title: Multigenerational shifts in liver molecular programming in rainbow trout raised from bisphenol A-laden eggs

city: Calgary

first: Vijayan

middle: M.

last: Mathilakath

state: Alberta

address: 2500 University drive NW

institute: University of Calgary

summary: Bisphenol A (BPA), a widely used chemical in the manufacture of plastics and epoxy resins, is prevalent in the aquatic environment and disrupts endocrine pathways in fish, but the long-term developmental implications are unknown. We demonstrate that BPA in eggs of rainbow trout (Oncorhynchus mykiss), a commercially important species of fish with a long life-cycle, has the potential to reprogram liver metabolism in the offspring and alter the developmental growth phenotype in multiple generations. Specifically, BPA reduces growth during early development, followed by a catch-up growth and obesity phenotype in juveniles. More importantly, we observed a shift in the liver transcripts supporting the transient growth phenotypes observed in the F1 generation and this was also evident in the F2 generation. These results reveal that maternal and/or ancestral exposure to BPA in eggs has long-lasting and multigenerational impacts in trout, with implications on salmonid fisheries and sustainability of ecosystem health.

overall_design: Liver of 48 individuals were sampled at 2 life stages in F1 and F2 generation after accumulation of bisphenol A (BPA) in the egg prior to fertilization

first: Bastien

last: Sadoul

first: Oana

last: Birceanu

first: Neel

last: Aluru

first: Jith

last: Thomas

first: Mathilakath

middle: M

last: Vijayan


title: Multilayered control of alternative splicing regulatory networks by transcription factors (SPAR-Seq)

status: Public on Feb 02 2017

city: Toronto

first: Ulrich

last: Braunschweig

state: Ontario

address: 160 College Street

department: Donnelly Centre

country: Canada

institute: University of Toronto

type: Expression profiling by high throughput sequencing

summary: Networks of coordinated alternative splicing (AS) events play critical roles in development and disease. However, a comprehensive knowledge of the factors that regulate these networks is lacking. We describe a high-throughput system for systematically linking trans-acting factors to endogenous RNA regulation events. Using this system, we identify hundreds of factors associated with diverse regulatory layers that positively or negatively control AS events linked to cell fate. Remarkably, more than one third of the new regulators are transcription factors. Further analyses of the zinc finger protein Zfp871 and BTB/POZ domain transcription factor Nacc1, which regulate neural and stem cell AS programs, respectively, reveal roles in controlling the expression of specific splicing regulators. Surprisingly, these proteins also appear to regulate target AS programs via binding RNA. Our results thus uncover a large ‘missing cache’ of splicing regulators among annotated transcription factors, some of which dually regulate AS through direct and indirect mechanisms.

overall_design:
Alternative splicing and/or expression of 50 genes was monitored in 1,536 siRNA-mediated knockdowns, including 120 controls, in CGR8 mouse ES cells and N2A neuroblastoma cells in duplicate.
KnockdownAnnotation.tab: Treatment annotation and well/plate position
ScreenJuncUp.20-77.fa: fasta; Sequences of upstream junctions
ScreenJuncDn.20-77.fa: fasta; Sequences of downstream junctions
ScreenEvents_junctions.tab: Junction combinations for PSI calculation
PSI.SSMD.CGR8.tab: Raw PSI and final SSMD for CGR8 samples
PSI.SSMD.N2A.tab: Raw PSI and final SSMD for N2A samples
Reads_perEvent_CGR8.tab: Raw read counts for gene expression in CGR8
Reads_perEvent_N2A.tab: Raw read counts for gene expression in N2A
Expression.CGR8.treatments.tab: Normalized expression and fold-change in CGR8 samples
Expression.N2A.treatments.tab: Normalized expression and fold-change in N2A samples

first: Hong

last: Han

first: Thomas

last: Gonatopoulos-Purnatzis

first: Robert

middle: J

last: Weatheritt

first: Calley

middle: L

last: Hirsch

first: Kevin

middle: C

last: Ha

first: Ernest

last: Radovani

first: Syed

last: Nabeel-Shah

first: Timothy

last: Sterne-Weiler

first: Juli

last: Wang

first: Dave

last: O'Hanlon

first: Qun

last: Pan

first: Debashish

last: Ray

last: Zheng

first: Frederick

last: Vizeacoumar

first: Alessandro

last: Datti

first: Lilia

last: Magomedova

first: Carolyn

last: Cummins

middle: R

last: Hughes

first: Jack

middle: F

last: Greenblatt

first: Jeffrey

last: Wrana

first: Jason

last: Moffat

first: Benjamin

last: Blencowe


title: Regulatory Role of SLFN5 in Type I Interferon Signaling

status: Public on Jan 31 2017

city: Berlin

first: Pawel

last: Lisowski

address: Hannoversche Str. 28

country: Germany

institute: Max-Delbrück-Center for Molecular Medicine (MDC) in the Helmholtz Association

summary: We provide evidence that a member of the IFN-regulated member of the Schlafen (SLFN) family of proteins, SLFN5, promotes the malignant phenotype in glioblastoma multiforme (GBM).  Our studies demonstrate that SLFN5  negatively regulates  expression of key interferon stimulated genes (ISGs) that mediate important biological functions, including anti-viral and antineoplastic responses.

