title: Identification and differential expression of gill microRNA in the Chinese surf Clam (Mactra chinensis) with Cd2+ exposure

city: Dalian

first: Hongjun

last: Li

address: 42 Linghe Street

institute: National Marine Environmental Monitoring Center

summary: The Chinese surf clam (Mactra chinensis) is an economically important clam, distributed in Liaoning and Shandong province. In recently years，because of coastal environmental deterioration and overfishing, the natural population of M. chinensis have considerably declined . In this paper, we study the microRNA transcriptome of gills, including control and experimental group was sequenced through Illumina Hi-seq 2500 CE. And the differential expression was used to find the functional microRNA response to the Cd2+ exposure. Through Illumina Hi-seq 2500, a total of 14,415,256 clean reads and 15,570,111 clean reads were yielded in the gill of control and experimental group respectively. A total of 14,584,077 sRNA, in which there are 12,505,055 sRNA shared by S01 & S02, including 187,859 unique sRNA. The distribution of the sRNA length in the two library was similar, most of them were 26-27 nt. 27 nt was the most abundant length in S01, followded by 28 nt, 26 nt, and 23 nt; 26 nt was the most abundant length in S02, and followed by 27 nt, 28 nt and 23 nt. 50 miRNA was found in unique sRNA, including 38 conserved and 12 novel genes. The most abundant length of microRNA in the two library was the same, 23 nt. Through the analyze of differential expression analysis, the expression of 5 miRNA was induced with significantly difference, and 17 miRNA was down regulated and 28 miRNA was up regulated without significantly difference. So the miRNA in gill of M. chinensis might involve the environmental stress. 542 target genes were yielded when the 50 miRNA were hit to mRNA genome. And the target genes of differential expression miRNA were annotated by hitting to the NCBI database, and 4 genes hit to the COG, 1 genes hit to the GO, 5 genes hit to the KEGG and 11 genes hit to the nr database. The genes hit to the NCBI database include E3 ubiquitin-protein ligase, Wnt signaling pathway and Regulator of G-protein signaling 22.

overall_design: MicroRNA transcriptome of gills, including control and experimental group was sequenced through Illumina Hi-seq 2500 SE. This series contains only the experimental CdCl2-treated sample.

first: Jingjing

last: Zhang


title: S. meliloti CspA2 CspA4 and CspA5 Native IP followed by RNA-seq

status: Public on Aug 01 2018

city: Pullman

first: Jason

last: Price

address: 100 Dairy Rd

country: USA

institute: Washington State University

type: Expression profiling by high throughput sequencing

summary: Rhizobia are soil bacteria that can associate with some legumes and participate in symbiotic nitrogen fixation. Bacterial CspA family members are small, single stranded nucleic acid binding proteins. Differentiation of rhizobial bacteria from a free-living to symbiotic state within legume root nodules follows a massive re-programming of bacterial gene expression. Here, the role of Sinorhizobium meliloti CspA family members in symbiotic development with Medicago sativa (alfalfa) was investigated. We defined expression patterns of CspA family members, identified CspA interacting RNAs, and investigated phenotypes and transcriptional defects associated with cspA deletion strains. We propose that these proteins affect rhizobial physiology through their global control of the cellular RNA secondary structure strength environment and through specific modulation of small non-coding RNA (sRNA) structures involved in cis-regulation of stress responsive sigma factor expression. This work describes an RNA structure mediated mechanism important for bacterial stress adaptation and symbiotic development within a plant host.

overall_design: Illumina sequencing was performed with input and bound RNA fractions from control, CspA2, CspA4, and CspA5 immunoprecipitations in duplicate

middle: P


title: S. meliloti 1021 WT and ΔcspA2 ΔcspA4 whole transcriptome sequencing from free-living and symbiotic nodules

overall_design: Illumina sequencing was performed with isolated total RNA from exponential phase free-living culture and symbiotic nodule tissue 28 dpi


title: Characterization and Targeting of Malignant Stem Cells in Patients with Advanced Myelodysplastic Syndromes (MDS)

city: Aurora

first: Brett

last: Stevens

state: CO

institute: University of Colorado

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

overall_design: Refer to individual Series


title: Small RNA (sRNA) sequencing from A. thaliana flowers

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

type: Non-coding RNA profiling by high throughput sequencing

summary:
Purpose:  To study small RNAs expressed in A. thaliana flowers
Methods: sRNA libraries were constructed as previously described (C Lu et al. 2007) and sequenced on an Illumina GAIIx or Illumina HiSeq 2000 instrument at the Delaware Biotechnology Institute. These libraries were prepared between 2010 and 2012.

overall_design: Two libraries prepared from unopened flower buds and one library from mixed stage inflorescence

first: Tzuu-fen

last: Lee

first: Atul

last: Kakrana

first: Stacey

last: Simon

middle: C


title: Endothelial cells derived from iPSC in response to diabetic medium

city: Vienna

first: Reiner

last: Wimmer

address: Dr. Bohrgasse 3

country: Austria

institute: IMBA

summary: Diabetes is prevalent worldwide and associated with severe health complications, including blood vessel damage that leads to cardiovascular disease and death. We report the development of 3D blood vessel organoids from human embryonic and induced pluripotent stem cells. These human blood vessel organoids contain endothelium, perivascular pericytes, and basal membranes, and self-assemble into lumenized interconnected capillary networks. We treat these vascular organoids with hyperglycemia and inflammatory cytokines in vitro, which leads to basement membrane thickening, a structural hallmark of diabetic patient. To compare differential gene expression we performed RNAseq on endothelial cells, derived from control (NG) or diabetic (DI) vascular organoids.

overall_design: Vascular organoids were differentiated from human iPS cells and treated for 3 weeks with a diabetic media containing 75mM Glucose, 1ng/mL TNF-α, 1ng/mL IL6 (DI) or left untreated in 17mM Glucose (NG). Endothelial cells were FACS sorted for CD31 directly into Trizol and stored at -80°C before RNA preparation. The 2 NG and 2 DI are pools of sorted endothelial cells from multiple vascular organoids (>100) from 2 independent differentiations/treatments.

first: Josef

last: Penninger


title: A genome-scale analysis of mitochondrial-associated mRNAs in plants: upstream AUGs in 5’UTRs alter mRNA targeting

city: Strasbourg

first: Anne-Marie

last: Duchêne

address: 12 rue du général Zimmer

department: Ibmp

country: France

institute: CNRS

summary: Intracellular sorting of mRNAs is an essential process to regulate gene expression and protein localization. Most of mitochondrial proteins are nuclear-encoded and imported into mitochondria, through post-translational or co-translational processes. To determine cytosolic mRNAs targeted to the mitochondrial surface, a genome-scale analysis of mRNAs associated with mitochondria has been performed in plants. As expected, many messengers encoding mitochondrial proteins were found associated with mitochondria, but numerous mRNAs encoding cytosolic proteins were also detected. This suggests multiple roles for mRNA targeting, in addition to the co-translational import of mitochondrial proteins. Moreover, correlations between mRNA targeting and function of mitochondrial proteins indicate a coordinated control of mRNAs localization within metabolic pathways. At last, upstream AUGs in 5'UTR, known to regulate translation efficiency of downstream sequences, affect mRNA targeting. A mutational approach coupled with in vivo mRNA visualization confirms this observation, and highlights the role of upstream AUGs as regulators of mRNA targeting to the mitochondrial surface.

overall_design: Analysis of two types of RNAseq data, each in triplicates. Total RNA from S. tuberosome cell, and mitochondrial associated RNA from S. tuberosum cells.

first: Timothée

last: Vincent

first: Elodie

last: Ubrig

first: Kevin

last: Azeredo

first: Valérie

last: Cognat

first: Stéfanie

last: Graindorge

first: Thalia

last: Salinas

first: Laurence

last: Maréchal-Drouard


title: Conditional DICER1 knockout hESCs

city: New York

first: Virginia

last: Teijeiro

state: NY

address: 430 E 67th St

department: Developmental Biology

institute: Memorial Sloan Kettering Cancer Center

summary: We report the generation and characterization of DICER1-deficient hESCs. We uncover an unexpected requirement for DICER1 as well as essential pro-survival roles of members of the mir-302- 367 and mir-371- 373 clusters in hESCs. Our work provides a robust platform for interrogating microRNA function in hESC and differentiation.

overall_design: For RNAsequencing, total RNA was isolated from Tra-1-60+ sorted cells from +DOX and -DOX conditions using the miRNeasy Mini Kit (Qiagen Cat. No. 217004), following manufacturer's guidelines. Three replicates were done for each sample.

first: Richard

last: Koche


title: Dynamic immune gene expression in young foals

city: Ithaca

first: Wojciech

last: Pawlowski

address: Bradfield Hall, Room 403

department: Plant Breeding and Genetics

institute: Cornell University

summary: This study was undertaken to obtain a global view of the temporal changes in equine immune gene expression between from the neonatal stage to adulthood. To this end, transcriptome analysis of peripheral blood mononuclear cells (PBMCs) from foals on the day of birth and again 6 weeks later was performed and contrasted with those of adult PBMCs. Differential gene expression analysis identified 2,280 genes with ≥2 fold change between PBMCs sampled on day 1 and 42 (p≤0.01). Approximately 1,000 genes differed between either day 1 or day 42 PBMC and adult PBMC. Progressive increases in expression of genes involved in adaptive and cell-mediated immunity were documented between days 1, 42, and adulthood. New insights of natural killer cell-specific genes were obtained, many of which increased expression levels between days 1 and 42 (p≤0.0005), when adult levels were achieved. Transcriptome data also demonstrated the profile of T cell receptor delta (TCRD) transcripts, representative of gamma delta T cells, which peaked in day 42 PBMCs (p=0.0136) although TCRD expression was equivalent between day 1 and adult PBMCs (p>0.05). Transcriptome data further revealed several aspects that may impair robust immune responses in the neonatal period. TLR3 gene expression was lowest in day 1 PBMC (p<0.0001) and this may contribute to viral susceptibility. Increased expression of IL27, IL13RA1, IREM-1, LAIR-1, SIRL-1, and SIRPalpha was observed in day 1 PBMC (p≤0.0198) compared to day 42 PBMC; these immunosuppressive molecules may dampen immune responses in early life. These results provide insight to the unique attributes of the equine neonatal and young immune system, and offer many avenues of future investigation.

overall_design: Peripheral blood mononuclear cell mRNA profiles of foals on day 1 of life, day 42 of life, and adult mares (n=4 per group) were obtained by sequencing Illumina TruSeq Stranded mRNA Libraries on an Illumina NextSeq500.

first: Rebecca

middle: L

last: Tallmadge

first: Qi

last: Sun

first: Minhui

last: Wang

first: Maria

middle: B

last: Felippe


title: High TCR self-reactivity drives regulatory T cell function during tissue-specific autoimmunity

status: Public on Aug 02 2018

city: Houston

last: Bettini

state: TX

address: 1102 Bates St

institute: Baylor College of Medicine

summary: Tregs with high self-reactivity are a potent suppressive population in preventing tissue-specific autoimmunity.

overall_design: 4 Islet T effector controls, 4 Splenic Treg samples, 6 Islet Treg samples

first: Mara

last: Sprouse

first: Marissa

middle: A

last: Scavuzzo

first: Malgorzata

last: Borowiak


title: mRNA transcriptome data of granulosa cells cultured at normal and low oxygen level

city: Dummerstorf

first: Vijay simha

last: Baddela

address: Wilhelm-Stahl-Allee 2

department: Reproductive biology

country: Germany

institute: Leibniz institute for farm animal biology

summary: The ovarian follicle is devoid of direct blood supply because of a blood follicle barrier. The intra follicular compartments are hypothesized to have low oxygen level. As the diameter of an ovarian follicle substantially increases during follicular development, the oxygen concentration is likely to decrease in the follicular fluid and reaches lowest levels in the ovulatory follicles. During the present investigation, transcriptome differences induced by low oxygen levels were comprehensively analyzed to understand the specific significance of low oxygen levels in ovulatory follicles.

