title: Novel neuroprotective and neurogenic phenotype of microglia

city: La Jolla,

first: Inge

last: Holtman

state: California

department: CMM

institute: UCSD

summary: Background: Tissue macrophages contribute to development and protection, both requiring appropriately timed and located source(s) of factors controlling growth, cell differentiation and migration. Goal: To understand the role of microglia (tissue macrophages of the central nervous system), in promoting neurodevelopment and controlling neuroinflammation. Summary of findings: We show that microglia fulfill both these roles. In contrast to adult cells, neonatal microglia show a unique neurogenic phenotype with stem cell-like potential. Neonatal microglia are protective against neuroinflammation, and their transplantation ameliorates experimental autoimmune encephalomyelitis. A CD11c+ microglial subset predominates in primary myelinating areas of the developing brain and expresses genes for neuronal and glial survival, migration and differentiation. CD11c+ microglia are also found in clusters of repopulating microglia after experimental ablation and in neuroinflammation in adult mice, but despite some similarities, they do not recapitulate neurogenic neonatal microglia characteristics. Conclusions: We therefore identify a unique phenotype of neonatal microglia that deliver signals necessary for neurogenesis and myelination and suppress neuroinflammation.

overall_design:
The overall design was to compare transcriptomes of subsets of microglia isolated from neonatal mice, healthy adults, and adult mice with a neuroinflammatory disease (Experimental autoimmune encephalomyelitis, EAE), and to compare anti-inflammatory function of adult and neonatal microglia. Microglia were isolated by cell-sorting based on surface phenotype, and RNAseq data was analyzed using WGCNA, GO and DAVID approaches. Expression of selected genes and pathways was confirmed by histology and flow cytometry. Functional analysis involved transfer of isolated microglia to the central nervous system of animals with EAE and evaluation of outcome.
EAE = Experimental autoimmune encephalomyelitis

first: Trevor

last: Owens


title: Epigenetic mechanisms underlie the crosstalk between growth factors and a steroid hormone [RNA polymerase ChIP-Seq]

status: Public on Sep 24 2017

city: Rehovot

first: Yehoshua

last: Enuka

address: Herzl 234

department: Biological Regulation

country: Israel

institute: Weizmann Institute of Science

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Growth factors (GFs) suppression by steroid hormones  recurs in embryology and is co-opted in pathology. While studying mammary cell migration, which is stimulated by GFs and antagonized by glucocorticoids (GCs), we found that GCs inhibit positive feedback loops activated by GFs and stimulate the reciprocal negative loops. Although no alterations in DNA methylation accompany the transcriptional events instigated by either stimulus, forced demethylation of distal regions broadened the repertoire of inducible genes. Our data indicate that the crosstalk involve transcription factors like p53 and NF-kB, along with reduced pausing (and traveling) of RNA polymerase II (RNAPII) at the promoters (and bodies) of GF-inducible genes. In addition, while GFs hyper-acetylated chromatin at unmethylated promoters and enhancers of genes involved in motility, GCs hypo-acetylated the corresponding regions. In conclusion, stably unmethylated genomic regions that encode feedback regulatory modules and differentially recruit RNAPII and acetylases/deacetylases underlie suppression of growth factor signaling by glucocorticoids.

overall_design: RNA polymerase ChIP-Seq – 2 biological replicates for each treatment


title: RNAseq data on HDAC Class IIa inhibitor (CHDI-00390576) dosed Q175 mice.

status: Public on Sep 23 2017

city: Princeton

first: Jeff

last: Aaronson

state: New Jersey

address: 155 Village Boulevard, Suite 200

department: Discovery & Systems Biology

country: USA

institute: CHDI

type: Expression profiling by high throughput sequencing

summary: WT and Q175 heterozygous (het) mice treated orally twice a day with vehicle (10% HPβCD), and Q175 mice treated with either 30 or 100 mg/kg orally twice a day  CHDI-00390576. CHDI-00390576 is a Class IIa HDAC inhibitor. Mice were dosed from 4 weeks to 6 months of age.

overall_design: Tibialis, striatum, cortex, heart and liver collected N = 8 per group (4M/4F).

first: Jim

last: Rosinski


title: The BvgAS-dependent regulon of Bordetella pertussis

status: Public on Sep 22 2017

city: BETHESDA

first: Deborah

middle: M

last: Hinton

state: MD

address: 8 center Dr., Building 8, Rm 2A21

institute: NIH

summary:
Purpose: Within the past 20 years, outbreaks of whooping cough, caused by Bordetella pertussis, have led to respiratory disease and infant mortalities, despite good vaccination coverage. This is due at least in part to the introduction of a less effective acellular vaccine in the 1990’s. It is crucial then to understand the molecular basis of B. pertussis growth and infection.  The two-component system BvgA/BvgS is the B. pertussis master regulator that regulates the expression of various virulence genes.  Previous genome wide studies to identify the bvgAS regulon in B. pertussis have been limited to microarray analyses.  The goal of this study is to define the bvgAS regulon using NGS based RNA-seq analysis and RT-qPCR and to compare the differences with the previous microarray data.
Method: To define the bvgAS regulon, transcriptomes were generated using B. pertussis Tohama I BP536 (WT) and a ΔbvgAS derivative in the presence and absence of phosphorylated BvgA. Bacteria were grown either under modulating (50 mM MgSO4) conditions, in which phosphorylated BvgA is undetectable (Bvg- mode), or non-modulating (no MgSO4) conditions in which BvgA is phosphorylated (Bvg+ mode). After total RNA extraction and rRNA removal, strand-specific DNA libraries were prepared for Illumina sequencing using the ScriptSeq 2.0 kit (Illumina) in duplicates.  Libraries were sequenced using a HiSeq 2000 sequencer (Illumina; University of Buffalo Next Generation Sequencing Core Facility). Sequence reads were mapped to the reference genome (NC_002929.2) and normalized against total reads. Differential expression analyses were performed using CLC Biomedical Genomic Workbench version 3.5.4 with default parameters. Differential gene expression profiles were obtained after Empirical DGE statistical test with FDR p-value. RT–qPCR validation was performed using SYBR Green assays.
Result: Using CLC Biomedical Genomic Workbench version 3.5.4, ~ 20-25 million reads per sample were mapped to the reference B. pertussis genome (NC_002929.2).  RNA-seq analyses identified >550 genes (15% of genome) that were regulated in a bvgAS-dependent manner with a fold difference ≥ 1.6 and FDR p-value < 0.05.  RT-qPCR was used for confirmatory analyses for 80 genes.  Overall, we identified 245 genes that were positively regulated and 326 genes that were negatively regulated by bvgAS.  362 members of the bvgAS regulon were newly identified by our study.  Most importantly, our analyses indicated that the expression of dozens of transcriptional regulators increases, while the expression of multiple metabolic genes decreases in the presence of BvgA~P.
Conclusion: We report here the first RNA-seq analysis of the bvgAS regulon in B. pertussis, revealing that > 550 genes are regulated by bvgAS. Our results suggest that metabolic changes in the Bvg- mode (absence of BvgA phosphorylation) may be participating in bacterial survival, transmission, and/or persistence and identify over 200 new genes negatively regulated by bvgAS that can be tested for function.

overall_design: Two strains were used to identify the bvgAS regulon: WT and an isogenic ΔbvgAS derivative.  No MgSO4 or addition of 50 mM MgSO4 to the growth medium was used to generate the BvgA+ mode (presence of BvgA phosphorylation) or the Bvg- mode (absence of BvgA phosphorylation), respectively.  B. pertussis mRNA profiles were generated by deep sequencing, in duplicates, using Illumina ScriptSeq 2.0 kit.

first: Kyung

last: Moon

first: Richard

middle: P

last: Bonocora

first: David

middle: D

last: Kim

first: Qing

last: Chen

first: JosephT

last: Wade

first: Scott

last: Stibitz


title: Regulation of gene expression by S. aureus and GAS (S. pyogenes) in murine bone marrow-derived dendritic cells (BMDC)

city: Toronto

first: Daniel

last: De Carvalho

state: ON

address: 101 College St

country: Canada

institute: Princess Margaret Cancer Centre

summary: We report the differential regulation of Th17-inducing cytokine genes in Dendritic cells by GAS and S. aureus

overall_design: RNAseq was performed in libraries derived from mRNA from bone-marrow derived (BMDC) infected with S. aureus or GAS in vitro

first: George

middle: Y

last: Liu

first: Gislaine

middle: A

last: Martins

first: Marisel

last: Sanchez

first: Rajat

last: Singhania


title: Integrated analysis of miRNA and mRNA expression profiles in genetically improved farmed tilapia (GIFT, Oreochromis niloticus) liver exposed to high temperature stress

city: Wuxi

first: Jun

last: Qiang

state: Jiangsu

address: 9 Shanshi East road

country: China

institute: Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences

type: Non-coding RNA profiling by high throughput sequencing

summary: MicroRNAs (miRNAs) are a class of small non-coding RNAs (18-25 nucleotides) that result in RNA silencing and post-transcriptional regulation of gene expression by binding to the 3'-untranslated regions of their target mRNAs. Mature miRNAs are widely reported in plants, animals and some viruses, which involved in the innate immune response, inflammatory diseases, cell signal transduction, and metabolism. Under temperature stress, miRNA expression is regulated to cope with the stress response. Up-regulation of 18 miRNAs and down-regulation of 11 miRNAs were found in the rat jejunum after heat treatment. 25 miRNA different expression under the cold and normal conditions were identified in zebrafish (Danio rerio). However, miRNAs involved in heat stress in GIFT have not been detected, and potentially important miRNA-signal pathway could have been overlooked. Study of the regulatory function of miRNA in heat-stress response is a crucial topic in the research of fish physiology. MiRNA expression profiles of tilapia in a variety of tissue have been studied recently by high-throughput next-generation sequencing technology (NGST). The expression levels of 218 miRNAs (e.g., miR-17, miR-29, miR-155 and miR-214) were significantly altered in tilapia kidney at 6-72h post- S. agalactiae infection. Additionally, 635 mature miRNAs were identified post-hatch day 5 in tilapia XX and XY gonads, in which 62 and 49 miRNAs showed different expression respectively (e.g., sex-biased miRNAs: miR-9, miR-21, miR-30a, miR-96, miR-200b, miR-212 and miR-7977). The gene expressions may contribute to immune regulation and stress adaptation in fish by heat stress. The levels of immune-related gene (e.g., immunoglobulin M, lysozyme, hepcidin and transferrin) expression were significantly up-regulated in turbot (Scophthalmus maximus) post-48h heat stress. HSPs play an important role in fish exposed to environmental stress. Some highly conserved HSPs could be synthesized in sculpins Oligocottus maculosus, turbot and GIFT in response to heat stress. Fatty acid composition and utilization in fish could be affected by heat stress. △6-desaturase-α and elongation of long chain fatty acids 5α (Elovl 5α) are involved in poly unsaturated fatty acid biosynthesis, which were obviously up-regulated in common carp (Cyprinus carpio) by heat stress, and help to increase fatty acid metabolism and maintain fluidity of cell membrane. However, in these studies the several genes were generated from known and functional protein-coding genes. The significance of mRNA transcriptome to heat-stress response in fish are far from clear. Thus, the study of miRNA and mRNA expression profiles may help us better understand the molecular mechanisms and signaling pathway of heat stress.

