semples are in three biological replicates

first: Angelo

last: Sicilia

first: Giorgio

last: Testa

first: Danilo

middle: F

last: Santoro

first: Salvatore

last: Cosentino

first: Angela


title: Steroids originating from bacterial bile acid degradation affect Caenorhabditis elegans and indicate potential risks for the fauna of manured soils

city: Muenster

first: Ruediger

last: Paul

address: Schlossplatz 8

department: Institute of Zoophysiology

institute: University of Muenster

summary: Bile acids are steroid compounds from the digestive tracts of vertebrates that enter agricultural environments in unusual high amounts with manure. Bacteria degrading bile acids can readily be isolated from soils and waters including agricultural areas. Under laboratory conditions, these bacteria transiently release steroid compounds as degradation intermediates into the environment. These compounds include androstadienediones (ADDs), which are C19-steroids with potential hormonal effects. Experiments with Caenorhabditis elegans showed that ADDs derived from bacterial bile acid degradation had effects on its tactile response, reproduction rate, and developmental speed. Additional experiments with a deletion mutant as well as transcriptomic analyses revealed that these effects might be conveyed by the putative testosterone receptor NHR-69. Soil microcosms showed that the natural microflora of agricultural soil is readily induced for bile acid degradation accompanied by the transient release of steroid intermediates. Establishment of a model system with a Pseudomonas strain and C. elegans in sand microcosms indicated transient release of ADDs during the course of bile acid degradation and negative effects on the reproduction rate of the nematode. This proof-of-principle study points at bacterial degradation of manure-derived bile acids as a potential and so-far overlooked risk for invertebrates in agricultural soils.

overall_design:
Two strains (N2 Bristol variety; nhr-69 deletion mutant, nhr-69(ok1926) I); two experimental conditions (control/test conditions: without/with 5 µM of the ADD 7a-HADD); 2-3 biological replicates per experimental condition; four contrasts between test and control conditions or strains functionally analyzed.
Please note that differential gene expression data calculated between samples, as indicated in the processed data file names, is provided as Series supplementary file.

first: Martha

last: Mendelski

first: Ramona

last: Doelling


title: Ablation of SetD2 impaired the lymphocyte development in mouse models.

first: zhongzhong

last: ji

state: Shanghai China

address: Huashan Rd. 1940, build 3.  Shanghai,

institute: SJTU CHINA

summary: The repertoire of diverse T-cell receptors (TCRs) and immunoglobulins is generated through restrictedly lineage and stage specific DNA rearrangements of variable (V), diversity (D) and Joining (J) gene segments at early T and B cell development. Histone modifications has been demonstrated to ensure proper VDJ recombination. However, the epigenetic mechanisms and the role of enzymes that catalyze epigenetic modifications in regulating VDJ recombination still remain largely unexplored. Herein we report that deletion of SetD2, the histone methyltransferase to catalyze the trimethylation of lysine 36 on histone 3, leads to severe lymphopenia due to development blockage of T lymphocyte at the double negative 3 (DN3) stage and differentiation arrest of B cell development at the pro-B stage in genetically engineered mouse models. SetD2 deficiency causes a loss of H3K36me3 and markedly impairs VDJ rearrangement of TCRβ and immunoglobulin heavy chain. Our study demonstrates that SetD2 and its mediated H3K36M3 modification are required for the VDJ recombination and normal lymphocyte development.

overall_design: Examination of transcriptional difference between SetD2-deficient mice DN3 thymocytes and control

first: Zhongzhong

last: Ji


title: Hybrid assembly of the genome of the entomopathogenic nematode Steinernema carpocapsae identifies the X-chromosome.

