title: Whole genome bisulfite sequencing of sperm from a mouse heterozygous for a mutation in Setdb1 (MommeD13) and a wildtype mouse.

city: Bundoora

first: Harald

last: Oey

state: Vic

address: Kingsbury Drive

department: Genetics

institute: La Trobe University

summary: DNA from mature sperm was obtained from a mouse heterozygous for a mutation in Setdb1 (MommeD13) and a wildtype control mouse. The DNA was bisulfite converted and sequenced on a HiSeq 2000 to ~30x coverage. After mapping the resulting reads to the mouse genome DNA methyalation values at CpG dinucleotides were obtained as the ratio of reads with unconverted Cs relative to the sum of converted and unconverted reads. The resulting values were used to identify sites with a shift in the percentage of methylated CpGs between wildtype and mutant sperm.

overall_design: Whole genome bisulfite sequencing of sperm DNA

first: Lucia

last: Daxinger

first: Emma

last: Whitelaw


title: GATA2 knockout study to investigated the role of GATA2 in human hematopoiesis

status: Public on Feb 09 2017

city: Guangzhou

first: qianyu

last: chen

address: 190 Kai Yuan Avenue, Science Park

country: China

institute: Guangzhou Institutes of Biomedicine and Health,Chinese Academy of Sciences

type: Expression profiling by high throughput sequencing

summary: We generated homozygous GATA2 knockout human embryonic stem cells (GATA2-/- hESCs) and analyzed their blood differentiation potential. Paritcularly at the hemogenic endothelium (HE) stage and hematopoietic progenitor cell (HPC) stage. Our result revealed that GATA2-/- hESCs displayed attenuated generation of CD34+CD43+ HPCs, due to the impairment of endothelial to hematopoietic transition (EHT). However, GATA2-/- hESCs retained the potential to generate erythroblasts, macrophages, but never granulocytes. Through RNA-Seq and further rescue experiment, we further identified that SPI1 was responsible for the defect of GATA2-/- hESCs in generation of CD34+CD43+ HPCs and granulocytes.

overall_design: We compared the transcriptome of GATA2-/- hESCs, HE, HPC and their wildtype counterparts by RNA-Seq.

first: Ke

last: Huang

first: Qianyu

last: Chen

first: Xi

last: Shi

first: Guangjin

last: Pan

first: Juan

last: Du


title: RNA-Seq analysis of glycosylation related gene expression in STZ-induced diabetic rat kidney inner medulla

city: Atlanta

first: Guangping

state: GA

address: 1639 Pierce Drive

department: Renal Division

country: USA

institute: Emory University

summary: The UT-A1 urea transporter is crucial to the kidney’s ability to generate concentrated urine. Native UT-A1 from kidney inner medulla (IM) is a heavily glycosylated protein with two glycosylation forms of 97 and 117 kDa. In diabetes, UT-A1 protein abundance, particularly the 117 kD isoform, is significantly increased corresponding to an increased urea permeability in perfused IM collecting ducts, which plays an important role in preventing the osmotic diuresis caused by glucosuria. In this study, using sugar-specific binding lectins, we found that the carbohydrate structure of UT-A1 is also changed under diabetic conditions with increased amounts of sialic acid, fucose, and increased glycan branching. These changes were accompanied by altered UT-A1 association with the galectin proteins, α-galactoside glycan binding proteins. To explore the molecular basis of the alterations of glycan structures, the highly sensitive next generation sequencing (NGS) technology, Illumina RNA-seq, was employed to analyze genes involved in the process of UT-A1 glycosylation using streptozotocin (STZ) - induced diabetic rat kidney as the tissue source. Differential expression analysis combining quantitative PCR revealed that a number of important glycosylation related genes were changed under diabetic conditions. These genes include the glycosyltransferase genes Mgat4a, the sialylation enzymes St3gal1 and St3gal4and glycan binding protein galectin-3, -5, -8 and -9. In contrast, although highly expressed in kidney IM, the glycosyltransferase genes Mgat1, Mgat2, and fucosyltransferase Fut8, did not show any changes. We conclude that the alteration of these glycosylation related genes may contribute to changing the UT-A1 glycan structure, and therefore modulate kidney urea transport activity under diabetic conditions.

overall_design: Examination of UT-A1 urea transporter glycosylation related genes under STZ-induced diabetic conditions

first: Xiaoqian

last: Qian

first: Xuechen

last: Li

first: Titilayo

middle: O

last: Ilori

first: Janet

middle: D

last: Klein

first: Rebecca

middle: P

last: Hughey

first: Cong-jun

first: Abdel

middle: A

last: Alli

first: Zhengyu

last: Guo

first: Peng

last: Yu

first: Xiang

last: Song


title: RNA-Seq analysis of Head and Neck Squamous cell carcinoma cell-lines

city: BUFFALO

first: SATRAJIT

last: SINHA

address: 701 ELLICOTT STREET

institute: SUNY AT BUFFALO

summary: Analysis of gene-probe expression data (FPKM) for HNSCC cell-lines using single-end RNA-Seq

overall_design: RNA was collected and analyzed from 6 HNSCC cell-lines ( SCC15, SCC4, SCC71, UMSCC103, UMSCC29, SCC351)

first: Isha

last: Sethi

first: Christian

last: Gluck

first: Michael

middle: J

last: Buck

first: Satrajit

last: Sinha


title: Genome-wide maps of histone acetylation and CREB/CRTC binding in Drosophila mushroom body.

city: Sai Kung

first: Yukinori

last: Hirano

address: Clear water bay

department: LIFS

country: Hong Kong

institute: The Hong Kong University of Science and Technology

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
Purpose: Exploring the alteration in histone acetylation colocalized with CREB/CRTC binding, which are important for long-term memory maintenance
Methods: The nuclei of Drosophila mushroom bodies were purified and the histone acetylation and CREB/CRTC binding were examined by ChIP-seq using specific antibodies. The sequencing was performed using SOLiD, and aligned to dm3 using Lifescope..The sequence reads that passed quality filters were analyzed by peak calling using PICS and ERD equipped on Strand NGS software. This method using two algorisms excludes false-positive calling of peaks. The PICS and ERD were run using a default setting except for the following parameters; for PICS, 120 bp as an average fragment length, 10 bp as a minimum distance between forward and reverse reads, 200 bp as a minimum distance between forward and reverse reads, 100 bp as a window width, with 5% false discovery rate; for ERD, 2 as an enrichment factor, 100 bp as a window size, 10 bp as a window slide size, 100 bp as a minimum region size. The peaks obtained by ERD analysis were filtered by an enrichment factor of 1.5, and a density of reads at 0.3 for H3K9Ac, 0.15 for H4K16Ac, 0.18 for CREB and 0.15 for CRTC. To determine the histone acetylation-increased sites, the peaks determined from 3 replicates of the trained samples were summed to analyze all peaks. Then the centers of the H3K9Ac and H4K16Ac peaks were extracted,  and then used to create neighboring 400 bp windows. The mapped reads were counted in these 400 bp windows for each biological replicate of ChIP-seq analysis. The counted read numbers in individual regions were normalized by elav for H3K9Ac ChIP-seq, and gapdh2 for H4K16Ac ChIP. The normalized read numbers in individual windows obtained from the spaced trained flies and the naïve flies were analyzed by Student’s t test (p < 0.05). Standard deviations of the normalized read numbers in individual windows from 3 replicates of naïve flies were 0.07 in H3K9Ac-ChIP-seq and 0.10 in H4K16Ac-ChIP-seq. Significantly increased peaks showing a more than 1.2-fold increase (>2SD) were determined as sites with an increase in H3K9Ac or H4K16Ac.
Results: Using an optimized data analysis workflow, the filtered reads amounted to 12-15 million reads for H3K9Ac in each of 3 replicates, 5-7 million reads for H4K16 in each of 3 replicates, 2.4 million reads for CREB, 2 million reads for CRTC, and 2.9 million reads for input. Using anti-H3K9Ac antibody, we found significant increases in H3K9Ac 1 day after training, and 75.0% of these mapped within 500bps of the transcriptional start sites (TSSs) of 1766 genes. Using anti-H4K16Ac antibody, we found significant increases in H4K16Ac 1 day after spaced training, and 61.6% of these mapped within 500bps of the TSSs of 1320 genes. Epigenetic changes in the vicinity of TSSs suggests that expression of these genes may be increased in LTM maintenance. We also examined CRTC and CREB binding 1 day after training. We identified 2390 CRTC binding sites, of which 79.6% of these were close to CREB binding sites. These CREB/CRTC binding sites mapped to 1394 genes, and were predominately located within 500bp from TSSs (55.4%). Of the 1394 CREB/CRTC target genes, 346 genes showed increases in H3K9Ac, 319 showed increases in H4K16Ac, and 135 showed increases in both.
Conclusions: Our study represents the first detailed analysis of chromatin state related to memory in Drosophila mushroom bodied. The optimized data analysis workflows reported here should provide a framework for comparative investigations of tissue-specific epigenetic alterations.

overall_design: Examination of 2 different histone modifications (H3K9Ac and H4K16Ac) and 2 different transcription factors (CREB and CRTC)

first: Kunihiro

last: Ihara

first: Tetsuya

last: Yamamoto


title: ∆DNMT3B4-del Contributes to Aberrant DNA Methylation Patterns in Lung Tumorigenesis

city: College Park

first: Jose

middle: Adrian

last: Carrillo

state: MD

address: 1413 Animal Sciences Center

department: Department of Animal and Avian Sciences

institute: University of Maryland

type: Methylation profiling by high throughput sequencing

summary: Aberrant DNA methylation is a hallmark of cancer but mechanisms contributing to the abnormality remain elusive. Here, we report that most of lung cancer cell lines tested expressed predominantly ∆DNMT3B-del whereas normal bronchial epithelial cells expressed equal quantities of ∆DNMT3B and ∆DNMT3B-del. We demonstrate biological impacts of ∆DNMT3B4-del, a ∆DNMT3B-del isoform, in a transgenic mouse model. Expression of ∆DNMT3B4-del in the mouse lungs resulted in an increased global DNA hypomethylation, focal DNA hypermethylation, epithelial hyperplastia and tumor formation when challenged with a tobacco carcinogen. In patients with non-small cell lung cancer, 83% of the primary tumors expressed predominantly ∆DNMT3B-del. Our results demonstrate ∆DNMT3B4-del as a critical factor in developing aberrant DNA methylation during lung tumorigenesis.

overall_design: Methyl binding domain protein-enriched genome sequencing (MBD-Seq) approach was employed to analyze methylated DNA regions in the genomic DNA samples. We constructed 6 libraries of genomic DNA samples from mouse lung tissues including 3 from wild-type mice and 3 from the transgenic mice. Each group (wild type or transgenic), therefore, consisted of three biological replicates.