overall_design: Total RNA was isolated from untreated and IFNβ-treated U87MG SLFN5 WT and U87MG SLFN5 KO human glioblastoma cell lines. Cells were treated for 6 hours with or without human IFNβ (5000 IU/ml).

first: Dirim

last: Arslan

first: Leonidas

last: Platanias


title: The Lung Microbiome in Rheumatoid Arthritis and Autoimmunity

city: New York

first: Leopoldo

middle: Nicolas

last: Segal

state: NY

address: 462 First Avenue NBV 6N5-6N8

department: Medicine

country: USA

institute: NYU School of Medicine

summary: Here we report 16s rRNA data in  patients with Rheumatoid Artrhitis as compared with patients with sarcoidosis and healthy volunteers. Our data shows that the BAL microbiota of RA patients was significantly less diverse and abundant when compared to healthy controls, but similar to sarcoidosis patients. This distal airways dysbiosis was attributed to the reduced presence of several genus (i.e., Actynomyces and Burkhordelia) as well as reported periodontopathic taxa, including Treponema, Prevotella and Porphyromonas. While multiple clades correlated with local and systemic levels of autoantibodies, the genus Pseudonocardia and various related OTUs were the only taxa overrepresented in RA BAL and correlated with higher disease activity and erosions.

overall_design:
16S rRNA was quantified and sequenced (MiSeq) from lung BAL of control, RA, and sarcoid patients.
The amplicons from a total of 58 samples are barcoded and the barcodes are provided in the complete_metadata.txt file.

middle: N

first: Jose

last: Scher


title: Promiscuous DNA-binding of a mutant zinc finger protein corrupts the transcriptome and diminishes cell viability

status: Public on Feb 01 2017

city: Melbourne

first: Kevin

middle: Robert

last: Gillinder

state: Victoria

address: 99 Commercial Road

department: Australian Centre for Blood Diseases

country: Australia

institute: Monash University

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
The rules of engagement between zinc finger transcription factors and DNA have been partly defined  by in vitro DNA-binding and structural studies, but less is known about how these rules apply in vivo. Here we demonstrate how a missense point mutation in the second zinc finger of Krüppel-like factor-1 (KLF1) leads to degenerate DNA-binding specificity in vivo, resulting in ectopic transcription and semi-dominant neonatal anemia. We employed RNA-seq, ChIP-seq and 4sU-RNA-seq to identify the direct transcriptional consequences of aberrant DNA-binding events genome wide.

Funding: National Health and Medical Research Council [APP1082429 to A.C.P.]; United States Public Health Service [R01 GM103544 to T.B., R01 DK100692 to L.L.P. and R01 DK46865 to J.J.B.]; Victorian Government Operational Infrastructure Support Scheme [St Vincent's Institute of Medical Research to M.W.P]. Funding for open access charge: Mater Research - UQ [APP1082429].

overall_design: mRNA sequencing Klf1Nan/+ and wild type fetal liver (E14.5) identified a requirement for in vitro studies. ChIP-seq and 4sU-RNA-seq were performed on replicate immortalized cell lines transfected with tamoxifen inducible  protein fusions of KLF1-ER or Nan-KLF1-ER.

first: Melissa

middle: D

last: Ilsley

first: Ravi

last: Sachidanandam

first: James

last: Bieker

first: Andrew

last: Perkins


title: Cdx is crucial for the timing mechanism driving collinear Hox activation and defines a trunk segment in the Hox cluster topology

city: Utrecht

first: Jacqueline

last: Deschamps

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

summary: Cdx regulates gradual Hox activation in the early embryo

overall_design: ChIP-sequencing for several antibodies and 4C-seq on epiblast stem cells (EpiSCs).

first: R

last: Neijts

first: S

last: Amin

first: C

last: van Rooijen

first: J


title: PC1/3 deficiency impacts POMC processing in human embryonic stem cell-derived hypothalamic neurons

city: Tarrytown

first: Yurong

last: Xin

address: 777 Old Saw Mill River Road

institute: Regeneron Pharmaceuticals, Inc.