status: Public on Mar 06 2019

city: Irvine

first: Ali

last: Mortazavi

address: 2300 E biological science 3

institute: University of California Irvine

summary: Entomopathogenic nematodes from the genus Steinernema are lethal insect parasites that quickly kill their insect hosts with the help of their symbiotic bacteria. Steinernema carpocapsae is one of the most studied entomopathogens due to its broad lethality to diverse insect species and its effective commercial use as a biological control agent for insect pests, as well as a genetic model for studying parasitism, pathogenesis, and symbiosis. In this study, we used long-reads from the Pacific Biosciences platform and BioNano Genomics Irys system to assemble the best genome of S. carpocapsae ALL strain to date, comprising 84.5 Mb in 16 scaffolds, with an N50 of 7.36Mb. The largest scaffold, with 20.9Mb, was identified as chromosome X based on sex-specific genome sequencing. The high level of contiguity allowed us to characterize gene density, repeat content, and GC content. RNA-seq data from 17 developmental stages, spanning from embryo to adult, were used to predict 30,957 gene models. Using this new genome, we performed a macrosyntenic analysis to Caenorhabditis elegans and Pristionchus pacificus and found S. carpocapsae’s chromosome X to be primarily orthologous to C. elegans’ and P. pacificus’ chromosome II and IV. We also investigated the expansion of protein families and gene expression differences between male and female stage nematodes. This new genome and more accurate set of annotations provide a foundation for new comparative genomic and gene expression studies within the Steinernema clade and across the Nematode phylum.

overall_design: we used long-reads from the Pacific Biosciences platform and BioNano Genomics Irys system to assemble the best genome of S. carpocapsae ALL strain and we performed Illumina sequencing of the DNA of males and females to identify chromosome X in our new assembly.

first: Lorrayne

last: Serra

first: Marissa

last: Macchietto

first: Aide

last: Munoz

first: Cassandra

last: McGill

first: Isaryhia

last: Rodriguez

first: Bryan

first: Rabi

last: Murad


title: A role for PICKLE in the regulation of cold stress response in Arabidopsis

city: West Lafayette

first: CHUNZHAO

last: ZHAO

state: Indiana

address: 209 AIRPORT ROAD, APT 5

institute: Chinese Academy of Science

summary: Our study showed that the CHD3 protein PKL plays a role in the regulation of cold stress response likely via the regulation of chlorophyll accumulation under low temperature conditions. Our results suggest that PKL may regulate cold response partly via a CBF3-mediated pathway. Besides, our results reveal that the PKL gene is also involved in the regulation of drought and salt stress resistance.

overall_design: RNA-Seq of 6 samples, each has 3 replicates. The samples are wild type ( WT ) and pkl-1 before and after cold treatment.

first: Rong

last: Yang

first: Chunzhao

last: Zhao


title: Small RNA  sequencing of Barley CI 16151 and fast-neutron-derived, immune-compromised mutants infected with the powdery mildew fungus (Blumeria graminis f. sp. hordei (Bgh); isolate 5874)

first: Roger

last: Wise

summary: Purpose: The powdery mildew fungus, Blumeria graminis, is an obligate biotrophic pathogen of cereals and has significant impact on food security (Dean et al., 2012. Molecular Plant Pathology 13 (4): 414-430. DOI: 10.1111/j.1364-3703.2011.00783.x). Blumeria graminis f. sp. hordei (Bgh) is the causal agent of powdery mildew on barley (Hordeum vulgare L.).  We sought to identify small RNAs (sRNAs) from both barley and Bgh that regulate gene expression both within species and cross-kingdom.

overall_design:
90 samples analyzed = 5 genotypes * 6 time points * 3 replications
Note: This experiment used the identical split-plot design, tissue, and source RNA as GEO submission # 101304 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE101304).

first: Matthew

last: Hunt

first: Gregory

last: Fuerst


title: Sex allocation plasticity on a transcriptome scale: socially-sensitive gene expression in a simultaneous hermaphrodite

city: Bielefeld

first: Steven

last: Ramm

address: Konsequenz 45

institute: Bielefeld University

summary: We report gene expression patterns for the flatworm Macrostomum lignano in four different social envirionments expected to influence allocation to the male and female sex functions

overall_design: Four replicate pools of worms worm raised in each of four different treatment groups: 'isolated' worms were kept alone for the duration of the experiment; 'joined' were kept alone for the duration of the experiment, except that for the final 24h always two worms were paired together (aimed at studying short-term responses to mating); 'paired', in which two worms were kept together for the duration of the experiment; and 'octet' , in which worms were kept together in groups of eight for the duration of the experiment. After 64 days in these groups, RNA was extracted and pooled to form the 16 independent cDNA libraries for sequencing on the Illumina HiSeq 2000 platform (single-end, 100bp reads).