first: Mark

middle: Z

last: Ma

first: Luxian

last: Lin

first: José

first: Manisha

last: Bhutani

first: Ashatosh

last: Pathak

first: Hening

last: Ren

first: Jiuzou

first: Li

last: Mao


title: Thymus Transcriptome Reveals Novel Pathways in Response to Avian Pathogenic Escherichia coli (APEC) Infection

city: Beijing

first: hongyan

last: sun

address: Poultry genetic group, College of Animal Science and Technology, China Agricultural Univeristy, Yuanmingyuan West Rd. No. 2, Haidian District, Beijing, China

institute: Iowa State University

summary:
Purpose: This study would be useful to characterize the molecular mechanisms of an effective anti-bacterial response of chicken immune system.
Methods: meat-type chickens were either infected with APEC O1 or given saline as a control. Thymii were collected on 1 and 5 days post-infection (dpi). The infected birds were classified based upon necropsy findings as having mild or severe pathology, representing resistant and susceptible phenotypes, respectively. Data from RNA sequencing experiments were analyzed using the R package, edgR, to identify the significantly differentially expressed (DE) genes. GO and pathway analysis using the R package GOseq identified many immune-related pathways.
Results: Thousands of genes were DE at 5 dpi in susceptible vs. non-infected birds and in susceptible vs. resistant birds, as well as in susceptible birds at 1 vs. 5 dpi. In the contrast of susceptible birds with resistant or non-challenged birds, many immune response and signal transduction pathways were strongly induced, whereas the TCR signaling pathway was deeply suppressed to affect T cell development, differentiation, proliferation, and maturation. The transcriptomes of resistant and non-challenged birds were similar.
Conclusions: These results provide the first comprehensive assessment of global gene networks and biological functionalities of DE genes in thymus in response to APEC infection, thus providing novel insights into key molecular genetic mechanisms that differentiate host resistance from susceptibility in this primary lymphoid tissue. These findings are foundational to the development of strategies to enhance host resistance to APEC infection.

overall_design: Thymus mRNA profiles of six treatment groups were generated by deep sequencing, in four replicates, using Illumina Hiseq2000.

first: Hongyan

last: Sun

first: Susan

last: Lamont


title: The Bcl2/Shp/Fgf15/lncRNA H19 molecular circuit: a key gatekeeper of bile acid homeostasis

city: Durham

first: Integrative

last: Bioinformatics

state: NC

address: 111 TW Alexander Drive

department: BCBB

institute: NIEHS

summary: Analysis of hepatic gene expression in mice transiently overexpressing Bcl2

overall_design: 3 control GFP mice and 5 GFP-Bcl2 mice, 8 mouse liver samples total

first: Lisa

last: Zhang

last: Wang


title: DLX3 alters transcriptomic profile of adhesion, cell cycle, and cell death in Squamous Cell Carcinoma Cells

city: Bethesda

first: Hong-wei

address: 9000 Rockville Pile

department: Office of Science & Technology

institute: NIAMS

summary: Reinstatement of DLX3 into SCC13 cells upregulates genes involved with cell cycle exit, signaling, and adhesion whiles downregulates genes involved with cell death, proliferation, and movement.

overall_design: We used RNA-sequencing data analysis to assess gene expression in SCC13 cells infected with Adeno-GFP or Adeno-DLX3 in order to understand the effects of DLX3 in a Squamous Cell Carcinoma Cell Line.  We identified a specific subset of genes involved in regulation of cell cycle arrest and inhibition of apoptosis.

first: E

last: Palazzo

first: M

last: Kellett

first: C

last: Cataisson

first: A

last: Gormley

first: P

middle: W

last: Bible

first: V

last: Pietroni

first: N

last: Radoja

first: J

last: Hwang

last: Blumemberg

first: S

middle: H

last: Yuspa

last: Morasso


title: Identification of candidate adherent-invasive E. coli signature transcripts by genomic/transcriptomic analysis

city: Stony Brook

first: Yuanhao

address: AMS Department,Stony Brook University

department: Applied Mathematics and Statistics

institute: Stony Brook University

summary: Our aim was to identify candidate transcripts that distinguish AIEC from non-invasive E. coli (NIEC) strains and might be useful for rapid and accurate identification of AIEC by culture-independent technology.  We performed comparative RNA-Sequence (RNASeq) analysis using AIEC strain LF82 and NIEC strain HS during exponential and stationary growth.

sample_organism:
Escherichia coli HS
Escherichia coli LF82

overall_design: Triplicate Luria broth cultures (37o C) of LF82 and HS were grown with continuous shaking for 2 hours (exponential phase) and 24 h without shaking (stationary phase).

first: Grace

last: Gathungu

first: Leahana

last: Rowehl

first: Erika

last: Orner

first: Edgar

middle: C

last: Boedeker

first: Xuejian

last: Xiong

first: ohn

last: Parkinson

first: Ellen

last: Li


title: Transcriptome sequencing of β-arr1 knockout DG astrocytes

city: Shanghai

first: Yezheng

last: Tao

address: No.130, Dong An Road

institute: IOBS, Fudan University

summary: WT and β-arr1-/- DG astrocytes with pooled cDNA library were sequenced.

overall_design: pooled cDNA libraries from WT and β-arr1-/- DG astrocytes were sequenced.

first: Lan

last: Ma


title: KPC vs Wild Type Pancreatic Fibroblasts

city: Columbus

first: Jason

middle: R

last: Pitarresi

state: Ohio

address: 460 W. 12th Ave

institute: Ohio State University Medical Center

summary: These experiments aim to determine global gene expression patterns in WT vs KPC isolated pancreatic fibroblasts

overall_design: WT or KPC mice were isolated from pancreas and RNA-seq was performed

first: Michael

last: Ostrowski


title: The effect of HOXB13 CRISPR knockout on the transcriptome in G401 cells

city: Los Angeles

first: Paul-Joseph

last: Aspuria

state: California

address: 8400 Beverly Blvd.

department: Women's Cancer Program

institute: Cedars-Sinai Medical Center

summary: We report the expression profiles of G401 rhabdoid tumor of the kidney cell lines with and without the expression of the homeobox transcription factor HOXB13.

overall_design: Single samples of G401-sg-control and G401-sg1-HOXB13 cells were subjected to RNAseq

first: Vincent

last: Funari

first: Sandra

last: Orsulic


title: Deep sequencing-based characterization of transcriptome and transcriptional profiling of trifoliate orange (Poncirus trifoliata (L.) Raf.) in response to cold stress

city: Wuhan

first: Wang

last: Min

address: No.1,Shizishan Street

institute: Huazhong Agricultural University

summary: A large number of high-quality transcripts were fistly obtained by sequencing the pooled RNAs from trifoliate orange under different stress treatments (cold, salt, drought). Four cold-treated libraries were further mapped to the assembled transcriptome, leading to identification of more 5,000 DEGs. Plant hormone signal transduction, plant-pathogen interaction, and secondary metabolism were most significantly enriched in the DEGs. A total of 60 transcription factors were revealed to be cold responsive.n addition, a number of genes involved in catabolism and signaling of hormones, such as abscisic acid, ethylene and gibberellin, were either up- or down-regulated under cold stress. These data provide valuable information for elucidating transcriptomic reprogramming and underlying mechanisms of trifoliate orange in response to cold and underpin exploitation of genes of interest in the future.

overall_design: High-throughput RNA sequencing of pooled library derived from trifoliate orange under different stress treatments (cold, salt, drought) and four cold-treated libraries.In detail,three-month-old trifoliate orange (Poncirus trifoliata (L.) Raf.) seedlings were collected from an experimental nursery at Huazhong Agricultural University. After a full wash, the plants were incubated in glass beakers filled with tap water and kept for 5 d at 25°C in a growth chamber. In order to enrich stress-responsive genes, the seedlings were treated with different stresses, including cold, salt, and drought. For cold treatment, the plants were placed at 4°C; the leaves were harvested at indicated time points (0, 6, 24, and 72 h). Salinity treatment was applied by placing the seedlings in 200 mM NaCl solution for same time schedule as cold. For drought treatment, the seedlings were placed on filter papers and dehydrated at ambient environment; the whole plants were sampled at 0, 0.5, 3, and 6 h.  These tissues were immediately frozen in liquid nitrogen after sampling and stored at -80 °C

first: Min

last: Wang

first: Ji-Hong

last: Liu


title: Transcriptional landscape of XYR1 in Trichoderma reesei during the degradation of cellulosic material

city: Campinas

first: Gabriela

middle: F

last: Persinoti

state: São Paulo

address: Rua Giuseppe Máximo Scalfaro, 10.000

department: Brazilian Biorenewables National Laboratory LNBR

country: Brazil

institute: Brazilian Center for Research in Energy and Materials CNPEM

summary: Hypocrea jecorina (anamorph Trichoderma reesei) is one of the most well studied fungi used in biotechnology industry. This fungus is today a paradigm for the comercial scale production of different plant cell wall degrading enzymes, mainly cellulases and hemicellulases. The objective of this study was to analyze the transcriptional profiling of T. reesei (Δxyr1) grown in presence of cellulose, sophorose and glucose as the carbon source using RNA-seq approach.

overall_design: T. reesei (Δxyr1) was grown in Mandels-Andreotti medium, supplemented with 1% of cellulose, 2% of glucose or 1mM of sophorose. The cultures were incubated on an orbital shaker (200 rpm) at 28°C for 8 and 24 hours using cellulose as carbon source; for 24 and 48 hours with glucose as the carbon; and 2, 4 and 6 hours with sophorose as the carbon source. In the latter, the mycelium was previously grown on glycerol for 24 hours and then transferred to 20 mL of Mandels-Andreotti medium without peptone. All experiments were performed in three biological replicates. The resultant mycelia were collected by filtration, frozen and stored at -80°C until RNA extraction. After growth, total RNA was isolated from the mycelia using TRIzol® reagent. RNA-seq experiments were performed by LGC Genomics GmbH (Berlin/Germany) using the platform Illumina/HiSeq2000.

first: Lílian

last: dos Santos Castro

first: Rafael

middle: S

last: Rocha

first: Amanda

last: Antoniêto

first: Renato

last: Graciano de Paula

first: Roberto

last: do Nascimento Silva


title: DLX3-dependent p53 signaling network controls keratinocyte cell cycle and squamous tumor growth

first: Hong-wei

last: Sun

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

overall_design: Refer to individual Series


title: Characterization of miRNomes in Human Embryonic Stem Cells and Erythroid Cells

first: yadong

last: yang

address: No.1-104 Beichen West Road, Chaoyang

institute: Beijing Institute of Genomics

type: Non-coding RNA profiling by high throughput sequencing

summary: In this study, we analyzed the genome-wide miRNAs dynamics that occur during the differentitation of HESCs into the erythroid lineage using high throughput sequencing technology.  Undifferentiated HESCs as well as erythroid cells at three developmental stages-ESER (embryonic stage), FLER (fetal stage) and PBER (adult stage) were analyzed.

overall_design: Compare the miRNomes of embryonic stem cells and three erythroid cell types at different development stages

first: X

last: Fang


title: miRNA expression profiling in liver of juvenile and egg-laying hens

city: Zheng

first: HONG

last: LI

address: 95 Wenhua Road, Jinshui District

institute: Henan Agriculture University

summary: A total of 565 miRNAs annotated in miRBase 20.0 were identified to be expressed in the liver of hen by high-throughput sequencing three biological reduplication libraries in juvenile and egg-laying hens, respectively. Compared with juvenile hen, 80 miRNAs (67 down-regulated and 13 up-regulated) were verified to be significant differential expression (SDE) in egg-laying physiological stage. Among these, miR-22-3p has the highest abundant expression, and miR-146b-5p has the highest fold-change. Additionally, 19 of the 71 novel miRNAs was significantly expressed. Furthermore, 648 putative target genes of the SDE miRNAs were obtained, and among these, FADS1, FADS2, ELOVL6, ACSL5, etc which are lipid metabolism related critical regulators are targeted by some SDE miRNAs. Gene Ontology (GO) analyses to the putative target genes of all the SDE miRNAs showed significantly enriched in Steroid biosynthesis, Glycerophospholipid metabolism, Biosynthesis of unsaturated fatty acids, and PPAR signaling pathway (P ≤ 0.05). Meanwhile, GO terms are also significantly enriched in lipid related biological processes.

