title: Oct4 binding and Histone modification profiling during OSKM-mediated 2nd reprogramming

city: Shanghai

first: Min

last: Li

address: 1239 Siping Road, Yangpu District

institute: Tongji University

summary: Forced expression of four transcription factors Oct4,Sox2, Klf4 and Myc (OSKM) induces somatic cell reprogramming towards pluripotency. Major efforts have been made to characterize the molecular events involved in this process. Yet, it remains elusive how gene expression change, epigenetic landscape remodelling and cell fate conversion are triggered by expression of these Yamanaka factors. To address this gap,we utilized a secondary inducible reprogramming system and performed genome-wide profilings of Oct4 binding, histone modification (H3K4me3/H3K27me3/H3K4me1/H3K27ac), and gene expression analysis during this process. Through integrative analysis, we revealed stage-specific Oct4 binding and enhancer signatures in consistence with gene expression changes, in which the initial regression of somatic program is followed by the gradual acquisition of pluripotent program. Oct4 preferatially binds to H3K4me1 marked enhancer regions and Oct4 binding is positively correlated with active mark H3K27ac. Moreover, we observed significant enhancer activation of epigenetic related genes, especially acetylation associated genes, prior to pluripotency network activation, suggesting a pivotal role of epigenetic remodelling in the process of pluripotency acquisition and maintenance.

overall_design: We used ChIP-seq to explore the global changes of Oct4 binding profiling during OSKM-mediated somatic cell reprogramming. The exogenous Oct4 was tagged with 3XFlag, thus we used anti-flag antibody to monitor exogenous Oct4 changes; anti-Oct4 antibody which recognizes both endogenous and exogenous Oct4 was used to monitor total Oct4 changes during iPSC induction. In addition, we also examined genome-wide H3K4me1/H3K27ac/H3K4me3/H3K27me3/RNAPII profiling during 3Flag-OSKM 2' reprogramming.


title: Circadian rhythm in NIH3T3 cells

status: Public on Dec 31 2015

city: Cambridge

first: Sudhir

last: Thakurela

address: 7 Divinity Avenue

country: USA

institute: HSCRB

type: Expression profiling by high throughput sequencing

summary:
Identification of cyclical expressed coding and non-coding genes during the circadian rhythm in NIH3T3 cells.
NIH3T3 cells were synchronized for their circadian rhythm and RNA sequencing were performed at several time points along the rhythm. This data was used to identify cyclical expressed genes as well as long intergenic non-coding RNAs.

overall_design: NIH3T3 cells were synchronized with 100 nM Dexamethasone for 2 hours, then medium was changed to normal culture medium (0h). Every 4 hours cells were harvested, RNA isolated and RNAseq performed.

first: Sandra

last: Schick

first: Kolja

last: Becker

first: David

last: Faurnier

first: Mareike

middle: H

last: Hampel

first: Stefan

last: Legewie

first: Vijay

middle: K

last: Tiwari


title: Small RNAs in stress-related rice cultivars

city: New Delhi

first: Mukesh

last: Jain

state: New Delhi

address: New Mehrauli Road

country: India

institute: Jawaharlal Nehru University

type: Non-coding RNA profiling by high throughput sequencing

summary: In this study, we sequenced small RNA content from three different rice cultivars employing Illumina technology. More than 15 million reads were generated using Illumina high-throughput sequencing platform. After pre-processing, distinct small RNA sequences were identified for each rice cultivars.

overall_design: We collected seedlings of different rice cultivars and total RNA isolated was subjected to Illumina sequencing. The sequenced data was further filtered using NGS QC Toolkit to obtain high-quality reads. The filtered reads were pre-processed using modified perl script provided in the miRTools software. After quality control, the identical reads were collapsed into a unique read and read count for each sequence was recorded. All the filtered unique reads from each sample were mapped on the rice genome to find their location.

first: Jain

last: Mukesh

first: Chevala

last: V Narayana

first: Shankar

last: Rama

first: Garg

last: Rohini


title: Expression profiling of miR-294 and Mbd2 siRNA transfected Dgcr8-/- mESCs by high throughput sequencing

city: Beijing

first: Yangming

last: Wang

address: 5 Yiheyuan Road

department: Institute of Molecular Medicine

country: China

institute: Peking University

summary: RNA-seq analysis on CTR, miR-294, and siMbd2 transfected Dgcr8-/- ESCs showed that Mbd2 is responsible for the change of expression of a significant portion of genes that are regulated by miR-290 cluster

overall_design: mRNA profiles of CTR, miR-294 and siMbd2 transfected Dgcr8-/- ESCs were generated by deep sequencing, in duplicate, using pair-end Illumina.

first: Yang

last: Cao

first: Wen-Ting

last: Guo


title: Genome-wide profiling of histone H3 lysine 27 and lysine 4 trimethylation in multiple myeloma reveals the importance of Polycomb gene targeting and highlights EZH2 as a potential therapeutic target

city: Uppsala

first: Prasoon

last: Agarwal

state: Sweden

address: Dag Hammarshkojlds vag 20

department: IGP

country: Sweden

institute: Rudbeck Laboratory, Uppsala University

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Mdm2 enhances stemness-promoting chromatin modifications through the Polycomb Repressor Complex 2 in a p53-Independent Manner

city: Goettingen

first: Magdalena

last: Wienken

address: Justus-von-Liebig-Weg 11

country: Germany

institute: University Medical Center Goettingen

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Chip-seq analysis of hrpRSL and Lon in Pseudomonas syringas

city: Hong Kong

first: Xin

last: Deng

address: To Yuen Building

department: Biomedical Sciences

country: Hong Kong

institute: City University of Hong Kong

summary: Pseudomonas syringae uses HrpRSL to regulate the expression of type III secretion system (T3SS) genes and bacterial virulence. However, the molecular mechanism and the regulons of HrpRSL have yet to be fully elucidated. Here, we performed chromatin immunoprecipitation followed by high-throughput DNA sequencing (ChIP-seq) on HrpRSL and Lon. The direct regulation of these genes by corresponding regulator has been confirmed by Electrophoretic mobility shift assays (EMSAs) and quantitative real-time polymerase chain reactions (qRT-PCR). Binding motifs are found by using MEME suite and verified by footprint assays in vitro. Collectively, this work provides new cues to better understand the detailed regulatory networks of T3SS systems in P. syringae.

overall_design: ChIP-seq analysis of HrpRSL and Lon in Pseudomonas syringas


title: The RNA-Seq transcriptome of human prostate cancer cell line depleted of CIC

city: Seoul

first: Tae-Young

last: Roh

state: --- Select One ---

address: 52 Ewhayeodae-gil, Seodaemun-gu

department: Life Sciences

country: South Korea

institute: Ewha Womans University

summary: To identify which genes were regulated by CIC in human prostate cancer cell, the effect of CIC knockdown on PC3 cell transcriptome was determined

overall_design: The transcriptome profiles were obtained from control PC3 and shCIC treated PC3

first: Nahyun

last: Choi

first: Hyeongrin

last: Jeon

first: Seung-Hee

last: Lee

first: Yoontae


title: Drug specific epigenetic reprogramming leads to increased cellular invasion in ERα positive breast cancer via de novo cholesterol biosynthesis.

city: London

first: Luca

last: Magnani

address: DuCane road

department: Surgery and Cancer

country: United Kingdom

institute: Imperial College London

summary: Endocrine therapy resistance remains a critical problem in the treatment of estrogen receptor alpha (ERα) breast cancer. Endocrine therapies target ERα via different modes of action. Drug resistance involves drug specific remodeling of the transcriptional and regulatory landscape. Using epigenomics and transcriptomics, we demonstrate that resistance to aromatase inhibitors (AI) induces phenotypical changes through epigenetic activation of cholesterol biosynthesis (CB) and keratin 80. Epigenetic activation is stable and involves both large topological domains and punctuated activation of single enhancers and super-enhancers. Specialized cancer cells expressing high levels of keratin 80 lead invasion through the extracellular matrix. Strikingly, we demonstrate that anti-cholesterol strategies can effectively arrest breast cancer invasion. Our work identifies a robust strategy to target resistant invasive breast cancer.

overall_design: All cell lines were grown in their respective media until they reached 70% confluency.  Specifically, MCF7 were grown in DMEM+10% FBS and 1% Pen-Sprep-Glutamine. MCF7T as MCF7 with the addition of 100nM Tamoxifen. MCF7F as MCF7 with the addition of 100nM Fulvestrant. LTED were grown in DMEM without phenol + 10% DCS-FBS and1% Pen-Sprep-Glutamine. LTEDT as LTED with the addition of 100nM Tamoxifen. LTEDF as LTED with the addition of 100nM of Fulvestrant. All chemicals are purchased from Sigma. ChIP-seq was performed using Illumina methodology.


title: Single-base resolution DNA methylation maps of rice cultivars under control and stress conditions

first: Mukesh

type: Methylation profiling by high throughput sequencing

summary: In this study, we aim to generate genome-scale DNA methylation profiles at single-base resolution in different rice cultivars (IR64, Nagina 22 and Pokkali) under control and stress conditions. Using high-throughput whole genome bisulfite Sequencing, we generated DNA methylation maps covering the vast majority of cytosines in the rice genome. More than 152 million high quality reads were obtained for each tissue sample using Illumina platform. We discovered extensive DNA methylation in rice cultivars, identified the context and level of methylation at each site.Numerous differentially methylated regions (DMRs) among different cultivars under control and stress conditions were identified and many of them were associated with differential gene expression. The high resolution methylome maps of different rice genotypes and differentially methylated regions will serve as reference for understanding the epigenetic regulation of stress responses in plants.

overall_design: Whole genome bisulfite sequencing of seven control/stressed samples from three rice cultivars (IR64, N22 and Pokkali)

last: VVS Narayana


title: Stress responsive gene expression in rice cultivars

last: Jain

summary: In this study, we aim to present a global view of transcriptome dynamics in different rice cultivars (IR64, Nagina 22 and Pokkali) under control and stress conditions. More than 50 million high quality reads were obtained for each tissue sample using Illumina platform. Reference-based assembly was performed for each rice cultivar. The transcriptome dynamics was studied by differential gene expression analyses between stress treatment and control sample.

overall_design: We collected seedlings of three rice cultivars subjected to control (kept in water), desiccation (transferred on folds of tissue paper) and salinity (transferred to beaker containing 200 mM NaCl solution) treatments. Total RNA isolated from these tissue samples was subjected to Illumina sequencing. The sequence data was further filtered using NGS QC Toolkit to obtain high-quality reads. The filtered reads were mapped to Japonica reference genome using Tophat software. Cufflinks was used for reference-based assembly and differential gene expression was studied using cuffdiff software. The differentially expressed genes during various abiotic stress conditions were identified.

first: Bhattacharjee

last: Annapurna

first: Jain


title: Epo-Induced Erythroid Maturation Is Dependent on Plcγ1 Signaling

city: Heidelberg

first: Daniel

middle: B.