overall_design: RNA from 21% oxygen (4n) and 1% oxygen (4n) treated GC were processed for microarray analysis

first: Vijay

middle: S

first: Jens

last: Vanselow


title: Deconstructing lincRNA regulation during ESC to NPC differentiation

city: Basel

first: Alex

middle: Charles

last: Tuck

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

summary: Using single-cell and bulk RNA-sequencing, we profiled mouse embryonic stem cells and neural precursor cells to identify lincRNAs with cell type- and subpopulation-specific expression. In contrast to mRNAs, we found that lincRNAs are prone to prematurely terminate transcription, are less abundant across single cells, and are degraded by the nuclear exosome. These properties indicate that lincRNA genes widely function without requiring their RNA product. To test this prediction experimentally, we developed a method that separates the role of a lincRNA gene from the role of its RNA product. This revealed RNA-independent lincRNA gene activities, underscoring the importance of distinguishing the roles of transcription, the genomic locus, and the RNA product when studying non-coding loci, for which we are providing suitable tools.

overall_design: Two mESC lines (BL6xCAST and CASTxBL6) were differentiated into neural precursor cells, as well as being sampled in 2i+LIF and in serum+LIF medium. Bulk RNA-seq was performed for all timepoints (2i+LIF, serum+LIF, day3, day6 and day8 of differentiation). Most timepoints were also sampled by single-cell RNA-seq (96 cells per sample, 7 samples in total). Cell lines with lincRNA genomic deletions, or with the hammerhead ribozyme genomically integrated into lincRNA loci, were also analysed by bulk RNA-seq (140 cell lines in total). We also performed CRosslinking and Analysis of CDNAs (CRAC) in wild-type cells or cells where endogenous Mtr4 is tagged with a FLAG-Bio tag, to examine transcriptome-wide targets of the nuclear RNA surveillance factor Mtr4. For normalisation, we performed NET-seq. To measure global RNA half-lives, we treated wild-type mESCs with actinomycin D, and performed bulk RNA-seq at several timepoints, in triplicate (3 wells of cells were analysed in parallel per timepoint).

first: Kedar

last: Natarajan

first: Fabio

last: Mohn


title: Analysis of the origin of stenospermocarpy under the control of the major seedlessness locus in grapevine

status: Public on Jul 31 2018

city: Logroño

first: NURIA

last: MAURI

state: La Rioja

address: Carretera de Burgos, km 6 "Finca La Grajera"

department: Genomics

country: Spain

institute: Instituto de Ciencias de la Vid y del Vino

summary: Seedlessness is greatly prized by consumers of fresh grapes. While stenospermocarpy determined by the Seed Development Inhibitor (SDI) locus is the usual source of seedlessness in commercial grapevine cultivars, the sdi mutation underlying this locus remained unknown and we undertook an integrative approach to identify it. Quantitative genetics and fine mapping studies in two Crimson Seedless (CS)-derived F1 populations confirmed the major effect of the SDI locus and delimited the sdi mutation to a region of 323 kb on chromosome 18. Transcriptomics comparing gene expression between seeds and seed traces in RG (Red Globe) × CS progeny identified processes triggered during sdi-determined seed abortion, including the activation of salicylic acid (SA)-dependent defenses. RNA-seq and NimbleGen microarray datasets were investigated for candidate genes and, while no evidence for causal cis-acting regulatory mutations was detected, deleterious nucleotide sequence changes in the seedless haplotype were predicted in two genes within the sdi fine mapping interval, VviPPAT2 and VviAGL11. Targeted re-sequencing of the two genes in a collection of 126 cultivars showed that only the point variation causing the Arg197Leu substitution in the seed morphogenesis regulator gene VviAGL11 was fully linked with seedlessness. Remarkably, this missense mutation was not detected in seeded clonal variants of Sultanina cultivar, the original donor of the sdi mutation, providing genetic evidence that this is the major cause of seedlessness in cultivated grapevines. The identification of the dominant effects of this amino acid substitution in seed abortion can be exploited to boost seedless grape breeding.

overall_design: A total of 6 independent cDNA libraries were sequenced. RNA from stenospermocarpic seed traces of three seedless (669-60, 670-17, 675-17) and from seeds of three seeded (665-17, 671-19, 677-06) Red Globe×Crimson Seedless F1 Vitis vinifera table grape hybrids was compared. Every sample was collected simultaneously and three replicates were analyzed for the two genotypically and phenotypically constrasting offspring classes.

first: Nuria

last: Mauri

first: Pablo

last: Carbonell-Bejerano


title: The DiGeorge Syndrome gene TBX1 is required to specify the nkx2.5+ cardiopharyngeal lineage

city: Charlestown

first: Caroline

last: Burns

state: MA

address: CVRC, 4th floor, 4138E 149 13th Street

department: Cardiovascular Research Center

institute: Massachusetts General Hospital, Harvard Medical School

summary: Hemizygous microdeletions on chromosome 22q11.2 cause a broad spectrum of congenital cardiovascular and craniofacial anomalies known collectively as DiGeorge Syndrome (DGS) that appear to arise from reduced expression of TBX1, a gene in the typically deleted region.  Although mice lacking tbx1 display similar, yet more severe, cardiovascular and craniofacial defects, the mechanisms underlying these devastating phenotypes remain incompletely understood. Here, we report that Tbx1 is required prior to pharyngeal arch development to specify the nkx2.5+ cardiopharyngeal cell lineage that gives rise to the cardiovascular and crainiofacial structures absent in tbx1 null zebrafish. Importantly, the role of Tbx1 during cardiopharyngeal lineage specification is conserved in mammals.  Further, we learned that DVR1, the zebrafish homolog of mammalian GDF1/3, functions downstream of Tbx1 for pharyngeal progenitor specification. Together, these studies unveil a new paradigm potentially underlying the cardiovascular and craniofacial defects observed in the DGS population.

overall_design: Determination of differentially expressed genes/pathways between tbx1 mutants and controls.

first: Burcu

last: Guner-Ataman

first: C

middle: G

middle: E


title: Sinorhizobium meliloti CspA family members mediate stability of structured sRNAs contributing to stress adaptation and effective symbiosis with alfalfa

first: Jason

last: Price


title: Identification and Differential Expression of MicroRNAs during Cold Acclimation of the Tea Plant (Camellia sinensis) by Deep Sequencing

city: Hangzhou

first: Lu

last: Wang

state: Zhejiang

address: 9th, South Meiling Road

country: China

institute: Tea Research Institute, Chinese Academy of Agricultural Sciences

summary: In this study, we performed deep sequencing and bioinformatics analyses of tea plant leaves to identify and characterize known and novel miRNAs. A total of 26,876,261 raw reads were produced from 2 libraries. We detected 422 known miRNAs belonging to 125 families, and 68 putative novel miRNAs.

overall_design: The miRNA profiles of non-acclimated (CK, the date for sample collection was 1st December, 2010) and fully acclimated (CA1, the date was 29th December, 2010) were generated by deep sequencing, using Illumina Solexa.

first: Xinchao

first: Yajun

last: Yang


title: Caenorhabditis japonica high resolution developmental transcriptomic time-course

city: Haifa

first: Harel

last: Zalts

state: Israel

address: Technion city

country: Israel

institute: Technion

summary: Transcriptomic studies typically examine expression at the gene level, although it has been long recognized that the same genetic locus may produce isoforms distinct in their splicing and site of polyadenylation. Here we examine alternatively polyadenylated (APA) transcripts throughout embryogenesis and discover distinct strategies for gene regulation. We introduce APA-Seq, an RNA-Seq method to study APA at a global level, and apply it to study individual C. elegans embryos throughout early development. Surprisingly, we find that genes, whose overall expression is constitutive throughout development, generally show highly dynamic expression for individual isoforms. Such genes tend to participate in cellular as opposed to developmental processes, and this trend was also evident in the closely related C. japonica nematode, providing evidence that the manner by which cellular processes are regulated during embryogenesis is evolutionarily conserved. Finally, we report that genes with dynamic isoform usage have significantly more miRNA binding sites relative to constitutively-expressed isoforms, suggesting strong miRNA regulation in the control of isoform expression. Our findings support a model distinguishing two modes of gene regulatory underlying embryonic development each with unique functions and mechanisms.

overall_design: 46 single embryo samples.

first: Michal

last: Levin

first: Itai

last: Yanai


title: Transcriptional profiling of macrophages derived from injured nerves at 3 and 8 days post-injury

city: Montreal

first: Jo Anne

last: Stratton

state: Quebec

address: 3801 University Road

department: Neurology and Neurosurgery

country: Canada

institute: McGill University

summary: Pro-regenerative macrophages are well known for their role in promoting tissue repair, however in nerve injury their role in promoting regenerative events is not well defined. Macrophage-targeted RNAseq revealed that macrophages expressed an array of ligands post nerve injury that interact with the injury environement to regulate regeneration.

overall_design: RNAseq experiment was performed on FACS-collected cells obtained from the nerves of adult female mice (n=7-8 per time point at Day 3 and 8 post-nerve injury) from a double macrophage reporter (Cx3cr1-GFP/Ccr2-RFP) mouse line (stock no.: 017586; stock No.: 005582, Jackson Laboratories). Samples were pooled to obtain 2 RNAseq sample replicates per time point. Monocytes were also included as a reference.

first: Jo

first: Jeff

last: Biernaskie


title: RNAseq of hPSC-derived cardiac progenitors: normal vs. polyI:C treated (functionally advanced), and TGFbeta treated (cardiac fibroblast progenitors)

city: Madison

first: Mitch

last: Biermann

state: Wisconsin

address: 917 Eagle Heights, Apt D

institute: University of Wisconsin

summary: Directed differentiation of human induced pluripotent stem cells creates billions of patient-specific cells. However, the differentiated derivatives of hiPS cells are immature relative to adult counterparts. Proliferative progenitor cells in these protocols are also therapeutically promising, but progenitors with enhanced potential for maturation have not been discovered. We hypothesized that brief epigenetic and innate immune modulation with polyinosinc cytidilic acid (pIC) could create cardiac progenitors with enhanced later maturation. Progenitor transcriptomic analysis revealed increases in cardiac crescent-like proliferative notch signaling by Jagged1, and activated progenitors spontaneously gave rise to cardiomyocytes with enhanced maturity and conductive microtissue with arrhythmogenic resistance. Furthermore, activated cardiac progenitors improved survival in animals after myocardial infarction compared to untreated progenitors. Our data suggest that future organization and maturation of cardiomyocytes are impacted by earlier pre-cardiomyocyte developmental signaling, and that progenitors modifying these pathways have translational promise. The forward epigenetic and immune modulation approach here utilized may be applicable to other cell lineages as well.

overall_design: 9 samples total: 3 sample types (1 control/normal cardiac progenitors, vs. 2 groups of treated progenitors--with polyI:C or TGFbeta) x 3 biological reps.