overall_design: Total two groups juvenile and egg-laying hens were included,and three replications for each group.Juvenile stage was designed as the reference group.The liver miRNAs expression profile of juvenile hens and laying hens were generated by Solexa microRNA-Seq

first: Hong

last: Li

first: Xiangtao

last: Kang

first: Xiaojun


title: Effect of Egg Protein Ovotransferrin-derived Peptide, IRW on Gene Expression of Vascular Tissues in Spontaneously Hypertensive Rats

city: Edmonton

first: Guanxiang

last: Liang

state: Alberta

address: 410 Agriculture/Forestry Centre

country: Canada

institute: University of Alberta

summary: In this study we tested the effect of orraly administered egg white ovotransferrin derived pepide, IRW on gene expression in spontaneously hypertensive rats. IRW is previously identified with antihypertensive effect and in this study we evaluated how IRW treatment can modulate various gene expression.

overall_design: Two groups of animal, group 1 is untreated control with 5 animals, receiving vehicle control for 18 days and group 2 is IRW treated (15mg/kg BW) for 18 days, 6 animals were used in this group

first: Kaustav

last: Majumder


title: Gene expression analysis of diploid and autotetraploids of Mulberry (Morus atropurpurea)

first: fanwei

last: dai

state: Guangdong

address: The Sericulture and Agri-Food Research Institute, Guangdong Academy of Agricultural Sciences

summary: Autotetraploid carries several phenotypic changes with larger leaves and fruit compared to diploid. To analysis of phenotypic changes in mulberry autotetraploids on the transcriptome, we performed RNA-Seq analyses on mulberry leaf samples of diploid and autotetraploids using Illumina HiSEq 2000.

overall_design: Mulberry leaves mRNA profiles of diploid and autotetraploids were generated by deep sequencing using Illumina HiSEq 2000.

first: Fanwei

last: Dai

first: Zhenjiang

first: Guoqing

last: Luo

first: Cuiming

last: Tang


title: The temporal patterning system governs the malignant susceptibility of neural progeny during Drosophila development

city: Marseille

first: Cedric

last: Maurange

address: Parc Scientifique de Luminy, case 907

country: France

institute: CNRS / Aix-Marseille University

summary: Pediatric neural tumors are initiated during embryonic/fetal stages and rapidly become malignant despite carrying few genetic alterations. However, the molecular basis of this early malignant susceptibility remains unknown. During Drosophila development, malignant neural tumors can arise from single gene inactivation triggering dedifferentiation towards a neural stem cell (NSC)-like state. Here, we find that these tumors originate from a sub-population of early-born neural progeny that transiently co-express the mRNA-binding proteins Lin-28 and Imp/IGF2BP, and the transcription factor Chinmo. These three genes compose an early growth module that is co-opted in a subset of dedifferentiated cells to propagate unlimited proliferation. In late NSCs, Chinmo, Imp and Lin-28 are silenced by temporal transcription factors for timely termination of neurogenesis. Consequently, late-born progeny do not express the module and become refractory to malignant transformation. Thus, this study identifies the NSC-intrinsic developmental program that predisposes neural progeny to malignant transformation according to their birth order.

overall_design: Tumors are induced during early larval stages by expressing UAS-prosperoRNAi transgenes in neuroblasts using nab-GAL4. Tumors are then dissected at the end of larval stages for RNA-seq. To investigate the role of Chinmo in the tumorigenic process, three conditions have been sequenced: 1) nab-GAL4, UAS-prosperoRNAi (referred to as "P"). 2) nab-GAL4, UAS-prosperoRNAi, UAS-chinmoRNAi (referred to as "PC"); 3) nab-GAL4, UAS-prosperoRNAi, UAS-chinmoFL (referred to as "PCC"). Conditions 2 and 3 respectively allow down-regulation and over-expression of Chinmo in prosperoRNAi tumors.

first: Elodie

last: Lanet

first: Sophie

last: Foppolo

first: Hugues

last: Parrinello

first: Stéphanie

last: Rialle

first: Cédric

first: Karine

last: Narbonne-Reveau

first: Caroline

last: Dillard


title: The maize genome encodes novel members of the purple acid phosphatase (PAP) subgroup Ia

city: Irapuato

first: Ruairidh

last: Sawers

state: Guanajuato

address: Km 9.6 Lib. N. Car. Irapuato-Leon

country: Mexico

institute: LANGEBIO-CINVESTAV

summary: In this study we perform a transcriptomics analysis of two maize (Zea mays) organs, roots and leaves, from plants grown in the presence of a sufficient (1000 uM) or limiting (10 uM) concentration of soil phosphate.

overall_design: Duplicate root and leaf mRNA profiles for plants grown in the presence of 1000 uM or 10 uM soil phosphate.

first: Aida-Odette

last: Avendaño-Vázquez

first: Patrick

last: Brown


title: SUVH1, a histone methyltransferase, is required for the expression of genes targeted by DNA methylation

first: shaofang

last: Li

state: Beijing

address: No 50, ZhanghuaLu, HAIDIAN

department: Beijing Vegetable Research Center

institute: Beijing Academy of Agriculture and Forestry Science

summary: Transposons and repeats are found throughout the genomes of all organisms. To prevent the harmful effects of these elements, repressive marks such as DNA methylation and H3K9me2 have evolved to control transposon activity and ultimately maintain genome integrity. However, how silencing mechanisms are themselves regulated to avoid stochastic silencing of genes remains unclear. Here, negative regulators of silencing were identified using a forward-genetic screen on a reporter line that harbors a LUCIFERASE (LUC) gene driven by a double 35S promoter. SUVH1, a SU(VAR)3-9 homolog, was isolated as a factor promoting the expression of the LUC gene. Treatment with a cytosine methylation inhibitor compromised the effect of the identified suvh1 mutation, indicating that SUVH1 is dispensable for LUC expression in the absence of DNA methylation. However, the suvh1 mutation did not alter DNA methylation levels at the LUC region or on a genome-wide scale; thus, SUVH1 may function downstream of DNA methylation. Histone methylation analysis revealed that suvh1 led to decreased H3K4me3 levels; in contrast, H3K9me2 levels remained unchanged. Moreover, the characterization of endogenous genes indicated that SUVH1 functions at genes with repressive marks in the promoter region. Taken together, these findings shed light on the regulatory network acting at genes with various epigenetic marks.

overall_design: The BS-seq and mRNA-seq were performed on the reporter line YJ and the mutant YJ suvh1 to assess the effect on DNA methylation and transcriptome caused by suvh1 mutation

first: Shaofang

first: Xuemei

last: Chen


title: Transcriptomic analysis of ABA influences on pigments, flavonoids and antioxidant system in tomato fruit ripening

city: Hangzhou

first: Wangshu

last: Mou

state: Zhejiang

address: Yuhangtang Road 866

department: College of Bio-engineering and Food Science

institute: Zhejiang University

summary:
Purpose: The goals of this study was to provide genome-wide data to investigate the molecular mechanism of ABA regulation in many ripening related biological processes, including fruit color variation, antioxidant capacity, flavonoids biosynthesis and photosynthesis.
Methods:By applying the next generation sequencing technology, we conducted a comparative analysis of exogenous ABA and NDGA effects on tomato fruit maturation.
Results:The high throughput sequencing results showed that 25728 genes expressed across all three samples, and 10388 of them were identified as significantly differently expressed genes (DEGs). Exogenous ABA was found to enhance the transcription of genes in pigments metabolism, including carotenoids biosynthesis and chlorophyll degradation, whereas NDGA treatment inhibited these progresses. The results also revealed the crucial role of ABA in flavonoids synthesis and regulation of antioxidant system. Intriguingly, we also found that an inhibition of endogenous ABA significantly enhanced the transcriptional abundance of genes involved in fruit photosynthesis.
Conclusions:next-generation sequencing enabled us to characterize the transcriptomes of tomato fruit treated with ABA and NDGA. By comparing these transcriptomes with control respectively, we observed that ABA could accelerate fruit maturation by positively regulating many genes related to ripening processes. Our study have turned spotlight on the pathways of fruit pigmentation, including carotenoid biosynthesis and chlorophyll metabolism. Exogenous ABA was able to up-regulate many genes in relation to the carotenoids accumulation and chlorophyll breakdown, thus promoting the color transition of tomato fruit. In addition, ABA has the potential to improve the genes related to antioxidant capacity, such as SODs, CATs, APXs, GSTs, GPXs, TrXs and PrxRs. Besides, the expression changes of genes involved in flavonoids biosynthesis after ABA exposure was striking, suggesting ABA could enhance the defense response by producing more secondary metabolite in tomato fruit. Moreover, the sequencing results also implied high level of ABA could negatively affect photosynthesis of tomato fruit, which needs more investigations to explore the interaction between ABA and photosynthesis in the future.

overall_design: Examination of genome-wide gene expression changes of the 9th day tomato fruits treated with ABA, NDGA and CK, stored at  20 oC,90% RH in the dark.

first: Tiejin

last: Ying


title: Identification and profiling of microRNAs in goat endometrium during Embryo Implantation

city: Yangling District

first: Lei

last: Zhang

state: Province, State or Region

address: No.22 Xinong Road,  Yangling District

department: College of Animal Science and Technology

institute: Northwest A&F University

summary: Our data revealed the first miRNA profile related to the biology of the goat receptive endometrium during embryo implantation. The results suggested that a subset of miRNAs might play important roles in the formation of endometrial receptivity. Thus, elucidating the physiological roles of endometrial miRNAs will help us better understand the genetic control of implantation, which is the gateway to a successful pregnancy.

overall_design: A total of 20 healthy 24-month-old multiparous dairy goats (Xinong Saanen) were induced to estrous synchronization for this study. The first day of mating was considered to be Day 0 of pregnancy. Gestational days 5 and 15 were important time points for the embryo implantation in goats [38]. The experimental goats were observed 3 times daily to ascertained estrous sign and mated naturally twice in estrus. And then the goats were euthanized when the goats lost consciousness caused by intravenous injection of barbiturate (30mg/kg) at gestational day 5 (pre-receptive endometrium) and gestational day 15 (receptive endometrium). Endometrium samples from 10 goats at gestational day 5 and 10 goats at gestational day 15 were obtained from the anterior wall of the uterine cavity.

first: Yu-Xuan

last: Song

first: Xiao-peng

last: An


title: Transcriptome analysis of the primary roots of Alhagi sparsifolia in response to water stress

first: WEIMIN

last: LI

address: No.12 Zhongguancun St.