middle: A

first: Lukas

last: Schärer


title: DNA hypermethylation encroachment at CpG island borders in cancer is predisposed by H3K4 monomethylation [mESC_WGBS]

status: Public on Jan 23 2019

city: Sydney

first: Ksenia

last: Skvortsova

state: NSW

address: 384 Victoria St, Darlinghurst

department: Genomics and Epigenetics

institute: Garvan Institute

summary: The crosstalk between H3K4 monomethylation and DNA methylation has been receiving little attention to date. We investigated DNA methylation profiles (using WGBS) of  wild-type (WT) mouse ESCs, Mll3/Mll4 (Kmt2c/Kmt2d) mutant (dKO) ESCs and catalytic SET domain mutant (dCD) ESCs, which were kindly provided by the Wysocka Laboratory (Dorighi et al., 2017).

overall_design: Genome-wide analysis of DNA methylation using WGBS in mouse wild-type ESCs (WT), Mll3/Mll4 (Kmt2c/Kmt2d) mutant (dKO) ESCs and catalytic SET domain mutant (dCD) ESC.

first: Phuc-Loi

last: Luu

first: Susan

middle: J

last: Clark

first: Clare

last: Stirzaker


title: Effects of naturally ocurring proto-Y chromosomes on house fly gene expression

status: Public on Feb 19 2019

city: Houston

first: Richard

last: Meisel

state: TX

address: 3455 Cullen Blvd

department: Biology and Biochemistry

institute: University of Houston

summary: We performed RNA-seq experiments to examine the effects of house fly proto-Y chromosomes on gene expression. Two different Y^M chromosomes were investigated, and two different III^M chromosomes were investigated. One of the Y^M genotypes also was also heterozygous for third chromosomes that do not carry a male-determining locus to evaluate the effect of third chromosomes on gene expression independent of being a proto-Y.

overall_design: Four different genotypes were assayed. For each genotype, expression was measured in both head and abdomen. Three biological replicates of each genotype and tissue were assayed.

first: Jae

middle: H

last: Son


title: RNA-seq profiling of HSC, MPPs and HPC-1s from Phf6-deleted and Phf6-intact mice

status: Public on Feb 20 2019

city: Parkville

first: Alexandra

last: Garnham

state: Victoria

address: 1G Royal Parade

institute: Walter and Eliza Hall Institute of Medical Research

summary: The study profiled the effect of Phf6 deletion on gene expression in hematopoietic stem cells (HSCs), multipotent progenitor cells (MPPs) and hematopoietic progenitor cells (HPC-1). Phf6lox/Y;Tie2-creTg/+ mice were prepared on a C57BL/6 background so that Phf6 deletion could be selectively mediated by Tie2-cre. Cell populations were sorted from bone marrow samples using standard surface markers  (Lin–SCA1+cKIT+(LSK) CD150+ CD48– for HSCs, Lin–SCA1+cKIT+(LSK) CD150– CD48– for MPPs and Lin–SCA1+cKIT+(LSK) CD150- CD48+ for HPC-1 cells). Phf6 intact and Phf6-delected cells of all three types were profiled by paired-end RNA-seq using an Illumina NextSeq 500 sequencer. RNA-seq libraries were prepared from the HPC-1 samples used a standard Illumina TruSeq library protocol whereas the libraries for the HSC and MPP samples used a SMART-seq ultra low input kit for cDNA synthesis and amplification. Statistical analysis of the TruSeq and SMART-seq samples was undertaken separately.

overall_design: HSC, MPP and HPC-1 cells were isolated from the bone marrow of 4 control mice and 4 mice with Phf6 deleted.