overall_design: In this study, the expression profiles of miRNA and mRNA both control- and heat-stress-treated GIFT liver were investigated by NGST. Differently expressed (DE) miRNAs and DE genes were jointly analyzed within a special biological pathway. The findings of the current study offer a deeper insight into the molecular regulated-mechanisms mediating heat-stress-induced various biological process.


title: Dynamic host-pathogen interactions in pathogen-challenged chicken embryo fibroblasts cells with Marek’s Disease Virus using 3’ end enriched RNA-seq

city: Guangzhou

first: Jie

last: Li

address: No. 135, Xingang Xi Road, Guangzhou, 510275, P. R. China

institute: Sun Yat-Sen University

summary: Marek’s disease is a contagious lymphoproliferative disease of chickens and is a unique model of viral oncogenesis. Mapping changes or states over the course of infection for both host and pathogen would have the potential to generate important insights into dynamic host-pathogen interactions. Here we introduced 3’ end enriched RNA-seq as a novel method to study host-pathogen interactions in Marek’s disease virus challenged chicken embryo fibroblasts cells, which allowed accurate profiling of gene expression and alternative polyadenylation sites for host and pathogen simultaneously. We totally identified 476 differentially expressed genes and 437 APA switching genes in host, including switching in tandem 3’ UTRs and switching between coding region and 3’ UTR. Most of these genes were related to innate immunity, apoptosis and metabolism, but two sets of genes overlapped a little suggesting two complementary mechanisms for regulating gene expression during infection. In summary, our results gave a relatively comprehensive insight into dynamic host-pathogen interactions in gene transcription regulation during Marek’s disease virus infection and suggested that 3’ end enriched RNA-seq was a promising method to investigate global host-pathogen interactions.

overall_design: Samples was collected at each time point after virus challenge. Thus, in total ten IVT-SAPAS libraries were constructed and sequenced with Illumina GA IIx.

first: Liangliang

last: He


title: Expression data of Frankia sp. strain CcI6 under salt stress, osmotic stress, and control conditions (no salt/osmotic stress)

city: Durham

first: Louis

middle: S

last: Tisa

state: NH

address: 46 College Rd

department: MCBS

institute: University of New Hampshire

summary: Purpose:to identify the response of  Frankia sp.strain CcI6 to salt and osmotic stress. Frankia sp.strain CcI6 was exposed to salt  and  osmotic stress for seven days. RNAseq analysis was carried out to ge an insight into the response of the bacterium under salt and osmotic stress conditons

overall_design: mRNA profiles of Frankia sp. CcI6 grown under three different condions (control, salt stress, and osmotic stress) were generated by deep sequencing and mapped to the genome by CLC Genomic workstation. The transcriptome profile of the strain under salt and osmotic stress conditions was compared to the transcriptome profile under control conditons (no salt stress)

first: Rediet

last: Oshone

first: Sheldon

last: Hurst IV


title: MicroRNA expression in a phosphaturic mesenchymal tumour

city: Oxford

first: Irina

last: Mohorianu

address: Headington

department: Medical Sciences Division

country: United Kingdom

institute: University of Oxford

summary:
An FGF23-producing phosphaturic mesenchymal tumour was surgically resected.
We performed small RNA sequencing to quantify the microRNAs/ small RNAs expression in the resulting library.

overall_design:
The tumour was resected from the patient's femoral head. RNA was extracted from the tumour.
Small RNA sequencing using HD adapters (Xu et al 2015) was performed using Illumina HiSeq 2500

first: Darrell

last: Green

first: Jeremy

last: Turner

first: Andoni

last: Toms

first: John

last: Nolan

last: Ball

first: Iain

last: McNamara

first: Tamas

last: Dalmay

first: William

last: Fraser


title: Identification and analysis of brown planthopper-responsive microRNAs in the resistant and susceptible rice plants

city: Wuhan

first: Yan

last: Wu

address: Bayi Street

institute: Wuhan University

summary: MicroRNAs (miRNAs) regulate a spectrum of development and defense response processes in plants. The brown planthopper (BPH) is the most devastating insect pest of rice, BPH resistance gene BPH15 has a strong resistance to BPH. In this study, we analyzed six miRNA profiles of BPH15 introgression line (P15) and susceptible recipient line (PC) in 3 time points (0h, 6h and 48h) after BPH attacked, and identified 464 known miRNAs and 183 novel miRNAs. Before BPH feeding we identified 23 miRNAs expressed differently in P15 and PC. Then after BPH feeding, 104 miRNAs were found expressed differently in P15, and 80 miRNAs were found expressed differently in PC. Among them, miR167, miR444d, miR1846e, miR3979-3p, miR531 were found to be involved in BPH stress response. The response to BPH of P15 was much wider and more rapidly than PC. The levels of a subset of miRNAs were confirmed by qRT-PCR. The targets of miRNAs were predicted and validated by gene expression profiling. Additionally, the target genes of 2 differently expressed miRNAs (miR160f-5p and miR167a-5p) were confirmed by detecting YFP fluorescence and western blotting. Our data provide an important basis for evaluating the role of miRNA in the regulation of BPH interactions in rice.

overall_design: Six miRNA profiles of BPH15 introgression line (P15) and susceptible recipient line (PC) in 3 time points (0h, 6h and 48h) after BPH attacked,

first: Guangcun


title: Genome-wide maps of H3K4me3 and H3K27me3 in SATB1-depleted breast cancer cells

city: Seoul

first: Hyoung-Pyo

last: Kim

address: Yonsei-ro 50-1

country: South Korea

institute: Yonsei University

summary: We used chromatin immunoprecipitation-coupled to deep sequencing (ChIP-seq) to profile genome-wide locations of H3K4 trimethylation (H3K4me3) and H3K27 trimethylation (H3K27me3) epigenetic marks in SATB1-depleted MDA-MB-231 aggressive breast cells.

overall_design: Examination of 2 different histone modifications in a breast cancer cell line

first: Mikyoung


title: Genome-wide identification and expression profiling of long non-coding RNAs in the auditory and vestibular systems

first: Igor

last: Ulitsky

address: Hertzl St.

summary: Mammalian genomes are highly complex and can be regulated at multiple levels, often imposed by a class of RNA molecules, long intervening non-coding RNAs (lincRNAs). Their transcripts are more than 200 nucleotides in length, they are capped, polyadenylated and spliced, similar to mRNAs, but less abundant, but with higher tissue specificity. lincRNAs are versatile and can act on numerous levels and have been linked to development, epigenetic processes and disease. We performed a whole-genome identification of lincRNAs using RNA-seq at two developmental stages of the mouse inner ear sensory epithelium of the cochlea and vestibule. We identified 1,921 lncRNA genes, 1369 of which are intergenic. Of these, 403 are novel, as they were not annotated in the latest Ensembl/GENCODE annotation (Ensembl release 84). We then examined specificity by analyzing the developmental profiles at embryonic day 16.5 and at birth. The spatial and temporal patterns were examined for three lincRNAs, which were in close proximity to genes associated with hearing and deafness. Our findings demonstrate that lincRNAs are prevalent in the sensory epithelium of the mouse cochlea and vestibule and are likely to play key roles in the regulation of critical pathways for hearing and balance.

overall_design:
RNA-seq of RNA from two tissues at two developmental times, each with three biological replicates

Please note that the P0 samples (GSM2560443-48) are re-analyzed sample records of GSM1975057-62 (in GSE76149).

first: Karen

middle: B

last: Avraham


title: Role of small RNAs in gene dosage regulation in the ciliate Oxytricha trifallax

status: Public on Sep 21 2017

city: New York

first: Jaspreet

last: Khurana

state: NY

address: 701 West 168th St.

institute: Columbia University

summary: Dicer-dependent small non-coding RNAs play important roles in gene regulation in a wide variety of organisms. Endogenous small interfering RNAs (siRNAs) are part of an ancient pathway of transposon control in plants and animals. The ciliate, Oxytricha trifallax, has approximately 16,000 gene-sized chromosomes in its somatic nucleus. Long non-coding RNAs establish high ploidy levels at the onset of sexual development, but the factors that regulate chromosome copy numbers during cell division and growth have been a mystery. We report a novel function of a class of Dicer (Dcl-1)– and RNA-dependent RNA polymerase (RdRP)– dependent endogenous small RNAs in regulating chromosome copy number and gene dosage in O. trifallax. Asexually growing populations express an abundant class of 21nt sRNAs that map to both coding and non-coding regions of most chromosomes. These sRNAs are bound to chromatin and their levels surprisingly do not correlate with mRNA levels. Instead, the levels of these small RNAs correlate with genomic DNA copy number. Reduced sRNA levels in dcl-1 or rdrp mutants lead to concomitant reduction in chromosome copy number. Furthermore, these cells show no signs of transposon activation, but instead display irregular nuclear architecture and signs of replication stress. In conclusion, Oxytricha Dcl-1 and RdRP-dependent small RNAs that derive from the somatic nucleus contribute to the maintenance of gene dosage, possibly via a role in DNA replication, offering a novel role for these small RNAs in eukaryotes.

overall_design: Datasets: 1) sRNAs from asexually growing O.trifallax cells from WT (mix of strain JRB310 and JRB510), dcl-123, dcl-141, rdrp13. 2) RNAseq from Poly(A) selected RNA from WT (strain JRB310),  dcl-141, rdrp13.  3) Whole cell Genomic DNA from WT (strain JRB310),  WT (F1 crossed between JRB310 and JRB510), dcl-141, rdrp13

first: Derek

last: Clay

first: Sandrine

last: Moreira

first: Xing

last: Wang

first: Laura

middle: F

last: Landweber


title: Transcriptional architecture of synaptic communication delineates cortical GABAergic neuron identity

city: Hershey

first: Anirban

last: Paul

state: PA

address: 500 University Drive

department: Neural and Behavioral Sciences

institute: Penn State College of Medicine

summary: We sequenced six types of interneurons from adult mouse frontal cortex across multiple library batches to determine GABAergic neuronal identity

overall_design: Cells were harvested from four animals and processed in batches of 16 cells each.

first: Josh

last: Huang

first: Megan

last: Crow

first: Jesse

last: Gillis


title: Streptococcus pneumoniae TIGR4 phase-locked opacity variants differ in virulence phenotypes

city: Birmingham

first: W

middle: Edward

last: Swords

state: Alabama

address: 1918 University Blvd. McCallum bldg, Room 798

department: Medicine, Division of Pulmonary, Allergy and Critical Care Medicine

institute: Univ. of Alabama at Birmingham

summary: Streptococcus pneumoniae (pneumococcus) is a leading human pathogen that can cause serious localized and invasive diseases. Pneumococci can undergo a spontaneous and reversible phase variation that is reflected in colony opacity, which allows the population to adapt to different host environments. Generally, transparent variants are adapted for nasopharyngeal colonization whereas opaque variants are associated with invasive disease. In recent work, colony phase variation was shown to occur by means of recombination events to generate multiple alleles of the hsdS targeting domain of a DNA methylase complex, which mediates epigenetic changes in gene expression. A panel of isogenic strains were created in the well-studied S. pneumoniae TIGR4 background that are “locked” in the transparent (n=4) or opaque (n=2) colony phenotype. The strains had significant differences in colony size which were stable over multiple passages in vitro and in vivo. While there were no significant differences in adherence for the phase-locked mutant strains to immortalized epithelial cells, biofilm formation and viability was reduced for opaque variants in static assays.  Nasopharyngeal colonization was stable for all strains, but the mortality rate differed between them.  Transcript profiling by RNA-seq analyses revealed that expression of certain virulence factors were increased in a phase-specific manner.  As epigenetic regulation of phase variation (often referred to as phasevarion) is emerging as a common theme for mucosal pathogens, these studies serve as a model for future studies of host-pathogen interactions.