institute: Biotechnology Research Institute, CAAS

summary: Alhagi sparsifolia Shap. is a perennial subshrub belonging to genus Alhagi, family Leguminosae. As a typical desert phreatophyte, this plant species has highly developed deep roots and displays a great capacity to withstand poor soil as well as extreme dry, cold and hot weather. A. sparsifolia is naturally distributed in the arid and salinized regions of northernwestern China and adjacent countries in Central Asia, and plays a fundamental role in maintaining the local ecosystem. In addition, this plant is usually used as a fodder for local animals due to its high protein content, and is important in the development of local livestock husbandry. Considering its great tolerance to harsh environments, A. sparsifolia represents an ideal species for deciphering the mechanism of plant adaption to abiotic stress, such as water deficit. However, understanding the stress adaption in this plant is limited. While a few studies were conducted on physiological responses of A. sparsifolia to water stress, research has never been done to explore the genomic basis for its drought-tolerance to date. In particular, as a non-model plant species, the genomic resource of A. sparsifolia is rather scarce, only one expressed sequence tag (EST) and one protein have been deposited in Genbank prior to Sept., 2014.   In aim to explore the genetic basis underlying drought tolerance in this species, recently we took advantage of transcriptome sequencing to survey the water stress responsive genes in A. sparsifolia primary roots. Using Illumina HiSeq™ 2000 platform, we sequenced the primary root samples individually collected at four different time points (0, 6h, 24 and 30h) from A. sparsifolia seedlings during 24h of water stress following 6h of rehydration. The resulting 38,763,230, 67,511,150, 49,259,804 and 54,744,906 high quality reads were pooled and assembled into 33,255 unigenes with an average length of 1,057 bp. All-unigenes were subjected to functional annotation by searching against the public databases including NR, NT, Swiss-Prot, Pfamm, GO, KOG and KEGG. On the basis of the established transcriptome database, we evaluated the gene expression profiles in A. sparsifolia primary roots at 0, 6, 24 and 30h in the course of water stress and subsequent rehydration. An extensive repertoire of the differently expressed genes (DEGs) reflecting the early response to water stress (6h), the late response to water stress (24h) and the response to post stress rehydration (30h) were identified. In addition, to unravel the dynamic changes of gene expression during water stress and subsequent rehydration, we further captured the DEGs commonly or specifically regulated at 6, 24 and 30h. Functional categorization of the DEGs disclosed the activation of oxidoreductase system in A. sparsifolia primary roots upon water stress, and particularly emphasized the significance of the ‘Glutathione metabolism pathway’.          To our knowledge, this is the first description of the genetic makeup of A. sparsifolia, thus providing a substantial contribution to the sequence resources for this species. The DEGs identified herein offers a deep insight into the molecular mechanism of A. sparsifolia in response to water stress, and merits further investigation.

overall_design: Identification of the differently expressed genes during 24h of water stress following 6h of rehydration in A. sparsifolia


title: Transcriptome analysis of the effect of Vibrio alginolyticus infection on the innate immunity-related complement pathway in Epinephelus coioides

city: Ilan

first: Jyh-Yih

address: 23-10, Dahuen Rd., Jiaushi, Ilan

country: Taiwan

institute: Academia Sinica

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized  analysis of the immune response to V. alginolyticus in Epinephelus coioides larvae, we used high-throughput deep sequencing technology to study the effect of infection on gene expression.
Methods: Epinephelus coioides larvae (30-days-old) were injected with V. alginolyticus , and fish were sacrificed at 24 h after infection. Ten wild-type Epinephelus coioides larvae were used to build an EST library for transcriptome analysis. The library products were prepared for sequencing analysis using an Illumina HiSeq™ 2000. Raw data were saved as fastq files. The following were removed: reads with adaptors, reads in which over 10% bases were unknown, and low quality reads (i.e., the percentage of bases of quality value ≤ 5 exceeds 50% in the read). Clean reads were mapped to reference sequences using SOAP aligner/soap2 . The randomness of RNA fragmentation was used to construct the library, and the numbers of reads mapped to the reference sequence were calculated. The RPKM method (Reads Per kb per Million reads) was used to calculate gene expression level, and differentially expressed genes (DEGs)
Results: A total of 114,851,002 reads were assembled, consisting of 9,687,355,560 nucleotides; these were further assembled into 209,082 contigs with a mean length of 372 bp. Gene ontology (GO) analysis of the transcriptome revealed 12 cellular component subcategories, 16 molecular function subcategories, and 42 biological process subcategories (P value < 0.05). A total of 32664 Epinephelus coioides genes were mapped to the Kyoto Encyclopedia of Genes and Genomes (KEGG); 1504 differentially expressed genes (DEGs) were subsequently identified, in 12 categories (P value < 0.05). Vibrio  infection affected the expression of genes involved in complementation, coagulation cascades, pathogen (Staphylococcus aureus) infection, phagosome activity, antigen processing, and the antigen presentation pathway.
Conclusions: We conclude that the complement pathway of innate immunity and the hepicidin antimicrobial peptide may play important roles in the defense of Epinephelus coioides larvae against V. alginolyticus, and the immune response may activate at 4h after bacterial infection. These results implicate the complement pathway signal pathway in immunity during V. alginolyticus infection at early developmental stages, enhancing our understanding of the mechanisms underlying the immune response to Vibrio infection in Epinephelus coioides.

overall_design: Comparing Vibrio infected mRNA profile with non-infected mRNA profile of Epinephelus coioides by RNA-seq

first: Yi-Da

last: Wang


title: Quantitative analysis of CD133+ liver cancer stem cells vs CD133- non cancer stem cell by RNA-Seq profiling

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

institute: The University of Hong Kong

summary: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goal of this study is to compare the differentially expressed transcriptomes between CD133+ liver cancer stem cells versus CD133- non cancer stem cells by RNA-Seq profiling

overall_design: mRNA profiles of sorted CD133+ and CD133- subsets isolated from HCC cell lines Huh7 and PLC8024 were generated by deep sequencing using Illumina GAIIx

first: Stephanie

last: Ma


title: The epigenetic reader protein SPIN1 controls proliferation and survival of liposarcoma by modulating the RET signaling pathway

city: Freiburg

first: Henriette

last: Franz

address: Alberstr: 17

department: Anatomy and Cellbiology

country: Germany

institute: University Freiburg


title: Genome-wide Analysis of Enterococcus faecalis OG1RF(pCF10) Gene Expression During Infection

city: Minneapolis

first: Kristi

middle: L

last: Frank

state: MN

address: 420 Delaware St SE, MMC196

department: Dept. of Microbiology

institute: University of Minnesota

summary: Changes in Enterococcus faecalis OG1RF(pCF10) gene expression at 4 hours post-infection in a rabbit model of subdermal abscess formation were studied using RNA-seq analysis.

overall_design: Samples consisted of RNA from the input inoculum and RNA collected from the subdermal chambers four hours after inoculation. Two biological replicates were performed.

first: Gary

middle: M

last: Dunny


title: Transcriptome alteration of cultured dental mesenchymal cells

city: Beijing

first: Yunfei

last: Zheng

address: 22 Zhongguancun Avenue South, Haidian District

department: Oral and Maxillofacial Surgery

institute: Peking University School and Hospital of Stomatology

summary: Dental mesenchymal cells (dMCs) differentiate into dentin-secreting odontoblasts and are utilized in the majority of tooth regeneration studies to produce an entire tooth organ. An in vitro culture platform of dMCs is useful in generating an adequate quantity of cells for experiments and regenerative therapy. However, culturing techniques may induce functional modification in dMCs. Here, we examined the transcriptomic alterations induced by in vitro culture and investigated the biological properties of cultured dMCs. Hierarchical clustering analysis and principal components analysis reveal an overall transcriptional similarity between the first and second passages that differed significantly from freshly obtained cells. Following in vitro culture, the biological processes of cell adhesion, chromatin organization, cell differentiation and development are significantly altered. Components of signaling pathways, including p53, transforming group factor β/bone morphogenetic protein (TGFβ/BMP), Hedgehog, and Wnt, as well epigenetic regulators are involved. Furthermore, the osteogenic potential of cultured dMCs is also impaired. Our study provides valuable insights for the modification of the current culturing methods to maintain the characteristics of in vivo dMCs.

overall_design: To determine the transcriptional regulation following in vitro culture, dMCs from developing molar germs in embryonic day 14.5 (E14.5) mouse embryos were isolated and designated as P0. The cells were then subcultured in standard medium and passaged once they reached 90% confluence, with the first-passage culture designated as P1 and the second-passage as P2. Illumina-based high-throughput sequencing (Illumina, San Diego, CA, USA) was used to obtain the transcriptome profiles of P0, P1 and P2 cells

first: Shicheng

last: Wei


title: Tag-based identification of differentially expressed genes under cold and freeze stress in seabuckthorn (Hippophae rhamnoides L.)

city: New Delhi

first: Prakash

middle: Chand

last: Sharma

state: Delhi

address: Sector 16-C, Dwarka

department: University School of Biotechnology

country: India

institute: GGS indraprastha University

summary:
Purpose: Tag-based approach for global gene expression analysis has been revolutionised with the advent of next generation sequencing (NGS) technology.  The aim of the present study is to present comprehensive view of differentially expressed genes under cold and freeze stress in seabuckthorn (Hippophae rhamnoides L.)
Methods: DeepSAGE, a tag based approach, was used to identify differentially expressed genes under cold and freeze treatments in seabuckthorn (Hippophae rhamnoides L.). The 30 days old plantlets, at six leaves stage, were subjected to cold stress (CS) at 4°C and freeze stress (FS) at -10°C treatment for 6 hr. The seedlings grown at 28°C were taken as control (CON). Total RNA from all the three samples was isolated. Illumina Gene Expression Sample Prep Kit and Solexa Sequencing Chip (Flowcell) were used for tag preparation and the main instruments used for sequencing included Illumina Cluster Station and Illumina HiSeqTM 2000 System. Bioinformatics analysis resulted in to high number of differentially expressed genes under cold and freeze stress.
Results: 36.2 million raw tags including 13.9 million distinct tags were generated from three leaf tissue libraries (control, cold stress and freeze stress). After removing low quality tags, 35.5 million clean tags including 7 million distinct clean tags were obtained. In total, 11922 differentially expressed genes (DEGs) were identified including 6539 up regulated and 5383 down regulated genes.
Conclusions: DeepSAGE data of seabuckthorn provided useful resource and reference dataset for further functional genomics analysis in seabuckthorn and other important crops. The present study implicated a large number of genes with different biological functions expressing differentially in response to cold and freeze stress treatment. Isolation and further characterization of these genes will help researchers in understanding their role in cold and freeze tolerance in seabuckthorn and may provide important gene resources to be exploited for the development of stress tolerant crop plants in future.

overall_design: Differential gene expression profile of seabuckthorn (Hippophae rhamnoides L.) under cold and freeze stress was generated through DeepSAGE. Tags were generated using mRNA isolated from all the three, control, cold stressed and freeze stressed leaf tissues samples. Tags generated were further sequenced using Illumina Cluster Station and Illumina HiSeqTM 2000 System.

first: Saurabh

last: Chaudhary


title: The epigenetic reader protein SPIN1 controls proliferation and survival of liposarcoma by modulating the RET signaling pathway [ChIP-Seq]

summary: The aim of this study is to identify the SPIN1 target genes in liposarcoma cells

overall_design: Liposarcoma is one of the most common histological subtypes of soft tissue sarcoma and causes high incidence of morbidity and mortality. Since therapeutic options for liposarcoma treatment are insufficient, there is an urgent need to identify novel therapeutic targets. Here, we show that knockdown of SPIN1, a reader of H3K4me3 and H3R8me2a chromatin marks, strongly reduces proliferation and survival of liposarcoma cells in vitro and in xenograft mouse models. Combining genome-wide chromatin binding and transcriptome analyses, we found that SPIN1 in cooperation with the transcription factor MAZ directly enhances expression of GDNF, an activator of the RET signaling pathway. Accordingly, knockdown of SPIN1 results in reduced levels of GDNF and activated RET explaining diminished liposarcoma cell proliferation and survival. In line with these observations, levels of SPIN1, GDNF, and activated RET are highly increased in human liposarcoma compared to lipoma or normal adipose tissue. Importantly, SPIN1-mediated transcriptional control depends on binding to H3K4me3 suggesting that targeting of this interaction with small molecule inhibitors is a novel strategy to treat liposarcoma.