last: Lipka

address: INF 280

department: Epigenomics and Cancer Risk Factors

institute: German Cancer Research Center

summary: Erythropoiesis is a tightly regulated process. Development of red blood cells occurs through differentiation of hematopoietic stem cells into more committed progenitors and finally into erythrocytes. Binding of erythropoietin to its receptor (EpoR) is strictly required for erythropoiesis as it promotes survival and late maturation of erythroid progenitors. In vivo and in vitro studies have highlighted the requirement of EpoR signaling through Jak2 tyrosine-kinase and Stat5a/b as a central pathway. Here, we demonstrate that phospholipase C gamma 1 (Plcγ1) is activated downstream of EpoR/Jak2 independently of Stat5. Plcγ1-deficient proerythroblasts and erythroid progenitors exhibited strong impairment in differentiation and colony-forming potential. In vivo, suppression of Plcγ1 in immunophenotypically defined hematopoietic stem cells (Lin-Sca1+KIT+CD48-CD150+) severely reduced erythroid development. To identify Plcγ1 effector molecules involved in regulation of erythroid differentiation we assessed for changes on the level of transcription and DNA methylation after inactivation of  Plcγ1. The single common downstream effector was H2AFY2, which encodes for the histone variant macroH2A2 (mH2A2). Suppression of macroH2A2 expression recapitulated the effects of Plcγ1 knockdown on erythroid maturation. Taken  together, our findings identify Plcγ1 and its downstream target macroH2A2, as a “non-canonical” signaling pathway essential for erythroid differentiation.

overall_design: MCIP-seq was used to interrogate methylation changes during Epo-induced differentiation of murine I/11 erythroblastic cell line upon knock-down of Plcy1 as compared to a mock control. Two different shRNA constructs that target Plcg1 were investigated at two different time points.

middle: B

first: Christoph

last: Plass

first: Tina

middle: M

last: Schnöder

first: Patricia

last: Arreba-Tutusaus

first: Inga

last: Griehl

first: Lars

last: Bullinger

first: Marcus

last: Buschbeck

first: Steven

middle: W

last: Lane

first: Konstanze

last: Döhner

first: Florian

last: Heidel

first: Thomas

last: Fischer


title: Cryptochromes interact directly with PIFs to control plant growth in limiting blue light

city: La Jolla

first: Joanne

last: Chory

state: California

address: 10010 N Torrey Pines RD

department: Plant Biology Laboratory

institute: Salk Institute for Biological Studies

summary: Sun-loving plants have the ability to detect and avoid shading through sensing of both blue and red light wavelengths. Higher plant cryptochromes (CRYs) control how plants modulate growth in response to changes in blue light. For growth under a canopy, where blue light is diminished, CRY1 and CRY2 perceive this change and respond by directly contacting two bHLH transcription factors, PIF4 and PIF5. These factors are also known to be controlled by phytochromes, the red/far-red photoreceptors; however, transcriptome analyses indicate that the gene regulatory programs induced by the different light wavelengths are distinct. Our results indicate that CRYs signal by modulating PIF activity genome-wide, and that these factors integrate binding of different plant photoreceptors to facilitate growth changes under different light conditions.

overall_design: We performed whole-genome transcriptome (mRNA-seq) analysis on 5-day-old Arabidopsis thaliana Columbia wild-type (WT) and pif4pif5 seedlings exposed to low blue-light (LBL) or mock-treated for 1, 6 and 24 hours. In addition we performed mRNA-seq on WT, 35S::PIF4-9xMyc-6x-His-3xFlag(Flash) and 35S::PIF5-9xMyc-6x-His-3xFlag (Flash) seedlings treated with LBL or mock-treated for 16 hours.

first: Ullas

middle: V

last: Pedmale

first: Shao-shan Carol

last: Huang

first: Joseph

middle: R

last: Ecker


title: mRNA sequencing of embryonic tails of sih mutants at 28 hours post fertilisation

city: Illkirch

first: Julien

last: Vermot

address: 1 rue Laurent Fries

country: France

institute: IGBMC

summary: We analysed the mRNA expression of embryos lacking blood flow at the onset of heart function.

overall_design: Examination of 3 WT and 3 sih mutants at 28 hpf


title: Genome-wide mapping of Tet3FL in neural progeniter cells

city: Duarte

first: Xiwei

last: Wu

state: CA

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

summary: We report that the 5-methylcytosine oxidase Tet3 exists as three isoforms and characterized the full-length isoform containing an N-terminal CXXC domain (Tet3FL). Presence of the CXXC domain reduces Tet3’s enzymatic activity. This CXXC domain binds not only to unmethylated CpGs but its highest affinity is towards 5-carboxylcytosine (5caC). We determined the structure of the CXXC domain - 5caC-DNA complex and showed that disruption of the CXXC-5caC interaction leads to enhanced Tet3 activity. Mapping of genomic binding sites of Tet3FL in neuronal cells shows that Tet3FL is targeted to transcription start sites of genes involved in lysosome function, mRNA processing and key genes of the base excision repair pathway. Our data suggest that the CXXC domain of Tet3FL restricts the protein to a set of unmethylated or 5caC-containing CpG islands and that Tet3FL functions both as a reader of 5caC and as a regulator of 5caC removal by base excision repair.

overall_design: Examination of genomic binding sites of Tet3FL in neural progeniter cells at day 2 upon neural differentiation and in E15.5 embryonic mouse brain.

first: Seung-Gi

last: Jin

first: Gerd

middle: P

last: Pfeifer


title: Analysis of Midgut Gene Expression Profiles from Different Silkworm Varieties after Exposure to High Temperature

city: Guangzhou

first: LI

last: QingRong

address: No. 133 Yihenglu,Dongguanzhuang,Tianhe District

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

summary: To identify genes and metabolic pathways involved in the heat-stress response, digital gene expression analysis was performed on the midgut of thermotolerant silkworm variety ‘932’ and thermosensitive variety ‘HY’ after exposure to high temperature (932T and HYT). Deep sequencing yielded 6,211,484, 5,898,028, 5,870,395, and 6,088,303 reads for the 932, 932T, HY, and HYT samples, respectively. After filtering adaptor sequences and removing low-quality tags, 6,139,297, 5,828,615, 5,799,074, and 6,005,746 clean tags remained, respectively. The annotated genes associated with these tags numbered 4357, 4378, 4296, and 4658 for the 932, 932T, HY, and HYT samples, respectively. In HY-vs-932, 932-vs-932T, and HY-vs-HYT comparisons, 561, 316, and 281 differentially expressed genes were identified, which could be assigned to 179, 140, and 123 biological pathways, respectively.

overall_design: mRNA expression profiles of midgut from  thermtolerant and thermsensitive varieties  by deep sequencing

first: Qingrong

last: Li

first: Qiong

last: Yang


title: Jmjd3-mediated H3K27me3 dynamics orchestrate brown fat cell fate transition and regulate white fat plasticity (RNA-Seq)

city: Worcester

first: Yongxu

last: Wang

state: MA

address: 364 Plantation Street

department: Program in Gene Function and Expression

institute: UMass Medical School

summary: We performed RNA-Seq for brwon fat, epididymal white fat and soleus muscle of mice to identify brown fat-selective, white fat-selective and common fat genes.

overall_design: RNA-Seq for brown fat, white fat and soleus muscle of wild type C56BL6 mice.

first: Dongning

last: Pan

first: Lihua

last: Zhu

first: Jianhong

last: Ou

first: Yong-Xu


title: RNAseq analysis of mature thymic NKT cells and immature thymic DN1eP cells

city: Yokohama

first: Takaho

middle: A.

last: Endo

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

department: IMS

country: Japan

institute: RIKEN

summary: We report the identification of immature thymic CD4(-),CD8(-) double-negative (DN)1e cells with the NKT cell lineage potential. We also analyzed the gene expression profiles of DN1e thymocytes compared with those of mature thymic NKT cell developmental stages termed NKT stage-1, 2, and -3, which are characterized by differential expression levels of NK1.1 and CD44 antigens in C57BL/6J mouse strain.

overall_design: Next generation sequencing of total transcriptomes using total RNA isolated from FACS sorted ex vivo thymic DN1eP (Lin-/CD44+/CD25-/CD24low/CD5+/CD27+/Ly108-/CXCR3+) fraction, and mature thymic alphaGalCer-loaded CD1d dimer+TCRbeta+ NKT cell developmental stage-1 (CD44-/NK1.1-), stage-2 (CD44+/NK1.1-), and stage-3 (CD44+/NK1.1+) cells, obtained from C57BL/6J wild-type mice.

first: Nyambayar

last: Dashtsoodol

middle: A


title: Jmjd3-mediated H3K27me3 dynamics orchestrate brown fat cell fate transition and regulate white fat plasticity

summary: We performed ChIP-seq to chart genome-wide maps of H3K27me3 in brown preadipocytes and mature brown adipocytes. We observed a subset of brown fat-specific genes, but not common fat genes or white fat-specific genes, possess the H3K27me3 mark in preadipocytes, and this mark is erased in mature adipocytes.

overall_design: H3K27me3 ChIP-seq in brown preadipocytes and mature adipocytes.

first: Yong

middle: X


title: Characterization of porcine chromosomal regions harboring QTL for water holding capacity of meta by tiling arrays and mRNA-seq

city: Dummerstorf

first: Klaus

last: Wimmers

state: Mecklenburg-Vorpommern

address: Wilhelm-Stahl-Allee 2

institute: Leibniz Institute for Farm Animal Biology

summary: To further characterize genomic regions previously identified which are linked with meat quality traits like drip loss, PH, conductivity and etc., we employed mRNA-seq experiment on the PiF1 animals used in the tiling array experiments. Total RNA were taken from muscle sample of M. longissimus dorsi of pigs selected from two phenotypic groups graded according to high (HI) and low (LO) drip loss.

overall_design: Muscle mRNA profiles of 12  were generated by deep sequencing, in triplicate, using Illumina GAIIx.

first: Nares

last: Trakooljul

first: Yang

last: Du


title: Discovery of novel and differentially expressed microRNAs between fetal and adult backfat in cattle

city: YANGLING

first: JIAJIE

last: SUN

state: SHANNXI

address: Taicheng Rd.

department: College of Animal Science and Technology

institute: Northwest A&F University

summary: The posttranscriptional gene regulation mediated by microRNA (miRNA) plays an important role in various species. Recently, a large number of miRNAs and their expression patterns have been identified. However, to date, limited miRNAs have been reported to modulate adipogenesis and lipid deposition in beef cattle. Total RNAs from Chinese Qinchuan bovine backfat at fetal and adult stages were used to construct small RNA libraries for Illumina next-generation sequencing. A total of 13,915,411 clean reads were obtained from a fetal library and 14,244,946 clean reads from an adult library. In total, 475 known and 36 novel miRNA candidates from backfat were identified. The nucleotide bias, base editing, and family of the known miRNAs were also analyzed. Based on stem-loop qPCR, 15 specific miRNAs were detected, and the results showed that bta-miRNAn25 and miRNAn26 were highly expressed in backfat tissue, suggesting these small RNAs play a role in the development and maintenance of bovine subcutaneous fat tissue. Putative targets for miRNAn25 and miRNAn26 were predicted, and the 61 most significant target transcripts were related to lipid and fatty acid metabolism. Of interest, the canonical pathway and gene networks analyses revealed that PPARα/RXRα activation and LXR/RXR activation were important components of the gene interaction hierarchy results. In the present study, we explored the backfat miRNAome differences between cattle of different developmental stages, expanding the expression repertoire of bovine miRNAs that could contribute to further studies on the fat development of cattle. The expression analysis of the differential target genes of miRNAn25 and miRNAn26 showed potential gene networks that affect lipid and fatty acid metabolism. These results may help in the design of new intervention strategies to improve beef quality.

overall_design: Examination of Chinese Qinchuan bovine backfat miRNAs by deep sequencing.