first: Timothy

last: Kamp


title: Targeting the MTF2-MDM2 Axis Sensitizes Refractory Acute Myeloid Leukemia to Chemotherapy [RNA-Seq]

city: Ottawa

first: William

last: Stanford

state: Ontario

address: 501 Smyth Road

institute: Ottawa Hospital Research Institute

summary: Deep sequencing has revealed that epigenetic modifiers are the most mutated genes in acute myeloid leukemia (AML). Thus, elucidating epigenetic dysregulation in AML is crucial to understand disease mechanisms. Here, we demonstrate that Metal Response Element Binding Transcription Factor 2/Polycomblike 2 (MTF2/PCL2) plays a fundamental role in the Polycomb repressive complex 2 (PRC2) and that its loss elicits an altered epigenetic state underlying refractory AML. Unbiased systems analyses identified the loss of MTF2-PRC2 repression of MDM2 as central to, and therefore a biomarker for, refractory AML. Thus, immature MTF2- deficient CD34+CD38- cells overexpress MDM2, thereby inhibiting p53 that leads to chemoresistance due to defects in cell cycle regulation and apoptosis. Targeting this dysregulated signaling pathway by MTF2 overexpression or MDM2 inhibitors sensitized refractory patient leukemic cells to induction chemotherapeutics and prevented relapse in AML patient-derived xenograft (PDX) mice. Therefore, we have uncovered a direct epigenetic mechanism by which MTF2 functions as a tumor suppressor required for AML chemotherapeutic sensitivity and identified a potential therapeutic strategy to treat refractory AML.

overall_design: Fold change analysis between treatment and control

first: Harinad

last: Maganti


title: Use of RNA sequencing to assess the expression patterns of microbial metabolite transporters present in children post-transplant with and without GVHD

city: Cincinnati

first: Stella

last: Davies

state: OH

address: 3333 Burnet Ave

department: Cancer & Blood Disease Institute

institute: Cincinnati Children's Hospital

summary: We report the expression of microbial metabolite tranporters in mucosal biopsies from children with GVHD

overall_design: RNA-Seq of GI mucosal tissue in children with GVHD and without GVHD

first: Lindsey

last: Romick-Rosendale


title: AKR1C3-mediated adipose androgen generation fuels an adverse metabolic phenotype in polycystic ovary syndrome (PCOS)

city: Birmingham

first: Wiebke

last: Arlt

address: Edgbaston

department: Institute of Metabolism and Systems Research  (IMSR)

country: United Kingdom

institute: University of Birmingham

summary: RNA-seq samples used to support a study into understanding of the association between androgens and adipose tissue

overall_design: Pairwise comparison of patients with and without PCOS and patients with PCOS and with PCOS on an oral hormone (DHEA)

first: Michael

middle: W

last: O’Reilly

first: Punith

last: Kempegowda

first: Angela

last: Taylor

last: Biehl

first: Konstantinos

middle: N

last: Manolopoulos

first: Farfia

last: Capper

first: Iwona

middle: J

last: Bujalska

first: Warwick

last: Dunn

last: Allwood

first: Robert

middle: K

last: Semple

first: Mark

last: Walsh

first: Daniel

last: Hebenstreit

first: Jeremy

last: Tomlinson


title: Metabolic oscillations on the circadian time scale in Drosophila cells lacking clock genes

city: Geneva

first: Guillaume

last: Rey

address: Campus Biotech, Chemin des Mines 9

institute: University of Geneva

summary: Circadian rhythms are cell-autonomous biological oscillations with a period of about 24 hours. Current models propose that transcriptional feedback loops are the primary mechanism for the generation of circadian oscillations1. In these models, Drosophila S2 cells are generally regarded as ‘non-rhythmic’ cells, as they do not express several canonical circadian components2,3. Using an unbiased multi-omics approach, we made the surprising discovery that Drosophila S2 cells do in fact display widespread daily rhythms. Transcriptomics and proteomics analyses revealed that hundreds of genes and their products, and in particular metabolic enzymes, are rhythmically expressed in a 24-hour cycle. Metabolomics analyses extended these findings and demonstrated that central carbon metabolism and amino acid metabolism are the principal pathways regulated in a rhythmic fashion. We thus demonstrate that 24-hour metabolic oscillations, coupled to gene expression cycles, take place in eukaryotic cells without the contribution of any known circadian regulators.

overall_design: RNA-Seq time courses over 57 h sampled at 3 h interval in Drosophila S2 cells at a constant temperature of 25C or 28C.

first: Nikolay

last: Milev

first: Utham

last: Valekunja

first: Ratnasekhar

last: Ch

first: Sandipan

last: Ray

first: Mariana

last: Silva Dos Santos

first: Andras

middle: D

last: Nagy

first: Robin

last: Antrobus

first: James

middle: I

last: MacRae

first: Akhilesh

last: Reddy


title: Transcription factor Etv6 controls functional differentiation of cross-presenting classical dendritic cells [RNA-Seq]

status: Public on Aug 03 2018

first: Colleen

last: Lau

state: New York

address: 930 Campus Road

department: Microbiology & Immunology

summary: An IRF8-dependent subset of classical dendritic cells (cDCs), termed DC1, effectively cross-primes CD8+ T cells and facilitates antitumor T cell responses. Etv6 is an ETS family transcription factor that controls hematopoietic stem and progenitor cell (HSPC) function. We report that like HSPC, cDCs express Etv6 but not its antagonist ETS1, whereas interferon-producing plasmacytoid dendritic cells (pDCs) express both factors. Deletion of Etv6 in the bone marrow reduced the generation of DC1-like cells in vitro and the differentiation of DC1 in vivo, including the loss of signature marker CD8a. Global expression and chromatin profiling of Etv6-deficient DCs revealed impaired lineage identity of DC1, including the reduction of cDC signature and upregulation of pDC signature. Accordingly, DC-specific Etv6 deletion impaired CD8+ T cell cross-priming and tumor-specific CD8+ T cell responses. These results identify Etv6 as a regulator of DC1 differentiation and functional fitness that indirectly facilitates T cell cross-priming and antitumor immunity.

overall_design: Examination of transcriptional profiles of Etv6-deficient dendritic cell subtypes

middle: M

first: Boris

last: Reizis


title: RNAseq analyze global transcriptome of changes between siIRF3 and siYAP in Gastric cancer cells

city: Shanghai

first: jingmin

last: Guan

address: 320 Yue Yang Road

department: Institute of Biochemistry and Cell Biolog

institute: Shanghai Institutes for Biological Sciences

summary:
Purpose: To investigate the signal crosstalk between IRF3 and YAP, RNA-sequencing (RNA-seq) was performed to analyze the genome-wide changes by the knockdown of IRF3 or YAP in HGC-27 cells.
Methods: Total RNA was extracted from HGC-27 cell after transfection with negative control siRNA (n.c.), IRF3 siRNA (siIRF3) or YAP siRNA (siYAP). Then total RNA was quality controlled and quantified using an Agilent 2100 Bioanalyzer. After converting to cDNA and building library, high-throughput sequencing was performed using the Illumina  HiSeq 2500 platform.
Results: Approximately one thousand transcripts showed differential expression between the siIRF3/siYAP and n.c., with a Fold-change>=2 and q-value <= 0.05. Gene ontology (GO) and gene set enrichment analysis (GSEA) showed a significant negative enrichment of YAP target genes identified by three independent studies in IRF3-knockdown condition.
Conclusions: We conclude that RNA-seq based transcriptome characterization would provide a framework for understanding the signal crosstalk between IRF3 and YAP.

overall_design: RNA was extracted from HGC-27 cells transfected with siRNAs for 48 h. The quality assessed on the Agilent 2100 and sequencing on the Illumina Hiseq2500.

first: Shi

last: Jiao

first: Jingmin


title: Attack-Phase Bdellovibrio bacteriovorus Responses to Extracellular Nutrients Are Analogous to Those Seen During Late Intraperiplasmic Growth

city: Ulsan

first: Robert

middle: J.

last: Mitchell

address: 50 UNIST-gil

department: School of Life Sciences

country: South Korea

institute: Ulsan National Institute of Science and Technology (UNIST)

summary: We sequenced whole transcriptome from attack phase (AP) Bdellovbrio bacteriovorus HD100 after incubating it for 4 hours either in a nutrient rich meium (nutrient broth, NB) or in absence of nutrients (HEPES buffer only, H) as a control. The aim is to know how the excracellular nutrients affect the gene expression pattern of AP B. bacteriovorus. We found that the nutrients induces AP B. bacteriovorus to up-regulate its transcription and translation machinery in a way that resembles what happen during the late intraperiplasmic stage of B. bacteriovorus life cycle

overall_design: B. bacteriovorus genome-wide gene expression pattern was compared upon incubating it in HEPES buffer versus Nutrient broth. Both are done in triplicate.

first: Mohammed

last: Dwidar

first: Hansol

last: Im

first: Jeong

last: Seo


title: Environmental and genetic regulation of white-opaque switching in Candida tropicalis

first: Jian

last: Bing

address: Songhu Road, Yangpu District

institute: Fudan University

summary: Phenotypic switching is a strategy by which microbial organisms adapt to environmental changes. The human fungal pathogens, Candida albicans and Candida tropicalis, are closely related species and capable of undergoing morphological transitions. C. albicans primarily exists in human or warm-blooded animals as a commensal, whereas C. tropicalis not only exists as a commensal but also is widely distributed in the environment. In this study, To elucidate the regulatory mechanism of environmental pH on white-opaque switching in C. tropicalis, we performed RNA-Seq analysis under three pH conditions (pH 5.0, pH 7.0, and pH 8.0).

overall_design: total RNA profiles of Candida tropicalis response to different PH

first: Guanghua

last: Huang

first: Qiushi

last: Zheng


title: Proteome allocation constraints determine cellular growth rates and demand fitness trade-offs

city: La Jolla

first: Edward

last: OBrien

state: CA

address: 417 Powell-Focht Bioengineering Hall, 9500 Gilman Drive La Jolla

institute: UCSD

summary: Protein synthesis is costly and the proteome size is constrained. Using a genome-scale computational model of proteome allocation together with absolute proteomics data sets from many growth environments, we determine how these fundamental limitations constrain growth and fitness in Escherichia coli. First, we show that the observed variation in growth rates across environments is largely determined by the expression of protein not utilized for growth in a given environment. We then elucidate the overall transcriptional regulatory logic that underlies the expression of unused protein. We systematically classify the unused proteome into segments devoted to environmental readiness and stress resistance functions. While expression of these proteome segments incurs a fitness cost of decreased growth in a fixed environment, they provide fitness benefits in a changing environment. Thus, the systems biology of the prokaryotic proteome can be quantitatively understood based on resource allocation to growth, environmental readiness, and stress resistance functions.