overall_design: RNA from pneumococcal strains TIGR4, MBO15, MBO20, MBO21, MBO22, MBO23, MBO24, and MBO25 were analyzed. TIGR4 was the parent strain. MBO15 was the hsdS deletion strain. MBO20 through MBO25 were the isogenic TIGR4 strains containing alleles A through F, respectively. RNA was extracted from a total of 8 strains, with three replicates per strain, resulting in 24 total samples analyzed.

first: Melissa

last: Oliver

first: Ankita

last: Basu Roy

middle: E


title: RNA seq_A375 gSMARCB1 +  A549 etoposide, Aurora kinases inhibitors treated

city: Amsterdam

first: Liqin

address: Plesmanlaan 121

country: Netherlands

institute: NKI-AVL

summary: To study the senescence gene signatures in the cells, which were  genetic SMARCB1 depleted or treated with aurora kinase inhibitors or etoposide, we performed next generation RNA sequencing on these cell, and 'FRIDMAN_SENESCENCE_UP' geneset was used to determine the enrichment of senescence-related genes. The RNA sequencing results include (1) A375 cells and SMARCB1 depleted counterparts. (2) A549 cells and aurora kinase inhibitor (Alisertib, barasertib or tozasertib) or etoposide treated counterparts.

overall_design:
RNA seq data of A375_gSMARCB1 +  A549_etoposide, Aurora kinases inhibitors treated, to check senescence gene expression signature
one replicate of A375 cells parental V.S SMARCB1 KO (by CRISPR) + duplicates of A549 parental V.S etoposide, or 3 indepdent aurora kinase inhibitors (MLN8237/Alisertib, VX680/Tozasertib, AZD1132/Barasertib)

first: Iris

last: de Rink

first: Cor

last: Lieftink


title: Genome editing reveals a role for OCT4 in human preimplantation development [MiSeq]

city: London

first: Kathy

last: Niakan

address: Mill Hill

institute: The Francis Crick Institute

summary: Despite their fundamental biological and clinical importance, the molecular mechanisms that regulate the first cell fate decisions in the human embryo are not well understood. Here we use CRISPR?Cas9-mediated genome editing to investigate the function of the pluripotency transcription factor OCT4 during human embryogenesis. We identified an efficient OCT4-targeting guide RNA using an inducible human embryonic stem cell-based system and microinjection of mouse zygotes. Using these refined methods, we efficiently and specifically targeted the gene encoding OCT4 (POU5F1) in diploid human zygotes and found that blastocyst development was compromised. Transcriptomics analysis revealed that, in POU5F1-null cells, gene expression was downregulated not only for extra-embryonic trophectoderm genes, such as CDX2, but also for regulators of the pluripotent epiblast, including NANOG. By contrast, Pou5f1-null mouse embryos maintained the expression of orthologous genes, and blastocys  t development was established, but maintenance was compromised. We conclude that CRISPR?Cas9-mediated genome editing is a powerful method for investigating gene function in the context of human development.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: 244 OCT4-targeted samples including controls. Each of the OCT4-targeted sites were sequenced using MISeq to evaluate targeting efficiency and to investigate the different types of mutation. Sequencing of pottential off-target sites was also performed to evaluate targeting specificity.

first: Norah

last: Fogarty

first: Afshan

last: McCarthy

first: Paul

last: Blakeley


title: Genome-wide Analysis of Binding Sites of the Caenorhabditis elegans NR4A Nuclear Receptor NHR-6 During Spermatheca Organogenesis

city: Monroe

first: Chris

middle: R

last: Gissendanner

state: LA

address: 700 University Avenue

institute: University of Louisiana Monroe

summary: The gene nhr-6 encodes the sole C. elegans NR4A nuclear receptor homolog which has a critical role in organogenesis by regulating the development of the spermatheca organ. Here we utilized chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq) to identify NHR-6 binding sites during both the late L3/early L4 and mid L4 developmental stages. Our results revealed 30,745 enriched binding sites for NHR-6 with sites specific to each developmental stage and sites found in both stages. Additionally, ~70% of enriched sites were found within 3 kb upstream of a gene transcription start site. Binding sites for a cohort of candidate target genes with probable functions in spermatheca organogenesis were validated through qPCR. Reproductive and spermatheca phenotypes were also evaluated for these genes following a loss-of-function RNAi screen which revealed several genes with critical functions during spermatheca organogenesis. Our results uncovered a complex nuclear receptor regulatory network whereby NHR-6 regulates multiple cellular processes including proliferation, differentiation, and metabolism.

overall_design: Identification of NHR-6 binding sites using ChIP-seq at two developmental stages

first: Brandon

last: Praslicka


title: Proteogenomic characterization of developmental defects in the forebrain resulting from hyperactivated mTOR signaling

city: Daejeon

first: Yukyung

last: Jun

address: 245 Daehak-ro, Yuseong-gu

department: Center for Supercomputing Applications

institute: Korea Institute of Science and Technology Information

summary:
Hyperactivated mTOR signaling in the developing brain has been implicated in multiple forms of pathology including tuberous sclerosis complex (TSC).
Here, we present an integrated analysis of transcriptomes and proteomes generated from wild-type and TSC1/Emx1-Cre forebrains.
This led to comprehensive lists of genes and proteins whose expression levels were altered by hyperactivated mTOR signaling.

overall_design: Comparative analyses of data from wild-type (WT) and TSC1/Emx1-Cre forebrains revealed sets of genes and proteins altered by TSC1 knockout.

first: Jiheon

last: Shin

first: Minhyung

last: Kim

first: Hee-Jung

last: Jung

first: Hye

middle: L

last: Cha

first: Haeyoung

last: Suh-Kim

first: Sanghyun

last: Ahn

first: Jaehoon

first: YounAh

first: Sanghyuk

last: Lee

first: Daehee

last: Hwang

first: Jaesang


title: 3′ sequencing from human Huntington's disease and control motor cortex and cerebellum.

city: Worcester

first: Neil

last: Aronin

state: MA

address: 368 Plantation St.

institute: University of Massachusetts Medical School

summary:
Purpose: We applied polyA site sequencing (Passeq) to human Huntington's disease and control motor cortex and cerebellum to test if any genes change 3′UTR isoforms abundance.
Methods: 3′ sequencing was performed on 6 motor cortices from grade 1 Huntington's patient brains, 4 motor cortices from grade 2 Huntington's patient brains, and 5 motor cortices from control brains.  Cerebellum samples included 9 cerebella from grade 2-3 Huntington's patient brains, and 7 cerebella from control brains. To verify HTT isoforms in mice, sequencing was performed on 5 Q140 mouse striata and 3 wild-type mouse striata.
Results: We report 11% of genes from Huntington's disease patient motor cortex exhibit a change in at least one of their 3′UTR isoforms, commensurate with the 11% of genes which show different total expression in HD motor cortex versus control.  In contrast, gene isoform and expression changes are minimal (<5%) in Huntington's disease cerebellum versus controls. In the motor cortex, we show isoform and gene expression differs between between grade 1 and grade 2 brains.  We identify a novel isoform of huntingtin mRNA which is conserved in wild-type and Huntington's model mice.
Conclusions: This is the first study characterizing widespread alterations in 3′UTR isoform abundance in Huntington's disease.  Alterations in isoform abundance may affect mRNA metabolism in Huntington's disease brains.

overall_design: Examination of 3′UTR isoform abundance in Huntington's disease and control motor cortex and cerebellum, and in Q140 and wild-type mouse striatum. 3′ sequencing was performed on 6 motor cortices from grade 1 Huntington's patient brains, 4 motor cortices from grade 2 Huntington's patient brains, and 5 motor cortices from control brains.  Cerebellum samples included 9 cerebella from grade 2-3 Huntington's patient brains, and 7 cerebella from control brains. To verify HTT isoforms in mice, sequencing was performed on 5 Q140 mouse striata and 3 wild-type mouse striata.

first: Lindsay

last: Romo

first: Ami

last: Ashar-Patel


title: Intestinal epithelial and intraepithelial T cell crosstalk mediates a dynamic response to infection

first: Daniel

last: Mucida

address: 1230 York Avenue

institute: The Rockefeller University

summary: Oral infection of mice with Salmonella Typhimurium leads to rapid changes in small intestinal TCRgd IEL behavior. How these changes are induced is currently unknown. By analyzing the transcriptome of TCRgd and intestinal epithelial cells in the steady state and after infection, we find a potential role for epithelial cell MYD88 expression in regulating the IEL response. By additionally analyzing the transcriptome of epithelial cell-specific, conditional Myd88 knockout animals after Salmonella infection, we address the role of epithelial cell Myd88 signaling in regulating the IEL and EC response to Salmonella infection.

overall_design: 3 types of mice were used: wildtype C57BL/6 mice, Villin-Cre Myd88ff and Cre negative control mice (C57BL/6 background). Wildtype mice were naïve or orally infected with 10^8 CFU of Salmonella enterica serovar Typhimurium (SL1344) and IELs were harvested from the small intestine after 18 hours. Villin-Cre Myd88ff and Cre negative control mice were treated  with Tamoxifen. 1 week after Tamoxifen treatment, mice were orally infected  with 10^8 CFU of Salmonella enterica serovar Typhimurium (SL1344) and IELs were harvested from the small intestine after 18 hours.

first: David

last: Hoytema van Konijnenburg

first: Bernardo

last: Reis

first: Virginia

last: Pedicord

first: Julia

last: Farache

first: Gabriel

last: Victora


title: A somatic mutation in erythro-myeloid progenitors causes (late-onset) neurodegenerative disease

first: Frederic

last: Geissmann

address: 1275 York Ave

department: Immunology Program

institute: Memorial Sloan Kettering Cancer Center (MSKCC)

summary: The pathophysiology of neurodegenerative diseases is poorly understood, and therapeutic options are few. Neurodegenerative diseases are hallmarked by progressive neuronal dysfunction and loss, associated with chronic glial and immune activation1. Microglia are the resident macrophages of the nervous system thought to be important for the clearance of debris after neuronal damage and aid to repair and regeneration. Their activation is viewed in general as a reactive process in neurodegeneration1-3. Whether microglia itself may be causative of neurodegenerative diseases is unclear. Late-onset neurodegenerative disease is frequently observed in patients with histiocytoses4-10, which are clonal myeloid diseases associated with somatic mutations in the RAS/MEK/ERK pathway such as BRAFV600E 5,11,12, suggesting a possible role of somatic mutations in neurodegeneration. Yet, expression of BRAFV600E in the hematopoietic stem cell (HSC) lineage does not cause neurodegeneration13,14. However, recent works from our laboratories and other have revealed that microglia belong to a lineage of adult tissue-resident myeloid cells that develop during organogenesis from yolk sac erythro-myeloid progenitors (EMP) distinct from HSC15-18. We thus hypothesized that somatic BRAFV600E mutations in the resident macrophage lineage may cause neurodegeneration. We found that while BRAFV600E expression in the HSC lineage causes leukemic and tumoral diseases13,14, its expression in the EMP lineage instead results in a severe late-onset neurodegenerative disorder. Neurological symptoms, neuronal death, astrogliosis, immune activation, and amyloid precursor protein deposition were driven by ERK-activated microglia clones and preventable by RAF inhibition. These results identify the fetal precursors of tissue-resident macrophages as a potential cell-of-origin for histiocytoses, and demonstrate that a somatic mutation in the EMP lineage can drive late-onset neurodegeneration. Moreover, these data identify activation of the MAP kinase pathway in microglia as a cause of neurodegenerative disease, and provide opportunities for therapeutic intervention aimed at preventing neuronal death in neurodegenerative diseases