first: Jiajie

last: Sun

first: Hong

last: Chen


title: Genome-wide mapping of TEL-AML1 targets in acute leukemia

city: Kuopio

first: Merja

last: Heinäniemi

address: Yliopistonranta 1

country: Finland

institute: university of eastern finland

summary: Around 20-25% of childhood acute lymphoblastic leukemias carry the TEL-AML1 (TA) fusion gene. It is a fusion of two central hematopoietic transcription factors, TEL (ETV6) and AML1 (RUNX1). Despite its prevalence, the exact genomic targets of TA have remained elusive. We evaluated gene loci and enhancers targeted by TA genome-wide in precursor B acute leukemia cells  using global nuclear run-on sequencing (GRO-seq).

overall_design: Nascent RNA expression profiles were generated with GRO-seq after TEL-AML1 expression in the Nalm6 pre-B-ALL cell line in four different time points (0, 4, 12 and 24 h). TEL-AML1-mut and luciferase induction cell lines were used as controls. Two replicates were included for all six samples.

first: Susanna

last: Teppo

first: Olli

last: Lohi


title: Next Generation Sequencing facilitates analysis of gene expression from Rehmannia glutinosa associated with  replanting disease

city: Zhengzhou

first: Xin Jian

state: Henan

address: Wenhua Road 95

department: College of Life Sciences

institute: Henan Agricultural University

summary:
Purpose: the technology of Solexa/Illumina (RNA-seq) is an attractive alternative to the transcriptome sequencing.  The goals of this study are to investigate transcriptional changes in replanted R. glutinosa leaves and identify genes responding to the disease.
Methods:Totally 6.01and 6.15 million raw tags were measured from leaves of the first year planted (L1) and the second year replanted R. glutinosa (L2) at the tuberous root expansion stage, respectively.  mRNA profiles of  leaves of the first year planted (L1) and the second year replanted R. glutinosa (L2) at the tuberous root expansion stage, were generated by deep sequencing (Illumina HiSeq™ 2000 system).  qRT–PCR validation was performed using SYBR Green assays.
Results: we obtained a total of 6.01 and 6.15 million total tags including 377,200 and 361,659 distinct tags from the L1 and L2 samples, respectively. Removal of low quality tags, 161,298 and 149,290 distinct clean tags were remained.With reference to the 94,544 non-redundant consensus sequences defined by the RNA-seq transcriptomic procedure, 60,574 genes had the diagnostic CATG site, which were taken as reference distinct sequences for DGE analysis. 47,458 of the L1 tag library and 42,247 of the L2 tag library were perfectly matched the reference sequences. we screened differentially expressed genes in the L1 and L2 libraries by digital gene expression (DGE) technique. Finally, a set of 1,954 genes may be in differential expression of L2. By bioinformatics and qRT-PCR, the 117 most strongly differentially expressed ones were considered to be prime candidates for responsible for replanting disease.
Conclusions: The study provides an important resource for further investigating the cause of replanting disease and developing the methods to control or subtract its injury.

overall_design: Leaf mRNA profiles of  L1 (The first year planted R. glutinosa leaves ) and L2 (the second year replanted R. glutinosa leaves) root expansion stage  were generated by deep sequencing (using Illumina HiSeq™ 2000 system)

first: Yan

first: Xin

middle: J


title: Altered microRNA expression in individuals at high risk of type 1 diabetes

city: Fitzroy

first: Mark

last: Chong

state: Victoria

address: 9 Princes Street

country: Australia

institute: St Vincent's Institute of Medical Research

summary: Type 1 diabetes (T1D) is an autoimmune disease characterized by the destruction of pancreatic insulin-producing β cells. CD4+ T cells are integral to the pathogenesis of T1D, but biomarkers that define their pathogenic status in T1D are lacking. miRNAs have essential functions in a wide range of tissues/organs, including the immune system. We reasoned that CD4+ T cells from individuals at high risk for T1D (pre-T1D) might be distinguished by an miRNA signature. We sorted CD4+ T cells from 9 healthy and 7 pre-T1D individuals into 6 subsets, namely naïve, resting regulatory (rTreg), activated regulatory (aTreg), transitional memory (Ttm), central memory (Tcm) and effector memory (Tem) cells, and then compared miRNA profiles between these subsets and between pre-T1D and healthy individuals by deep sequencing. Differential expression of miRNAs was detected in each of the CD4+ T cell subsets. For example, expression of miRNAs that induce apoptosis (miR-15a) or FOXP3 instability (miR-31) was increased in rTreg and aTreg cells, respectively, in pre-T1D individuals, whereas miR-150 was increased in Tem cells of pre-T1D individuals. Importantly, increased miR-150 expression could be detected by qRT-PCR in total CD4+ T and PBMCs of pre-T1D individuals. Consistent with it being a marker of pathogenic CD4+ T cells, we showed that miR-150 regulates IFN-γ production in mouse CD4+ T cells. Thus, comprehensive profiling identifies miRNA profiles that not only distinguish CD4+ T cell subsets but also discriminate individuals with preclinical T1D. The ability to detect differentially expressed miRNAs in total CD4+ T cells or PBMCs should facilitate clinical application of miRNAs as biomarkers.

overall_design: CD4+T cells from healthy and individuals at high risk for autoimmune type 1 diabetes were sorted into 6 subsets, which resulted in 80 samples, 38 for healthy and 42 for high risk individuals. Each sample was barcoded and miRNA libraries were constructed and subsequently subjected to deep-sequencing on the Illumina GAII or HiSeq platform. The Fastq files are have deconvoluted and stripped of the barcode adaptor sequences.


title: Vascular niche induction of hematopoietic progenitors from pluripotent stem cells

city: New York

first: Olivier

last: Elemento

state: NY

address: 1305 York Avenue

institute: WEILL MEDICAL COLLEGE OF CORNELL UNIV

summary: Pluripotent stem cells (PSC) represent an alternative source of hematopoietic stem cells (HSCs). Clinical translation is impeded by limited engraftment of human (h)PSC-multipotent progenitor cells (MPP). This barrier suggests that additional cues are required for definitive hematopoiesis. We hypothesized that vascular niche producing Notch ligands Jagged-1 (JAG1) and Delta-like ligand-4 (DLL4) would drive definitive hematopoiesis. To test our hypothesis, hes2 human embryonic stem cells (hESC) 2 and Macaca nemestrina (Mn) iPSC line-7 were differentiated with cytokines ± endothelial cells (EC), which express JAG1 and DLL4. EC co-culture supported emergence of 8-fold more CD34+CD45+ cells compared to co-culture with cytokines ± ECs with JAG1 or DLL4 knockdown. EC-induced cells exhibit Notch activation and express HSC-specific targets of Notch signaling RUNX1 and GATA2. EC-induced PSC-MPP engraft at a higher level in NSG mice compared to cytokine-induced cells (10% >5 months), and selection increased engraftment (30%). Long-term engraftment and the myeloid-to-lymphoid ratio achieved with vascular niche induction is similar to levels achieved for cord blood MPP and up to 20-fold higher than hPSC-MPP engraftment. Our findings identify a previously underappreciated role for endothelial Notch ligands in PSC definitive hematopoiesis and production of long-term engrafting CD34+ cells and suggest they are critical for HSC emergence.

sample_organism:
Macaca nemestrina
Homo sapiens

platform_organism:
Macaca nemestrina
Homo sapiens

overall_design: Transcriptome sequencing of Macaca nemestrina (Mn) iPSCs

first: Jennifer

last: Gori

first: Shahin

last: Rafi

first: Hans-Peter

last: Kiem


title: Mapping N6-methyladenosine methylome in mouse embryonic stem cells

city: Cambridge

first: Yue

last: Li

state: Massachusetts

address: 32 Vassar Street, 32-D528

institute: Massachusetts Institute of Technology

summary: m6A-seq of undifferentiated and differentiated mouse embryonic stem cell

overall_design: m6A-mRNA library for undifferentiated and differentiated mouse embryonic stem cell each having one biological replicate were generated using HiSeq2000 v3 flowcell (Illumina) and sequenced for 100 bases with separate 7 base indexing read in a single lane.

last: Wang

first: Zhaolei

last: Zhang

first: Philip

last: Ordoukhanian

first: Steven

last: Head

first: Qing

last: Liu

first: Jing

middle: C

last: Zhao


title: Global Analysis of the Transcriptional Response of Chinese cabbage (Brassica rapa ssp. pekinensis) to Methyl Jasmonate Reveals JA Signaling on Enhancement of Secondary Metabolism Pathways

city: Lin’an

first: Yunxiang

last: Zang

address: Huanchengbei Road 88#

institute: Zhejiang A & F university

summary: We conducted a RNA-Seq analysis of MeJA-treated Chinese cabbage leaf transcriptome. Total 14,619,469 sequence reads were generated to produce 27,461 detected genes, among which 1,451 genes were up-regulated and 991 genes were down-regulated as differentially expressed genes (DEGs) (log2 ratio ≥1, false discovery rate ≤0.001). More than 90% of the DEGs (2,278) were between 1.0- and 3.0-fold (log2 ratio). The most highly represented pathways by 1,674 annotated DEGs were related to “metabolic pathways” (333 members), “ribosome” (314 members), “biosynthesis of secondary metabolites” (218 members), “plant-pathogen interaction” (146 members), and “plant hormone signal transduction” (99 members). Fourteen genes involved in JA biosynthesis pathway were up-regulated. As many as 182 genes for the biosynthesis of several secondary metabolites were induced, and the level of indole glucosinolate was highly increased by MeJA treatment. The genes encoding sugar catabolism and some amino acids synthesis were up-regulated, which could supply structural intermediates and energy for the biosynthesis of secondary metabolites. The results demonstrated a high degree of transcriptional complexity with dynamic coordinated changes in global gene expression of Chinese cabbage in response to MeJA treatment. It expands our understanding of the complex molecular events on JA-induced plant resistance and accumulation of secondary metabolites. It also provides a foundation for further studies on the molecular mechanisms of different pathways in other Brassica crops under MeJA treatment.

overall_design: Transcriptomic analysis of MeJA-treated Chinese cabbage leaf

first: Zhujun

last: Zhu


title: Multiple waves of transcriptome changes during extended hypoxic induction in human pulmonary microvascular endothelial cells

city: Los Angeles

first: Kevin

last: Huang

address: Gonda BLDG Rm. 6554, P.O.Box 957088

department: Human Genetics

institute: UCLA

summary: We profile the expression pattern of human pulmonary microvascular endothelial cells (HPMECs) at different time points of hypoxic stress. Through mRNA-seq, we identify functional waves of minor gene up-regulation at 8 and 24h hypoxia exposure followed by a massive wave of transcriptional activation after 48 hours. By weighted gene co-expression network analysis, we identify hub genes that likely play central roles in hypoxia transcription program. Strikingly, these hub genes included a prominent group of lincRNAs, suggesting non-coding RNAs may also have pivotal roles in the hypoxia regulatory circuit.  HPMECs share a core hypoxia signature profile, but with some notably differences, indicating a portion of HPMECs hypoxia response is cell-specific. Collectively, our study comprehensive surveys the hypoxia transcriptome, and provides insight into the temporal dynamics of hypoxia transcriptional response.