first: Helen

last: McRae

first: Anne

last: Voss

first: Tim

last: Thomas

first: Gordon

middle: K

last: Smyth


title: Transcriptome of microbiome for the nematode Caenorhabditis elegans

status: Public on Feb 25 2019

city: Kiel

first: Hinrich

last: Schulenburg

address: Am Botanischen Garten 1-9

department: Evolutionary Ecology and Genetics, Zoological Institute

summary: Host-microbe associations underlie many key processes of host development, immunity, and life history. Yet, none of the current research on the central model species Caenorhabditis elegans considers the worm’s natural microbiome. Instead, almost all laboratories exclusively use the canonical strain N2 and derived mutants, maintained through routine bleach sterilization in monoxenic cultures with an E. coli strain as food. Here, we characterize for the first time the native microbiome of C. elegans and assess its influence on nematode life history characteristics via transcriptomics.

overall_design: mRNA profiles of wild type (WT) C.elegans fed to either Ochrobactrum strain MYb65, MYb71, mixture of MYb65 and MYb71 or standard lab food E. coli OP50 at different life stages (from L2 to adults) were generated by deep sequencing, in triplicate, using Illumina HiSeq2000.

first: Carola

last: Petersen

first: Barbara

last: Pees

first: Katja

last: Dierking


title: Induction and Therapeutic Targeting of Human NPM1c+ Myeloid Leukemia in the Presence of Autologous Immune System in Mice

status: Public on Jan 03 2019

city: Cambridge

first: Guangan

last: Hu

state: MA

address: 500 Main Street

department: Koch Institute

institute: MIT

summary: Purpose: To understand the molecular mechanisms underlying NPM1c-mediated tumorigenesis by comparing the transcriptome of de novo generated bulk human leukemic cells and leukemic stem cells

overall_design: Human hematopoietic stem/progenitor cells (HSPC) are transduced with lentiviruses expressing a mutated form of Nucleophosmin (NPM1c). Following engraftment into immunodeficient mice, transduced HSPCs give rise to human myeloid leukemia whereas untransduced HSPCs give rise to human immune cells in the same mice. The de novo AML, with CD123+ leukemic stem cells (LSC), resembles NPM1c+ AML from patients.

first: Mandeep

last: Kaur


title: VD3-VDR axis regulates the homeostasis and function of alveolar macrophage [RNA-Seq]

status: Public on Jan 08 2019

summary: Purpose: To understand the regulation of gene expression of alveolar macrophages by VD3-VDR axis

overall_design: Fresh isolated WT alveolar macropahges (AM) were treated with or without 50 nM Vitamin D3 in vitro for 24hrs. Fresh AMs were isolated from WT and VDR knockout mice in 4 and 10 weeks old. RNA was isolated and purified by Qiagen Rneasy micro kit and applied to RNAseq.

first: Jianzhu

last: Chen


title: VD3-VDR axis regulates the homeostasis and function of alveolar macrophage [RNA-Seq LPS]

overall_design: Fresh isolated WT alveolar macropahges (AM) were treated with LPS (100ng/mL) or LPS plus 50 nM Vitamin D3 in vitro for 4hrs. RNA was isolated and purified by Qiagen Rneasy micro kit and applied to RNAseq.


title: VD3-VDR axis regulates the homeostasis and function of alveolar macrophage [ChIP-Seq]

overall_design: Fresh isolated WT alveolar macropahges (AM) were cultured in vitro and treated with or without 50 nM Vitamin D3 in vitro for 24hrs. Cells were fixed to prepare for ChIP using anti-VDR or IgG. ChIP DNA was isolated and applied to ChIP-seq.


title: A Myt1 family transcription factor defines neuronal fate by repressing non-neuronal genes