overall_design: RNA-seq from YFP+ and  from BRAFVE and BRAFWT mice in brain stem from 1 and 6-month-old and liver 1 month-old

first: Elvira

last: Mass

first: Alessandro

last: Pastore


title: Differential gene regulation and tumor inhibitory activities of alpha-, delta- and gamma-tocopherols in estrogen-mediated mammary carcinogenesis

status: Public on Sep 30 2017

city: Piscataway

first: Nanjoo

last: Suh

state: NJ

address: 164 Frelinghuysen Road

institute: Rutgers University

summary:
Purpose: Examination of different forms of tocopherol treatment in mammary tumorigenesis by comparing NGS-derived transcriptome profiling (RNA-seq)
Methods: Use of cDNA library construction and Illumina sequencing (NextGen 75 bp pair-end) and quality control using FastQC.
Results: Differential transcriptome profiling of mammary tumors between different forms of tocopherol treatment was observed.
Conclusions: Our study represents the first detailed analysis of mammary tumor transcriptomes with different tocopherol treatment generated by RNA-seq technology. The optimized data analysis reported here should provide a framework for comparative investigations of expression profiles with tocopherols.

overall_design: mRNA profiles of mammary tumors from ACI rats treated with different tocopherols for 30 weeks were generated by cDNA library construction/illumina sequencing


title: Whole genome sequencing of Drosophila melanogaster from different microclimates at 'Evolution Canyon'

status: Public on Sep 20 2017

city: Stanford

first: Jin

middle: Billy

last: Li

state: CA

address: 300 Pasteur Drive, Alway M-341

department: Genetics

institute: Stanford University

summary: We sequenced the genomes of 32 isofemale fly lines from two divergent microclimates at 'Evolution Canyon' in Israel (16 fly lines from each microclimate).

overall_design: We sequenced the whole genomes of single male flies from each of the 32 isofemale fly lines from 'Evolution Canyon'.

first: Arielle

last: Yablonovitch

first: Kexin

first: Eugenia

last: Rashkovetsky

first: Abraham

last: Korol

first: Pawel

last: Michalak

first: Eviatar

last: Nevo


title: Organism-level analysis of vaccination reveals networks of protection across tissues

city: Chicago

first: Nicolas

last: Chevrier

state: Illinois

address: 5640 South Ellis Avenue

department: Pritzker School of Molecular Engineering

institute: The University of Chicago

summary: To study the response of single lung and liver memory CD8+ T cells to reactivation, mice vaccinated subcutaneously with MVA (10^7 PFUs/mouse) were subsequently challenged intranasally with: (1) PBS; (2) WR (10^7 PFUs/mouse); or (3) Vaccinia virus-derived B8R20-27 peptide (20 µg/mouse). Sixteen hours after challenge, single-cell suspensions were generated from lung or liver and lymphocytes were enriched using Percoll density centrifugation prior to immunostaining and cell sorting. Single memory CD8+ T cells from lung and liver were profiled using plate-based or droplet-based single-cell RNA-seq.

overall_design: Three datasets were generated from single memory CD8+ T cells isolated from lung or liver using plate-based (2,423 cells) or droplet-based (7,292) single-cell RNA-seq methods, which included: (i) 947 cells from lung of MVA-vaccinated mice challenged with PBS, WR or B8R20-27 peptide (plate-based – experiment 1); (ii) 1,476 cells from lung or liver of MVA-vaccinated mice challenged with PBS or WR (plate-based – experiment 2); and (iii) 7,292 cells from lung of MVA-vaccinated mice challenged with PBS or WR (droplet-based – experiment 3). Libraries from each experiment were sequenced as a single pool on an Illumina NextSeq500 sequencer.

first: Motohiko

last: Kadoki


title: Gene-Edited Human Kidney Organoids Reveal Mechanisms of Disease in Podocyte Development

city: Box

first: Stuart

last: Shankland

state: WA

address: 1959 NE Pacific Avenue

department: Nephrology

institute: University of Washington, Seattle

summary: A critical event during kidney organogenesis is the differentiation of podocytes, specialized epithelial cells that filter blood plasma to form urine. Podocytes derived from human pluripotent stem cells (hPSC-podocytes) have recently been generated in nephron-like kidney organoids, but the developmental stage of these cells and their capacity to reveal disease mechanisms remains unclear. Here, we show that hPSC-podocytes phenocopy mammalian podocytes at the capillary loop stage (CLS), recapitulating key features of ultrastructure, gene expression, and mutant phenotype. hPSC-podocytes in vitro progressively establish junction-rich basal membranes (nephrin+ podocin+ ZO-1+) and microvillus-rich apical membranes (podocalyxin+), similar to CLS podocytes in vivo. Ultrastructural, biophysical, and transcriptomic analysis of podocalyxin-knockout hPSCs and derived podocytes, generated using CRISPR/Cas9, reveals defects in the assembly of microvilli and lateral spaces between developing podocytes, resulting in failed junctional migration. These defects are phenocopied in CLS glomeruli of podocalyxin-deficient mice, which cannot produce urine, thereby demonstrating that podocalyxin has a conserved and essential role in mammalian podocyte maturation. Defining the maturity of hPSC-podocytes and their capacity to reveal and recapitulate pathophysiological mechanisms establishes a powerful framework for studying human kidney disease and regeneration.

overall_design: 6 biological sample were isolated from wild type and PODXL mutant human pluripotent stem cells (12 samples in total). RNA-seq was performed on each sample.

first: Benjamin

last: Freedman

first: Yuliang

last: Wang

first: Kelly

last: McNagny


title: Transcriptomic responses of the endangered freshwater mussel Margaritifera margaritifera to trace metal contamination in the Dronne River, France

city: Arcachon

first: Anthony

last: Bertucci

address: Place du Dr Peyneau

country: France

institute: University of Bordeaux

summary: The freshwater pearl mussel Margaritifera margaritifera is one of the most threatened freshwater bivalves worldwide. In this study, we aimed (i) to study the processes by which water quality might affect freshwater mussels in situ and (ii) to provide insights into the ecotoxicological significance of water pollution to natural populations in order to provide necessary information to enhance conservation strategies. M. margaritifera specimens were sampled in two close sites located upstream or downstream from an illegal dumping site. The renal transcriptome of these animals was assembled and gene transcription determined by RNA-seq. Correlations between transcription levels of each single transcript and the bioaccumulation of 9 trace metals, age (estimated by sclerochronology) and condition index were determined in order to identify genes likely to respond to a specific factor. Amongst the studied metals, Cr, Zn, Cd and Ni were the main factors correlated with transcription levels, with effects on translation, apoptosis, immune response, response to stimulus and transport pathways. However, the main factor explaining changes in gene transcription appeared to be the age of individuals with a negative correlation with the transcription of retrotransposons-related genes. To investigate this effect further, mussels were classified into 3 age classes. In young, middle-aged and old animals, transcription levels were mainly explained by Cu, Zn and age, respectively. This suggests differences in the molecular responses of this species to metals during its lifetime that must be better assessed in future ecotoxicology studies.

overall_design: 32 samples - In april 2009 and march 2010, 8 specimens were sampled on two sites (upstream and dowstream a wild dumping site).

first: Fabien

last: Pierron

first: Julien

last: Thébault

first: Christophe

last: Klopp

first: Julie

last: Bellec

first: Patrice

last: Gonzalez

first: Magalie

last: Baudrimont


title: Host transcriptome analysis of Aspergillus fumigatus infection in Airway Epithelial Cells

city: Farmington

first: Reinhard

last: Laubenbacher

state: CT

address: 263 Farmington Avenue

department: Center for Quantitative Medicine MC 6029

institute: University of Connecticut Health Center

summary: The goal of this study is to determine the transcriptional response of primary normal human bronchial epithelial (NHBE) cells following interaction with A. fumigatus conidia at 2, 6, and 12 hours in order to examine the infection of airway epithelial cells at multiple time points of co-incubation. After total RNA isolation, the Illumina® HiSeq 2000 next generation sequencing system was used to characterize the transcriptional response, in untreated and A. fumigatus exposed cells.

overall_design: 12 samples were analyzed for this study. Triplicates of each sample were pooled together to form a sample. 2 samples generated in this fashion was used for each time point and condition. Since we have 2 samples, 2 conditions (control vs. infected with A. fumigatus), and 3 time points (2, 6, and 12 hrs), this produces our 12 samples.

first: Shernita

last: Lee

middle: C


title: RNAseq study of synovial biopsies after triple DMARD treatment

city: Spring House

first: Alice

last: Walsh

address: Welsh & McKean Roads

department: Immunology

institute: Janssen R&D

summary: Total RNA sequencing was performed on samples isolated from joint synovial biopsies from subjects with rheumatoid arthritis before and after 6 months of triple DMARD treatment

overall_design: One biopsy sample per subject/time point was analyzed without replicates

first: Yanxia

last: Guo


title: Alpha TC1 and Beta-TC-6 genomic profiling uncovers both shared and distinct transcriptional regulatory features with their primary islet counterparts

first: Michael

last: Stitzel

address: 10 Discovery Drive

institute: The Jackson Laboratory

summary:
Alpha TC1 (αTC1) and Beta-TC-6 (βTC6) mouse islet cell lines are cellular
models of islet (dys)function and type 2 diabetes (T2D). However, genomic characteristics of these cells, and their similarities to primary islet alpha and beta cells, are undefined. Here, we report the epigenomic (ATAC-seq) and transcriptomic (RNA-seq) landscapes of αTC1 and βTC6 cells. Each cell type exhibits hallmarks of its primary islet cell counterpart including cell-specific expression of beta (e.g., Pdx1) and alpha (e.g., Arx) cell transcription factors (TFs), and enrichment of binding motifs for these TFs in αTC1/βTC6 cis-regulatory elements. αTC1/βTC6 transcriptomes overlap significantly with the transcriptomes of primary mouse/human alpha and beta cells. Our data further indicate that ATAC-seq detects cell-specific regulatory elements for cell types comprising ≥ 20% of a mixed cell population. We identified αTC1/βTC6 cis-regulatory elements orthologous to those containing type 2 diabetes (T2D)-associated SNPs in human islets for 33 loci, suggesting these cells’ utility to dissect T2D molecular genetics in these regions. Together, these maps provide
important insights into the conserved regulatory architecture between αTC1/βTC6 and primary islet cells that can be leveraged in functional (epi)genomic approaches to dissect the genetic and molecular factors controlling islet cell identity and function.