overall_design: Time-course expression profiling of HPMECs exposed to hypoxia

first: Guoping

last: Fan


title: Cell cycle-dependent resolution of DNA double-strand breaks repair

status: Public on Dec 30 2015

city: Naples

first: Stefano

last: Amente

address: via pansini, 5

department: Department of  Molecular Medicine and Medical Biotechnologies

country: Italy

institute: University of Naples "FEDERICO II"

summary: Damage to genomic DNA, especially as DNA double strand breaks (DSB), elicits prompt activation of DNA damage response (DDR) which arrest cell-cycle either G1/S or G2/M to avoid entering S and M phase with DNA damage. In mammalian organs cells are in both proliferating and quiescent states. Quiescent cells are already arrested in G0, therefore there may be fundamental difference in DDR between proliferating and quiescent cells. To address these differences we studied recruitment of DSB repair factors and resolution of DNA lesions induced at site-specific DSBs occurring at different cell cycle phases, i.e. in asynchronously proliferating, G0, and G1 arrested cells. Strikingly, DSBs occurring in G0 quiescent cells are irreparable with a sustained activation of p53-pathway. Conversely, reentry of G0-damaged cells into cell cycle progression, show a delayed clearance of recruited DNA repair factors bound at DSBs, indicating an inefficient repair when compared to DSBs induced in asynchronously proliferating or G1 cells. Moreover, we found that initial recognition of DSBs and assembly of DSB factors is largely similar at different cell cycle phases. Our study thereby demonstrates the crucial role of cell cycle phases in repair and resolution of DSBs.

overall_design: Examination of the resolution of DNA damage-associated marker gH2AX in growing and G0 arrested MCF10a cells.

first: Susanna

last: Ambrosio

first: Giacomo

last: Di Palo

first: Giuliana

last: Napolitano

first: Gaetano

middle: I

last: Dellino

first: Mario

last: Faretta

first: Pier

middle: G

last: Pelicci

first: Luigi

last: Lania

first: Barbara

last: Majello


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

city: Beltsville

first: Sunchung

last: Park

state: MD

address: 10300 Baltimore ave, Bldg001

department: ARS-NEA

institute: USDA -ARS

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

overall_design: Examination of mRNA levels in the Arabidospsis ecotypes of Italian and Swedish plants grown at warm, cold for 1 week, and for 2 weeks.

first: Malia

last: Dong

first: Michael

last: Thomashow


title: Expression of IRF8 in gastric epithelial cells confers protective innate immunity against Helicobacter pylori infection

city: Bethesda

first: Peng

last: Li

address: 9000 Rockville Pike

department: NHLBI

institute: NIH

summary: The transcription factor IRF8 is expressed in many types of blood cells and plays critical roles in cellular differentiation and function. However, the role of IRF8 in nonhematopoietic systems remains poorly understood. In this study, we examined the role of IRF8 in gastric epithelial cells (GECs) and provided evidence that IRF8 is a transcriptional modulator of the gastric mucosa necessary for limiting H. pylori colonization. H. pylori infection significantly upregulated expression of IRF8, which in turn promoted IFN-γ expression by GECs. Mice deficient of IRF8 exhibited increased H. pylori colonization and aborted induction of mucosal  IFN-γ. Genome-wide analyses of  IFN-γ-treated GECs by ChIP-seq and RNA-seq led to identification of IRF8 target genes with many belonging to the IFN regulated gene family that was previously observed in immune cells. Our results identify the IRF8- IFN-γ circuit as a previously unrecognized gastric innate immune mechanism in defense against infection of H. pylori.

overall_design: Genome-wide transcription factors mapping and binding of IRF8 in mouse gastric epithelial cells (GECs). RNA-Seq is performed in mouse GECs, treated with or without IFN-γ.

first: Ming

last: Yan

first: Hongsheng

last: Wang

first: Jiafang

last: Sun

first: Wei

last: Liao

first: Yin

first: Chengfu

last: Xu

first: Jungsoo

last: Joo

first: Yan

first: Sadia

last: Abbasi

first: Alexander

last: Kovalchuk

first: Nonghua

last: Lv

first: Warren

last: Leonard

first: Herbert

last: Morse III


title: pH regulates white-opaque switching and sexual mating in Candida albicans

city: Beijing

first: guanghua

last: huang

address: NO.1 West Beichen Road, Chaoyang District

institute: Institute of Microbiology

summary: As a successful commensal and pathogen of humans, Candida albicans encounters a wide range of environmental changes. Among them, ambient pH is an important factor, which changes frequently and affects many biological processes in this species. The ability to adapt to pH changes is tightly linked with pathogenesis and morphogenesis. In this study, we report that pH has a profound effect on white-opaque switching and sexual mating in C. albicans. Acidic pHs promote white-to-opaque switching but repress sexual mating of opaque cells. The cAMP signaling and Rim101-mediated pH sensing pathways are involved in the regulation of pH-regulated white-opaque switching. Interestingly, white and opaque cells of the cyr1/cyr1 mutant, which is defective in producing cAMP, show distinct growth defects under acidic and alkaline conditions. Phr2 could play a major role in acidic pHs-induced opaque cell formation. We further discover that acidic pH conditions repress sexual mating due to the failure of activation of the Ste2-mediated a-pheromone response pathway. The effects of pH changes on phenotypic switching and sexual mating could be a balance behavior between host adaptation and sexual reproduction.

overall_design: total RNA profiles of cells grown in different pH

first: Guanghua

last: Huang

first: Yuan

first: Chengjun

last: Cao


title: Identification of microRNAs in Caragana intermedia by high-throughput sequencing and expression analysis of 12 microRNAs and their targets under salt stress

first: Zhu

last: Jianfeng

address: Haidian District, Xiang Shan Road

department: Research Center of Saline and Alkali Land of State Forestry Administration

institute: Chinese Academy of Forestry

summary: MicroRNAs (miRNAs) are endogenous small RNAs that play important roles in various biological and metabolic processes in plants. Caragana intermedia is an important ecological and economic tree species that is prominent in the desert environment of west and northwest China. To date, no investigation into C. intermedia miRNAs has been reported. In this study, high-throughput sequencing of small RNAs was performed to identify both conserved and novel miRNAs, and also their target mRNA genes in C. intermedia. Based on sequence similarity and hairpin structure prediction, 132 putative conserved miRNAs (12 of which were confirmed to form hairpin precursors) belonging to 31 known miRNA families were identified. Ten novel miRNAs (including the miRNA* sequences of three novel miRNAs) were also discovered. The expression of 12 miRNAs was validated in different tissues, and the 12 miRNAs were further assessed by qRT-PCR after salt treatment. Furthermore, 36 potential target genes of 17 known miRNA families and two potential target genes of one novel miRNA were predicted, and some target genes were also assessed by qRT-PCR after salt treatment. Our study provides a basic catalog of miRNAs and their targets, which will promote further understanding of the important roles of miRNAs in C. intermedia and in other species of the leguminous genus, Caragana.

overall_design: Examination of small RNA expression profiling in three-weeks-old seedings of Caragana intermedia.

first: Liwang

last: Qi

first: Jianfeng

last: Zhu


title: Genome-wide occupancy of RNA polymerase II before and after heat shock in mouse cells

city: Boulder

first: Jennifer

middle: F

last: Kugel

state: CO

address: 596 UCB

department: Biochemistry

institute: University of Colorado Boulder

summary: The goal of this study was to understand changes that occur in RNA polymerase II occupancy upon heat shock using ChIP-seq in mouse cells.

overall_design: ChIP-seq of Pol II from control cells (no heat shock) and heat shocked cells.  Input chromatin before and after heat shock was also sequenced.

first: Petro

last: Yakovchuk

first: James

last: Goodrich


title: LncRNA DINO guides DNA damage signaling

city: Stanford

first: Adam

last: Schmitt

address: 269 Campus Drive

department: Department of Dermatology

institute: Stanford University

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

overall_design: Refer to individual Series


title: KLF15 dependent REV-ERBa binding in the heart

city: Cleveland

first: Mukesh

last: Jain

state: OH

address: 2103 Cornell Road, Room 4537

department: Case Cardiovascular Research Institute

institute: Case Western Reserve University

summary: By comparing the ChIPseq signal of REV_ERBa in control (Flox) and cardiomyocytic KLF15 knockout (cKO), we identified the KLF15 dependent REV-ERBa binding and repression in the heart. We further compared the differential binding sites to KLF15 binding site, using a FLAG tagged cardiomyocytic transgenic (cTG1) mice.

overall_design: Examination of REV_ERBa binding in cardiomyocytic KLF15 knockout (cKO) and control (Flox) mice hearts.

first: Lilei

last: Zhang


title: Genetic variation contribute to different susceptibility to HP-PRRSV infection across pig breeds

first: Ning

last: Li

state: Beijing

address: Yuanmingyuan West Rd. 2,Haidian District

institute: China Agriculture University

summary:
Purpose: To characterize the differential mRNA expression profiles of lung tissues upon PRRSV infection in different pig breeds, using NGS techonology, we sequenced mRNAs of the lungs of Tongcheng and Landrace pigs before (0 dpi) and after (3, 5, 7 dpi) infection with high-pathogenic PRRSV (HP-PRRSV).
Methods: The mRNA expression profiles of the lungs of Tongcheng and Landrace pigs before (0 dpi) and after (3, 5, 7 dpi) HP-PRRSV infection were produced by using solexa platform. The raw reads with low qualities were filtered and the clean high quality reads were mapped to Ensembl Sus reference genome 10.2.71 using BOWTIE2. The unique mapped reads were retained for mRNA expression analysis. The raw reads counts of each mRNA were calculated by HTseq and the differentially expressed mRNA (Fold change >2; FDR <0.05) were called using DEGseq.

overall_design: Comparasion of the mRNA expression profiles of lungs from two pig breeds: Tongcheng and Landrace, at 0, 3, 5, 7 dpi infected with HP-PRRSV.

first: Jia


title: EB-transcriptome in Drosophila midgut

city: Lausanne

first: ZongZhao

last: Zhai

address: EPFL-SV-GHI-UPLEM station 19

country: Switzerland

institute: EPFL

summary: gene expression profiling in EBs of wild-type and Sox21a mutant fly midgut by RNA-seq using FACS-sorted cells

overall_design: 2 genotypes, and biological triplicates

first: Zongzhao

first: Bruno

last: Lemaitre


title: RNA polymerase II ChIP-seq in HSV-1 and mock infected cells

summary: The goal of this study was to determine how RNA poymerase II (Pol II) occupancy changed in response to herpes simplex virus-1 (HSV-1) infection using ChIP-seq of Pol II. ChIP assays were performed 4 hours after cells were infected (or mock infected) with HSV-1. Because host cell Pol II transcribes the HSV-1 genome, the ChIP-seq data also reveal polymerase occupancy on the viral genome.