status: Public on Jan 26 2019

city: Stanford

first: Kang

last: Shen

state: CA

address: 385 Serra Mall, Herrin lab 144

institute: Stanford University

summary: Cellular differentiation requires both activation of target cell programs and repression of non-target cell programs. Transcriptional repressors such as RE1-silencing transcription factor (REST) and Hairy/Enhancer of Split (Hes) repress neuronal genes in non-neuronal cells. However, it is unknown whether transcriptional repressors of non-neuronal genes in neuronal precursors are required to specify neuronal fate during development. The Myt1 family of zinc finger transcription factors contributes to fibroblast to neuron reprogramming in vitro by repressing Notch signaling. Here, we show that ztf-11 (Zinc-finger Transcription Factor-11), the sole Caenorhabditis elegans Myt1 homolog, is required for neurogenesis in multiple neuronal lineages, including an in vivo developmental epithelial-to-neuronal transdifferentiation event. ztf-11 is exclusively expressed in all neuronal precursors with remarkable specificity at single cell resolution. Loss of ztf-11 leads to upregulation of non-neuronal genes and reduced neurogenesis. Ectopic expression of ztf-11 in epidermal lineages is sufficient to produce additional neurons. Our genetic and genomic experiments show that ZTF-11 indeed functions as a transcriptional repressor to suppress the activation of non-neuronal genes in neurons; however, it does not function via repression of Notch signaling. Instead, ZTF-11 binds to the MuvBco-repressor complex, which we show is also required for neurogenesis. These results dovetail with ability of Myt1l (Myt1-like) to drive neuronal transdifferentiation in vitro in vertebrate systems. Together, we identified an evolutionarily conserved mechanism to specify neuronal cell fate by repressing non-neuronal genes.

overall_design: 4 biological replicates each under 2 experemental conditions (ztf-11 KD and negative control) were used for total of 8 samples

first: Joo

last: Lee

first: Emerson

last: Stewart

first: Caitlin

last: Taylor

first: Kristopher

last: Barnes

first: Allison

first: Zhirong

last: Bao

first: Ao


title: RIG-I-Like-Receptors Induce Unique and Complimentary Transcriptional Programs Following West Nile Virus Infection Leading to Macrophage Polarization and Protection

city: Minneapolis

first: Michael

last: Gale

state: Minnesota

address: 689 23rd Ave SE

department: Microbiology and Immunology

institute: University of Minnesota

summary: The study shows that RLRs drive distinct immune gene activation and polarization of the immune response. In our data, the RLR-dependent, WNV-induced immune response polarization overshadows the classical drivers of viral innate immune responses, interferon I (IFN) and IFN-stimulated genes, thus underscoring the importance of innate immune activation for channeling the adaptive immune system into specific effector pathways

overall_design: We conducted genome-wide RNAseq and bioinformatics analysis of WNV infection in bone marrow derived macrophages from the RLR-deficient mice.

first: Amy

last: Stone

first: Courtney

last: Wilkins

first: Richard

last: Green

last: Gale Jr


title: The gene expression analysis of TDP knocked down MIN6 cells.

city: Nagoya

first: Kunihiko

last: Araki

state: Outside the United States or Canada

address: 65 Tsurumai-cho, Showa-ku

department: Neurology

institute: Nagoya University

summary:
TAR DNA-binding protein 43 kDa (TDP-43), encoded by TARDBP, is an RNA-binding protein, the nuclear depletion of which is the histopathological hallmark of amyotrophic lateral sclerosis (ALS). Here, we show that ALS subjects have reduced early-phase insulin secretion and that the nuclear localization of TDP-43 is lost in the islets of autopsied ALS pancreas. Loss of TDP-43 inhibits exocytosis, thereby reducing early-phase insulin secretion in a cultured β cell line (MIN6).
Using microarray analysis, we identified the genes causing insulin impaired in TDP knocked down MIN6 cells.

overall_design: We examined the MIN6 cells treated by control siRNA and TDP siRNA. RNA was extracted from control and TDP knockdown MIN6 cells of each 3 groups.

first: K

first: M

last: Katsuno


title: ATAC-seq on primate adipose tissue

status: Public on Jan 21 2019

city: Durham

first: Devjanee

last: Swain Lenz

state: NC

address: 130 Bioscience Drive

institute: Duke University

summary: To better understand the evolution of primate adipose, we performed compartive analyses of adipose tissue from human, chimpanzee and macque adipose.

sample_organism:
Macaca mulatta
Pan troglodytes
Homo sapiens

overall_design: 13 male adipose samples - human (3 biological replicates, 1 - 3 technical replicates), chimpanzee (2 biological replicates, 2 - 3 technical replicates), macaque (2 technical replicates)

first: Gregory

last: Wray