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: nitrogen-limited and carbon-limited chemostats both at 2 different growth rates

last: O'Brien

first: Jose

last: Utrilla

first: Bernard

last: Palsson


title: Differential RNASeq of human bronchial and nasal epithelial cells stimulated with RIG-I ligand SLR14

status: Public on Jul 30 2018

city: New Haven

first: Ellen

middle: Flescher

last: Foxman

state: CT

address: 330 Cedar St.

department: Laboratory Medicine

institute: Yale University

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

overall_design: Refer to individual Series


title: Hepatic miRNA profile in dengue hemorrhagic fever associated with apoptosis regulation, vascular injury and inflammation

city: Ananindeua

first: Layanna

middle: Freitas de

last: Oliveira

state: Pará

address: BR 316 Km 7

department: Arbovirology Section

country: Brazil

institute: Evandro Chagas Institute

summary:
Purpose: Dengue virus (DENV) causes dengue hemorrhagic fever (DHF) and have been often associated to fatal cases worldwide. The liver is one of the most important target tissues in severe cases, due to its intense viral replication and role in metabolism. microRNAs (miRNA) role during infection is crucial to understand the regulatory mechanisms of DENV infection, and can help in diagnostic and anti-viral therapies development.
Methods: miRNoma sequencing of ten fatal cases and compared to controls, to characterize the miRNAs expression profile of the human formalin fixed paraffin embedded (FFPE) liver tissue during DHF
Results: Eight miRNAs were differentially expressed in hepatic FFPE tissue: miR-126-5p (log2FC 3.09; p< 0,001), a regulatory molecule of endothelial cells, and miR-133a-3p (100-fold, p<0,001) were up regulated in DHF and miR-122-5p (a liver-specific miRNA), miR-146a-5p (Interferon-regulator), miR-10b-5p, miR-204-5p, miR-148a-5p and miR-423-5p were down regulated. Enrichment analysis of KEGG pathways and GO terms with predicted target genes of overexpressed miRNAs revealed regulatory pathways of apoptosis, involving MAPK, RAS, CDK and FAS and immune response pathways were related to NF- kB, CC and CX families, IL and TLR. The enrichment analysis using target genes of down regulated miRNAs in DHF also identified in most pathways of apoptosis and biosynthetic pathways.
Conclusions: This is the first description of the human miRNA profile in liver tissues from DHF cases. The results demonstrated the association of miR-126-5p, miR-122-5p and miR-146a-5p with DHF liver pathogenesis, involving endothelial repair and vascular permeability regulation, control of homeostasis and expression of inflammatory cytokines.

overall_design: miRNA profile from ten FFPE hepatic tissue of dengue hemorragic fever fatal cases compared with five control FFPE tissue from non hepatic injury individuals sequenced by MiSeq Illumina.

middle: F

first: João

last: Vianez

first: Carla

last: Pagliari

first: Leda

middle: V

last: Carvalho

first: Taiana

last: Silveira

first: Jedson

last: Cardoso

first: André

last: Telles

first: Janaina

last: Vasconcelos

first: Caroline

last: Moreira-Nunes

first: Rommel

middle: R

last: Burbano

first: Márcio

middle: T

last: Nunes

first: Eduardo

last: Santos


title: Linking prostate cancer cell AR heterogeneity to distinct castration and Enzalutamide responses

city: Buffalo

first: Xin

last: Chen

address: Elm & Carlton Streets

department: Pharmacology & Therapeutics

institute: Roswell Park Cancer Institute

summary: Molecular mechanisms underlying resistance to androgen deprivation therapy (ADT) and, in particular, to antiandrogen Enzalutamide, in treating castration-resistant prostate cancer (CRPC), remain incompletely understood. Through screening >120 CRPC patient samples, we observed 3 expression patterns of androgen receptor (AR) protein: primarily nuclear (nuc-AR), mixed nuclear/cytoplasmic expression (nuc/cyto-AR), and low/no expression (AR-/lo). Xenograft CRPC modeling in 4 models (i.e., LNCaP, VCaP, LAPC4, and LAPC9) recapitulated the 3 AR expression patterns in castration-resistant tumors developed from parental androgen-dependent tumors. Strikingly, although the 3 CRPC models that retained AR expression (LNCaP, VCaP, and LAPC4)  responded, to different levels and in different kinetics, to Enzalutamide, the AR-/lo LAPC9 CRPC was completely refractory to Enzalutamide. By combining whole-genome RNA-Seq and biochemical analyses together with experimental combinatorial therapy in the LNCaP and LAPC9 models, we identified BCL-2 as a critical therapeutic target in both AR+/hi and AR-/lo, Enzalutamide-resistant CRPC models.

overall_design: 1) In LNCaP model, total RNA profiles of 4 pairs of LNCaP AD, LNCaP Primary CRPC and LNCaP Secondary CRPC tumors were generated by deep sequencing. 2) In LAPC9 model, total RNA profiles of 5 paris of LAPC9 AD and LAPC9 CRPC tumors were generated by deep sequencing.

first: Hsueh-Ping

last: Chao

first: Yue

last: Lu

first: Qiuhui

last: Li

first: Dean

last: Tang


title: Epigenome editing of microsatellite repeat enhancers reveals specific regulatory functions and tumor dependencies [NRO-Seq]

city: Boston

first: Sowmya

last: Iyer

department: Pathology

institute: Massachusetts General Hospital

summary: Various types of repetitive sequences are dysregulated in cancer but their contributions to oncogenesis are yet to be determined. Here we combine nascent transcription profiling with epigenome editing to test the function of GGAA microsatellites in Ewing sarcoma, a pediatric bone cancer where the oncogenic fusion protein EWS-FLI1 induces chromatin features of active enhancers at this class of repeats. Silencing of chromatin through epigenome editing at specific GGAA repeats abolished local nascent transcription, decreased the expression of neighboring target genes and, in the case of a repeat associated with the SOX2 locus, reduced the growth of tumor xenografts. Our studies directly demonstrate that repeat elements can acquire enhancer functions in cancer and become critical components of oncogenic gene regulation programs.

overall_design: Nascent transcription was measured using NRO-seq in Ewing sarcoma cells (A673 and SKNMC). EWS-FLI1 was knocked-down with lentiviral shRNA.

first: Gaylor

last: Boulay

first: Angela

last: Volorio

first: Miguel

last: Rivera


title: Expression of MLL-ENL in hematopoietic stem cells induces mixed lineage acute leukemia

city: Basel

first: Antoine

last: Peters

address: Maulbeerstrasse 66

institute: Friedrich Miescher Institute for Biomedical Research (FMI)

summary: The t(11;19)(q23;p13.3) translocation leading to the expression of an MLL-ENL fusion is one of the most prevalent alterations affecting the mixed lineage leukemia 1 (MLL1) gene, mostly associated with B-cell acute lymphoblastic leukemia (ALL). Using a doxycycline (DOX)-inducible transgenic mouse model (“iMLL-ENL”) we show that direct induction or induction following transplantation of hematopoietic stem cells (HSC) but not of committed myeloid granulocyte-macrophage progenitors (GMP) leads to reversible acute mixed lineage leukemia. Disease induction was associated with iMLL-ENL levels exceeding the endogenous Mll1. iMLL-ENL leukemia was composed of small B220High cells with higher leukemia-initiating potential than co-existing larger-sized B220Low cells. Collectively, characterization of a novel transgenic mouse model indicates that the cell-of-origin and the expression levels above Mll1/MLL1 are both critical determinants for mixed lineage leukemia induced by the MLL-ENL fusion.

overall_design: RNA-sequencing of hematopoietic stem cells in control and iMLL-ENLleukemic mice  (total bone marrow or sorted for HIGH and LOW expression levels of the surface marker B220)

first: Hélène

last: Royo

first: Vaia

last: Stavropoulou

first: Jürg

last: Schwaller


title: Epigenome editing of microsatellite repeat enhancers reveals specific regulatory functions and tumor dependencies [ChIP-Seq]

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
Various types of repetitive sequences are dysregulated in cancer but their contributions to oncogenesis are yet to be determined. Here we combine nascent transcription profiling with epigenome editing to test the function of GGAA microsatellites in Ewing sarcoma, a pediatric bone cancer where the oncogenic fusion protein EWS-FLI1 induces chromatin features of active enhancers at this class of repeats. Silencing of chromatin through epigenome editing at specific GGAA repeats abolished local nascent transcription, decreased the expression of neighboring target genes and, in the case of a repeat associated with the SOX2 locus, reduced the growth of tumor xenografts. Our studies directly demonstrate that repeat elements can acquire enhancer functions in cancer and become critical components of oncogenic gene regulation programs.

Raw data for MSC Samples GSM2857574-GSM2857587 are subject to privacy restrictions and were not submitted.

overall_design: ChIP-seq for the histone modifications H3K4me1, H3K4me3, H3K9ac, H3K27ac, H3K27me3 and the transcription factor EWS-FLI1 in mesenchymal stem cells (MSC). EWS-FLI1 was expressed in MSCs with lentiviral expression vectors. ChIP-seq for the histone modifications H3K27ac, H3K9me3 and the transcription factor EWS-FLI1 in Ewing sarcoma cells (A673). dCas9-KRAB and specific guide RNAs targeting a GGAA repeat enhancer either near NKX2-2 or SOX2 were expressed in Ewing sarcoma cells (A673) using a lentiviral expression vector. ChIP-seq for the histone modifications H3K4me3 and H3K27ac in the lung carcinoma cells NCI-H810.


title: Evolutionary rewiring of the ROX genes controlling hypoxic response in yeasts

city: Zürich

first: Markus

middle: S

last: Schröder

state: Zürich

address: Otto-Stern-Weg 7

department: Biology, Molecular Health Sciences

institute: ETH Zürich

summary: Unusually among fungi, Saccharomyces cerevisiae is able to grow in environments containing almost no oxygen. A major feature of its response to hypoxia is a transition in expression from aerobic to hypoxic genes, which often code for duplicated isoforms of the same protein. In aerobic conditions, expression of the hypoxic gene set is repressed by the HMG domain protein Rox1. Here, we examined the evolution of ROX1 and related genes in the subphylum Saccharomycotina and find that a substantial reorganization of hypoxic gene regulation occurred during yeast evolution. S. cerevisiae lost ROX2, an ancient paralog of ROX1, which is almost universally present in other yeast species. ROX2 is orthologous to Candida albicans RFG1, a regulator of filamentous growth. Many yeasts, such as Candida glabrata, lack ROX1 and contain only ROX2. Others such as Naumovozyma castellii retain both genes. Although the ancestral function of ROX2 is uncertain, we find that it is not a regulator of hypoxic genes except in C. glabrata where it has taken over this function from the absent ROX1. We also find that N. castellii has a greatly attenuated transcriptional response to hypoxia as compared to other species, but that the ergosterol pathway which is normally induced by hypoxia can be induced by cobalt chloride stress in N. castellii.

overall_design: N. castellii mRNA profiles of three biological replicates of wild type (WT) and rox2-/-, and two biological replicates of rox1-/-, rox1/rox2-/-, WT + CoCl2, rox1-/- + CoCl2, rox2-/- + CoCl2 and rox1/rox2-/- + CoCl2 were generated by deep sequencing, using Illumina GAII X. N. castellii mRNA profiles of WT in normoxic and hypoxic conditions with three biological replicates each were generated by BGI using Illumina HiSeq 2000.

first: Can

last: Wang

first: Sixiang

last: Sai

first: Kenneth

middle: H

last: Wolfe

first: Geraldine

last: Butler


title: Transcriptomic blood responses to mycobacteria in a BCG challenge model

city: Oxford

first: Julius

last: Muller

state: Oxfordshire

address: ORCRB, Roosevelt Drive

department: Nuffield Department of Medicine

institute: The Jenner Institute, University of Oxford

summary:
Cattle were vaccinated at week 0 with the live attenuated M. bovis BCG SSI vaccine strain; some animals remain as non-vaccinated controls. After eight weeks animals were challenged intranodally with 108 BCG Tokyo cfu. Lymph nodes were harvested at week 11 and bacterial load in lymph nodes evaluated. Some BCG vaccinates had bacterial loads similar to those found in non-vaccinated animals (not-protected) and some animals had lower bacterial loads (protected) than non-vaccinated animals. Immune responses to mycobacteria were monitored in vitro by stimulation of whole blood with medium, purified protein derivative from M. bovis (PPD-B) or live BCG Tokyo longitudinally. Blood samples from 6 BCG-protected, 6 BCG-not-protected and 6 not-vaccinated.
Challenged cattle stimulated with mycobacterial antigens or not were used to prepare RNA for RNAseq analysis at weeks 0 (vaccination), 8 (challenge), 9, 10 and 11. The outcome of this project would help not only in the selection of vaccine candidates but would also inform on the formulation of novel vaccines/vaccination strategies.