first: Holger

last: Greschik

first: Dominica

last: Willmann

first: Roland

last: Schüle


title: The epigenetic reader protein SPIN1 controls proliferation and survival of liposarcoma by modulating the RET signaling pathway [RNA-Seq]


title: Identification of boron-deficiency-responsive microRNAs in Citrus sinensis roots by Illumina sequencing

city: Fuzhou

first: Chen

last: Lisong

address: Shangdian street NO.15

institute: Fujian Agriculture and Forestry University

summary:
Background: Boron (B)-deficiency is a widespread problem in many crops, including Citrus. MicroRNAs (miRNAs) play important roles in nutrient deficiencies. However, little is known on B-deficiency-responsive miRNAs in plants. In this study, we first identified miRNAs and their expression pattern in B-deficient Citrus sinensis roots by Illumina sequencing in order to identify miRNAs that might be involved in the tolerance of plants to B-deficiency.
Results: We isolated 52 (40 known and 12 novel) up-regulated and 82 (72 known and 10 novel) down-regulated miRNAs from B-deficient roots, demonstrating remarkable metabolic flexibility of roots, which might contribute to the tolerance of plants to B-deficiency. A model for the possible roles of miRNAs in the tolerance of roots to B-deficiency was proposed. miRNAs might regulate the adaptations of roots to B-deficiency through following several aspects: (a) inactivating reactive oxygen species (ROS) signaling and scavenging through up-regulating miR474 and down-regulating miR782 and miR843; (b) increasing lateral root number by lowering miR5023 expression and maintaining a certain phenotype favorable for B-deficiency-tolerance by increasing miR394 expression; (c) enhancing cell transport by decreasing the transcripts of miR830, miR5266 and miR3465; (d) improving osmoprotection (miR474) and regulating other metabolic reactions (miR5023 and miR821). Other miRNAs such as miR472 and miR2118 in roots increased in response to B-deficiency, thus decreasing the expression of their target genes, which are involved in disease resistance, and hence, the disease resistance of roots.
Conclusions: Our work demonstrates the possible roles of miRNAs and related mechanisms in the response of plant roots to B-deficiency.

overall_design: Two libraries were constructed from C. sinensis roots subjected to 0(B-deficient) or 10(B-sufficient,control) μM B   for 15 weeks, and sequenced by Illumina sequencing. Size fractionated small RNAs (16-30 bp) from total RNA extracts was ligated to 5' and 3' adapters, and reverse transcribed. After PCR amplification the sample was subjected to Solexa sequencing. The clean tags were used for further analysis.

first: Yi-Bin

last: Lu

first: Lin-Tong

last: Yang


title: High-throughput deep sequencing reveals that microRNAs play important roles in salt adaptation of euhalophyte Salicornia europaea

first: Yinxin

last: Li

address: Nanxincun No. 20, Xiangshan, Haidian District

department: Chinese Academy of Sciences

institute: Institute of Botany

summary:
Backgroud: microRNA (miRNA) is implicated in plant development processes, playing pivotal roles in plant adaptation to environmental stresses. Salicornia europaea, a salt mash euhalophyte, is a good model plant to study salt adaptation mechanisms. It is also attractive in being vegetables, forage and oilseed that can be used for saline land reclamation and biofuel precursor production on marginal lands. However, none of the miRNAs from S. europaea have been identified so far.
Results: Deep sequencing was performed to investigate small RNA transcriptome of S. europaea. Two hundred and twelve conserved miRNAs comprising 51 families and 31 novel miRNAs (including 7 miRNA star sequences) belonging to 30 families were identified. Interestingly, about half (13 out of 31) of the novel miRNAs were only detected in salt-treated samples. The expression of 43 conserved and 13 novel miRNAs changed significantly in response to salinity. In addition, 53 conserved miRNAs and 13 novel miRNAs were differentially expressed between shoots and roots. Furthermore, a total of 306 and 195 S. europaea unigenes were predicted to be targets of 41 conserved and 29 novel miRNA families, respectively. These targets encode a wide range of proteins, and genes involved in transcription regulation constitute the largest category. Four of them, which encode laccase, F-box family protein, SAC3/GANP family protein, and nadph-cytochrome P450 oxydoreductase, were validated using 5'-RACE.
Conclusions: Our results indicate specific miRNAs are tightly regulated by salinity in shoots and/or roots of S. europaea, which play important roles in salt adaptation of this euhalophyte. The S. europaea salt-responsive miRNAs and miRNAs that target transcription factors, nucleotide binding site-leucine-rich repeat proteins and enzymes involved in lignin biosynthesis as well as carbon and nitrogen metabolism may be applied in genetic engineering of crops with higher stress tolerance, and genetic modification of biofuel crops with higher biomass and regulatable lignin biosynthesis.

overall_design: The aim of this study is to investigate the miRNAs transcriptome in S. europaeaand identify salt-responsive miRNAs in this euhalophyte. Six sRNA libraries were constructed from the shoots and roots of S. europaea seedlings treated with 200 mM NaCl for 0, 12 hours and 7 days and were sequenced using Illumina HiSeq 2000.

first: Juanjuan

last: Feng

first: Jinhui

first: Pengxiang

last: Fan

first: Weitao

last: Jia

first: Lingling

last: Nie

first: Ping

last: Jiang

first: Xianyang

last: Chen

first: Sulian

last: Lv

first: Lichuan

last: Wan

first: Sandra

last: Chang

first: Shizhong


title: Small RNA profiles in mangroves

city: Guangzhou

first: Ming

last: Wen

address: No. 135, Xingang Xi Road

department: Life Science

institute: Sun Yat-sen University

summary: MicroRNAs (miRNAs) and endogenous small interfering RNAs (siRNAs) play an important role in plant stress responses but the small RNA (sRNA) repertoire is poorly characterized in extremphophiles. We report sRNA transcriptomes of leaf and flower tissues of two mangrove species Bruguiera gymnorrhiza and Kandelia candel (Rhizophoraceae) based on Illumina sequencing. A total of 32 known and 5 novel miRNA families were identified collectively.Besides the conserved miR390-TAS3-ARF pathway, B. gymnorrhiza possessed additional high-abundance tasiRNAs derived from the less-conserved regions of TAS3 transcripts with expanded potential targets.his study provides the first comprehensive sRNA transcriptome for mangroves B. gymnorrhiza and K. candel. Comparative analyses revealed that these two species systematically optimize sRNA expression levels, accompanied with rewiring of sRNA regulatory networks, as an evolutionarily strategy for stress adaptations.  Furthermore, 24-nt sRNAs mapped to the telomeric repeats (CCCTAAA)n were highly abundant in both B. gymnorrhiza and K. candel.

sample_organism:
Bruguiera gymnorhiza
Kandelia candel

platform_organism:
Bruguiera gymnorhiza
Kandelia candel

overall_design: 8 samples

first: M

first: X

last: Lin

last: Xie

first: S

last: Shi

first: T

last: Tang


title: RNA-Seq of LPA derived macrophages

status: Public on Feb 08 2017

city: Bhubaneswar

first: Vivek

last: Rai

state: Orissa

address: Nalco Square

institute: Institute of Life Sciences

summary: Monocytes and macrophages constitute important components of immune system. Monocytes differentiate into macrophages following stimulation with cytokines and/or microbial molecule. Macrophages play central role in the maintenance of tissue homeostasis, development and its restoration after injury, as well as the initiation and resolution of innate and adaptive immunity. Though macrophages were long considered to be derived from differentiation of bone marrow monocytes, recent studies have proved that tissue resident macrophages are derived from yolk sac macrophages, fetal liver macrophages, can self-replicate from local proliferation. However, during homeostatic adaptations, injury and inflammation macrophages of different phenotypes can be recruited from the monocyte reservoirs of blood, spleen and bone marrow. Our studies show that Lysophosphatidic acid (LPA), a small lipid molecule converts monocytes into macrophages. We report the gene expression profile of primary mouse bone marrow monocytes treated for 5 days with LPA with respect to control monocytes.

overall_design: We have performed RNA-seq in mouse bone marrow monocytes and LPA derived macrophages from bone marrow monocytes.

first: Rashmi

last: Ray


title: Genome-wide microRNA expression profiles of rat hippocampus in a chronic temporal lobe epilepsy model induced by amygdala stimulation

city: Nanjing

first: Teng

state: Jiangsu

address: No.140 Hanzhong Road

department: Neurology

institute: Nanjing Medical University

summary: MicroRNAs (miRNAs) have been found to participate in the pathogenesis of several neurological diseases including epilepsy. To date, the expression and functions of miRNAs in chronic temporal lobe epilepsy (TLE), the most common type of refractory epilepsy in adults, have not been well characterized. Here, we adopted high-throughput sequencing to investigate miRNA expression profile in a chronic TLE model induced by amygdala stimulation

overall_design: Hippocampus miRNA profiles of TLE group and control group were generated by deep sequencing, using Hiseq 2000.

first: Meng-Meng

last: Li

first: Jin-Tai

last: Yu


title: Down-regulation of E protein activity augments an ILC2 differentiation program in the thymus

city: Oklahoma City

first: Xiao-Hong

last: Sun

state: OK

address: 825 NE 13th street

institute: Oklahoma Medical Research Foundation

summary: Innate lymphoid cells (ILCs) are important regulators in various immune responses.  Current paradigm states that all newly-made ILCs originate from common lymphoid progenitors (CLP) in the bone marrow.  Id2, an inhibitor of E protein transcription factors, is indispensable for ILC differentiation.  Unexpectedly, we found that ectopically expressing Id1 or deleting two E protein genes in the thymus drastically increased ILC2 counts in the thymus and other organs where ILC2 normally reside.  Further evidence suggests a thymic origin of these mutant ILC2s.  The mutant mice exhibit augmented spontaneous infiltration of eosinophils and heightened responses to papain in the lung and increased ability to expulse the helminth parasite, Nippostrongylus brasiliensis.  These results prompt the question whether the thymus naturally has the capacity to produce ILC2s and E proteins restrain such a potential.  The abundance of ILC2s in Id1 transgenic mice also offers a unique opportunity for testing the biological functions of ILC2s.

overall_design: For RNA-seq analyses, ILC2s (Lin-Thy1+ST2+) were sorted from thymocytes and mesenteric lymph node cells and processed for RNA-seq.  In addition, MLN cells were also cultured in the presence of IL-, IL-25 and IL33.  Duplicate samples were analyzed.