overall_design: RNA-seq and ATAC-seq profiling of mouse islet cell lines (alpha TC1 and beta TC6). SRA study accession SRP108440 and BioProject acession PRJNA388786

first: Nathan

last: Lawlor

first: Ahrim

last: Youn

first: Romy

last: Kursawe

first: Duygu

last: Ucar


title: Fundamental molecular bases for differential transcriptional programs of top leaves during grain-filling in rice

city: Mainz

first: Hyobin

last: Jeong

state: Germany

address: Richard shirrmann Str 12.

country: Germany

institute: IMB

summary: Flag (FL) and second leaves (SL) in rice show differential aging patterns during monocarpic senescence. Coordination of aging programs in the top leaves is important for effective grain-filling. However, molecular bases for differential aging programs in the top leaves have not been systematically explored in rice. Here, we performed mRNA-sequencing of FL and SL at six time points during the grain-filling period. mRNA expression data revealed 6,365 genes showing aging-dependent expression changes in FL and/or SL. Of them, while 3047 genes showed shared aging-dependent expression patterns between FL and SL, 3058 genes showed differential expression patterns, which were classified into 5 major groups (G1-5) based on their differential expression patterns. Of the groups, G3 representing amino acid (AA) transport showed consistent differential age-dependent expression patterns in independent samples, whereas the other groups showed inconsistent differential expression patterns. Moreover, of AA transporters (AATs) in G3, long-distance AATs showed invariant differential age-dependent expression patterns after panicle removal, consistent to panicle removal-invariant differential nitrogen contents between FL and SL, known to be associated with protein concentration in grains. Our results suggest that long-distance AA transport is an invariant core transcriptional program of differential aging in rice top leaves for nitrogen remobilization during grain-filling.

overall_design: mRNA expression profiles of the flag leaf and 2nd leaf of Oryza Sativa during grain filling (Day After Heading, DAH, 4-44) were examined by Illumina Hi-seq 2500.

first: Hong

middle: G

last: Nam

first: Daehee

last: Hwang


title: Impeding transcription of expanded microsatellite repeats by deactivated Cas9

city: Gainesville

first: Eric

middle: T

last: Wang

state: FL

address: 2033 Mowry Rd

institute: University of Florida

summary: Transcription of expanded microsatellite repeats is associated with multiple human diseases, including myotonic dystrophy, Fuchs’ endothelial corneal dystrophy, and C9orf72-ALS/FTD. Eliminating or reducing production of RNA and proteins arising from these expanded loci holds therapeutic benefit. Here, we tested the hypothesis that a deactivated form of the Cas9 enzyme impedes transcription across expanded microsatellites. We observed a repeat length-, PAM-, and strand-dependent reduction in the abundance of repeat-containing RNAs upon targeting dCas9 directly to repeat sequences. Aberrant splicing patterns were rescued in DM1 cells, and production of RAN peptides characteristic of DM1, DM2, and C9orf72-ALS/FTD cells was drastically decreased. Systemic delivery of dCas9/gRNA by adeno-associated virus led to reductions in pathological RNA foci, rescue of chloride channel 1 protein expression, and decreased myotonia. These observations suggest that transcription of microsatellite repeat-containing RNAs is more sensitive to perturbation than transcription of other RNAs, indicating potentially viable strategies for therapeutic intervention.

overall_design: RNA-Seq was perfomed on DM1 and non-DM1 myoblasts treated dCas9 plus control gRNA or (CAG)6 gRNA.

first: Belinda

last: Pinto

first: Tanvi

last: Saxena

first: Ruan

last: Oliveira

first: Hector

last: Mendez-Gomez

first: John

last: Cleary

first: Lance

last: Denes

first: Ona

last: McConnell

first: Juan

last: Arboleda

first: Guangbin

last: Xia

first: Maurice

last: Swanson


title: The influence of microRNAs and poly(A)-tail length on endogenous mRNA-protein complexes

city: Toronto

first: Olivia

last: Rissland

address: 686 Bay Street

institute: The Hospital for Sick Children

summary: All mRNAs are bound in vivo by proteins to form mRNA–protein complexes (mRNPs), but changes in the composition of mRNPs during post-transcriptional regulation remain largely unexplored. Here, we have analyzed, on a transcriptome-wide scale, how microRNA-mediated repression modulates the associations of core components (eIF4E, eIF4G, and PABP) and of the decay factor DDX6 in human cells. Despite the transient nature of repressed intermediates, we detected significant changes in mRNP composition, marked by dissociation of eIF4G and PABP, and by recruitment of DDX6. Furthermore, although poly(A)-tail length has been considered critical in post-transcriptional regulation, differences in steady-state tail length explained little of the variation in either PABP association or mRNP organization more generally. Instead, relative occupancy of core components correlated best with gene expression. Together, these results indicate that posttranscriptional regulatory factors influence the associations of PABP and other core factors, and do so without substantially affecting steady-state tail length.

sample_organism:
Drosophila melanogaster
Homo sapiens

platform_organism:
Drosophila melanogaster
Homo sapiens

overall_design: Total and immunoprecipitated samples analyzed by RNA-seq and PAL-seq

first: Alexander

middle: O

last: Subtelny

first: Miranda

first: Andrew

last: Lugowski

last: Laver

first: Sachdev

last: Sidnu

first: Craig

last: Smibert

first: Howard

last: Lipshitz

first: David

last: Bartel


title: RNAseq of T-ALL upon long non coding rna purturbation

city: New York

first: Iannis

last: Aifantis

address: 550 First Avenue, Smilow Research Building Room 1301

department: Pathology

institute: New York University School of Medicine

summary: T cell leukemia cell lines transciptome changes upon long non coding RNA knockdown by CRISPR and ASO. The target lncRNA is a novel lncRNA called "lnrCXCR4". The sequence of this lncRNA is available at the foot of this page.

overall_design: Examination of transcriptome changes of T cell leukemia cell lines upon CRISPR modification or ASO of novel lncRNA lnrCXCR4.

first: Yixiao

last: Gong

first: Yoon

last: Yap


title: Investigation of the Molecular Action of Actinorhodin

first: Stefanie

last: Mak

state: Ontario

address: 661 University Avenue, Suite 1600

department: Biochemistry

institute: University of Toronto

summary: Actinorhodin is a blue-pigmented, redox-active pigmented secondary metabolite that is produced by the bacterium Streptomyces coelicolor. Although actinorhodin has been used as a model compound for studying secondary metabolism, its mechanism is not well understood. In this work, we have conducted a comprehensive chemical genetic investigation of actinorhodin’s antibacterial effect on target organisms.

overall_design: Transcriptome profiles of actinorhodin-, H2O2-, and dioxane-treated Staphylococcus aureus were generated in duplicate using Illumina MiSeq platform.

first: Justin

last: Nodwell


title: Comparison of gene expression profiles between SCD1 knockdown and vector control of Huh7 cells and PLC/PRF/5 cells by RNA-sequencing

city: Hong Kong

first: Chi Ho

last: Lin

address: 6th Floor, The Hong Kong Jockey Club Building for Interdisciplinary Research, 5 Sassoon Road, Pokfulam

department: Centre for PanorOmic Sciences

country: Hong Kong

institute: The University of Hong Kong

summary: The purpose of this experiment is to search for the downstream target of SCD1

overall_design: We subjected SCD1 knockdown and vector control of Huh7 cells and PLC/PRF/5 cells to RNA-sequencing, and analyzed the genes that were shown to be differentially expressed between the two groups.

first: Mark

middle: K

last: Ma

first: Terence

last: Lee


title: Large scale sequencing of PSTVd-I sRNA in tomato plants

city: Sherbrooke

first: Charith Raj

last: Adkar-Purushothama

state: Quebec

address: 3201 rue Jean-Mignault

institute: Université de Sherbrooke

summary: In order to analyze the production of small RNA (sRNA) by Potato spindle tuber viroid-intermediate strain (PSTVd-I) upon infecting the plants, the tomato plants (Lycopersicum esculentum cv. Rutgers) were inoculated with the PSTVd-I. After 21-days of post inoculation, total RNA was extracted and subjected for deep-sequencing using Illumina MiSeq platform. The primers were trimmed and the 21- to 24-nt long small RNA species were filtered after quality check of the raw data.

overall_design: Examination for the production of viroid specific small RNA by PSTVd upon infection in tomato plants.

first: Charith

first: Jean-Pierre

last: Perreault


title: Parallel analysis of 5'-RNA ends in mock inoculated tomato plants

summary: 5′ RNA ligase mediated rapid amplification of cDNA ends (5′ RLM-RACE) is the widely used tool for confirming the direct cleavage of target mRNA by a miRNA. Recently, 5′ RLM-RACE combined with high-throughput sequencing such as parallel analysis of RNA ends (PARE) are gaining importance as these techniques allows to assess the large number of sample in a single experiment. In order to verify the cleavage of predicted a target mRNA in potato spindle tuber viroid (PSTVd) infected tomato plants, the the leaf samples collected from the mock inoculated (control/healthy) at 21-days were subjected for RNA extraction. A custom RNA adaptor containing MmeI restriction endonuclease was ligated to the free 5'-phosphate end of an uncapped mRNA using T4 RNA ligase, followed by reverse transcription (RT) and second strand synthesis using poly (T) primers. Obtained product was slightly amplified, cleaved with MmeI restriction endonuclease and then, a dsDNA adaptor was added to the 3’-end of the MmeI restriction endonuclease cleavage site. Resulted products were sequence in  an Illumina Mi-Seq machine. Retrieved data was then used to verify the 5’-termini of predicted target mRNA.

overall_design: In order to verify the PSTVd mediated cleavage of mRNAs, the  PARE data obtained from control plants were compared with the PARE data obtained with PSTVd infected plants.


first: Nicolas

last: Chevrier

summary: Whole organs or CD8+ T cell populations sorted by FACS from tissues were isolated at various time points following vaccination with Vaccinia virus strain Modified Vaccinia Ankara (MVA; subcutaneously) and/or infection with strain Western Reserve (WR; intranasally). Total RNA was extracted from whole organs or sorted cell populations, RNA-seq libraries were prepared with a custom protocol, and sequenced at an average depth of ~5M/sample.

overall_design:
We compared three types of immune responses in vivo: (1) vaccinating (MVA only; 10^7 PFUs subcutaneously), (2) lethal (WR only; 10^7 PFUs intranasally), and (3) protective (MVA followed by WR challenge; same doses and routes as in 1 and 2, respectively). Overall, 6 datasets were generated from the following experiments and samples:
(i) Whole-tissue samples from MVA, WR, MVA+WR cohorts with WR challenge at day 7, 21 (Exp. 1), or 80 (Exp. 2) in wild-type mice;
(ii) Whole-tissue samples from MVA+WR at day 21 in wild-type versus knockout animals: Tcra-/- (Exp. 3), and Ifng-/-, Il22-/-, and Csf2-/- (Exp. 5);
(iii) Sorted CD8+ T cell populations profiled from tissues of MVA-vaccinated (day 21) and control mice with (Exp. 6) or without (Exp. 4) intravascular staining (anti-CD45-PE antibody) to distinguish parenchyma-associated from vasculature-associated cells.

first: Motohiko

last: Kadoki


title: Large scale sequencing of PSTVd-RG1 sRNA in tomato plants

summary: In order to analyze the production of small RNA (sRNA) by Potato spindle tuber viroid- RG1 strain (PSTVd-RG1) upon infecting the plants, the tomato plants (Lycopersicum esculentum cv. Rutgers) were inoculated with the PSTVd-RG1. After 21-days of post inoculation, total RNA was extracted and subjected for deep-sequencing using Illumina MiSeq platform. The primers were trimmed and the 21- to 24-nt long small RNA species were filtered after quality check of the raw data.