summary: We developed a technique for generating hypothalamic neurons from human pluripotent stem cells. Here, as proof-of-principle, we examine the use of these cells in modeling of a monogenic form of severe obesity: PCSK1 deficiency. We generated PCSK1 (PC1/3)-deficient human embryonic stem cell (hESC) lines using both shRNA and CRISPR-Cas9, and investigated pro-opiomelanocortin (POMC) processing using hESC-differentiated hypothalamic neurons.

overall_design: We tried to idenitify transcripitional profiles and specific transcription factors that involved in of different stages during hypothalamic neuron differentiation from single cell sequencing for hESC-derived Day27 hypothalamic neurons, Day 12 neuron progenitors and undifferentiated stem cells

first: Liheng

last: Wang


title: The Drosophila speciation factor HMR localizes to genomic insulator sites

city: Planegg-Martinsried

first: Axel

last: Imhof

address: Großhadernerstr. 9

institute: Ludwig-Maximilians-University of Munich

summary: Hybrid incompatibility between Drosophila melanogaster and D. simulans is caused by a lethal interaction of the proteins encoded by the Hmr and Lhr genes. In D. melanogaster the loss of HMR results in mitotic defects, an increase in transcription of transposable elements and a deregulation of heterochromatic genes. To investigate the molecular mechanisms that mediate HMRs function, we measured genome-wide localization of HMR in D. melanogaster by chromatin immunoprecipitation. Interestingly, we find HMR localizing to genomic insulator sites that can be classified into two groups. One group that belongs to the gypsy class of insulators and another one that separates HP1a binding regions from active promoters. The activity of these promoters is strongly affected in Hmr mutant flies. Our data provide a novel link between HMR and insulator proteins and suggest a key role for genome organization in the formation of species.

overall_design: Examination of HMR binding in Drosophila S2 cells. Experiments were verified with replicates, unrelated antibody (IgG control) and HMR RNAi knock-down. CP190 RNAi knock-down experiments in combination with HMR ChIP and H3 ChIP were further used to dissect HMR binding dependencies.

first: Thomas

middle: A

last: Gerland

first: Bo

last: Sun

first: Pawel

last: Smialowski

first: Andrea

last: Lukacs

first: Andreas

middle: W

last: Thomae


title: Benchmarking of RNA-sequencing analysis workflows using whole-transcriptome RT-qPCR expression data

city: Ghent

first: Celine

last: Everaert

address: De Pintelaan 185

country: Belgium

institute: University Ghent

summary: RNA-sequencing has become the gold standard for whole-transcriptome gene expression quantification. Multiple algorithms have been developed to derive gene counts from sequencing reads. While a number of benchmarking studies have been conducted, the question remains how individual methods perform at accurately quantifying gene expression levels from RNA-sequencing reads. We performed an independent benchmarking study using RNA-sequencing data from the well established MAQCA and MAQCB reference samples. RNA-sequencing reads were processed using five popular workflows (Tophat-HTSeq, Tophat-Cufflinks, STAR-HTSeq, Kallisto and Salmon) and resulting gene expression measurements were compared to expression data generated by wet-lab validated qPCR assays for all protein coding genes. All methods showed high gene expression rank correlations with qPCR data. When comparing gene expression fold changes between MAQCA and MAQCB samples, about 85% of the genes showed consistent results between RNA-sequencing and qPCR data. Of note, each method revealed a small but specific set of genes with inconsistent expression measurements. A significant proportion of these method-specific inconsistent genes were reproducibly identified in independent datasets. These genes were typically smaller, had fewer exons and were lower expressed compared to genes with consistent expression measurements. We propose that careful validation is warranted when evaluating RNA-seq based expression profiles for this specific set of genes.

overall_design: MAQCA and MAQCB polyA+-RNA-seq raw data in duplicate.

first: Pieter

last: Mestdagh


title: Transcriptome analysis of human lung epithelial cells

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

institute: Walter and Eliza Hall Institute of Medical Research

summary: Human lung epithelial subpopulations (alveolar type 2, basal and airway luminal cells) freshly dissociated from human lung were isolated by FACS. RNA-seq gene expression profiling was used to determine gene signature from each population.