sample_organism:
Mus musculus
Human alphaherpesvirus 1 strain KOS

overall_design: ChIP-seq of Pol II in mock infected and HSV-1 infected cells

first: Robert

last: Abrisch

first: Tess

last: Eidem


title: Expression profiling of skeletal muscle in two breeds of duck (Anas platyrhynchos)

city: Ya’an

first: Rongping

state: Sichuan

address: NO.46 xinkang road

institute: Sichuan Agricultural University

summary:
Background: Skeletal muscle growth and development is highly orchestrated in gene expressions. Understanding the location-specific and breed-specific genes and pathways are agriculturally important on meat products and meat quality. In the present study, RNA-Seq was performed to elucidate the difference of muscle deposition between locations and breeds for functional genomics studies. To achieve those goals, skeletal muscle samples were collected for pectoral muscle (PM) and leg muscle (LM) of two genetically different duck breeds, Heiwu duck (H) and Peking duck (P), at embryonic 15 days. Functional genomics studies were performed in two experiments: Experiment 1 directly compared location-specific genes between PM and LM, while Experiment 2 compared the two breeds (H and P) at the same development stage (embryonic 15 days).
Results: Almost 13 million clean reads was generated using Illumina technology on each library, and more than 70% reads mapped to Anas platyrhynchos breed Peking duck genome. We identified 246, 258, 20 and 54 differentially expressed genes (DEGs) (log2.fold-change >0.5, and P-value <0.05) for H-PM vs H-LM, P-PM vs P-LM, H-LM vs P-LM and H-PM vs P-PM library, separately. A total of 168 genes were differentially expressed by over locations in experiment 1, while only 8 genes were differentially expressed by over breeds in experiment 2. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathways (KEGG) were used to functionally annotate DGEs. In experiment 1, DEGs mainly involved in Focal adhesion, PI3K-Akt signaling pathway and ECM-receptor interaction pathways (corrected P-value<0.05). In experiment 2, DEGs only associated with ribosome signal pathway (corrected P-value<0.05). In addition, quantitative real-time PCR was employed to confirm 15 differentially expressed genes detected by RNA-Seq.
Conclusions: Comparative transcript analysis of leg muscle and pectoral muscle of two duck breeds not only improves our understanding of those location-specific and breed-specific genes and pathways, but also provides some candidate molecular targets for increase muscle products and meat quality by genetic control.
Conclusions: Our study represents the first detailed analysis of duck breed muscle transcriptomes generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

overall_design: Total RNA of duck skeletal muscle at embryonic 15 days for four group muscles was extracted using Trizol reagent (Takara, china) according to manufacturer’s instructions. Five RNA samples per group were equally mixed to get a RNA pool.

first: Jiwen

last: Wang


title: Genome-wide profiling of histone H3 lysine 27 and lysine 4 trimethylation in multiple myeloma reveals the importance of Polycomb gene targeting and highlights EZH2 as a potential therapeutic target [Seq]

city: Uppsala

first: Prasoon

last: Agarwal

state: Sweden

address: Dag Hammarshkojlds vag 20

department: IGP

institute: Rudbeck Laboratory, Uppsala University

summary: Multiple myeloma (MM) is a hematopoietic malignancy characterised by the accumulation of neoplastic post-germinal centre, isotype-switched, long-lived plasma cell within the bone marrow. In genetic and clinical terms MM is highly heterogeneous and remains fatal. Here we present the first epigenomic map of MM derived from freshly isolated bone marrow plasma cells from four patients. Using ChIP- and RNA-sequencing we define a set of silent H3K27me3 targets, active genes bearing H3K4me3, and bivalent genes.

overall_design: Examination of 2 different histone modifications in four Multiple myeloma patients and two normal plasma cells samples.  A single patient RNA-seq sample was also examined.

first: Mohammad

last: Alzrigat

first: Alba

last: Párraga

first: Antonia

last: Kalushkova

first: Stefan

last: Enroth

first: Fredrik

last: Ã–berg

first: Helena

last: Wiklund


title: Usp16

city: Richmond

first: Hengbin

state: VA

address: 401 College Street

department: Massey Cancer Institute

institute: Virginia Commonwealth University


title: Usp16 WT and KO RNA-Seq ckit and sca1 positive cells

summary: RNA-seq in wt and Usp16 deleted HSC/P

overall_design: Examination of changes in gene expression in wt and Usp16 deleted HSC/P.

first: H


title: PLURIPOTENCY REGULATOR ZIC3 IS AN EARLY LINEAGE SPECIFIER

city: Singapore

first: Vibhor

last: Kumar

address: 60 Biopolis Street, Genome, #02-01

country: Singapore

institute: Genome Institute of Singapore

summary: Sustained expression of the key pluripotency transcriptional regulators and proliferative factors is needed for the maintenance of embryonic stem cells and early progenitors of various lineages. Zic3 is one of those factors which has been shown to be important for embryonic stem cell pluripotency. Through combinatorial analysis of transcription factor binding sites and the corresponding gene-regulation, we show that Zic3 not only activates key pluripotency genes but also acts cooperatively with them in connecting important circuits of regulation in ES cell in proliferation and maintenance of early progenitors.

overall_design: Chromatin immunoprecipitation was performed as previously described (Loh, Y.H. et al, Nat Genet 38, 431-440 (2006)). Briefly, cells were treated with 1% formaldehyde for 10 mins at RT. The reaction was quenched with 125 mM glycine. Chromatin was harvested from nuclear extracts. Chromatin extracts were sonicated to an average size of 500 bp. Immunoprecipitation was performed using 10 µg of Zic3 antibody previously generated (Lim, L.S. et al., Mol Biol Cell 18, 1348-1358 (2007)). Immunoprecipitated chromatin extracts were subjected to sequencing.

first: Felicia

middle: H

last: HONG

first: Lawrence

last: STANTON


title: Hierarchical folding and reorganization of chromosomes are linked to transcriptional changes in cellular differentiation

city: Montreal

first: Josee

last: Dostie

state: Quebec

address: 3655 Prom. Sir-William-Osler

country: Canada

institute: McGill University

summary: Mammalian chromosomes fold into arrays of megabase‐sized topologically associating domains (TADs), which are arranged into compartments spanning multiple megabases of genomic DNA. TADs have internal substructures that are often cell type specific, but their higher‐order organization remains elusive. Here, we investigate TAD higher‐order interactions with Hi‐C through neuronal differentiation and show that they form a hierarchy of domains‐within‐domains (metaTADs) extending across genomic scales up to the range of entire chromosomes. We find that TAD interactions are well captured by tree‐like, hierarchical structures irrespective of cell type. metaTAD tree structures correlate with genetic, epigenomic and expression features, and structural tree rearrangements during differentiation are linked to transcriptional state changes. Using polymer modelling, we demonstrate that hierarchical folding promotes efficient chromatin packaging without the loss of contact specificity, highlighting a role far beyond the simple need for packing efficiency.

overall_design: Hi-C was performed in mouse embryonic stem cells (ESC), neural progenitor cells (NPC), and midbrain-like neurons (Neurons) using both HindIII and NcoI restriction enzymes

first: James

last: Fraser

first: Carmelo

last: Ferrai

first: Ana

last: Pombo


title: Usp16 ChIP-seq of ckit and sca1 positive cells

summary: anti-Usp16 ChIP-seq in ckit and sca1 hematopoietic stem/progenitor cells

overall_design: Identification of Usp16 enriched genes in HSC/P


title: 3D chromosomal capture of X. laevis

status: Public on Dec 29 2015

city: La Jolla

first: Ian

middle: K

last: Quigley

state: CA

address: 10010 North Torrey Pines Road

department: Molecular Neurobiology Lab

institute: Salk Institute

summary: To determine 3D chromosomal structure in differentating ectoderm of the frog  Xenopus laevis, we performed tethered conformation capture (TCC) (PMID: 22198700) on wild-type dissected ectoderm and ectoderm injected with multicilin. We used these data to investigate possible differences between these conditions (we found very few) and also to determine the positions of topologically-associated domains (TADs). These data were also used to facilitate chromosome-level assembly of the X. laevis genome.

overall_design: Some embryos were harvested as wild-types (stage 10). In other experiments, we injected some embryos with mRNAs encoding an inducible form of multicilin (mcidas-HGR).  After injecting, we isolated ectoderm surgically and, when injected with multicilin, induced at mid-stage 11. We then harvested chromatin at 9 hours after induction (roughly stage 18) and performed tethered conformation capture on all harvested tissues (PMID: 22198700). We then sequenced these libraries, aligned the reads to the X. laevis genome (version 9.1 to interrogate 3D structure and the more fragmented genome version 7.1 to assist with chromosome assembly). TADs were called with HOMER, and chromosomes were assembled with both Lachesis (PMID: 24185095) and HighRise (arXiv:1502.05331).

first: Chris

last: Kintner


title: MethlyC-Seq of met18-1(SALK_121963) and met18-2(SALK_147068) mutant

status: Public on Dec 27 2015

city: West Lafayette

first: Jian-Kang

last: Zhu

state: IN

address: 625 Agriculture Mall Dr.

department: Department of Horticulture and Landscape Architecture

institute: Purdue University

summary: Using MethylC-Seq to provide single-base resolution of DNA methylation status in  met18-1 and met18-2 mutants

overall_design: MethylC-Seq: 2 mutants examined, met18-1 and met18-2, each mutant has two bilogical replicates

first: Cheng-Guo

last: Duan

first: Xingang

last: Wang

first: Kai

last: Tang


title: Deep Transcriptome Sequencing of a Rice Line Immune to Bacterial Blight Provides Novel Insights into Incompatible Interactions between Rice and Xanthomonas oryzae pv. oryzae

first: Fan

last: Zhang

address: 12 South Zhong-Guan-Cun St.

institute: CAAS

summary:
In this study, simultaneous gene expression, of both the host and pathogen, in the incompatible interaction between rice immune line H471 and Xoo race PXO99A with strong virulence, and in compatible ones between H471’s parents and PXO99A, were analyzed in the same infected leaf blades at 1 day and 3 days post-inoculation (dpi) using the RNA-Seq technique.This study provides the first insights into the differantial gene expression profiles of both organisms interacting simultaneously in the incompatible and compatible interactions between Xanthomonas oryzae pv. oryzae and host.
Gene groups of differentially expressed genes were identified for PXO99^A and H471. In the Xoo case, a set of  genes associated with two-component systems, involved in Quorum sensing (QS) and protecting the cell from reactive oxygen species (ROS) and oxidative stress, and genes encoding type III secretion systems and Type III (T3) effectors were sequentially up-regulated in the incompatible interaction. In the rice case, differentially regulated genes encoding a set of signal transduction components, sixty-six transcription factors, six genes encoding PPRs and three genes encoding tetratricopeptide repeat (TPR)-like superfamily proteins, and twenty-one resistance proteins have been identified in the incompatible interaction. Among them, six rice genes encoding response regulator receivers and histone proteins in the incompatible interaction uniquely differentially up-regulated in H471 at 1 dpi

sample_organism:
Oryza sativa
Xanthomonas oryzae pv. oryzae

overall_design: Simultaneous gene expression, of both the host (Rice) and pathogen(Xoo), in the incompatible interaction between rice immune line H471 and Xoo race PXO99A with strong virulence, and in compatible ones between H471’s parents and PXO99A, were analyzed in the same infected leaf blades at 1 day and 3 days post-inoculation (dpi) using the RNA-Seq technique.