overall_design: Examination for the production of viroid specific small RNA by PSTVd-RG1 upon infection in tomato plants.


title: A Distinct Population of Thirst-Associated Preoptic Neurons Encodes an Aversive Motivational Drive

first: Liqun

last: Luo

address: Herrin Labs, Rooms 152 and 154

summary: We FACS-isolated single thirst-associated neurons from the median preoptic hypothalamus of mice and determined their individual transcriptomes. This characterization revealed a molecularly distinct population of excitatory thirst-associated neurons that is responsible for producing thirst motivational dirve.

overall_design:
Thirst-associated cells in the preoptic hypothalamus of mice were labeled using the Fos-p2A-CreER; Ai14 reporter mouse after 48 hour water deprivation. The preoptic hypothalamus was dissociated, and individual tdTomato+ cells were sorted into 96 well plates with lysis buffer. The transcriptomes of 570 putative cells were amplified using SmartSeq2 single-cell RNA-seq (Picelli et al., 2014). Libraries were prepared using an Illumina Nextera XT following Illumina's protocols, and sequenced on an Illumina NextSeq 500. Data were processed using RSEM, and mapping directly to the ENSEMBL transcriptome, and quantified at a per-transcript level in TPM units.
FASTQ files containing few reads (<1 MB in size for first paired-end read) were not mapped or subsequently analyzed; final dataset comprises 505 cells.

first: William

last: Allen


title: Meg3 binding sites in mouse insulinoma cells

city: Bethesda

first: Sunita

last: Agarwal

state: MD

address: Bldg. 10, Room 8C-101

department: NIDDK

institute: National Institutes of Health

summary: We have shown that increased β-cell proliferation in functioning pancreatic neuroendocrine tumors (insulinomas) correlated with reduced expression of the long non-coding RNA Meg3 and increased expression of the oncogenic receptor c-Met. To investigate the target binding sites of Meg3 in and around the c-Met gene, we did ChIRP-Seq using biotinylated probes from the mouse Meg3 RNA sequence. This would help us better understand how Meg3 regulates ithe expression of c-Met to control β-cell proliferation in insulinoma cells.

overall_design: Glutaraldehyde cross-linked chromatin was prepared from 10 million cells of a mouse pancreatic islet β-cell line (MIN6-4N) stably transfected with Vector or stably overexpressing Meg3.  Chromatin isolation by RNA purification (ChIRP) as performed using 2 pools of odd-numbered or even-numbered biotinylated probes from the mouse Meg3 RNA sequence using standard protocols (Sigma). ChIRP-Seq libraries (input, odd probe and even probe) were prepared with Diagenode's MicroPlex Library Preparation kit and IP-Star Compact protocol. ChIRP-Seq libraries were sequenced for single-end 50 bp, and sequences were analyzed (NIDDK genomics core facility and Genomatix).

first: Sucharitha

last: Iyer


title: Parallel analysis of 5'-RNA ends in PSTVd-RG1 inoculated tomato plants

summary: 5′ RNA ligase mediated rapid amplification of cDNA ends (5′ RLM-RACE) is the widely used tool for confirming the direct cleavage of target mRNA by a miRNA. Recently, 5′ RLM-RACE combined with high-throughput sequencing such as parallel analysis of RNA ends (PARE) are gaining importance as these techniques allows to assess the large number of sample in a single experiment. In order to validate the cleavage of predicted a target mRNA in potato spindle tuber viroid-RG1 (PSTVd-RG1) infected tomato plants, the leaf samples collected at 21-days post inoculation were subjected for RNA extraction. A custom RNA adaptor containing MmeI restriction endonuclease was ligated to the free 5'-phosphate end of an uncapped mRNA using T4 RNA ligase, followed by reverse transcription (RT) and second strand synthesis using poly (T) primers. Obtained product was slightly amplified, cleaved with MmeI restriction endonuclease and then, a dsDNA adaptor was added to the 3’-end of the MmeI restriction endonuclease cleavage site. Resulted products were sequence in  an Illumina Mi-Seq machine. Retrieved data was then used to verify the 5’-termini of predicted target mRNA.

overall_design: Verification of RISC mediated cleavage of target mRNAs by PSTVd-RG1 derived small RNA.


title: Large scale sequencing of small RNAs in tomato plants

summary: In order to compare the small RNA (sRNA) population between the control and  Potato spindle tuber viroid (PSTVd) upon infecting the plants, the tomato plants (Lycopersicum esculentum cv. Rutgers) were mock  inoculated. At 21 dpi,tTotal RNA was extracted and subjected for deep-sequencing using Illumina MiSeq platform. The primers were trimmed and the 21- to 24-nt long small RNA species were filtered after quality check of the raw data.

overall_design: Examination for the small RNA population in tomato plants.


title: Elucidation of the molecular responses to waterlogging in Sesbania cannabina roots

city: yantai

first: cheng-gang

last: ren

state: shandong

address: 17 Chunhui Road, Laishan District

institute: Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, China

summary: To better understand the molecular mechanisms of the response of S. cannabina to soil waterlogging, the transcriptional profile in both short and long term of waterlogged S. cannabina roots were performed using the Illumina HiSeq™ 2000 sequencing platform (Illumina Inc., San Diego, CA, USA). Bioinformatic analysis of transcriptome data was performed to allow identification and functional annotation of differentially expressed genes (DEGs). By comparing the different genes appeared in control and treatment groups, we can learn more about the species-specific responses employed by S. cannabina and find novel associated genes or strategies in waterlogging resistant species.

overall_design: S. cannabina root mRNA profiles of 30-day old control (untreated) , 3h and 27h waterlogging treatment were generated by deep sequencing, in duplicate, using Illumina GAIIx.

first: Cheng-Gang

last: Ren

first: Cun-Cui

last: Kong


title: RNA-seq of Wistar-rat skin from young and old animals

status: Public on Sep 19 2017

city: Jena

first: Marco

last: Groth

address: Beutenbergstraße 11

department: Core Facility - Next Generation Sequencing

institute: Leibniz Institute on Aging - FLI

summary: Comparison of gene expression level by Illumina sequencing of rat skin from young and old animals. We identified differentially expressed genes and provide functional profiles, which give insights into the aging process of short-lived rodents.

overall_design: 9 skin samples, 4-5 animals per group, 2 groups: 1) young males, 2) old males

first: Arne

last: Sahm

first: Karol

last: Szafranski

first: Martin

last: Bens

first: Matthias

last: Schwab

first: Philip

last: Dammann

last: Platzer


title: Dental Pulp Stem Cells Model Early Life and Imprinted DNA Methylation Patterns.

city: Davis

first: Keith

last: Dunaway

address: 3318 Tupper Hall

department: MMI

institute: UC Davis

type: Methylation profiling by high throughput sequencing

summary: Early embryonic stages of pluripotency are modeled for epigenomic studies primarily with human embryonic stem cells (ESC) or induced pluripotent stem cells (iPSCs). For analysis of DNA methylation, however, ESCs and iPSCs do not accurately reflect the DNA methylation levels found in preimplantation embryos. Whole genome bisulfite sequencing (WGBS) approaches have revealed the presence of large partially methylated domains (PMDs) covering 30-40% of the genome in oocytes, preimplantation embryos, and placenta. In contrast, ESCs and iPSCs show abnormally high levels of DNA methylation compared to inner cell mass (ICM) or placenta. Here we show that dental pulp stem cells (DPSCs), derived from baby teeth and cultured in serum-containing media, have PMDs and mimic the ICM and placental methylome more closely than iPSCs and ESCs. By principal component analysis, DPSC methylation patterns were more similar to two other neural stem cell types of human derivation (EPI-NCSC and LUHMES) and placenta than were iPSCs, ESCs or other human cell lines (SH-SY5Y, B lymphoblast, IMR90). To test the suitability of DPSCs in modeling epigenetic differences associated with disease, we compared methylation patterns of DPSCs derived from children with chromosome 15q11.2-q13.3 maternal duplication (Dup15q) to controls. Differential methylation region (DMR) analyses revealed the expected Dup15q hypermethylation at the imprinting control region, as well as hypomethylation over SNORD116, and novel DMRs over 147 genes, including several autism candidate genes. Together these data suggest that DPSCs may be useful model for epigenomic and functional studies of human neurodevelopmental disorders.

overall_design: Examination of DNA Cytosine methylation in DPSCs, EPI-NCSC, and LUHMES:    DPSC_Control: 5 different DPSCs derived from patients with no diagnosed neurological disorders;   DPSC_Dup15: 4 different DPSCs derived from patients diagnosed with Dup15q Syndrome;   DPSC_Dup15: 1 DPSC derived from a patient diagnosed with Dup15q Syndrome that also had a duplication of part of chromosome 17;   EPI-NCSC: 1 EPI-NCSC derived from a single patient;   LUHMES: 2 biological replicates of the LUHMES cell line

first: K

first: J

last: LaSalle


title: Parallel analysis of 5'-RNA ends in PSTVd-I inoculated tomato plants

first: Charith Raj

last: Adkar-Purushothama

summary: 5′ RNA ligase mediated rapid amplification of cDNA ends (5′ RLM-RACE) is the widely used tool for confirming the direct cleavage of target mRNA by a miRNA. Recently, 5′ RLM-RACE combined with high-throughput sequencing such as parallel analysis of RNA ends (PARE) are gaining importance as these techniques allows to assess the large number of sample in a single experiment. In order to validate the cleavage of predicted a target mRNA in viroid infected tomato plants, the leaf samples collected at 21-days post inoculation were subjected for RNA extraction. A custom RNA adaptor containing MmeI restriction endonuclease was ligated to the free 5'-phosphate end of an uncapped mRNA using T4 RNA ligase, followed by reverse transcription (RT) and second strand synthesis using poly (T) primers. Obtained product was slightly amplified, cleaved with MmeI restriction endonuclease and then, a dsDNA adaptor was added to the 3’-end of the MmeI restriction endonuclease cleavage site. Resulted products were sequence in  an Illumina Mi-Seq machine. Retrieved data was then used to verify the 5’-termini of predicted target mRNA.

overall_design: Verification of RISC mediated cleavage of target mRNAs by viroid derived small RNA.

first: Charith

first: Jean-Pierre

last: Perreault


title: The TREM2-APOE pathway drives the transcriptional phenotype of dysfunctional microglia in neurodegenerative diseases IV

city: Boston

first: Oleg

last: Butovsky

address: 77 Avenue Louis Pasteur, Office 614

department: Center of Neurologic Diseases

institute: Brigham and Women's Hospital, Harvard Medical School

summary: Microglia play a pivotal role in the maintenance of brain homeostasis, but lose their homeostatic function during the course of neurodegenerative disorders. We identified a specific APOE-dependent molecular signature in microglia isolated from mouse models of amyotrophic lateral sclerosis, multiple sclerosis and Alzheimer’s disease (SOD1, EAE and APP-PS1) and in microglia surrounding neuritic A-plaques in human Alzheimer’s disease brain. This is mediated by a switch from a (M0)-homeostatic to (MGnD)-neurodegenerative phenotype following phagocytosis of apoptotic neurons via the TREM2-APOE pathway. TREM2 induces APOE signaling which is a negative regulator of the transcription program in M0-homeostatic microglia. Targeting the TREM2-APOE pathway restores the M0-homeostatic signature of microglia in APP-PS1 and SOD1 mice and prevents from neuronal loss in an acute model of neurodegeneration. In SOD1 mice, TREM2 regulates MGnD in a gender-dependent manner. APOE-mediated MGnD microglia lose their tolerogenic function. Taken together, our work identifies the TREM2-APOE pathway as a major regulator of microglial functional phenotype in neurodegenerative diseases and serves as a novel target to restore homeostatic microglia.