overall_design: Cattle were divided into three groups as follows: naïve, vaccinated protected and vaccinated not-protected. Blood samples that had been stimulated with PPD-B or BCG Tokyo (105 cfu/ml) or cultured with medium alone (negative control) from 6 animals of each group were used to prepare RNA for sequencing. Samples were obtained at four time points: week 0, week 8 (pre-challenge), week 9 (one week post-challenge) and week 10 (two weeks post-challenge); giving a total of 216. Three out of 216 mRNA samples did not pass the minimal QC criteria and were therefore removed.

first: Bernardo

last: Villarreal-Ramos

first: Martin

last: Vordermeier

first: Adaikalavan

last: Ramasamy


title: Epigenome editing of microsatellite repeat enhancers reveals specific regulatory functions and tumor dependencies

first: Sowmya

last: Iyer


title: Potential role of the CBF Pathway contributing to local adaptation of ecotypes collected from Italy and Sweden

city: Beltsville

first: Sunchung

last: Park

state: MD

address: 10300 Baltimore ave, Bldg001

department: ARS-NEA

institute: USDA -ARS

summary:
The two Arabidopsis ecotypes that are adapted to Italy and Sweden, respectively, showed different degree of freezing tolerance.
By comparing the low temperature transcriptomes of the IT and SW ecotypes with the CBF pathway being knocked out, we showed the CBF pathway plays a significant role in natural variation of freezing tolerance.

overall_design: Examination of mRNA levels in cbf CRISPR mutants in background of the Arabidospsis Italian and Swedish ecotype plants grown at warm, cold for 24h, and cold for 2 weeks.

first: Sarah

last: Gilmour

first: Michael

last: Thomashow


title: Metabolic and Expression Regulation by the rex Gene in Caldicellulosiruptor bescii

city: Oak Ridge

first: Kyle

last: Sander

state: TN

address: 1 Bethel Valley Road, MS 6038

department: Biosciences

institute: University of Tennessee/Oak Ridge National Laboratory

overall_design: A total of 18 samples were analyzed.  Each sample was sequenced on two different sequencing lanes, generating two sequence read files for each sample.  A knockout strain (delta_rex) and its parent strain (JWCB005) were each grown in three relicate fermenters and sampled at three different time points throughout batch growth; early, mid and late log phase.

first: Daehwan

last: Chung

first: Doug

last: Hyatt

first: Janet

last: Westpheling

first: Dawn

last: Klingeman

first: Miguel

last: Rodriguez

first: Brian

last: Davison

first: Steven

last: Brown


title: Global gene expression analysis of macrophage response induced by nonporous and porous silica nanoparticles

status: Public on Jul 28 2018

city: Salt Lake City

first: Philip

last: Moos

state: UT

department: Pharmacology & Toxicology

institute: University of Utah

summary: Little is known about the global gene expression profile of macrophages in response to changes in size and porosity of silica nanoparticles (SNPs). Spherical nonporous SNPs of two different diameters, and mesoporous spherical SNPs with comparable size were characterized. Reactive oxygen species, mitochondrial membrane potential, lysosome degradation capacity, and lysosome pH were measured to evaluate the influence of nonporous and mesoporous SNPs on mitochondrial and lysosomal function. RNA-sequencing was utilized to generate transcriptional profiles of RAW264.7 macrophages exposed to non-toxic SNP doses. DESeq2, limma, and BinReg2 software were used to analyze the data based on both unsupervised and supervised strategies to identify genes with greatest differences among NP treatments. Utilizing GATHER and DAVID software, possible induced pathways were studied. We found that mesoporous silica nanoparticles are capable of altering gene expression in macrophages at doses that do not elicit acute cytotoxicity, while gene transcription was minimally affected by nonporous SNPs.

overall_design: Examination of 4 different silica nanoparticles influence on gene response of RAW264.7 macrophages in triplicate

first: Mostafa

last: Yazdimamaghani

first: Hamidreza

last: Ghandehari


title: Transcriptional Regulation of Nitrogen and Nitrogen-Related Metabolism in Arabidopsis

city: Davis

first: Siobhan

last: Brady

address: 451 Health Sciences Drive, 4303 GBSF

department: GBSF

institute: UC Davis

summary:
Purpose: Investigate transcriptional changes by genetic perturbation of specific transcription factors under sufficient and limiting nitrate conditions.
Methods: 9 day old roots were harvested between 1-2pm (get hours after “sunrise”) and frozen in liquid N2. RNA-seq libraries were prepared following the BRAD-Seq DGE protocol (four biological replicates per genotype and treatment).  Libraries were sequenced using the Ilummina HiSeq 3000 in SR50 mode. Two technical replicates libraries were created from each RNA sample; after assessing sufficient reproducibility, counts across technical replicates were pooled together. Reads were processed with fastx_trimmer for barcode removal (-f 9 -v -Q 33) and trimmed by quality with reaper (paremeters: -geom no-bc -dust-suffix-late 10/ACTG -dust-suffix 10/ACTG --noqc -nnn-check 1/1 -qqq-check 33/10 -clean-length 30 -tri 20 -polya 5 --bcq-late), then mapped to the reference genome of Arabidopsis thaliana (TAIR v10) using bowtie (-a --best --strata -n 1 -m 1 -p 4 --sam --tryhard) with subsequent conversion to BAM format using samtools and counts were obtained with HTSeq-count.

overall_design: Wild-type and 12 T-DNA insertion lines were grown in media with 1 or 10 mM KNO3. mRNA from 9 days old roots was collected for RNA-seq libraries using BRAD-seq.

first: Allison

last: Gaudinier

first: Joel

last: Rodriguez-Medina


title: Effects of anticholinergic agent on miRNAs profile and transcriptome in murine model of allergic rhinitis

city: Changsha

first: Minghua

last: Hou

state: Hunan

address: 138 Tong-Zi Po Street, Yue-lu District

department: Department of Otolaryngology-Head Neck Surgery

institute: Third Xiangya Hospital, Central South University

summary:
Purpose: Ipratropium bromide (IB) is able to ameliorate symptoms of allergic rhinitis (AR) by neuroimmunologic mechanism. We intended to explorer whether IB induced effect through modulating specific alteration of miRNA profiling or not.
Methods: Nasal sRNAs (miRNAs) profiles of control mice and OVA-induced AR mice that were pre-treated with IB or normal saline before intranasal OVA challenge for 2 or 4 weeks were generated by high-throughput sequencing using Illumina Hiseq 2000.Raw data for sRNA (miRNA) profiles were processed to obtain corresponding clean data which were mapped to reference sequence(mm10) by TopHat(v2.0.9).The expression levels for these resulting mapped miRNAs were estimated by TPM (transcript per million),afterwards, the differentially expressed miRNAs were identified, and the candidate allergic-related miRNAs were further determined by RT-qPCR.
Results: Using an optimized data analysis workflow,our data showed that in nasal mucosa of allergic mice with ipratropium bromide (IB) treatment 87 miRNAs are differentially expressed whereas in the nasal mucosa of non-allergic mice 113 miRNAs are differentially expressed, when compared with allergic mice treated with normal saline.IB treatment significantly up-regulated the levels of mmu-miR-124-3p/5p, -133b-5p, -133a-3p/5p, -384-3p, -181a-5p, -378a-5p, -3071-5p. RT-qPCR data further validated these miRNAs expression.
Conclusions: Our study represents the detailed analysis of nasal mucosa miRNAs profiles of OVA-induced allergic mice treated with IB, generated by RNA-seq technology. Moreover, IB treatment orchestrated expression of allergic immune-related miRNAs of nasal mucosa in allergic mice, which may associate with ameliorated nasal allergic symptoms

overall_design: Nasal mucosa sRNAs (miRNAs) profiles of control mice and OVA-induced AR mice that were pre-treated with IB or normal saline before intranasal OVA challenge for 2 or 4 weeks were generated by high-throughput sequencing using Illumina Hiseq 2000. The candidate allergic-related identified differentially expressed miRNAs were determined by RT-qPCR

first: Wei

last: Li

first: Zuozhong

last: Xie

first: Jingang

last: Ai

first: Bo

last: Sun

first: Guolin

last: Tan


title: Novel Principles of Cellular Reprogramming Revealed by Prospective Isolation and Characterization of Rare Intermediates Poised to Generate iPSCs [RNA-seq 1]

status: Public on Jul 27 2018

first: Benjamin

middle: A

last: Schwarz

state: MA

address: 185 Cambridge St.

department: Molecular Biology

institute: MGH

summary: Cellular reprogramming converts differentiated cells into induced pluripotent stem cells (iPSCs). However, this process is extremely inefficient, complicating mechanistic studies. Here, we identified and molecularly characterized rare, early intermediates poised to reprogram with up to 100% efficiency, without perturbing additional genes or pathways. Analysis of these cells uncovered transcription factors (e.g., Tfap2c, Bex2), which are critical for reprogramming but dispensable for pluripotency maintenance. Additionally, we observed striking patterns of chromatin hyperaccessibility at pluripotency loci, which preceded gene expression in poised intermediates. Finally, inspection of these hyperaccessible regions revealed a previously unappreciated early wave of DNA demethylation, which is uncoupled from de novo methylation of somatic regions late in reprogramming. Overall, our study underscores the importance of investigating the rare intermediates poised to produce iPSCs, provides novel insights into the mechanisms of reprogramming, and offers a valuable resource for the dissection of transcriptional and epigenetic dynamics intrinsic to cell fate change.

overall_design: RNA-seq of reprogramming intermediates (11 cell types in triplicate).

first: Murat

last: Cetinbas

first: Kendell

last: Clement

first: Ryan

last: Walsh

first: Sihem

last: Cheloufi

first: Hongcang

last: Gu

first: Alexander

last: Meissner

first: Ruslan

last: Sadreyev

first: Konrad

last: Hochedlinger


title: Novel Principles of Cellular Reprogramming Revealed by Prospective Isolation and Characterization of Rare Intermediates Poised to Generate iPSCs [RNA-seq 2]

overall_design: RNA-seq of reprogramming intermediates (6 cell types in duplicate).


title: Novel Principles of Cellular Reprogramming Revealed by Prospective Isolation and Characterization of Rare Intermediates Poised to Generate iPSCs [WGBS]

type: Methylation profiling by high throughput sequencing

overall_design: Whole genome bisulfite sequencing (WGBS) of reprogramming intermediates.


title: Novel Principles of Cellular Reprogramming Revealed by Prospective Isolation and Characterization of Rare Intermediates Poised to Generate iPSCs [ATAC-seq]

overall_design: ATAC-seq of reprogramming intermediates (6 cell types in duplicate).


title: Thermal adaptation in closely related virbios

city: Beaufort

first: Dana

last: Hunt

state: NC

address: 135 Duke Marine Lab Road

institute: Duke University Marine Lab

summary: Here, we investigate the genetic mechanisms that underlie thermal specialization of closely-related vibrios isolated from coastal water at the Beaufort Inlet (Beaufort, NC, USA). This location experiences large seasonal temperature fluctuations (annual range of ~20°C), and a clear seasonal shift in vibrio diversity has been observed (Yung et al. 2015). This previous study suggested that the mechanisms of thermal adaptation apparently differ based on evolutionary timescale: shifts in the temperature of maximal growth occur between deeply branching clades but the shape of the thermal performance curve changes on shorter time scales (Yung et al. 2015). The observed thermal specialization in vibrio populations over relatively short evolutionary time scales indicates that few genes or cellular processes may contribute to the differences in thermal performance between populations. In order to understand the molecular mechanisms that underlie adaptation to local thermal regimes in environmental vibrio populations, we employ genomic and transcriptomic approaches to examine transcriptomic changes that occur within strains grown at their thermal optima and under heat and cold stress. Moreover, we compare two closely-related strains with different laboratory thermal preferences to identify in situ evolutionary responses to different thermal environments in genome content and alleles as well as gene expression.