first: Hong-Cheng

last: Wang

first: Liangyue

last: Qian

first: Ying

last: Zhao

first: Joni

last: Mengarreli

first: Indra

last: Adrianto

first: Courtney

last: Montgomery

first: Joseph

last: Urban

first: Kar-Ming

last: Fung


title: Genome-wide Transcription-coupled Repair in E.coli is Mediated by the Mfd Protein

city: Istanbul

first: Ogun

last: Adebali

address: Orta Mah. Universite Cad No 27

department: Faculty of Natural Sciences and Engineering

country: Turkey

institute: Sabanci University

summary: Transcription-coupled DNA repair is widespread in nature having been found in organisms from E. coli to yeast to humans. In E. coli, the transcription-repair coupling factor (TRCF) encoded by the mfd gene recognizes RNA polymerase (RNAP) stalled at a damage site and recruits the excision repair proteins to the stalled RNAP and promotes damage recognition while displacing RNAP and the truncated transcript from the damage site and in doing so, enhances the rate of repair of the transcribed strand (TS). Recently, it has been reported that there are other E. coli proteins that mediate transcription-coupled repair (TCR) independently of the Mfd protein. To understand the relative contributions of various proteins to and mechanisms of TCR we used the recently developed nucleotide excision repair sequencing (XR-seq) method for genome-wide analysis of excision repair to generate excision repair maps of entire genomes of various E. coli strains with deletions of genes implicated in TCR. Our data show that the Mfd protein catalyzes TCR throughout the genome.

overall_design: Examination of excision products in E.coli: WT and mutants of phr, mfd, uvrD.

first: Yi-ying

last: Chiou

first: Junchuan

last: Hu

first: Aziz

last: Sancar

first: Christopher

last: Selby


title: Abraxane, the Nanoparticle Formulation of Paclitaxel can Induce Drug Resistance by Up-regulation of P-gp

first: yadong

last: yang

address: No.1-104 Beichen West Road, Chaoyang

institute: Beijing Institute of Genomics

summary: Abraxane, a nanoparticle (NP) formulation of paclitaxel (PTX), has been demonstrated to be more effective than Taxol, the small molecule formulation, for the treatment of breast cancer and non-small cell lung cancer (NSCLC). It was reported that Abraxane existed in plasma as particles with the size of ~10 nm. NPs get in and out of the cells by endocytosis and exocytosis, whereas small molecules by diffusion and efflux. It is intriguing to know whether the improved pharmaceutical performance is related to the “too-big-to-be-pumped-out” phenomenon. Here we established an Abraxane-resistant NSCLC cell line A549/Abr and compared its transcriptomes with that of the Abraxane-sensitive parental cell line by RNA-Seq technology. To our surprise, the most significantly up-regulated genes were ABC transporters, the common efflux pump for small molecules. We further found that the ABCB1 inhibitor Verapamil reversed the drug resistance and confirmed the important role of ABCB1 in Abraxane resistance.

overall_design: mRNA profiles of A549 and A549/Abr cells were generated using Illumina Hiseq 2000 and compared.

first: Xiangdong

last: Fang

first: Zhiyuan


title: RNA-seq of Tumor-associated Endothelial Cells from Different Immunodeficient Backgrounds

city: New York City

first: Lin

last: Tian

state: New York

address: Mortimer B. Zuckerman Research Center, 417 East 68th Street

department: Cancer Biology & Genetics Program

institute: Memorial Sloan Kettering Cancer Center

summary: To investigate the impact of CD4+ T cells on tumor vasculature, we performed transcriptome profiling on tumor-associated endothelial cells in mice with or without functional CD4 T cells. In addition to examining four pathways that affect vessel maturation (VEGFA, ANGPT1/ANGPT2, TGFbR, and sphingolipid metabolism), we ran Gene Set Enrichment Analysis (GSEA) and found a down-regulation of cellular adhesion and extracellular matrix assembly-related pathways in the CD4 T cell deficient group. This suggests that CD4+ T cells play an important role in promoting tumor vessel integrity and normalization.

overall_design: Transcriptome profiling of E0771 murine tumor-associated endothelial cells isolated from CD4+ T cell competent (CD8KO, Tie2Cre, WT) or deficient mouse strains (CD4KO, Tie2Cre;H2Ab flox  and TCRKO) .

first: Xiang

last: Zhang

first: Hai

first: Amit

last: Goldstein


title: Inhibition of Ubc13-mediated ubiquitination by GPS2 regulates multiple stages of B cell development

city: Boston

first: Valentina

last: Perissi

address: 72 E. Concord St

institute: Boston University

summary: Non-proteolytic ubiquitin signaling mediated by K63 ubiquitin chains plays a critical role in multiple pathways converging on NFKB activation that are key to the development and activation of immune cells. However, a complete understanding of how the regulation of ubiquitin signaling affects immune cells development and functionality is still missing. G Protein Suppressor 2 (GPS2) is a multi-functional protein that recently emerged as an important regulator of inflammation and lipid metabolism through inhibition of Ubc13 activity. Here, we have deleted GPS2 in the B cell lineage results and performed RNAseq of WT and KO splenic B cells.

overall_design: RNA-seq of WT and_KO of GPS2 in Bcells.

first: Claudia

last: Lentucci

first: Anna

last: Belkina

first: Carly

middle: T

last: Cederquist

first: Michelle

last: Chan

first: Holly

middle: E

last: Johnson

first: Sherry

last: Prasad

first: Amanda

last: Lopacinski

first: Barbara

last: Nikolajczyk

first: Stefano

last: Monti

first: Jennifer

last: Cappione

first: Bogdan

last: Tanasa

first: Maria

last: Cardamone


title: Antennae transcriptomics of Varroa-hygienic and Nurse/Forager bees

city: Avignon

first: Cedric

last: Alaux

address: Domaine Saint Paul, Site Agroparc

institute: INRA

summary: The Varroa mite represents the main threat of honey bees (Apis mellifera). Bees from some colonies can limit the proliferation of this parasite by detecting and removing parasitized brood, such behavior is defined as Varroa sensitive Hygiene (VSH). This is an important issue for selecting colonies that can survive Varroa outbreaks. We therefore study the molecular meachnisms underlying this behavior by comparing the antennae transcriptomic profile of VSH and non-VSH bees. Those profiles were further compared to to the profiles of nurses and forager profiles involved in brood care and food collection, respectively.

overall_design: mRNA profiling of bees performing or not Varroa hygienic behavior (4 replicates) and nurse and forager bees (2-3 replicates)

first: Fanny

last: Mondet

first: Dany

last: Severac

first: Marine

last: Rohmer

first: Alison

last: Mercer

first: Yves

last: Le Conte


title: Transcriptome analysis in sheep Milk Somatic Cells

city: Pisa

first: Tommaso

last: Giordani

address: via del Borghetto 80

department: Department of Agricolture, Food and Enviroment

country: Italy

institute: University of Pisa

summary: To investigate the molecular bases of diet induced differences in milk composition, we collected milk from mid lactation dairy ewes  and after 3 weeks of diet supplementation with extruded linseed. RNAs were isolated from milk somatic cells isolated from milk of 3 sheep and Illumina RNA sequencing was performed to analyze RNA synthesis in these cells.

overall_design: Transcriptional profiling of milk somatic cells of sheep fed with normal diet and with a supplementation with extruded linseed. Sequence data were generated by deep sequencing, on three replicates, using Illumina HiSeq2000.

first: Alberto

last: Vangelisti

first: Giuseppe

last: Conte

first: Marcello

last: Mele

first: Andrea

last: Cavallini


title: A new developmental mechanism for the separation of the mammalian middle ear ossicles from the jaw

city: Urbana

first: Daniel

last: Urban

state: Illinois

address: 515 Morrill Hall, 505 S. Goodwin Ave

department: Animal Biology

institute: University of Illinois at Urbana-Champaign

summary: Multiple mammalian lineages independently evolved a definitive mammalian middle ear (DMME) through breakdown of Meckel’s cartilage (MC). However, the cellular and molecular drivers of this evolutionary transition remain unknown for most mammal groups. Here, we identify such drivers in the living marsupial opossum Monodelphis domestica, whose MC transformation during development anatomically mirrors the evolutionary transformation observed in fossils. Specifically, we link increases in cellular apoptosis and TGF-BR2 signalling to MC breakdown in opossums. We demonstrate that a simple change in TGF-b signalling is sufficient to inhibit MC breakdown during opossum development, indicating that changes in TGF-b signalling might be key during mammalian evolution. Furthermore, the apoptosis that we observe during opossum MC breakdown does not seemingly occur in mouse, consistent with homoplastic DMME evolution in the marsupial and placental lineages.

overall_design: RNA-seq of tissues from 3 time points (N=3 at each point) to analyze differential gene expression levels.

first: Neal

last: Anthwal

first: Zhe-Xi

last: Luo

last: Maier

first: Alexa

last: Sadier

first: Abigail

last: Tucker

first: Karen

last: Sears


title: Molecular Biomarkers Screened by Next-generation RNA Sequencing for non-sentinel lymph node status predicting in breast cancer patients with metastatic sentinel lymph node

first: yadong

last: yang

summary: Six candidates (all ER/PR+, HER2−, Ki-67 <20 %) with metastatic SLNs selected from 305 patients were equally categorized as NSLN negative and positive. We identified 103 specifically expressed genes in the NSLN negative group and 47 in the NSLN positive group. Among them, FABP1 (negative group) and CYP2A13 (positive group) were the only 2 protein-encoding genes with expression levels in the 8th to 10th deciles. Using a false discovery rate threshold of <0.05, 62 up-regulated genes and 98 down-regulated genes were discovered in the NSLN positive group. Furthermore, 10 gene fusions were identified in this group with the most frequently fused 23 gene being IGLL5.

overall_design: examination of transcriptome differences between NSLN positive and negative breast patients

first: X

middle: D

last: Fang


title: In vivo binding of PRDM9 reveals interaction with non-canonical genomic sites

city: Montpellier cedex 5

first: Julie

middle: A. J.

last: Clement

address: 141, rue de la Cardonille

department: IGH

institute: CNRS

summary: In mouse and human meiosis, DNA double strand breaks (DSBs) initiate homologous recombination and occur at specific sites called hotspots. The localization of these sites is determined by the sequence specific DNA binding domain of the PRDM9 histone methyl transferase. Here we performed an extensive analysis of PRDM9 binding in mouse spermatocytes. Unexpectedly, we identified a non-canonical recruitment of PRDM9 to sites which are devoid of both, recombination activity and the PRDM9-binding consensus motif. These sites include transcription promoters, where PRDM9 is recruited in a DSB-dependent manner. Another subset of non-canonical sites also reveals DSB-independent interactions between PRDM9 and genomic sites, which include binding sites for the insulator protein CTCF. We propose that these DSB-independent sites result from interactions between hotspot bound PRDM9 and genomic sequences located on the chromosome axis.

overall_design: PRDM9-, H3K4me3-, H3K36me3-, DMC1-ChIPseq experiments were performed on testis from different mouse lines

first: Corinne

last: Grey

last: Clément

first: Jérôme

last: Buard

first: Benjamin

last: Leblanc

first: Ivo

last: Gut

first: Marta

first: Laurent

last: Duret

first: Bernard

last: de Massy


title: Epigenetic Gene Regulation by Janus Kinase 1 in Diffuse Large B Cell Lymphoma (ChIP-Seq)

city: Bethesda

first: Louis

middle: M.