overall_design:
Illumina NextSeq500 was used to identify disease-associated vs. homeostatic molecular microglia signature in microglia in different disease models and transgenic models.
Bulk microglia (1,000 cells/sample) FCRLS+ sorted microglia.


title: The TREM2-APOE pathway drives the transcriptional phenotype of dysfunctional microglia in neurodegenerative diseases V


title: Cytochalasin treatment of Ciona embryos

city: Manhattan

first: Michael

last: Veeman

state: KS

address: 116 Ackert Hall

department: Division of Biology

institute: Kansas State University

summary: Cleavage and morphogenesis of Ciona embryos was blocked by treatment with cytochalasin B prior to gastrulation. Drug treated embryos and DMSO treated controls were harvested at stage 19.5 (after control embryos had undergone neurulation and were completing notochord intercalation). Only 55 genes showed a significant difference in expression between the two treatments.

overall_design: Dechorionated embryos were treated with 10 uM cytochalasinB or with DMSO alone as a control. Drug was added at 3.75 hpf at 21.5C (64 cell stage). For each of the replicates, 400 experimental and 400 control embryos were harvested at stage 19.5 (7.5hpf) for RNA purification. Triple biological replicates of purified RNA were analyzed by RNAseq and transcript enrichment was calculated using the Cufflinks software suite

first: Wendy

middle: M

last: Reeves

first: Yuye

last: Wu

first: Matthew

last: Harder


title: Ectopic expression of the Brachyury transcription factor upregulates only a subset of notochord expressed genes

summary: The key notochord transcription factor Brachyury was ectopically expressed in Ciona embryos under the control of the FoxAa cis-regulatory region (which drives expression in neural, endodermal and mesenchymal lineages in addition to notochord). Misexpression of Brachyury induced 925 genes compared to a control reporter plasmid (Bra>GFP). There was only modest overlap with a set of notochord-enriched genes previously identified by RNAseq of flow-sorted notochord cells, indicating that Brachyury is not a notochord master regulator gene as strictly defined.

overall_design: Fertilized dechorionated eggs were electroporated with either FoxAa>Venus-Bra plasmid or control plasmid (Bra<GFP). For each of the replicates, 400 experimental and 400 control embryos were collected at stage 19.5 (7.5hpf at 21.5C). Triple biological replicates of purified RNA were analyzed by RNAseq and transcript enrichment was calculated using the Cufflinks software suite


title: Aging in naked mole-rats and rats

first: Marco

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

sample_organism:
Rattus norvegicus
Heterocephalus glaber

platform_organism:
Rattus norvegicus
Heterocephalus glaber

overall_design: Refer to individual Series


title: RNA-seq of Wistar-rat liver from young and old animals

summary: Comparison of gene expression level by Illumina sequencing of rat liver from young and old animals. We identified differentially expressed genes and provide functional profiles, which give insights into the aging process of short-lived rodents.

overall_design: 9 liver samples, 4-5 animals per group, 2 groups: 1) young males, 2) old males

first: Arne


title: The Ciona notochord transcriptome reveals a core set of broadly conserved notochord effector genes

summary: The notochord is the eponymous feature of the chordates and an essential organ in chordate development. The notochord of the invertebrate chordate Ciona consists of only 40 cells, and is a longstanding model for studying differentiation and morphogenesis in a small, simple embryo. Here we perform RNAseq analysis on flow-sorted notochord cells from multiple stages of development to define a comprehensive Ciona notochord transcriptome. We identify 1364 genes with enriched expression in the notochord and extensively validate the results by in situ hybridization. This notochord gene set is highly enriched for Gene Ontology codes related to the extracellular matrix, cell adhesion and cytoskeleton, and contains numerous genes with intriguing potential functions in morphogenesis. Orthologs of 112 of the Ciona notochord genes have known notochord expression in vertebrates, more than twice as many as would be predicted by chance alone. This set of putative effector genes with notochord expression conserved from tunicates to vertebrates will be invaluable for testing hypotheses about the evolution of the notochord.

overall_design: Ciona notochord cells were fluorescently labeled by electroporation of fertilized eggs with the notochord reporter construct Bra>GFP. At two timepoints (Hotta St16 and St19/20, embryos were dissociated to single cells and then flow-sorted to isolate populations of notochord-enriched GFP+ cells and notochord-depleted GFP- cells. Triple biological replicates of purified RNA were analyzed by RNAseq and transcript enrichment was calculated using the Cufflinks software suite

first: Veeman

last: Michael

first: Reeves

last: Wendy

first: Wu

last: Yuye

first: Harder

last: Matthew


title: Pitx1 directly controls the core limb development program to implement hindlimb identity [RNA-Seq]

city: Montreal

first: Stephen

last: Nemec

address: 110 Av. des Pins Ouest

institute: IRCM

summary: Pitx1, critical regulator of a limited hindlimb-specific gene network, targets the limb development program common to both fore- and hindlimbs in order to implement hindlimb-specific limb morphology.

overall_design: The gene regulatory networks governing forelimb vs. hindlimb development in mouse were investigated using expressing profiling of morphologically stage-matched e10.5 forelimbs and e11.0 hindlimbs, ChIPseq of chromatin marks, and ChIPseq of limb-specific transcription factors Pitx1 and Tbx5. The makeup of the Pitx1-directed components of the hindlimb gene network were investigated using expression profiling of Pitx1 null hindlimbs at two stages (e11.0 and e11.5).

first: Maëva

last: Luxey

first: Aurélie

last: Sung

first: Deepak

last: Jain

first: Tomi

last: Pastinen

first: Jacques

last: Drouin


title: The SAGA coactivator regulates the expression of nearly all genes transcribed by RNA polymerase II

city: Seattle

first: Sebastian

last: Gruenberg

state: Washington

address: 1100 Fairview Ave N

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

summary: The SAGA coactivator complex facilitates transcription initiation through chromatin-modifying activities and interaction with TBP. SAGA was suggested to regulate the expression of about 10% of yeast genes, leading to the longstanding distinction of SAGA-dominated from TFIID-dominated genes, depending on the complex used to recruit TBP to promoters. We reassessed the genome-wide localization of SAGA by using ChEC-seq and its role on transcription through quantification of newly-synthesized mRNA. Here we show that SAGA binds to the upstream activating sequences of a majority of yeast genes. Deletion analyses reveal a global role for SAGA in transcription and a synergistic effect of Spt3 (TBP-binding subunit) with the acetyltransferase Gcn5. Our data demonstrate that SAGA acts as a general cofactor required for essentially all RNA polymerase II transcription. Hence, differential gene regulation, largely attributed to either SAGA or TFIID dominancy, is not accurate, but instead depends on other features of genes promoters.

overall_design: We used ChEC-seq to map the genome-wide binding of the SAGA coactivator complex in budding yeast. ChEC-seq was performed as described in PMID 27797823.

first: Tiago

last: Baptista

last: Grünberg

first: Nadège

last: Minoungou

first: Maria

middle: J

last: Koster

first: Marc

middle: H

last: Timmers

first: Steven

last: Hahn

first: Didier

last: Devys

first: László

last: Tora


title: Nuclear and cellular mRNA sequencing of 1 cm root tips of 7 days Oryza sativa seedlings

city: Riverside

first: Mauricio

middle: A

last: Reynoso

address: 4126 Genomics Bldg

department: Botany and Plant Sciences

institute: University of California Riverside

summary: Plants dynamically regulate chromatin architecture, transcription and post-transcriptional processes in accordance with developmental programs and environmental cues. Isolated nuclei can provide access to early steps in gene regulation involving chromatin as well as transcript production and processing. Here we describe transfer of the Isolation of Nuclei from TAgged specific Cell Types (INTACT) to the monocot rice (Oryza sativa L.). The purification of biotinylated nuclei was redesigned by replacing the outer nuclear envelope-targeting domain with an outer nuclear envelope-anchored domain in the Nuclear Tagging Fusion protein and codon optimization of E. coli BirA, combined in a single T-DNA construct. We also developed an inexpensive methods for INTACT, T-DNA insertion mapping, and profiling of the complete nuclear transcriptome, including a rRNA degradation procedure that minimizes pre-rRNA transcripts. The comparison of nuclear and steady-state poly(A)+ transcript populations of seedling root tips confirmed the capture of pre-mRNA and exposed distinctions between the nuclear and total RNA pool. The improved INTACT plasmid configuration for monocots and accompanying methods provide access to chromatin and pre-mRNA, paving the way for monitoring nuclear transcriptome and epigenome dynamics of specific cell-types in rice and other crop species.

overall_design: 8 samples, 1 condition (1X MS, 1 % [w/v] Sucrose, pH 5.8). 4 bioreplicates of 2 RNA pools (total mRNA, rRNA degraded nuclear RNA)

first: Germain

last: Pauluzzi

first: Julia

last: Bailey-Serres


title: Human tissue-resident memory T cells are defined by core transcriptional and functional signatures in lymphoid and mucosal sites

city: Pittsburgh

first: Mark

middle: Jay

last: Shlomchik

state: PA

address: W1052 Biomedical Science Tower 200 Lothrop St

department: Department of Immunology

institute: University of Pittsburgh

summary: Tissue resident memory T cells (TRM) mediate optimal protection to site-specific pathogens in mouse models and are key targets for vaccines. In humans, the existence and defining properties of Positive remain unclear. Here, we performed in-depth transcriptome profiling and phenotypic and functional analyses of circulating and resident memory CD4+ and CD8+T cells from lungs, spleens, blood and intestines of 72 individuals, revealing a core gene set conserved between tissues, species, and T cell lineages. Human Positive exhibit increased expression of specific adhesion and regulatory molecules, increased capacity for pro-inflammatory and regulatory cytokine production, and downregulation of molecules controlling responses to chemokines, tissue egress, and cell cycle control compared with circulating Negative cells. We further identify subsets of genes exhibiting tissue-specific expression patterns for mucosal and lymphoid sites. Our results indicate that human Positive constitute a subset distinct from circulatory Negative, with important implications for promoting anatomic localization of memory responses.

overall_design: mRNA profiling of CD69+ and CD69- T cells in lung, spleen and blood (CD69- only) for CD4 and CD8, each has 3 biological replicates

first: Brahma

middle: V

last: Kumar

first: Donna

last: Farber

first: Wenji

last: Ma

first: Yufeng

last: Shen


title: Cell origin dictates programming of resident versus recruited macrophages during acute lung injury

city: Denver

first: Kara

last: Mould

state: CO

address: 1400 Jackson Street

department: Medicine

institute: National Jewish Health

summary: The primary objective of this study was to compare global differences in transcriptional programming of resident and recruited alveolar macrophages in a time-limited murine model of lung inflammation. We first performed RNA sequencing of the resident and recruited alveolar macrophages from initiation through resolution of LPS-induced lung inflammation in the mouse.  Our results indicate that despite existing in a shared environment, cell origin is the major determinant of programming of resident and recruited AMs during an acute inflammatory response.  Major areas of difference include cell proliferation, inflammatory cytokine production and metabolism.