sample_organism:
Vibrio sp. PID17_43
Vibrio sp. PID23_8

platform_organism:
Vibrio sp. PID17_43
Vibrio sp. PID23_8

overall_design:
We sequenced the transcriptomes of  two environmental strains (Vibrio sp. PID17_43 and Vibrio sp. PID23_8) grown under three temperature conditions: heat stress, temperature of optimal growth and cold stress.
The draft genome assemblies were deposited in the NCBI whole genome shotgun archive under project ID PRJNA292554, However, the WGS submission has not been released yet.

middle: E

first: Cheuk

last: Yung


title: Artificial transcription factor-induced salinity tolerance in Arabidopsis

city: Leiden

first: Christiaan

last: Henkel

address: Sylviusweg 72

department: Institute of Biology

country: Netherlands

institute: University Leiden

summary: RNA sequencing of salinity tolerant Arabidopsis thaliana mutants expressing zinc finger artificial transcription factors (ZF-ATFs), with and without salt treatment (0 mM and 75 mM NaCl).

overall_design: RNA sequencing of Arabidopsis thaliana mutants

first: Niels

last: van Tol

first: Bert

last: van der Zaal


title: Enhancement of Arabidopsis growth characteristics using genome interrogation

summary: RNA sequencing of Arabidopsis thaliana mutants expressing zinc finger artificial transcription factors (ZF-ATFs) that induce an increase in rosette surface area and biomass.


title: Novel Principles of Cellular Reprogramming Revealed by Prospective Isolation and Characterization of Rare Intermediates Poised to Generate iPSCs

overall_design: Refer to individual Series


title: Analysis of gene expression in populations of adult undifferentiated spermatogonia

status: Public on Jul 26 2018

city: CLAYTON

first: Robin

middle: Mark

last: Hobbs

state: VIC

address: 27-31 Wright Street

department: Centre for Reproductive Health

country: Australia

institute: Hudson Institute of Medical Research


title: RNA-seq analysis of canonical and adaptive human NK cell and CD8+ T cell subsets from HCMV seropositive donors

city: Minneapolis

first: Frank

last: Cichocki

state: MN

address: 420 Delaware Street SE MMC 480

institute: University of Minnesota

summary: We report our results of RNA-seq analysis on freshly isolated, sorted subsets of cytotoxic lymphocytes

overall_design: RNA was isolated from sorted cells. Libraries were created using standard Illumina reagents and analyzed using a HiSeq2500.


title: Analysis of gene expression in populations of adult undifferentiated spermatogonia [RNA-seq]

summary: The undifferentiated spermatogonial population of mouse testis is known to be functionally heterogeneous and contain both stem cells and committed progenitor cells. However, gene expression patterns marking these distinct cell fractions are poorly defined. We found that a subset of undifferentiated spermatogonia were marked by expression of a PDX1-GFP transgene but properties of these cells were unclear. Undifferentiated cells were therefore isolated from adult testes and separated according to expression of PDX1-GFP+ for gene expression analysis by RNA-seq. Our goal was to identify differentially expressed genes from PDX1-GFP+ vs PDX1-GFP- with that of known markers of stem and committed progenitor cells.

overall_design: 4 independent sets of PDX1-GFP-positive and PDX1-GFP-negative undifferentiated spermatogonia were isolated by flow sorting from adult mouse testes.

first: Hue

last: La

first: Juho-Antti

last: Mäkelä

first: Ai-Leen

last: Chan

first: Fernando

middle: J

last: Rossello

first: Christian

last: Nefzger

first: Julien

last: Legrand

first: Mia

last: De Seram

first: Jose

last: Polo


title: Mtf2-PRC2 control of canonical Wnt signaling is required for definitive erythropoiesis

city: Ottawa

first: William

last: Stanford

address: 501 Smyth Road

institute: Ottawa Hospital Research Institute

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


title: Deficiency of SIRT6 results in developmental retardation in cynomolgus monkeys

city: Beijing

first: Qi

last: Zhou

address: Datun Road, Chaoyang District

institute: Institute of Zoology,CAS

summary: To know whether SIRT6-/- monkey sustains embryonic features at transcriptome level, we compare the transcriptional profiles of SIRT6 null monkey to datasets of fetal organs.

overall_design: Examination of gene expressive levels in WT and SIRT6-/- monkey tissue samples by RNA-Seq

first: Weiqi

last: Zhang

first: Haifeng

last: Wan

first: Guihai

last: Feng


title: Recapitulation of Human Neural Microenvironment Signatures in iPSC-Derived NPC 3D Differentiation

city: Oeiras

first: Daniel

last: Simão

address: Av. República, Qta. do Marquês, Estação Agronómica Nacional, Edificio IBET/ITQB

country: Portugal

institute: iBET, Instituto de Biologia Experimental e Biológica

summary: Brain microenvironment plays an important role in neurodevelopment and function, where extracellular matrix (ECM) components and soluble factors modulate cellular features, as migration, proliferation survival and neuronal function. Disruption of microenvironment’s homeostasis is often related to pathological conditions. Here, we addressed the microenvironment remodeling occurring during in vitro differentiation of human neural stem cells (NSC) in a three-dimensional (3D) culture system.  Proteome and transcriptome dynamics revealed significant changes namely at cell membrane and ECM composition during 3D differentiation, diverging significantly from the profile of monolayer cultures (2D). Structural proteoglycans typically found in brain ECM were enriched during 3D differentiation, while 2D cultures presented increased levels of basement membrane constituents (e.g., laminins, collagens and fibrillins). Moreover, higher expression levels of synaptic machinery and ion transport machinery constituents observed for 3D cultures, both at mRNA and protein levels, suggested a higher degree of neuronal maturation and organization relative to 2D differentiation. This work demonstrated that neural cellular and extracellular features can be recapitulated in the presented 3D neural cell model,  highlighting  its value to address molecular defects in cell-ECM interactions associated with neurological disorders.

overall_design: mRNA profiles of day 0, 12 ad 30 of hiPSC-NSC 3D differentiation were generated by RNA sequencing for two hiPSC-NSC lines in duplicates, using Illumina HiSeq 4000.

first: Marta

last: Silva

first: Ana

middle: P

last: Terrasso

first: Francisca

last: Arez

first: Marcos

last: Sousa

first: Patrícia

last: Gomes-Alves

first: Nuno

last: Raimundo

first: Paula

last: Alves

first: Catarina

last: Brito


title: Mtf2-PRC2 control of canonical Wnt signaling is required for definitive erythropoiesis. [ChIP-seq]

summary: genomic loci or increase enzymatic activity, while PRC2 core proteins are required for complex stability and global levels of trimethylation of histone 3 at lysine 27 (H3K27me3). Here, we demonstrate a role for the classical PRC2 accessory protein Mtf2/Pcl2 in the hematopoietic system that is more akin to that of a core PRC2 protein. Mtf2-/- erythroid progenitors demonstrate markedly decreased core PRC2 protein levels and a global loss of H3K27me3 at promoter-proximal regions. The resulting de-repression of transcriptional and signaling networks blocks definitive erythroid development, culminating in Mtf2-/- embryos dying by e15.5 due to severe anemia. Gene regulatory network (GRN) analysis demonstrated Mtf2 directly regulates Wnt signaling in erythroblasts, leading to activated canonical Wnt signaling in Mtf2-deficient erythroblasts, while chemical inhibition of canonical Wnt signaling rescued Mtf2-deficient erythroblast differentiation in vitro. Using a combination of in vitro, in vivo and systems analyses, we demonstrate that Mtf2 is a critical epigenetic regulator of Wnt signaling during erythropoiesis and recast the role of polycomb accessory proteins in a tissue-specific context.

overall_design:
ChIP-Seq based binding measurements of H3K4me3, PCL2 and IgG controls for mouse embryonic fetal liver cells; for PCL2 wt and knockout sorted for Ter119 presence/absence
CD71+Ter119-/lo and CD71+Ter119high cell fractions from fetal livers of e14.5 WT and Pcl2-/- embryos were FACS-sorted and crosslinked by formaldehyde.  ChIP-Seq was performed for H3K27me3 (and IgG control) in both cell fractions from both genotypes.  Pcl2 ChIP-seq and its IgG control was performed on both cell fractions from wild-type embryos.

middle: L

first: Janet

last: Rothberg


title: Sensitive and powerful single-cell RNA sequencing using mcSCRB-seq

city: Martinsried

first: Christoph

last: Ziegenhain

state: Bavaria

address: Großhaderner Str. 2

department: Department Biology II

institute: Ludwig-Maximilians University Munich

summary: Single-cell RNA sequencing (scRNA-seq) has emerged as a central genome-wide method to characterize cellular identities and processes. Consequently, improving its sensitivity, flexibility, and cost-efficiency can advance many research questions. Among the flexible plate-based methods, single-cell RNA barcoding and sequencing (SCRB-seq) is highly sensitive and efficient. Here, we systematically evaluate experimental conditions of this protocol and find that adding polyethylene glycol considerably increases sensitivity by enhancing cDNA synthesis. Furthermore, using Terra polymerase increases efficiency due to a more even cDNA amplification that requires less sequencing of libraries. We combined these and other improvements to develop a scRNA-seq library protocol we call molecular crowding SCRB-seq (mcSCRB-seq), which we show to be one of the most sensitive, efficient, and flexible scRNA-seq methods to date.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: single-cell RNA-sequencing protocols were benchmarked on J1, JM8 and Universal Human Reference RNA (UHRR) and human PBMCs

first: Johannes

middle: W

last: Bagnoli


title: Mtf2-PRC2 control of canonical Wnt signaling is required for definitive erythropoiesis [RNA-Seq]

first: William

last: Stanford

state: Ontario

summary: Polycomb repressive complex 2 (PRC2) accessory proteins play substoichiometric, tissue-specific roles to recruit PRC2 to specific genomic loci or increase enzymatic activity, while PRC2 core proteins are required for complex stability and global levels of trimethylation of histone 3 at lysine 27 (H3K27me3). Here, we demonstrate a role for the classical PRC2 accessory protein Mtf2/Pcl2 in the hematopoietic system that is more akin to that of a core PRC2 protein. Mtf2-/- erythroid progenitors demonstrate markedly decreased core PRC2 protein levels and a global loss of H3K27me3 at promoter-proximal regions. The resulting de-repression of transcriptional and signaling networks blocks definitive erythroid development, culminating in Mtf2-/- embryos dying by e15.5 due to severe anemia. Gene regulatory network (GRN) analysis demonstrated Mtf2 directly regulates Wnt signaling in erythroblasts, leading to activated canonical Wnt signaling in Mtf2-deficient erythroblasts, while chemical inhibition of canonical Wnt signaling rescued Mtf2-deficient erythroblast differentiation in vitro. Using a combination of in vitro, in vivo and systems analyses, we demonstrate that Mtf2 is a critical epigenetic regulator of Wnt signaling during erythropoiesis and recast the role of polycomb accessory proteins in a tissue-specific context.