last: Staudt

state: MD

address: 9000 Rockville Pike, Bldg 10, Rm 4N114

department: Lymphoid Malignancies Branch

institute: National Cancer Institute

summary: JAK kinases classically signal by activating STAT transcription factors, but can also regulate gene expression by epigenetically phosphorylating histone H3 on tyrosine 41 (H3Y41-P). In diffuse large B cell lymphomas (DLBCL), JAK signaling is a feature of the ABC subtype and is triggered by autocrine production of IL-6 and IL-10. Whether this signaling involves STAT activation, epigenetic modification of chromatin or both mechanisms is unknown. Here we use genetic and pharmacological inhibition to show that JAK1 signaling sustains the survival of ABC DLBCL cells. While STAT3 contributed to the survival of ABC DLBCL cell lines, forced STAT3 activity could not protect these cells from death following JAK1 inhibition, suggesting epigenetic JAK1 action. JAK1 regulated the expression of nearly 3,000 genes in ABC DLBCL cells, and the chromatin surrounding many of these genes was modified by H3Y41-P marks that were diminished by JAK1 inhibition. These JAK1 epigenetic target genes encode important regulators of ABC DLBCL proliferation and survival, including IRF4, MYD88 and MYC. A small molecule JAK1 inhibitor cooperated with the BTK inhibitor ibrutinib in reducing IRF4 levels and acted synergistically to kill ABC DLBCL cells, suggesting that this combination should be evaluated in clinical trials.

overall_design: TMD8 cells were treated with either DMSO or AZD 1480 (2uM) for 16 hours. Chromatin immunoprecipitation was performed with a phospho-H3Y41 antibody (Abcam #ab26310), and normal rabbit IgG (Santa Cruz #sc-2027) as a negative control (n=4).


title: Impact of laminin α1 chain on colorectal cancer progression

city: Strasbourg

first: Olivier

last: Lefebvre

address: 3 Avenue Molière

institute: Inserm

summary: Expression analysis of control HT29 or Laminin α1 expressing HT29 xenografts in nude mice

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: RNA from 3 independents subcutaneous tumors per group were analyzed.


title: Integrated Systems Biology Analysis of KSHV Latent Infection Reveals Viral Induction and Reliance on Peroxisome Mediated Lipid Metabolism

city: Seattle

first: Terri

last: DiMaio

state: WA

address: 750 Republican St.

department: Microbiology

institute: University of Washington

summary: Kaposi’s Sarcoma herpesvirus (KSHV), an oncogenic virus, modulates host cell signaling and metabolism to maintain latent infection. To unravel the underlying cellular mechanisms modulated by KSHV, we identified changes in the host proteome, phosphoproteome and transcriptome landscape upon KSHV infection of endothelial cells. A Steiner Forest algorithm was used to integrate proteomic, phosphoproteomic and transcriptomic data with transcriptome based predicted transcription factor activity to identify cellular networks altered by latent KSHV.

overall_design: RNA was isolated from hTert-immortalized microvascular endothelial (TIME) cells either infected with KSHV or mock-infected in 3 biological replicates

first: Zoi

last: Sychev

first: Alex

last: Hu

first: Anthony

last: Gitter

first: Nathan

last: Camp

first: William

last: Noble

first: Alejandro

last: Wolf-Yadlin

first: Michael

last: Lagunoff


title: Aberrant H3.3 dynamics in NAc promote vulnerability to depressive-like behavior

city: New York

first: Ian

last: Maze

state: NY

address: 1470 Madison Avenue, 9-109

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

summary: Human major depressive disorder (MDD), along with related mood disorders, is among the world’s greatest public health concerns, however, its pathophysiology remains poorly understood. Persistent changes in gene expression are known to promote physiological aberrations implicated in MDD. More recently, histone mechanisms affecting cell-type and regional specific chromatin structures have also been shown to contribute to transcriptional programs related to depressive behaviors, as well as responses to antidepressants (ADs). Although much emphasis has been placed in recent years on roles for histone posttranslational modifications (PTMs) and chromatin remodeling events in the etiology of MDD, it has become increasingly clear that replication-independent histone variants (e.g., H3.3), which differ in primary amino acid sequence from their canonical counterparts, similarly play critical roles in the regulation of activity-dependent neuronal transcription, synaptic connectivity and behavioral plasticity. Here, we demonstrate a novel role for increased H3.3 dynamics in nucleus accumbens (NAc)––a key limbic brain reward region––in the regulation of aberrant social stress-mediated gene expression, abnormal dendritic morphology and the precipitation of depressive-like behaviors in mice. We find that molecular blockade of these dynamics promotes resilience to chronic social stress and results in a partial re-normalization of stress-associated transcriptional patterns in NAc. In sum, our findings establish H3.3 dynamics as a critical, and previously undocumented, regulator of mood, and suggest that future therapies aimed at modulating striatal histone dynamics may potentiate beneficial behavioral adaptations to negative emotional stimuli.

overall_design: H3.3 ChIP-seq profiles generated for 3 conditions (control, acute social defeat stress, and chronic social defeat stress + acute re-exposure to social defeat stress), plus Inputs, all performed in triplicate


title: Epigenetic Gene Regulation by Janus Kinase 1 in Diffuse Large B Cell Lymphoma

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

overall_design: Refer to individual Series


title: Left-right asymmetry of maturation rates in human embryonic neural development

city: Nijmegen

first: Clyde

last: Francks

address: Wundtlaan 1

department: Language & Genetics

country: Netherlands

institute: Max Planck Institute for Psycholinguistics

summary:
Left-right asymmetry is a fundamental organizing feature of the human brain, and neuro-psychiatric disorders such as schizophrenia sometimes involve alterations of brain asymmetry. As early as 8 weeks post conception, the majority of human foetuses move their right arms more than their left arms, but because nerve fibre tracts are still descending from the forebrain at this stage, spinal-muscular asymmetries are likely to play an important developmental role.

Here we have used gene expression profiling in 18 human embryos to show that the left side of the human spinal cord, between four and eight weeks post conception, matures slightly faster than the right side, even though both sides transition from transcriptional profiles associated with cell division and proliferation at earlier stages, to later neuronal differentiation and function. The hindbrain showed a left-right mirrored pattern compared to the spinal cord.

overall_design:
RNA was extracted from left and right spinal cord and left and right hindbrain from 18 human embryos ranging in age from Carnegie stage 13 to Carnegie stage 23.

For library preparation, Illumina TruSeq RNA-kits (Illumina, San Diego, CA, USA) were used according to the manufacturer’s instructions. The library was sequenced using Illumina HiSeq(TM) 2000 at BGI, yielding paired reads of 90bp. The clean reads were aligned to the reference sequence GRCh37 (hg19) with SOAPaligner/SOAP2 v2.21 and Tophat (v2.08).

first: Carolien

last: de Kovel

first: Steven

last: Lisgo

first: Guy

last: Karlebach

first: Jia

last: Ju

first: Gang

last: Cheng

first: Simon

last: Fisher


title: Comparative transcriptomics reveals the different gene expression pattern related to wilt disease resistance and susceptibility in biodiesel plants of Vernicia

city: Hangzhou

first: Yicun

last: Chen

address: Fuchun Street

department: Institute of Subtropical Forestry

institute: Chinese Academy of Forestry

summary:
Background: Vernicia fordii (Tung oil tree) is a popular tree for biodiesel production in China. Unfortunately, the devastating Fusarium wilt disease caused great losses in production. Its sister species (Vernicia montana) was shown resistant to this pathogen. Vernicia fordii and Vernicia montana are main Vernicia species. V. fordii owns superior oil and agronomic traits, but susceptible to tung wilt disease, while V. nontana is resistant the wilt. However, the plants response mechanism remains largely unknown.

Method: To define the divergence of gene expression modules between the resistant and susceptible Vernicia species responding to tung wilt pathogen, we generated comparative transcriptome atlases of two species during the process of infection with the pathogen F. oxysporum by RNA Sequencing in three biological replicates.

Results: We describe the de novo assembly of the transcriptome of V. fordii and V. montana, comprising 258,430 and 245,240 non-redundant transcripts with N50 of 1,776 and 2,452 respectively. About 44,310 pair of putatively one-to-one orthologous genes between V. fordii and V. montana transcriptoms were identified. Overall, a high proportion of orthologous genes shared remarkably similar expression mode between Vernicia species. K means clustering indicated 2 cluster appear opposite expression mode. The highly connected gene expression analysis were conducted among genes with significantly differential expression mode, and the result indicated D6PK and LRR-RLK CLAVATA2 were top hub genes and hub genes glycosyltransferase (Gts), GLABRA2, PERK15 and EREBP-like factor were significantly associated with pathologic grades in resistant V. montana. Moreover, the result showed the resistant is a crucial signaling network, where MAPK signaling pathway, Plant-pathogen interaction, Circadian rhythm, Calcium signaling pathway and apoptosis fulfill distinct function. Additionally, dozens of unigenes were validated by quantitative real-time PCR (qRT-PCR). The study provided insight into the resistance gene expression modules.

Conclusion: We first conducted a system analyses of the dynamics of gene expression both in susceptible and resistant Vernicia species with pathogen F. oxysporum infection. The results will serve as the important foundation to further deeply validation the resistance mechanism and breeding of the woody biodiesel plants V. fordii and V. montana.

sample_organism:
Vernicia fordii
Vernicia montana

platform_organism:
Vernicia fordii
Vernicia montana

overall_design: We generated 24 comparative transcriptome between V. fordii (F) and V. montana (M), consisting of three biological replicates of four different stages for each species infected with pathogen F. oxysporum, including F0, F1, F2, F3, M0, M1, M2, M3

first: Yangdong

last: Wang


title: Digital Restriction Enzyme Analysis of Methylation (DREAM) of HL60 genomic DNA

city: Philadelphia

first: Takahiro

last: Sato

state: PA

address: 3307 North Broad Street

department: Fels Institute for Cancer Research and Molecular Biology

institute: Temple University

summary: We analyzed levels of 5-methyl cytosine nnnn CCCGGG target sites by sequential restriction digest by SmaI and XmaI enzymes, ligating Illumina adaptors to the restriction fragments and reading methylation-specific signatures at the ends of restriction fragments by paired ends Illumina high throughput sequencing.

overall_design: Digital restriction enzyme analysis of methylation (DREAM) was performed to determine the methylation profile of HL60 genomic DNA. Genomic DNA spiked in with unmethylated, partially methylated and fully methylated standards was sequentially cut at CCCGGG sites with the methylation-sensitive enzyme SmaI (blunt ends) and its methylation-tolerant neoschizomer XmaI (5'CCGG overhangs), creating different end sequences that represented methylation status of the CCCGGG sites. These end sequences were analyzed by Illumina high throughput sequencing. Methylation status at individual CCCGGG sites across the genome was determined by counting the methylated reads with the CCGGG signature and unmethylated reads with the GGG signature at the beginnings of the sequencing reads after alignment to the human genome.

first: Matteo

last: Cesaroni

first: Woonbok

last: Chung

first: Shoghag

last: Panjarian

last: Tran

first: Jozef

last: Madzo

first: Yasuyuki

last: Okamoto

first: Hanghang

last: Zhang

first: Xiaowei

first: Jaroslav

last: Jelinek

first: Jean-Pierre

middle: J

last: Issa


title: Analysis of the expression profile of skin macrophages FACS-sorted from mice overexpressing activin and/or oncogenes of human papilloma virus 8 in keratinocytes.