overall_design: Comparison of two alveolar macrophage cell types transcriptomes at days 0,3,6,9, and 12 following lung injury.

first: William

last: Janssen

first: Thomas

last: Danhorn

first: Sonia

last: Leach

first: Claudia

last: Jakubzick

first: Michael

last: Mohning

first: Alexandra

last: McCubbrey

first: Stacey

last: Thomas

last: Bratton

first: Tasha

last: Fingerlin

first: Brian

last: O'Connor

first: Julie

last: Reisz

first: Angelo

last: D'Alessandro


title: Zika virus infections of porcine fetal brain

status: Public on Sep 18 2017

middle: Joseph

last: Cox

address: 1 King's College Circle, Rm 3360

department: Physiology

summary: Zika virus was inoculated at mid gestation (day 50) in to either intra cerebrally, or interperotoneally and intra amniotic. Controls were mock injected and subject to similar surgical proceedures. Fetal tissue were obtained. Sampled fetal brains are from littermates and are not the fetus directly infected.  After 28 days post infection.

overall_design: examination of zika infection and route of infection

first: Uladzimir

last: Karniychuk


title: The TREM2-APOE pathway drives the transcriptional phenotype of dysfunctional microglia in neurodegenerative diseases VI

first: Oleg

last: Butovsky


title: Transcriptional profiles of female VMHpvlm and VMHpvll

first: Koichi

last: Hashikawa

address: 1959 NE Pacific St. HSB J135

department: Neuroscience

institute: University of Washington

summary: To investigate whether female VMHpvlm and VMHpvll have distinct transcriptional profiles, we conducted RNAseq onto these subnuclei that were microdissected by laser capture microdissection. Our results demonstrate that each subnucleus had distinct set of enriched genes.

overall_design: VMHpvlm and VMHpvll of VgluT2-cre/Ai6 female mice were microdissected using Laser capture microdissection.  Subsequent RNAseq generated transcriptional profiles of the subnucleus.

first: Yoshiko

first: koichi

first: Dayu

last: Lin


title: Next Generation sequencing and quantitative transcriptomic analysis in -77+/+ and -77-/- erythroid precursors

city: Madison

first: Charu

last: Mehta

state: Wisconsin

address: 1111 Highland Avenue 4028 WIMR

department: Cell and Regenerative Biology

institute: University of Wisconsin Madison

summary:
Gene expression profiles of sorted erythroid precursors from E14.5 wild-type (WT) and -77 enhancer knockout (-77-/-)  mouse fetal liver were generated by next generation sequencing, in triplicate, using Illumina Hiseq2500 (1X50).
We showed that the Gata2 -77 enhancer generated the vital erythroid precursor Burst Forming Unit-Erythroid by two mechanisms, GATA-1 upregulation to establish the erythroid transcriptome and GATA-2-dependent, GATA-1-independent transcriptional regulation.

overall_design: Erythroid precursor gene expression profiles of E14.5 mouse -77+/+ and -77-/- mouse fetal livers were generated by next generation sequencing, in triplicate, using Illumina Hiseq2500 (1X50).

first: Kirby

middle: D

last: Johnson

first: Irene

last: Ong


title: RNA-seq of Wistar-rat liver and skin from young and old animals

first: Marco

last: Groth


title: Transcriptome profiling of mutants of CALMODULIN-LIKE (CML) family genes and CALMODULIN-BINDING PROTEIN 60 (CBP60) family genes in response to Pseudomonas syringae pv maculicola ES4326

city: Saint Paul

first: You

last: Lu

state: MN

address: 1500 Gortner Avenue

department: Department of Plant and Microbial Biology

institute: University of Minnesota, Twin Cities

summary: We observed that mutations in CBP60a, CML46, CML47 and WRKY70 enhanced plant resistance to Pma likely through different mechanisms. To investigate their contributions to enhanced resistance at the transcriptome level, we designed this experiment to measure their response to Pma using the SMART-3Seq method.

overall_design: Mature leaves of Arabidopsis plants of seven different genotypes were infiltrated with mock or Pma. Samples were collected 24 hours after treatment. Each experiment contains one sample consisted of two leaves for each genotype-treatment combination. In total three independent experiments were conducted.

first: Fumiaki

last: Katagiri

first: Jane

last: Glazebrook


title: Developmental stage specific chromosome architecture in human erythroid cells (Capture-C)

city: Guangzhou

first: Peng

last: Huang

state: Guangdong

address: Xinzao, Panyu District

department: GMU-GIBH Joint School of Life Sciences

institute: Guangzhou Medical University

summary: Chromatin structure is tightly intertwined with transcription regulation. Here we compared the chromosomal architectures of fetal and adult human erythroblasts and find that globally, chromatin structures and compartments A/B are highly similar at both developmental stages. At a finer scale, we detect distinct folding patterns at the developmentally controlled b-globin locus. Specifically, new fetal stage-specific contacts are uncovered between a region separating the fetal (g-) and adult (b-) globin genes (encompassing the HBBP1 and BGLT3 non-coding genes) and two distal chromosomal sites (HS5 and 3'HS1) that flank the locus. In contrast, in adult cells the HBBP1-BGLT3 region contacts the embryonic e-globin gene, physically separating the fetal globin genes from the enhancer (LCR). Removal of the HBBP1 gene strongly reactivates g-globin expression, accompanied by increased LCR-g-globin and decreased BGLT3-e-globin interactions, mimicking the effects of deleting the fetal globin repressor BCL11A. Our results uncover a new critical regulatory region as a potential target for therapeutic genome editing for hemoglobinopathies and highlight the power of chromosome conformation analysis in discovering new cis control elements.

overall_design: We compared the chromatin structures of the developmentally controlled β-globin locus by Capture-C.

first: Gerd

last: Blobel


title: Developmental stage specific chromosome architecture in human erythroid cells (Hi-C)

overall_design: We compared the chromosomal architectures of fetal and adult human erythroblasts by Hi-C.


title: Episomal S/MAR-based replicons do not alter expression profile of host genome

city: Gießen

first: Andreas

last: Gogol-Döring

address: Wiesenstraße 14

department: MNI

institute: Technische Hochschule MIttelhessen

summary:
Methods: Autonomously replicating vectors represent a simple and versatile model system for genetic modifications, but their localisation in the nucleus is largely unknown. Using circular chromosome conformation capture we mapped genomic contact sites of S/MAR-based replicons in HeLa cells. The influence of cis-active sequences on genomic localisation was assessed using replicons containing either an insulator sequence or an intron
Results: While the original and the insulator-containing replicons displayed distinct contact sites, the intron-containing replicon showed a rather broad genomic contact pattern. Our results indicate a preference for certain chromatin structures and a rather non-dynamic behaviour during mitosis. Independent of inserted cis-active elements established vector molecules reside preferentially within actively transcribed regions, especially within promoter sequences and transcription start sites.
Conclusions: S/MAR-based episomal replicons have a limited number of preferential contact sites and seem to be fairly non-dynamic during mitosis. We show that cis-acting elements do have an impact on the chormosomal localisation of episomal replicons, even though the epigenetic signatue of these contact sites are similar. Independently of the inserted cis-acting element, these contact sites are preferentially located within actively transcribed regions, especially promoter sites. Knowledge of preferred contact sites of exogenous DNA, e.g. viral or non-viral episomes, contribute to our understanding of episome behaviour in the nucleus and can be used for vector improvement and guiding of DNA sequences to specific subnuclear sites.

overall_design: Genome-wide mapping of chromosomal contact sites of S/MAR-based replicons

first: Claudia

last: Hagedorn

first: Hans

last: Lipps


title: Time course of the Arabidopsis thaliana root meristem

city: Ames

first: Natalie

last: Clark

state: IA

address: Advanced Teaching and Research Building 2213 Pammel Drive

department: Plant Pathology and Microbiology

institute: Iowa State University

summary: We isolated cells in the different developmental zones of the A. thaliana root at 3,4,5,6 and 7 days old (DO)

overall_design: PET111:GFP seedlings were grown for 3,4,5,6, or 7 days (2 biological replicates per time point). GFP negative cells were collected from the meristematic zone (MZ) and elongation zone (EZ) to eliminate columella cells from root tip. RNA was extracted from GFP negative cells and sequenced

first: Rosangela

last: Sozzani


title: Developmental stage specific chromosome architecture in human erythroid cells (RNA-seq)

overall_design: We compared the expression profiles of fetal and adult human erythroblasts at two differentiation stages by RNA-seq.


title: H3K27 Acetylation profile of hypothyroid NCoR1KO mice

city: new york

first: arturo

last: mendoza

state: ny

address: 1 east loop 15a

department: Division of Endocrinology, Diabetes and Metabolism

institute: weill cornell medicine

summary: We ablated the expression of the Nuclear Receptor Corepressor 1 specifically in mice livers and rendered them hypothyroid. Then we performed H3K27 acetylation CHIP-Seq. We found decreased H3K27ac in the livers of hypothyroid wild type and NCoR1KO mice. Therefore, we concluded that the thyroid hormone receptor may recruit histone deacetilases independently of NCoR1.

overall_design: Examination of H3K27ac by Chip-Seq in euthyroid and hypothyroid Wt and NCoR1KO mouse

first: A

middle: N

last: Hollenberg

last: Mendoza


title: Inferring Gene Regulatory Networks that control maintenance and identity of the Arabidopsis Root Stem Cells

city: Raleigh

first: Maria

middle: Angels

last: de Luis Balaguer

state: NC

address: 2115 Gardner Hall, Box 7612

department: Plant and Microbial Biology

institute: North Carolina State University

summary: We isolated QC cells and obtained their cell-type specific transcriptional profiles in a WT and in a pan mutant background by sorting GFP+ cells marked with pWOX5::GFP.

overall_design: Seedlings were grown for 5 days.  WOX5::GFP sorted fluorecent cells were harvested for RNA extraction.

first: Adam

middle: P

last: Fisher


title: Widespread epistasis regulates glucose homeostasis and gene expression

city: Cleveland

first: David

last: Buchner

state: OH

address: 10900 Euclid Ave

department: Genetics and Genome Sciences

institute: Case Western Reserve University

summary: Liver gene expression analysis in mouse chromosome substitution strains

overall_design: RNA was isolated from liver tissue of fasted 5-week-old mice

first: Nathan

last: Morris


title: High-throughput Sequencing Reveals Differential expression of MicroRNAs during intestine regeneration of sea cucumber Apostichopus japonicus

city: Qingdao

first: Lina

last: Sun

address: Nanhai Road 7

institute: Institute of Oceanology, Chinese Academy of Sciences

summary: We applied high-throughput sequencing to investigate the alterations of miRNAs expression in regenerative intestine (3dpeA, 3dpeB, 3dpeC)  Vs normal intestine (ControlA, ControlB, ControlC).

overall_design: 9 individuals (3 biological replicates×3 sea cucumbers per biological replicate) at 3 days post evisceration (dpe) were used for our experiments (3 biological replicates: 3dpeA, 3dpeB and 3dpeC). 9 non-eviscerated sea cucumbers (3 biological replicates×3 sea cucumbers per biological replicate) served as the control (3 biological replicates: ControlA, ControlB and ControlC).

first: Hongsheng

last: Yang