overall_design: CD71+Ter119-/lo and CD71+Ter119high cell fractions from fetal livers of e14.5 WT and Pcl2-/- embryos were FACS-sorted and RNA was isolated isolated. RNAseq was performed to determine gene expression. (560Iplus the WT sample, 548Bminus is the Pcl2-/- sample)


title: Gene expression profiling of HepG2 cells treated with  hawk tea extracts vs. DMSO-treated control group

status: Public on Jul 25 2018

first: Juan

address: No.30, Shuangqing Road, Haidian District

department: School of Medicine

institute: Tsinghua University

summary:
Hawk tea (Litsea coreana var. lanuginose) is a traditional Chinese tea, widely cultivated and consumed in southwestern China. It has been widely used to treat gastrosis, hepatitis, and inflammatory diseases for hundreds of years. Modern pharmacological studies demonstrate that hawk tea has protective effects against liver fibrosis, hypercholesterolemia, hyperglycemia, and inflammatory diseases . However, the molecular mechanism of hawk tea against hypercholesterolemia remains unclear. The aims of this study were to investigate the mechanisms of hawk tea extract (HTE) to lower cholesterol. Therefore, we performed genome-wide transcriptional analysis of hawk tea extracts treated HepG2 cells.
Hawk tea extracts (HTE) induced significant gene modulation on HepG2 cells.

overall_design: Analysis used DMSO-treated RNA as control samples for comparison to the experimental samples treated with hawk tea extracts. Indirect comparisons were made across multiple arrays with raw data pulled from different channels for data analysis and comparison to the control data.

first: Lan

last: Xie


title: GLP-1 induced transcriptomic profile in INS-1 cells

city: Brisbane

first: Justin

last: Mitchell

state: Queensland

address: 306 Carmody Road, Queensland Bioscience Precinct (Building 80), The University of Queensland

institute: Institute for molecular Bioscience

summary:
Aim: The purpose of this RNAseq study is to gain insight into the effect that Glucagon Like Peptide-1(GLP-1) or BMS-21 (11 amino acid GLP-1 mimetic) has on the transcriptomic profile of an insulin secreting pancreatic beta cell line INS-1 at 1h and 6h.
Methods: The mRNA-focussed libraries (constructed using TruSeq RNA Library Prep Kit v2) of GLP-1 or BMS-21 treated INS-1 cells at 1h or 6h were generated by sequencing, in quadruplicate, using an Illumina Hiseq2000. De-multiplexing and FASTQ sequence data was generated using the Illumina CASAVA1.8.2 pipeline. The sequence reads that passed quality filters were analyzed at the transcript level using the following. Alignment using TopHat (2.0.12) + Bowtie (2.2.3.0) to the illumina rat iGenome (build 75 - Rnor_5.0 (GCA_000001895.3)), reads summarised using Subread-feature counts (1.4.6) and differential gene analysis using DESeq2 (1.6.3) within Rstudio (0.98.945).
Results: GLP-1 treatment of INS-1 cells induced many transcriptomic changes in gene expression at both 1h and 6h relative to control at 1h and 6h. At 1h following GLP-1 treatment there were 674 genes differentially expressed (470 up-regulated and 204 down-regulated, p-adj <0.05). Further, at 6h following exposure to GLP-1 treatment there were 3192 genes differently expressed (1709  up-regulated and 1,483 down-regulated, p-adj <0.05). Comparison of GLP-1 and BMS-21 treatments revealed highly similar transcriptomic profiles at both the 1h and 6h timepoints.
Conclusion: GLP-1 has a varied effect on the transcriptomic profile of INS-1 cells.

overall_design: RNAseq generated mRNA profiles of Insulin secreting pancreatic cell line INS-1 at 1h and 6h following stimulation by GLP-1, BMS-21 or Control (DMSO) in quadruplicate, using Illumina Hiseq2000.

middle: M

first: Abishek

last: Iyer

first: David

last: Fairlie


title: Next Generation Sequencing Facilitates Quantitative Analysis of S. aureus subsp. aureus ST398 and ST239 transcriptomes

status: Public on Jul 29 2018

city: Shanghai

first: Min

last: Li

state: China

address: Department  of  Laboratory  Medicine,  Renji  Hospital,  School  of  Medicine,  8 Shanghai Jiao Tong University, Shanghai, China

department: Department  of  Laboratory  Medicine

institute: Renji  Hospital

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goal of this study is to investigate the significantly different pathways and genes between ST398 and ST239.
Methods: mRNA profiles of ST398 and ST239 at mid-logarithmic growth phase (4h) were generated by deep sequencing, respectively in quadruplicate and duplicate samples, using the Hiseq2000 (Illumina, CA) sequencer. The four samples of ST398 are J-92 (Sample1), W-604 (Sample2), R-1025 (Sample3) and R-1089 (Sample4) and grouped to G1, while the two samples of ST239 are J-95 (Sample5) and J-99 (Sample6) and grouped to G2. The sequence reads of ST398 and ST239 that passed quality filters were respectively aligned to S. aureus subsp. aureus ST398 (RefSeq accession number AM990992) and S. aureus subsp. aureus TW20 (RefSeq accession number NC _017331) using the Burrows-Wheeler Alignment tool (BWA) followed by ANOVA (ANOVA). Only the consistent data between the four ST398 samples and two ST239 samples were reserved for further analysis. qRT–PCR validation was performed using SYBR Green assays.
Results: Using an optimized data analysis workflow, RNA-seq analyses revealed four types of significantly differentially expressed genes between ST398 and ST239 (G1 only, G2 only, G1/G2>2, G2/G1>2), and only the type of G1/G2>2 was included in this study. The type of G1/G2>2 included 164 genes in total, in which there are 14 top genes showing G1/G2>5 including essB gene.
Conclusions: Our data provide new information to the signicantly different genes between ST239 and ST398, especially the highly expressed genes in ST398 compared to ST239 which might be closely related to the high virulence of ST398.

sample_organism: Staphylococcus aureus subsp. aureus ST398

overall_design: mRNA profiles of ST398 and ST239 were generated by deep sequencing, in duplicate, using the Hiseq2000 (Illumina, CA) sequencer.

first: Yanan

last: Wang


title: mRNA-seq and ORC2 ChIP-seq in Drosophila larval fat body

city: Cambridge

first: Terry

middle: L.

last: Orr-Weaver

address: 455 Main Street

institute: Whitehead Institute


title: Hippocampal single-nucleus sequencing identifies a unique transcriptional signature that is predictive of reactivity in dentate granule neurons

city: La Jolla

first: Fred

last: Gage

state: CA

address: 10010 N Torrey Pines Rd

institute: The Salk Institute for Biological Studies

summary: Neuronal circuits are constantly remodeled in response to activity, but the extent and the specificity of activity-induced transcription are unknown. In this study, we used single nucleus RNA-seq to compare transcriptional responses to activity throughout the hippocampus following exposure to a novel environment. By comparing activated and non-activated nuclei, we found that dentate granule cells (DGCs) have a unique transcriptional response to activity that differs in both magnitude and quality compared to CA1 pyramidal cells and vasoactive intestinal polypeptide (VIP) interneurons. We further used single nuclei RNA-seq to compare transcriptional responses to activity throughout the dentate gyrus following exposure to two contexts and identified that DGCs generate a transcriptional signature that is predictive of reactivity.

overall_design: Single-nucleus RNA-seq of mouse hippocampal neurons after exposure to a novel experience or remaining in the home cage and stained for cell type-specific markers, NEUN, PROX1 and CTIP2 as well as the activity-dependent marker FOS. In addition, single-nucleus RNA-seq of mouse DG neurons after exposure to two separate contexts stained for cell type-specific markers, PROX1 and CTIP2, as well as two temporally distinct activity-dependent markers, FOS and ARC.

first: Baptiste

middle: N

last: Jaeger

first: Sara

middle: B

last: Linker

last: Parylak


title: ORC2 ChIP-seq in Drosophila larval fat body

summary: We analyzed Origin Recognition Complex Subunit 2 (ORC2) ChIP-seq from hand-dissected fat body tissue from 68hr (after egg laying, AEL), 92hr AEL, and late-third wandering Drosophila melanogaster larvae. Fat body was dissected from wild-type (OrR) males and testes were removed. We examined ORC2 binding genome-wide with particular focus on the underreplicated regions in the fat body.

overall_design: ChIP-seq of ORC2 bound to fat body chromatin from 68hr AEL, 92hr AEL, and late-third wandering wild-type (OrR) Drosophila melanogaster male larvae. Sequences analyzed by Illumina sequencing. Two biological replicates are included for each ChIP reaction.

first: Brian

last: Hua

first: Helena

last: Kashevsky

first: George

last: Bell

first: Jessica

last: Von Stetina


title: Functional divergence of a global regulatory complex governing fungal filamentation

status: Public on Jul 24 2018

city: Québec

first: Faiza

last: Tebbji

address: 2705 Boulevard Laurier

institute: CHU Québec

type: Genome binding/occupancy profiling by genome tiling array

summary: Morphogenetic transitions are prevalent in the fungal kingdom. For a leading human fungal pathogen, Candida albicans, the capacity to transition between yeast and filaments is key for virulence. For the model yeast Saccharomyces cerevisiae, filamentation enables nutrient acquisition. A recent functional genomic screen in S. cerevisiae identified Mfg1 as a regulator of morphogenesis that acts in complex with Flo8 and Mss11 to enable transcriptional responses crucial for filamentation. In C. albicans, Mfg1 also interacts physically with Flo8 and Mss11 and is critical for filamentation in response to diverse cues, but the mechanisms through which it regulates morphogenesis remained elusive. Here, we explored the consequences of perturbation of Mfg1, Flo8, and Mss11 on C. albicans morphogenesis, and identified functional divergence of complex members. We observed that C. albicans Mss11 was dispensable for filamentation, and that overexpression of FLO8 caused constitutive filamentation even in the absence of Mfg1. Epistasis experiments suggested that Mfg1 acts downstream of protein kinase A, as does Flo8. Harnessing transcriptional profiling and chromatin immunoprecipitation coupled to microarray analysis, we identified divergence between transcriptional targets of Mfg1 and Flo8 in C. albicans. A key direct transcriptional target of Mfg1 is TEC1, for which overexpression was sufficient to restore filamentation in the absence of Mfg1. To identify additional Mfg1 downstream effectors, we employed a novel strategy to select for mutations that restore filamentation in the absence of Mfg1. Whole genome sequencing of filamentation-competent mutants revealed chromosome 6 amplification as a conserved adaptive mechanism. A key determinant of the amplification on chromosome 6 is FLO8, as deletion of one allele blocked morphogenesis, and chromosome 6 was not amplified in evolved lineages for which FLO8 was re-located to a different chromosome. Thus, this work highlights rewiring of key morphogenetic regulators over evolutionary time and aneuploidy as an adaptive mechanism driving fungal morphogenesis.