first: Yongli

last: Zhou


title: Association between Hypomethylation of Noncoding Regions and Overexpression of the lnc-RNA, AFAP1-AS1, in Barrett’s Esophagus

status: Public on Dec 26 2015

city: Bronx

first: Yiting

last: Yu

address: 1300 Morris Park Ave

institute: Albert Einstein College of Medicine

summary: Background & Aims: Alterations in methylation of protein-coding genes have been associated with development of Barrett’s esophagus (BE) and esophageal adenocarcinoma (EAC). Deregulation of non-coding RNAs has been associated with carcinogenesis, but never studied in BE or EAC cells. We used high-resolution methylome analysis to identify changes at genomic regions that encode non-coding RNAs in BE and EAC cells.  Methods: We analyzed the methylation status of 1.8 million CpG sites using the massively parallel sequencing-based HELP-tagging assay in matched sets of BE and healthy esophageal tissues from the same patients. We also analyzed human EAC cell lines (OE-33, SK-GT-4, and FLO-1) and human primary non-immortalized esophageal epithelial cells (HEEpiC).  Results: BE was characterized by genome-wide loss of methylation that significantly affected intragenic and repetitive elements of the genome. A high proportion of non-coding regions were hypomethylated in BE tissues. The changes in methylation affected small and long non-coding (lnc) regions, and discriminated healthy esophageal from BE tissues, even in matched samples. One lncRNA, AFAP1-AS1, was highly hypomethylated and overexpressed in EAC cells, compared with primary non-malignant esophageal epithelial cells. Knockdown of AFAP1-AS1 with small interfering RNA inhibited proliferation and colony-forming ability of EAC cells, inducing apoptosis; knockdown also significantly reduced EAC cell migration and invasion in Matrigel assays.  Conclusions: BE tissues have reduced genome-wide methylation, compared with healthy esophageal tissues, that includes many non-coding regions. Methylation of the long noncoding RNA AFAP1-AS1 is reduced in EAC cells, increasing its expression and the aggressive behavior of cells in culture, similar to activation of protein-coding oncogenes.

overall_design: We did methylation tests for three normal esophagus and three Barrett’s esophagus

first: Wenjing

last: Wu

first: Tushar

last: Bhagat

first: Verma

last: Amit

first: Stephen

last: Meltzer


title: Expression profiles of microRNAs in Glioma-Initiating Cells (GICs) cultured under hypoxia and normoxia

status: Public on Dec 28 2015

first: Hai-Ri

last: Li

address: 9500 Gilman Dr.

department: Medicine

institute: University of California, San Diego

summary: Glioblastoma (GBM) is the most common and aggressive primary brain tumor in adults, with glioma initiating cells (GICs) implicated to be critical for tumor progression and resistance to therapy. The hypoxic tumor microenvironment has been shown to play an important role to maintain the GICs; however, the mechanisms regulating responses of GICs to hypoxia remain poorly understood.

overall_design:
We used RNA-Sequencing to  to detail the global change of microRNA expression in GICs cultured under hypoxia compared to normoxia and identified de-regulated microRNAs during hypoxia.
CD133+ 110040 GICs were cultured under 1% O2 for 0h, 6h, 12h and 24 hs. Then RNA was extracted and microRNA expression was profiled by RNA-Sequencing.

first: Jing

last: Hu

first: Xiao-Fan


title: Profiling of three leiomyosarcoma molecular subtypes with RNA-sequencing

status: Public on Dec 25 2015

first: Xiangqian

last: Guo

address: 300 Pasteur Dr.

department: Department of Pathology

summary: Leiomyosarcoma (LMS) is a malignant neoplasm with smooth muscle differentiation, and there are three molecular subtypes of LMS which have been defined previously by our lab. To further validate these subtypes and identify potential therapeutic targets in each subtype, we profiled the LMS cases from each subtype with RNA-Seq technology.

overall_design: 8 LMS cases from subtype I, 6 cases from subtype II, 3 cases from subtype III and 7 cases of normal tissues, were selected for RNA-Seq. Then the expression levels and potential mutations were analyzed on these cases.

first: Shirley

first: Sushama

last: Varma

first: Robert

last: West

first: Matt

last: van de Rijn


title: RING1 links retinoic acid signaling to the early proximal-distal specification of forelimb bud via Meis2 repression (ChIP-Seq)

city: Yokohama

first: Takaho

last: Endo

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

department: IMS

institute: RIKEN

summary: Polycomb group (PcG) proteins play a pivotal role in silencing of development-related genes and contribute to maintain various stem and precursor cells and regulate their differentiation. However, it is not well understood how PcG factors regulate dynamic and complex morphogenetic processes particularly in mammals. In this study, we focused on proximal-distal (PD) patterning of forelimb bud to elucidate how PcG factors contribute to regulation of morphogenetic processes that depends on developmental signals. Depletion of RING1 proteins, which are common components of both canonical and variant Polycomb repressive complex-1 (PRC1), led to dramatic deficiencies in forelimb formation. By using Ring1-deficient forelimb buds, we revealed the early defects in distal specification, which is due to the functional coupling of RING1 and retinoic acid (RA) signaling. RING1 activity is shown to antagonize with RA signals at Meis2 and likely Meis1, which are superior suppressors of distal formation program, in the prospective distal region of outgrowing forelimb bud. This study exhibits a first example showing how PcG factors interplay with developmental signals to mediate compartmentalization of elongating anlagen by regulating the expression of developmental genes.

overall_design: ChIP analysis of mouse E11.5 proximal or distal forelimb buds against anti-RING1B antibody.

first: N

last: Yakushiji-Kaminatsui

first: T

first: H

last: Koseki


title: Transcriptomes of lineage-specific Drosophila neuroblasts profiled via genetic targeting and robotic sorting

city: Ashburn

first: Ken

last: Sugino

address: 19700 Helix Dr

institute: Janelia Research Campus

summary: A brain consists of numerous distinct neurons arising from a limited number of progenitors, called neuroblasts in Drosophila.  Each neuroblast makes a specific neuronal lineage.  To unravel the transcriptional networks that underlie the development of distinct neuroblast lineages, we marked and isolated lineage-specific neuroblasts for RNA sequencing.  We labeled particular neuroblasts throughout neurogenesis by activating a conditional neuroblast driver in specific lineages using various intersection strategies.  The targeted neuroblasts were efficiently recovered using a custom-built device for robotic single cell picking.  Transcriptome analysis on the mushroom body, antennal lobe, and type II neuroblasts besides non-selective neuroblasts, neurons, and glia revealed a rich repertoire of transcription factors expressed among neuroblasts in diverse patterns.  In addition to those likely pan-neuroblast transcription factors, there exist many transcription factors selectively enriched or repressed in certain neuroblasts.  The unique combinations of transcription factors present in different neuroblasts may govern the diverse lineage-specific neuron fates

overall_design: Examination of 5 different cell types

first: Ching-Po

last: Yang

first: Zhiyong

last: Liu

first: Chi-cheng

last: Fu

first: Tzumin

last: Lee


title: Expression data for KDM1B knockdown in Glioma-Initiating Cells (GICs)

first: Hai-Ri

summary: Glioblastoma (GBM) is the most common and aggressive primary brain tumor in adults, with glioma initiating cells (GICs) implicated to be critical for tumor progression and resistance to therapy. KDM1B is involved in regulating GICs' responses to hypoxia, since over-expression of KDM1B delays the cell growth under hypoxia while knocking-down of KDM1B in GICs promotes their survival and tumorigenic abilities.

overall_design:
We used RNA-Sequencing to detail the global change of gene expression in GICs with knockdown of KDM1B, and identified de-regulated genes and pathways downstream of KDM1B.
CD133+ D456MG GICs were infected with non-targeting control and shRNA of KDM1B. Then RNA was extracted and gene expression was profiled by RNA-Seq.

last: Wang


title: Cross-species comparative analysis of Dicer proteins during Sindbis virus infection

city: Strasbourg

first: Sébastien

last: Pfeffer

address: 2 allée Konrad Roentgen

department: UPR 9002 - Architecture et Réactivité de l'ARN

institute: CNRS - Institut de Biologie Moléculaire et Cellulaire (IBMC)

summary: The role of RNA silencing as a defense mechanism against viruses remains to be formerly established in mammalian somatic cells. Here, we determined the antiviral properties of human and Drosophila Dicer proteins in a heterologous setup. We expressed human Dicer (hDicer) in Drosophila, and Drosophila Dicer-2 in human cells, and measured the impact on the response to Sindbis virus (SINV) infection. In flies, hDicer presents a low processing activity, but partially rescues a Dcr2 null mutation in flies. Expression of Dicer-2 in HEK293 cells allows the processing of SINV RNA into 21-nt-long small RNAs. Nevertheless, instead of conferring a protective effect against SINV, Dicer-2 expression increases viral replication in HEK293 cells. We present evidence that this effect is due to a competition with the interferon pathway. Our results therefore suggest that adding functionial RNA silencing machinery in IFN-competent differentiated mammalian cells can be detrimental for antiviral defense.

sample_organism:
Drosophila melanogaster
Homo sapiens
Sindbis virus

overall_design: Small RNA profiles of SINV-infected transgenic flies expressing RFP tagged hDicer or Dicer-2 in a Dicer-2 null background, 5 dpi (Df = Dicer-2 Deficiency = control, RFP-hDicer, RFP-Dicer-2) and of SINV-infected HEK293 stable cell lines, expressing or not some D. melanogaster RNAi components, 6 and 16 hpi (empty (e) = control, Dicer-2, DAR = Dicer-2 + R2D2) were generated by deep-sequencing, without replicate, using Illumina HiSeq 2500.

first: Erika

last: Girardi

first: Mathieu

last: Lefèvre

first: Béatrice

last: Chane-Woon-Ming

first: Simona

last: Paro

first: Bill

last: Claydon

first: Jean

middle: L

last: Imler

first: Carine

last: Meignin


title: MicroRNA transcriptome profiles during swine muscle development

city: Sichuan

first: Chaowei

last: Zhou

summary: Studies have been done to search for changes in miRNA expression during the muscle development in different pigs. However, research in this area has largely focused on dissecting miRNAs that are important for fetal and young muscle development. Little is known about the role of miRNAs in adult muscle development. In this study, we performed a comprehensive study on miRNA expression pattern across the muscle developmental process from embryo to adult (E90-7Years). We identified a number of differentially expressed muscle development-associated miRNAs including new members during developmental stages.

overall_design: Nine small RNA libraries at five stages of muscle development including one prenatal stages (90-day post-gestation fetuses, E90) and four postnatal stages (0, 30, 180 days and 7 year after birth) from fifteen Jinhua female pigs were sequenced.

first: Mingzhou

last: Li

first: Xuewei


title: RING1 proteins contribute to early proximal-distal specification of the forelimb bud by restricting Meis2 expression

first: Takaho

last: Endo

type: Genome binding/occupancy profiling by genome tiling array

summary:
Polycomb group (PcG) proteins play a pivotal role in silencing developmental genes and help to maintain various stem and precursor cells and regulate their differentiation. PcG factors also regulate dynamic and complex regional specification, particularly in mammals, but this activity is mechanistically not well understood. In this study, we focused on proximal-distal (PD) patterning of the mouse forelimb bud to elucidate how PcG factors contribute to a regional specification process that depends on developmental signals. Depletion of the RING1 proteins RING1A (RING1) and RING1B (RNF2), which are essential components of Polycomb repressive complex 1 (PRC1), led to severe defects in forelimb formation along the PD axis. We show that preferential defects in early distal specification in Ring1A/B-deficient forelimb buds accompany failures in the repression of proximal signal circuitry bound by RING1B, including Meis1/2, and the activation of distal signal circuitry in the prospective distal region. Additional deletion of Meis2 induced partial restoration of the distal gene expression and limb formation seen in the Ring1A/B-deficient mice, suggesting a crucial role for RING1-dependent repression of Meis2 and likely also Meis1 for distal specification. We suggest that the RING1-MEIS1/2 axis is regulated by early PD signals and contributes to the initiation or maintenance of the distal signal circuitry.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: RNAseq profiling of multiciliated cells

first: Ian

last: Quigley

summary: To determine what genes are upregulated in multiciliated cells, we manipulated Xenopus laevis ectoderm to either make more or fewer of this cell type with multiple approaches  across multiple timepoints. By finding differentially expressed genes in common across all comparisons in which multiciliated cell number changed, we obtained a robust, but conservative, core group of multiciliated cell genes.