city: Zurich

first: Maria

last: Antsiferova

state: Schweiz

address: HPL F16.1, Otto-Stern-Weg 7

country: Switzerland

institute: ETH Zurich

summary: We have shown that activin promoted skin tumorigenesis in mice induced by the human papilloma virus 8 oncogenes. Activin attracted blood monocytes to the skin as revealed by depletion of CCR2-positive monocytes. To determine if activin also altered the gene expression profile of these cells, we performed RNA-Sequencing of macrophages FACS-sorted from the pre-cancerous ear skin. We have found that activin induces a pro-migratiory, pro-angiogenic and pro-tumorigenic genes in skin macrophages in vivo. This largely contributes to the pro-tumorigenic function of activin, since macrophage depletion delayed spontaneous tumorigenesis in HPV8-transgenic mice by reducing keratinocyte proliferation and angiogenesis.

overall_design: F4/80+CD11b+CD45+ cells were FACS-sorted from the pre-cancerous ear skin of wt/wt, HPV8/wt, wt/Act and HPV8/Act mice and their expression profile was analysed by RNA-Sequencing. Experiment was performed in triplicates, for each replicate ear skin of 3-6 mice of corresponding genotype was pooled.

first: Sabine

last: Werner


title: RNA-seq of HL60 cells treated with epigenetic therapy

summary: RNA-seq was performed after HL60 cells were treated with S2101, UNC0638, GSK343, depsipeptide alone or in combination with decitabine

overall_design: Biological triplicates were performed for a total of 30 samples. Fold change of each gene was calculated by comparing change in expression after inhibitor treatment to expression in the control samples

first: Anthony


title: Postnatal Development is Associated with Genome-scale Changes in DNA Methylation in Mouse Liver

city: Columbus

first: Matt

last: Cannon

state: OH

address: 700 Children's Dr.

department: Center for Childhood Cancer

institute: Nationwide Children's Hospital

summary: DNA methylation marks are thought to be set up during early development and to remain static thereafter in healthy tissues. Here, we characterize the liver DNA methylation patterns of mice before birth, during early postnatal development (from birth until weaning) and in adulthood. Our analyses show extensive epigenetic reprogramming in the liver occurring during postnatal development. 118,877 of 261,317 CpGs analyzed throughout the genome significantly changed their methylation level by more than 5% from birth to nine weeks of age, with some changing by up to 86%. Interestingly, changes in DNA methylation occur primarily in intergenic enhancer regions while gene promoters seem little affected. Analysis of 166 CpGs at multiple time points by locus-specific bisulfite sequencing reveals that this reprogramming primarily occurs between postnatal day 1 and day 20. This time period coincides with two major cellular changes in the liver: the differentiation of hepatocytes and extensive cell division. While cell multiplication leaves a distinct footprint on the DNA methylation patterns, we show that the extensive epigenetic reprogramming likely results from differentiation of hepatoblasts into hepatocytes. Overall, our data suggest that epigenetic remodeling is an important aspect of normal liver maturation and involves a large number of gene enhancers.

overall_design: Methylation was measured across six ages by RRBS, and by locus specific bisulfite sequencing across seven ages

first: Matthew

middle: V

first: Genay

last: Pilarowski

first: Xiuli

last: Liu

first: David

middle: A

last: Serre


title: Digital Restriction Enzyme Analysis of Methylation (DREAM) of normal breast epithelial cells and MCF7 genomic DNA

first: Takahiro

overall_design: Digital restriction enzyme analysis of methylation (DREAM) was performed to determine the methylation profile of normal breast epithelial cells and MCF7 genomic DNA. Genomic DNA spiked in with unmethylated, partially methylated and fully methylated standards was sequentially cut at CCCGGG sites with the methylation-sensitive enzyme SmaI (blunt ends) and its methylation-tolerant neoschizomer XmaI (5'CCGG overhangs), creating different end sequences that represented methylation status of the CCCGGG sites. These end sequences were analyzed by Illumina high throughput sequencing. Methylation status at individual CCCGGG sites across the genome was determined by counting the methylated reads with the CCGGG signature and unmethylated reads with the GGG signature at the beginnings of the sequencing reads after alignment to the human genome.

first: Matteo

last: Chen


title: Target Specificity of Epigenetic Therapy

last: Sato


title: GATA2/eGFP knockin study to trace the endothelial to hematopoietic transition and hematopoietic progenitor cells in human hematopoiesis.

city: Guangzhou

first: Hao

last: Sun

address: Kaiyuan avenue 190

institute: GIBH

summary: We generated GATA2/eGFP knockin human embryonic stem cells (H1-GATA2W/eGFP hESCs) and analyzed eGFP expression at different hematopoietic stages, paritcularly the hemogenic endothelium (HE) and hematopoietic progenitor cell (HPC) stage. Our results revealed that, at the HE stage,  eGFP expression discriminates authentic HE from non-hematopoietic endothlial cells (EC) and, at the HPC stage, eGFP expression marks the HPC. Further transcriptome comparison analysis revealed distinct characteristics of the HE and EC. Our study provided ideal model to study the EHT and HPC generation, therefore underpining further study on human ESC modeled hematopoiesis.

overall_design: We compared the transcriptome of eGFP+CD34+CD31+CD43- hemogenic endothelium and eGFP-CD34+CD31+CD43- endothelial cells derived from GATA2w/eGFP hESCs by RNA-Seq.

first: Ke

last: Huang

first: Qianyu

first: Zhongzhou

last: Yang

first: Andrew

last: Hutchins

first: Guangjin

last: Pan

first: Juan

last: Du


title: Postnatal Development is Associated with Genome-scale Changes in DNA methylation in Mouse Liver

overall_design: Methylation was measured across three ages by RRBS in 21 samples, and by locus specific bisulfite sequencing across eight ages in 31 samples, RRBS samples from another study (9wk old animals(GSM1262175, GSM1262176, GSM1262177, GSM1262187, GSM1262166, GSM1262167, GSM1262202)) were used to compare to P1 samples


title: Hotspots of aberrant enhancer activity punctuate the colorectal cancer epigenome

city: Cleveland Heights

first: Peter

last: Scacheri

address: 10900 Euclid Ave; BRB 647

institute: Case Western Reserve University

summary: We sought to identify hotspots of aberrant enhancer activity in colorectal cancer (CRC) through interrogation of the enhancer epigenomes of a large cohort of genetically diverse CRC samples and normal colonic crypts, representing the cell type of origin for CRC. Through characterization of loci that exhibit differential enhancer activity, we identified sets of enhancers that are recurrently commissioned and decommissioned in CRC relative to normal crypts. The set of recurrently commissioned, or “acquired”, enhancers are of particular interest. Many originate from primed chromatin and activate known and potentially novel oncogenes in CRC. They are also frequently constituents of super enhancers and loaded with AP-1 and cohesin complex proteins. Nearly half of all GWAS CRC risk loci identified to date map to these enhancer hotspots. Through functional studies and integrative analyses we further demonstrate that CRC growth can be mitigated through pharmacologic inhibition or targeted knockout of genes activated by recurrent enhancers.

overall_design: H3K27ac profiles in 28 CRC cell lines, 4 primary CRC specimens, and 4 normal colon crypt samples; H3K4me1 profiles in 27 CRC cell lines, 4 primary CRCs, and 4 crypt samples; H3K27me3 profiles in 1 CRC cell line and 1 crypt sample; DNase hypersensitivity site profiles in 3 CRC cell lines and 3 crypt samples; and associated input DNA. Gene expression profiles for 6 CRC cell lines without treatment and at 4 time points of treatments with JQ1.

first: Andrea

last: Cohen

first: Alina

last: Saiakhova


status: Public on Feb 07 2017

city: wuhan

first: songsong

last: wu

state: Hubei

address: No. 1  Shizishan Street

department: College of Plant Science and Technology,

institute: Huazhong Agricultural University

summary: Transcriptome analysis the genes expression in SsMYRV4-infected strain Ep-1PNA367T1 and SsMYRV4-free strain Ep-1PNA367. the two strains were grown on a cellophane membrane overlaid onto PDA medium at 20℃ for 3 days,  samples were collected for total RNA extraction. The RNA samples were sequenced and anlysized by the BGI Co., Ltd. Total clean reads of each sample above 5000000.The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks.

overall_design: mRNA profiles of 3-day old strains Ep-1PNA367T1 and  Ep-1PNA367  were generated by deep sequencing using Illumina HiSeq 2000.

first: Daohong

last: Jiang

first: Jiatao

last: Xie

first: Songsong

last: Wu


title: piwi mutations and c-Fos overexpression on Drosophila ovarian germline

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

summary:
This project aims to identify molecular effects of piwi mutations and c-Fos overexpression on the formation of Drosophila ovarian germline
RNA-seq was utilized to compare transcript levels between wild type, piwi mutant, and c-Fos over-expressing ovarian tissues

overall_design: Three biological replicate samples from wild type, piwi mutant, and c-Fos over-expression, were used.

first: Jonathon

last: Klein

first: Jamy

last: Peng


title: Differential Gene Expression and Alternative Isoform Regulation in caper mutant embryos compared to wild-type

city: Sheridan

first: Kenneth

last: Jones

state: Wyoming

address: 1309 Coffeen Avenue STE 10090

institute: Bioinformatic Solutions LLC

summary: We find that Caper dysfunction leads to differential expression of many genes associated with neural development, as well as alternative exon usage, as compared to control embryos.

overall_design: RNA-Seq was performed on Drosophila OreR and caperCC01391 embryos using 3 biological replicates. Differential gene expression and alternative isoform regulation was performed.

first: Eugenia

last: Olesnicky

first: Jeremy

last: Bono

first: Meghan

last: Lybecker

first: Laura

last: Bell

first: Logan

last: Schachtner


title: Different microRNA Profiles Reveal the Diverse Outcomes Induced by EV71 and CA16 Infection in Human Umbilical Vein Endothelial Cells Using High-Throughput Sequencing

city: Kunming

first: Jie

last: Song

state: Yunnan

address: Number 935 Jiaoling Load

institute: Institute of Medical Biology, Chinese Academy of Medicine Science and Peking Union Medical College

summary: We performed comprehensive miRNA proﬁling in EV71- and CA16-infected human umbilical vein endothelial cells (HUVECs) at multiple time points using high-throughput sequencing. The results showed that 135 known miRNAs exhibited remarkable differences in expression. Of these, 30differentially expressed miRNAs presented opposite trends in EV71- and CA16-infected samples. Subsequently, we mainly focused on the 30 key differentially expressed miRNAs through further screening to predict targets.Gene ontology (GO) and pathway analysis of the predicted targets showed the enrichment of 14 biological processes, 9 molecular functions, 8 cellular components, and 85 pathways. The regulatory networks of these miRNAs with predicted targets, GOs, pathways, and coexpression genes were determined, suggesting that miRNAs display intricate regulatory mechanisms during the infection phase. Consequently, we specifically analyzed the hierarchical GO categories of the predicted targets involved in biological adhesion. The results indicated that the distinct changes induced by EV71 and CA16 infection may be partly linked to the function of the blood-brain barrier. Taken together, this is the first report describing miRNA expression profiles in HUVECs with EV71 and CA16 infections using high-throughput sequencing. Our data provide useful insights that may help to elucidate the different host-pathogen interactions following EV71 and CA16 infection and offer novel therapeutic targets for these infections.

overall_design: There are 6 samples, including EV71-0h, EV71-72h, EV71-96h,CA16-0h CA16-72h, CA16-96h.

first: Longding

last: Liu