overall_design: We performed chromatin immunoprecipitation coupled with microarray analysis (ChIP-chip) with strains harboring Flo8 or Mfg1 epitope-tagged with a tandem affinity purification (TAP) epitope in yeast (YPD 30°C) and hyphal condition (YPD 37°C). To identify the Flo8 and Mfg1 targets that are also transcriptionally modulated by these regulators, we performed microarray analysis comparing the gene expression profiles of mfg1Δ/mfg1Δ, flo8Δ/flo8Δ and flo8Δ/flo8Δ mfg1Δ/mfg1Δ mutants with a wild-type strain under basal (yeast condition) and filament-inducing conditions

first: Elizabeth

last: Polvi

first: Amanda

last: Veri

first: Sabrina

last: Hyde

first: Saif

last: Hossain

first: Sang

last: Kim

first: Jinglin

first: Rebecca

last: Shapiro

first: Malcolm

last: Whiteway

first: Nicole

last: Robbins

first: Anna

last: Selmecki

first: Leah

last: Cowen


title: Gene expression profiling of subclinical acute kidney rejection II

first: Sunil

last: Kurian

address: 10550 N Torrey Pines Road

department: Molecular and Experimental Medicine

institute: The Scripps Research Institute

summary: Sub-clinical acute rejection (subAR) in kidney transplant recipients (KTR) leads to chronic rejection and graft loss. Non-invasive biomarkers are needed to detect subAR. 307 KTR were enrolled into a multi-center observational study. Precise clinical phenotypes (CP) were used to define subAR. Differential gene expression (DGE) data from peripheral blood samples paired with surveillance biopsies were used to train a Random Forests (RF) model to develop a gene expression profile (GEP) for subAR. A separate cohort of paired samples was used to validate the GEP. Clinical endpoints and gene pathway mapping were used to assess clinical validity and biologic relevance. DGE data from 530 samples (130 subAR) collected from 250 KTR yielded a RF model: AUC 0.85; 0.84 after internal validation with bootstrap resampling. We selected a predicted probability threshold favoring specificity and NPV (87% and 88%) over sensitivity and PPV (64% and 61%, respectively). We tested the locked model/threshold on a separate cohort of 138 KTR undergoing surveillance biopsies at our institution (rejection 42; no rejection 96): NPV 78%; PPV 51%; AUC 0.66. Both the CP and GEP of subAR within the first 12 months following transplantation were independently associated with worse graft outcomes at 24 months, including de novo donor-specific antibody (DSA). Serial GEP tracked with response to treatment of subAR.  DGE data from both cohorts mapped to gene pathways indicative of allograft rejection.


title: mRNA-seq in Drosophila larval fat body

first: Terry

last: Orr-Weaver

summary: We performed mRNA-seq from hand-dissected fat body tissue from 68hr (after egg laying, AEL) and 92hr AEL Drosophila melanogaster larvae. Fat body was dissected from wild-type (OrR) males and testes were removed. We examined gene expression genome-wide with particular focus on genes in the underreplicated regions in the fat body.

overall_design: Sequencing of poly-A selected RNA from 68hr AEL and 92hr AEL wild-type (OrR) Drosophila melanogaster male larvae. Sequences analyzed by Illumina sequencing. Two biological replicates are included for each developmental sample.

first: Brian


title: RNA changes in the cortex of 1-month old ICR mice overexpressing microRNA142-GFP compared to controls overexpressing tdtomato in the cortical neurons as determined by mRNA deep sequencing.

city: Bloomington

first: Salil

last: Sharma

state: Indiana

address: 702 North Walnut Grove Ave

department: Psychological & Brain Sciences

institute: Indiana University Bloomington

summary: The overall goal of the project is to assess the mRNA alterations in the cortex of mice overexpressing microRNA142 (miR142). The wildtype ICR mice were electroporated with miR142-GFP plasmid DNA construct and tdtomato plasmid DNA control construct at embryonic day 14.5 (E14.5) using the technique in-utero electroporation (IUE). At this age, only cortical neurons get electroporated. At one-month of age, the cortices of these mice were evaluated for the global expression of mRNAs by mRNA deep sequencing. The levels of several mRNAs were altered. Ingenuity pathway network analysis (IPA) was performed on differentially altered mRNAs.

overall_design: Five samples per each plasmid construct.

first: Hui-Chen

last: Lu


title: RNA changes in hippocampus of transgenic murine model of tauopathy (rTg4510 mice) compared to controls at asymptomatic stage (2 months) of neurodegeneration as determined by mRNA deep sequencing.

summary: The overall goal of the project is to assess the mRNA alterations in tauopathy conditions that occur at the presymptomatic stage of neurodegeneration. The animal model selected for this study is a well characterized tauopathy animal model, known as rTg4510 murine model. rTg4510 (tau) is a transgenic mouse model of human tauopathy expressing human tau containing the P301L mutation that is associated with familial frontotemporal dementia and parkinsonism linked to chromosome 17.  The expression of P301L tau driven by CaMKII promoter peaks around two month-of-age and mainly in the forebrain. 2-month of age is considered the presymptomatic stage of neurodegeneration. The global expression of mRNAs was evaluated by mRNA deep sequencing in the hippocampus of tau mice at 2 months of age. The levels of several mRNAs were altered in the hippocampus of tau mice at 2 months. Many important candidates were further evaluated for their molecular and functional contributions to the process of neurodegeneration.

overall_design: Tauopathy (rTg4510 mice) compared to controls at asymptomatic stage (2 months)


title: Parvovirus Minute Virus of Mice Localizes to Sites of Cellular DNA Damage to Establish and Amplify its Lytic Infection

city: Madison

first: Kinjal

last: Majumder

state: WI

address: 1525 Linden Drive

department: Oncology

institute: University of Wisconsin

summary: We have developed a generally adaptable, novel high-throughput chromosome conformation capture assay for use in trans (V3C-seq) that allows genome-wide identification of the direct associations of a lytic virus genome with discreet regions of the cellular chromosome. Upon infection, the parvovirus Minute Virus of Mice genome associated directly with sites of cellular DNA damage. These sites also exhibited damage in uninfected cells when cycling through S-phase. As infection proceeded, new sites of DNA damage were induced, and virus subsequently also associated with these.

overall_design: Identification of cellular interaction site of the parvovirus MVM, and the localization of the resultant DNA damage response. Independent replicates of chromosome conformation capture (designated as V3C in the file name) and ChIP-seq experiments (the target epitope provided in the name) have been performed. For each time-point or treatment, at least two independent replicates of the indicated assays have been performed. ChIP-seq assays have been normalized to total input DNA prior to rpm normalization. Chromosome conformation capture assays have been rpm normalized. A total number of twenty three samples have been deposited. "hpt" designates hours post treatment with hydroxyurea, "hpr" designates hours post release from cell cycle synchronization and "hpi" designates hours post infection with the parvovirus Minute Virus of Mice.

first: David

last: Pintel


title: Contributory role of presymptomatic and symptomatic microRNAs in Tau pathogenesis

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

overall_design: Refer to individual Series


title: Small RNA changes in hippocampus of transgenic murine model of tauopathy (rTg4510 mice) compared to littermate controls at asymptomatic stage (2 months) of neurodegeneration as determined by small RNA deep sequencing.

summary: The overall goal of the project is to assess whether small RNA, especially microRNA (miR) alterations in tauopathy conditions contribute to pathological changes that later lead to neurodegeneration. The animal model selected for this study is a well characterized tauopathy animal model, known as rTg4510 murine model. rTg4510 (tau) is a transgenic mouse model of human tauopathy expressing human tau containing the P301L mutation that is associated with familial frontotemporal dementia and parkinsonism linked to chromosome 17.  The expression of P301L tau driven by CaMKII promoter peaks around two month-of-age and mainly in the forebrain. 2-month of age is considered the asymptomatic stage of neurodegeneration. The global expression of miRs was evaluated by small RNA sequencing in the hippocampus of tau mice at 2 months of age. The levels of several miRs were altered in the hippocampus of tau mice at 2 months. Many important candidates were further evaluated for their molecular and functional contributions to the process of neurodegeneration.

overall_design: Examination of small RNAs in the hippocampus tissue of control vs tau mice at 2-month of age.


title: Small RNA changes in hippocampus of transgenic murine model of tauopathy (rTg4510 mice) compared to littermate controls at symptomatic stage (6 months) of neurodegeneration as determined by small RNA deep sequencing.

summary: The overall goal of the project is to assess whether small RNA, especially microRNA (miR) alterations in tauopathy conditions contribute to pathological changes that later lead to neurodegeneration. The animal model selected for this study is a well characterized tauopathy animal model, known as rTg4510 murine model. rTg4510 (tau) is a transgenic mouse model of human tauopathy expressing human tau containing the P301L mutation that is associated with familial frontotemporal dementia and parkinsonism linked to chromosome 17.  The expression of P301L tau driven by CaMKII promoter peaks around two month-of-age and mainly in the forebrain. 6-month of age is considered the aymptomatic stage of neurodegeneration. The global expression of miRs was evaluated by small RNA sequencing in the hippocampus of tau mice at 6 months of age. The levels of several miRs were altered in the hippocampus of tau mice at 6 months which were compared to deep sequencing data from 2-month of age. Many important candidates were further evaluated for their molecular and functional contributions to the process of neurodegeneration.

overall_design: Examination of small RNAs in the hippocampus tissue of control vs tau mice at 6-month of age.


title: ETS1 induction by the omental microenvironment promotes ovarian cancer metastasis [RNA-Seq]

first: Peter

last: Hollenhorst

state: IN

address: 1001 E Third St, Jordan Hall 104

institute: Indiana University

summary: ETS1 expression is induced by the microenvironment of ovarian metastasis and this expression allows ETS1 to activate a gene expression program involved in cell invasion and epithelial mesenchymal transision.

overall_design: mRNA profiles of luciferase knockdown (negative control) and ETS1 knockodwn in the ovarian cancer cell line HEYA8 were generated using deep sequencing, in triplicate, using Illumina HiSeq. Knockdowns were stable shRNA expression from a lentiviral construct selected with puromycin.

first: Joshua

last: Plotnik

middle: C

first: Anirban

middle: K

last: Mitra


title: MEF2C phosphorylation is required for chemotherapy resistance in acute myeloid leukemia [inhibitor MRT199665]

status: Public on Jul 23 2018

city: New York

first: Richard

last: Koche

state: New York

institute: Memorial Sloan Kettering Cancer Center

summary: In acute myeloid leukemia, chemotherapy resistance remains prevalent and poorly understood. Using functional proteomics of patient AML specimens, we identified MEF2C S222 phosphorylation as a specific marker of primary chemoresistance. We found that transgenic Mef2cS222A/S222A mice engineered to block MEF2C phosphorylation exhibited normal hematopoiesis, but were resistant to leukemogenesis induced by MLL-AF9. MEF2C phosphorylation was required for leukemia stem cell maintenance, induced by MARK kinases in cells, and blocked by selective MARK inhibitor MRT199665, which caused apoptosis of MEF2C-activated human AML cell lines and primary patient specimens, but not those lacking MEF2C. These findings identify signaling-dependent dysregulation of transcription factor control as a determinant of therapy response in AML, with immediate potential for improved diagnosis and therapy for this disease.

overall_design: RNA-sequencing of human leukemia cell line with treatment of MARK inhibitor MRT199665.

first: Fiona

last: Brown

first: Alex

last: Kentsis


title: MEF2C phosphorylation is required for chemotherapy resistance in acute myeloid leukemia [ATAC-seq]

overall_design: ATAC-sequencing of human leukemia cell line with induction of wildtype or mutant MEF2C.


title: MEF2C phosphorylation is required for chemotherapy resistance in acute myeloid leukemia


title: Single-cell RNA-seq reveals the diversity of trophoblast subtypes and patterns of differentiation in the human placenta

first: Rui

last: WANG

address: No.5 Yiheyuan Road, Haidian District

department: Biodynamics Optical Imaging Center (BIOPIC)

institute: Peking University

summary: In this study, we isolated human villous stromal cells (STRs), CTBs, the STB, and EVTs at the first and second trimester of pregnancy and monitored the transcriptome dynamics of 1567 cells at single-cell resolution. We identified 14 subtypes of placental cells and characterized their functions, especially the unexpected secretion of 102 polypeptide hormone using bioinformatics analyses and immnunostaining verifications. Our study builds a strong foundation for understanding how the human placenta develops and functions to maintain a healthy pregnancy.

overall_design: single cell transcriptome profiles of stomal cells and trophoblast cells from 8 week and 24 week gestation of placenta were generated by next generation sequencing using Illumina Hiseq4000.

first: Xiaoying

last: Fan

first: Yawei

last: Liu

last: Wang