overall_design: We suppressed multiciliated cell development by activating the notch pathway with an injected mRNA encoding the intracellular domain of notch (icd) or by injecting an mRNA encoding a dominant-negative form of multicilin (dnmcidas). Conversely, we promoted multiciliated cell differentiation by blocking notch signaling with a DNA-binding mutant of Suppressor of Hairless (dbm), or by overexpressing an inducible form of multicilin (mcidas). We also coinjected these constructs in a way aimed at causing the greatest change in multiciliated cells and reducing background transcriptional programs not associated with these cells: for example, we coinjected icd with mcidas, in order to reduce other cell types specified by notch. After injecting, we isolated ectoderm surgically and, when injected with multicilin, induced at mid-stage 11. We then harvested RNA at 3, 6, and 9 hours after induction, roughly corresponding to stages 13, 16, and 18 and performed poly-a+  RNAseq (Illumina Truseq v2). We then aligned reads to X. laevis gene models (Mayball version, Chung and Kwon et al. 2014) and took the intersection of genes differentially expressed between all comparisons in which the multiciliated cell number dramatically changed (icd vs. icd + mcidas, icd vs. dbm, dbm vs. dbm + dnmcidas) to obtain a core list of  multiciliated cell genes.

first: Chris

last: Kintner


title: Thousands of novel translated open reading frames in humans inferred by ribosome footprint profiling.

city: Chicago

first: Sidney

state: IL

address: 920 E. 58th Street, CLSC 317

institute: University of Chicago

summary: Accurate annotations of protein coding regions are essential for understanding how genetic information is translated into biological functions. The recent development of ribosome footprint profiling provides an important new tool for measuring translation. Here we describe riboHMM, a new method that uses ribosome footprint data along with gene expression and sequence information to accurately infer translated sequences. We applied our method to human lymphoblastoid cell lines and identified 7,863 previously unannotated coding sequences, including 445 translated sequences in pseudogenes and 2,442 translated upstream open reading frames. We observed an enrichment of harringtonine-treated ribosome footprints at the inferred initiation sites, validating many of the novel coding sequences. In aggregate, the novel sequences exhibit significant signatures of purifying selection indicative of protein-coding function, suggesting that many of the novel sequences are functional. We observed that nearly 40% of bicistronic transcripts showed significant negative correlation in the levels of translation of their two coding sequences, suggesting a key regulatory role for these novel translated sequences. Despite evidence for their functional importance, the novel peptide sequences were detected by mass spectrometry at a lower rate than predicted based on data from annotated proteins, thus suggesting that many of the novel peptide products may be relatively short-lived. Our work illustrates the value of ribosome profiling for improving coding annotations, and significantly expands the set of known coding regions.

overall_design: Ribosome profiling assays were performed on cell lines treated with Harringtonine to generate data for validating translation initiatoin site prediction

first: Anil

last: Raj

first: Heejung

last: Shim

first: Yoav

last: Gilad

first: Jonathan

last: Pritchard

first: Matthew

last: Stephens

first: Brett

last: Engelmann

first: Yang

first: Arbel

last: Harpak


title: FOXD3 is a novel tumor suppressor in lung cancer

status: Public on Dec 24 2015

city: Shanghai

first: Jianru

last: Xiao

address: 415 Fengyang Road

department: Department of Orthopedics Oncology

institute: Changzheng Hospital, Second Military Medical University

summary: The transcription factor forkhead box D3 (FoxD3) is a transcriptional factor which belongs to forkhead box (Fox) transcription factor family. The functions of FOXD3 in embryogenesis and in the development of neural crest cells have been clearly defined. Its tumor suppressor function hasbeen found in many types of cancer in recent years. However, the study about its roles in lung cancerdevelopment is still lacking. Our study found that deficiency of FoxD3 in lung cancer enhanced cell growth and cell invasion. RNA-sequence analysis demonstrated that loss of FoxD3 mainly affected cell cycle progression related gene expression. Knockdown of FoxD3 led to G2-M cell accumulation with up-regulation of DNA replication licensing factor MCM5 and MCM4 as well as cell cycle regulator polo-like kinase-1 (PLK1) and CDC6. Over-expression of those genesin lung cancer was associated with poor clinical outcomes of lung cancer patients. We also identified high mobility group box-1(HMGB1), Hras and Ephrin B1 gene expression increase after FoxD3 silencing which may participate in enhanced lung cancer cell invasion. Our study identifiedtumor suppressor function of FoxD3 in lung cancer andwe did the first comprehensive analysis of the genes regulated by FoxD3 for cell proliferation and invasion in lung cancer. The identified genes regulated by FoxD3 through our analysis will provide valuable information to uncover the mechanism of FoxD3 tumor suppressor function.

overall_design: Three control and three FOXD3 knockdown A549 cell lines were subjected to RNA sequencing.

first: Wei

last: Xu


title: Gene expression differences associated with light cycle

status: Public on Dec 23 2015

city: St Andrews,

first: Darren

middle: James

last: Parker

state: Fife

address: Dyers Brae House

department: Centre for Biological Diversity

institute: University of St. Andrews

summary: We examined gene expression differences associated with changes in light cycle in Drosophila montana

overall_design: Whole fly RNAseq was carried out on females reared in different light cycles

first: Michael

last: Ritchie

first: Maaria

last: Kankare


title: Grape skin transcriptome to reveal genes related with resveratrol accumulation

city: Yangling

first: Yuejin

last: Wang

state: Shaanxi

address: Shaanxi, China

institute: Northwest A&F University

summary: Methods:transcriptomes of the different development stages of Vitis vinifera cv. Cabernet Sauvignon and Vitis quinquangularis accession Danfeng-2 were analyzed using Illumina Hiseq 2500. The sequence reads that passed quality filters were analyzed: TopHat followed by Cufflinks.

sample_organism:
Vitis vinifera
Vitis quinquangularis

platform_organism:
Vitis vinifera
Vitis quinquangularis

overall_design: mRNA profiles of  different development stages of Vitis vinifera cv. Cabernet Sauvignon and Vitis quinquangularis accession Danfeng-2 were generated by deep sequencing, in triplicate, using Illumina Hiseq 2500.

first: Ruimin


title: Genome-Wide Identification of microRNAs and Their Targets in Cold-Stored Potato Tubers by Deep Sequencing and Degradome Analysis

city: Wuhan

first: Yongbin

last: Ou

state: Hubei

address: No.1 Shizishan Street, Hongshan Distrit

department: Key Laboratory of Horticultural Plant Biology

institute: Huazhong Agricultural University

summary: Two small RNA libraries and 2 degradome libraries were constructed from potato tubers stored at room temperature or exposed to cold stress for deep sequencing. Through small RNA sequencing, 53 known miRNAs and 59 novel miRNAs were identified. Seventy genes were identified as miRNA targets by degradome sequencing.

overall_design: Small RNA sequencing and degradome sequencing of control and cold treated Solanum tuberosum tubers

first: Xun

last: Liu

first: Botao

last: Song

first: Conghua

last: Xie

first: Jun


title: Parallel single-cell bisulfite- and RNA-sequencing link transcriptional and epigenetic heterogeneity [RNA-seq]

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

institute: Altos Labs

summary: We report scM&T-seq, a method for parallel single-cell genome-wide methylome and transcriptome sequencing, allowing discovery of associations between transcriptional and epigenetic variation. Profiling of 61 mouse embryonic stem cells confirmed known links between DNA methylation and transcription. Notably, the method reveals novel associations between heterogeneous methylation of distal regulatory elements and transcriptional heterogeneity of key pluripotency genes.

overall_design:
E14 ES cells were grown in either serum/LIF or 2i culture conditions and separated into single cells. RNA-Seq or Bisulfite-Seq libraries were prepared. This Series includes only the RNA-Seq data.

The list of 61 samples that passed QC in both BS-seq and RNA-seq is included in "Supplementary Table 1" of the associated manuscript.

first: Christof

last: Angermueller

first: Stephen

last: Clark

first: Heather

last: Lee

first: Iain

last: Macaulay

first: Mabel

last: Teng

first: Tim

last: Hu

first: Sebastien

last: Smallwood

first: Chris

last: Ponting

first: Thierry

last: Voet

first: Gavin

last: Kelsey

first: Oliver

last: Stegle

first: Wolf

last: Reik


title: Pervasive polymorphic imprinted methylation in the human placenta

address: Babraham Research Campus

institute: The Babraham Institute

summary: The maternal and paternal copies of the genome are both required for mammalian development and this is primarily due to imprinted genes, those that are mono-allelically expressed based on parent-of-origin. Typically, this pattern of expression is regulated by differentially methylated regions (DMRs) that are established in the germline and maintained after fertilisation. There are a large number of germline DMRs that have not yet been associated with imprinting and their function in development is unknown. In this study, we developed a genome-wide approach to identify novel imprinted DMRs, specifically in the human placenta, and investigated the dynamics of imprinted DMRs during development in somatic and extra-embryonic tissues. DNA methylation was evaluated using the Illumina HumanMethylation450 array in 116 human tissue samples, publically available reduced representation bisulfite sequencing in the human embryo and germ cells, and targeted bisulfite sequencing in term placentas. 43 known and 101 novel imprinted DMRs were identified in the human placenta, by comparing methylation between diandric and digynic triploids and female and male gametes. 72 novel DMRs showed a pattern consistent with placental-specific imprinting and this monoallelic methylation was entirely maternal in origin. Strikingly, these DMRs exhibited polymorphic imprinted methylation specifically in placenta. These data suggest that imprinting in human  development is far more extensive and dynamic than previously reported and that the placenta preferentially maintains maternal germline-derived DNA methylation.

overall_design: Multiplexed targeted bisulfite seequencing of 151 assays for imprinted differentially methylated regions in human placental villous, trophoblast and whole blood samples

first: Courtney

last: Hanna

first: Maria

middle: S

last: Peñaherrera

first: Heba

last: Saadeh

first: Simon

last: Andrews

first: Deborah

middle: E

last: McFadden

first: Wendy

last: Robinson


title: Parallel single-cell bisulfite- and RNA-sequencing link transcriptional and epigenetic heterogeneity [Bisulfite-Seq]

first: Felix

last: Krueger

overall_design:
E14 ES cells were grown in either serum/LIF or 2i culture conditions and separated into single cells. RNA-Seq or Bisulfite-Seq libraries were prepared. This Series includes only the Bisulfite-Seq data.

The list of 61 samples that passed QC in both BS-seq and RNA-seq is included in "Supplementary Table 1" of the associated manuscript.

first: Christof

last: Angermueller

first: Stephen

last: Clark


title: Integration of ATAC-seq and RNA-seq Identifies Human Alpha Cell and Beta Cell Signature Genes

city: Philadelphia

first: Paul

last: Wang

state: PA

address: 3700 Hamilton Walk

institute: University of Pennsylvania

summary:
Objective: Although glucagon-secreting α-cells and insulin-secreting β-cells have opposing functions in regulating plasma glucose levels, the two cell types share a common developmental origin and have overlaps in their transcriptome and epigenome profiles. Notably, destruction of one of these cell populations can stimulate repopulation via transdifferentiation of the other cell type, at least in mice, suggesting plasticity between these cell fates. Furthermore, dysfunction of both α- and β-cells contributes to the pathophysiology of type 1 and type 2 diabetes, and β-cell de-differentiation has been proposed to contribute to type 2 diabetes. Our objective was to delineate the molecular properties that maintain islet cell type specification yet allow for cellular plasticity.  We hypothesized that correlating cell type-specific transcriptomes with an atlas of open chromatin will identify novel genes and transcriptional regulatory elements such as enhancers involved in α- and β-cell specification and plasticity.
Methods: We sorted human a- and b-cells and performed the “Assay for Transposase-Accessible Chromatin with high throughput sequencing” (ATAC-seq) and mRNA-seq, followed by integrative analysis to identify cell type-selective gene regulatory regions.
Results: We identified numerous transcripts with either α-cell- or β-cell-selective expression and discovered the cell type-selective open chromatin regions that correlate with these gene activation patterns. We confirmed cell type-selective expression on the protein level for two of the top hits from our screen.  The “group specific protein” (GC; or vitamin D binding protein) was restricted to a-cells, while CHODL (chondrolectin) immunoreactivity was only present in b-cells.  Furthermore, α-cell- and β-cell-selective ATAC-seq peaks were identified to overlap with known binding sites for islet transcription factors, as well as with common single nucleotide polymorphisms (SNPs) previously identified as risk loci for type 2 diabetes.
Conclusions: We have determined the genetic landscape of human α- and β-cells based on chromatin accessibility and transcript levels, which allowed for detection of novel α- and β-cell signature genes not previously known to be expressed in islets. Using fine-mapping of open chromatin, we have identified thousands of potential cis-regulatory elements that operate in an endocrine cell type-specific fashion.

overall_design: ATAC-seq on 3 human alpha cell samples, 3 human beta cell samples, and 2 human acinar cell samples.  RNA-seq on 7 human alpha cell samples and 8 human beta cell samples.

first: Amanda

middle: M

last: Ackermann

first: Zhiping

first: Jonathan

last: Schug

first: Ali

last: Naji

first: Klaus

last: Kaestner


title: Unique cell cycle-dependent variations in the pluripotent epigenetic landscape define novel cohorts of temporal expressed bivalent genes during hESCs differentiation

city: Worcester

first: Troy

middle: W.

last: Whitfield

address: 55 Lake Ave. N.

institute: University of Massachusetts Medical School

summary: By mapping the genomic enrichments  of H3K4me3 and H3K27me3 modifications in pure populations of hESCs during the G2, mitotic and G1 phases of the cell cycle, we characterize cell cycle-dependent variations in the epigenetic landscape of bivalent genes, altering the current view of mitotic inheritance in pluripotent cells. We identified novel classes of bivalent domains that are highly enriched with H3K4me3 during mitosis, depleted during G1 only, and ubiquitously bivalent. These bivalent domains are associated with specific genes and expression patterns during differentiation. These cell cycle-dependent epigenetic profiles are unique to hESCs and are not observed following initiation of phenotype commitment. Our results establish a new dimension in cell cycle-dependent chromatin regulation that advances understanding of contributions the pluripotent epigenetic landscape to hESC identity.

overall_design: Study of two histone modifications, H3K4me3 and H3K27me3, during three cell cycle phases in two cell types. Study of gene expression from these two cell types in asynchronous cells.

first: Rodrigo

last: Grandy

middle: W


title: Mitochondrial Membrane Potential Identifies Cells with Enhanced Stemness for Cellular Therapy

city: Bethesda

first: Peng

last: Li

address: 9000 Rockville Pike

department: NHLBI

institute: NIH

summary: Long-term survival and antitumor immunity of adoptively transferred CD8+ T cells is dependent on their metabolic fitness, but approaches to isolate therapeutic T cells based on metabolic features are not well established. Here we utilized a lipophilic cationic dye tetramethylrhodamine methyl ester (TMRM) to identify and isolate metabolically robust T cells based on their mitochondrial membrane potential (ΔΨm). Comprehensive metabolomic and gene expression profiling demonstrated global features of improved metabolic fitness in low-ΔΨm-sorted CD8+ T cells. Transfer of these low-ΔΨm T cells was associated with superior long-term in vivo persistence and an enhanced capacity to eradicate established tumors compared with high-ΔΨm cells. Use of ΔΨm-based sorting to enrich for cells with superior metabolic features was observed in CD8+, CD4+ T cell subsets, and long-term hematopoietic stem cells. This metabolism-based approach to cell selection may be broadly applicable to therapies involving the transfer of HSC or lymphocytes for the treatment of viral-associated illnesses and cancer.

overall_design: mRNA-Sequencing of gene expression profiles in mouse CD8 cells (TMRM high and TMRM low).

first: Madhusudhanan

last: Sukumar

first: Jie

last: Liu

first: Gautam

middle: U

last: Mehta

first: Shashank

last: Patel

first: Rahul

last: Roychoudhuri

first: Joseph

last: Crompton

first: Christopher

last: Klebanoff

first: Yun

last: JI

first: Zhiya

last: Yu

first: Greg

middle: D

last: Whitehill

first: David

last: Clever

first: Robert

last: Eil

first: Douglas

last: Palmer

first: Suman

last: Mitra

first: Mahadev

last: Rao

first: Keyvan

last: Keyvanfer

last: Schrump

first: Ena

first: Francesco

last: Marincola

first: Luca

last: Gattinoni

first: Warren

last: Leonard

first: Pawel

last: Muranski

first: Toren

last: Finkel

first: Nicholas

middle: P

last: Restifo


title: AGM hematopoietic stem cells are differentially regulated by BMP and Hedgehog signalling pathways

status: Public on Dec 22 2015

city: Edinburgh

first: Elaine

last: Dzierzak

address: 47 Little France Crescent

department: MRC Centre for Inflammation Research

institute: University of Edinburgh

summary: The first HSCs are produced in the aorta-gonadmesonephros (AGM) region of the embryo through endothelial to a hematopoietic transition. BMP4 and Hedgehog affect their production/expansion, but it is unknown whether they act to affect the same HSCs. In this study using the BRE GFP reporter mouse strain that identifies BMP/Smad-activated cells, we find that the AGM harbors two types of adult-repopulating HSCs upon explant culture.

overall_design: Embryonic day 11 AGM are dissected and either analyzed directly, or after explant culture in conditions containing BMP/Hedgehog with or without cyclopamine. EC: endothelial enriched (CD31+Kit-); MC: mesenchymal cell enriched (CD31-Kit-); HPSC: hematopoietic progenitor/stem cell enriched; AGM11: E11 fresh AGMs; AGMex: AGM after explant culture; AGMcy: AGM after explant in presence of cyclopamine; CD31p: CD31 positive; CD31n: CD31 negative; KITp: c-Kit positive; KITn: c-Kit negative; BREp: BRE-GFP positive; BREn: BRE-GFP negative

first: Mihaela

last: Crisan

first: Parham

last: Solaimani Kartalaei


title: The role of antigen presenting cells in the induction of HIV-1 latency in resting CD4+ T-cells

city: Clayton

middle: Richard

last: Powell

state: VIC

address: Wellington Road

department: Bioinformatics Platform

institute: Monash University

summary:
BACKGROUND: Combination antiretroviral therapy (cART) is able to control HIV-1 viral replication, however long-lived latent infection in resting memory CD4+ T-cells persist. The mechanisms for establishment and maintenance of latent infection in resting memory CD4+ T-cells remain unclear. Previously we have shown that HIV-1 infection of resting CD4+ T-cells co-cultured with CD11c+ myeloid dendritic cells (mDC) produced a population of non-proliferating T-cells with latent infection. Here we asked whether different antigen presenting cells (APC), including subpopulations of DC and monocytes, were able to induce post-integration latent infection in resting CD4+ T-cells, and examined potential cell interactions that may be involved using RNA-seq.

RESULTS: mDC (CD1c+), SLAN+ DC and CD14+ monocytes were most efficient in stimulating proliferation of CD4+ T-cells during syngeneic culture and in generating post-integration latent infection in non-proliferating CD4+ T-cells following HIV-1 infection of APC-T-cell co-cultures. In comparison, plasmacytoid DC (pDC) and B-cells did not induce latent infection in APC-T-cell co-cultures. We compared the RNA expression profiles of APC subpopulations that could and could not induce latency in non-proliferating CD4+ T-cells. Gene expression analysis, comparing the mDC, SLAN+ DC and CD14+ monocyte subpopulations to pDC identified 53 upregulated genes that encode proteins expressed on the plasma membrane that could signal to CD4+ T-cells via cell-cell interactions (32 genes), immune checkpoints (IC) (5 genes), T-cell activation (9 genes), regulation of apoptosis (5 genes), antigen presentation (1 gene) and through unknown ligands (1 gene).

CONCLUSIONS: APC subpopulations from the myeloid lineage, specifically mDC subpopulations and CD14+ monocytes, were able to efficiently induce post-integration HIV-1 latency in non-proliferating CD4+ T-cells in vitro. Inhibition of key pathways involved in mDC-T-cell interactions and HIV-1 latency may provide novel targets to eliminate HIV latency.

overall_design: mRNA profiles of sorted, pure antigen presenting cells including, CD1c+ myleoid dendirtic cells (mDC), SLAN+ mDC, CD14+ monocytes and plasmacytoid DC (pDC), were generated using next generation sequencing in triplicate, using Illumina Illumina Hiseq 2000.

first: Nitasha

last: Kumar

first: Paul

last: Cameron

middle: R


title: Functional and molecular characterization of mouse Gata2-independent hematopoietic progenitors

summary: The Gata2 transcription factor is a pivotal regulator of hematopoietic stem cell (HSC) development and maintenance. Gata2 functions in the embryo during endothelial cell to hematopoietic cell transition (EHT) to affect hematopoietic cluster, HPC and HSC formation. Although previous studies of cell populations phenotypically enriched in HPCs and HSCs show expression of Gata2, there has been no direct study of Gata2 expressing cells during normal hematopoiesis. In this study we generate a Gata2 Venus reporter mouse model with unperturbed Gata2 expression to examine the hematopoietic function and transcriptome of Gata2 expressing and nonexpressing cells.

overall_design: Gata2Venus- HPCs 1 replicate, Gata2Venus+ HPCs 1 replicate

first: Christina

last: Eich

first: Polinikies

last: Kaimakis

first: Emma

last: De Pater


title: Intrinsic age-dependent changes and cell-cell contacts regulate nephron progenitor lifespan

city: Cincinnati

first: Raphael

last: Kopan

state: Ohio

address: 3333 Burnet Avenue

department: Developmental Biology

institute: Cincinnati Children's Hospital

summary:
Purpose: To use single-cell RNA-Seq analysis of nephron progenitors in order to determine transcrptional differences as nephron progenitors age.
Methods: Using a combination of FACS sorting and a Fluidigm Single-cell auto-prep system, we generated high-throughput RNA-SEQ data of nephron progenitors during development
Results: Single cells transcriptome profiling of nephron progenitors  revealed  progressive age-dependent changes with heterogeneity increasing in older populations.

overall_design: 96-single cell transcriptomes were determined from nephron progenitors of e14.5, e18.5 and P0 using Cited1GFP transgenic animals

first: Shuang

last: Chen

first: Eric

last: Brunskill