overall_design: Cells were isolated from the small airway (SA) and large airway (LA) of 3 human lungs

first: Yunshun

last: Chen

first: Clare

middle: E

last: Weeden

first: Marie-Liesse

last: Asselin-Labat


title: Phosphatidylinositol 3-Kinase (PI3K) delta blockade increases genomic instability in B cells

city: Boston

first: Roberto

last: Chiarle

state: Massachusetts

address: 300 Longwood Avenue

department: Department of Pathology

institute: Children’s Hospital Boston and Harvard Medical School

summary:
Activation-induced cytidine deaminase (AID) is a B-cell specific enzyme that targets immunoglobulin (Ig) genes to initiate class switch recombination (CSR) and somatic hypermutation (SHM). Through off-target activity, however, AID has a much broader impact on genomic instability by initiating oncogenic chromosomal translocations and mutations involved in lymphoma development and progression. AID expression is tightly regulated in B cells and its overexpression leads to enhanced genomic instability and lymphoma formation. The phosphatidylinositol 3-kinase (PI3K) δ pathway plays a key role in AID regulation by suppressing its expression in B cells. Novel drugs for leukemia or lymphoma therapy such as idelalisib, duvelisib or ibrutinib inhibit PI3Kδ activity directly or indirectly through inhibition of the Bruton tyrosine kinase (BTK), thus possibly affecting AID expression and, consequently, genomic stability in B cells.
Here we show that treatment of primary mouse B cells with idelalisib or duvelisib, and to a lesser extent ibrutinib, enhanced the expression of AID and increased somatic hypermutation (SHM) and chromosomal translocation frequency to the Igh locus and to several AID off-target sites. These effects were both completely abrogated in AID deficient B cells. PI3Kδ inhibitors or ibrutinib increased the formation of AID-dependent tumors in pristane-treated mice. Consistently, PI3Kδ inhibitors enhanced AID expression and translocation frequency to IgH and AID off-target sites in human chronic lymphocytic leukemia (CLL) and mantle cell lymphoma (MCL) cell lines, and patients treated with idelalisib showed increased SHM in AID off-targets. In summary, we show that PI3Kδ or BTK inhibitors increase genomic instability in normal and neoplastic B cells by an AID-dependent mechanism. Since such inhibitors are administered for years to patients, their genotoxic potential should be carefully considered while planning therapeutic protocols.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: We applied a genome-wide translocation technique we previously developed (High-Throughput Genomic Translocation Sequencing approach, HTGTS) to identify translocation partners from DNA double strand breaks (DSBs) introduced into the c-myc locus (Chiarle et al, Cell 2011) in Mouse and Human B cell treated with PI3K inhibitors. We also re-sequenced selected mouse and human genomic regions from template DNA for somatic hypermutation (SHM) analysis in samples treated with PI3K delta inhibitors. We also performed GRO-Seq experiments in activated B cells treated with PI3K delta inhibitors to find correlations between transcription and translocation junction frequency.

first: Mara

last: Compagno

first: Qi


title: Next Generation Sequencing Facilitates Quantitative Analysis of Skeletonema marinoi Transcriptomes

city: Qingdao

first: Hualong

address: Songling road

country: China

institute: Ocean University of China

summary: Purpose:Using Illumina high-throughout sequencing technology, the transcriptome and expression profiles of S. marinoi were sequenced and analyzed. Comprehensive and systematic study of transcriptomic characteristics, analysis of characteristics of Digital Gene Expression Profiling during different growth phase and deep exploration of molecular mechanism for response to the temperature and low silicate stress environment will provide a comprehensive insight into gene expression profiles and provides an important gene resource for future genetic and molecular studies of S. marinoi and other Skeletonema family diatom.

overall_design: Three biological replicates for each treatment: exponential phase (2 replicates, control), declining phase, Stationary phase, low temperature, high temperature (1 replicate), low silicate

first: Tiezhu

last: Mi

first: Yu

last: Zhen

first: Baozhong

last: Fu

first: Xiaoli

last: Jing

first: Zhigang

last: Yu


title: RNA-seq of normal breast epithelial cells

city: Philadelphia

first: Takahiro

last: Sato

state: PA

address: 3307 North Broad Street

department: Fels Institute for Cancer Research and Molecular Biology

institute: Temple University

summary: RNA-seq was performed on primary normal breast epithelial cells that were grown briefly in culture

overall_design: Biological triplicates were performed for a total of 3 samples.

first: Matteo

last: Cesaroni

first: Shoghag

last: Panjarian

first: Anthony

last: Tran

first: Jozef

last: Madzo

first: Yasuyuki

last: Okamoto

first: Hanghang

last: Zhang

first: Xiaowei

first: Jaroslav

last: Jelinek

first: Jean-Pierre

last: Issa


title: Disruption of the ATXN1-CIC complex causes a spectrum of neurobehavioral phenotypes in mice and humans

city: Edmonton

first: Qiumin

last: Tan

address: 6-16 Medical Sciences Building

department: Cell Biology

institute: University of Alberta

summary: We isolated RNAs from Otp-lineage cells in the mouse brain using translating ribosome affinity purification (TRAP) approach. We compared two groups of mice: Otp-cre; ROSAfsTRAP (control) and Otp-cre; Cicf/f; ROSAfsTRAP (conditional knockout). Following RNA isolation, RNAseq was performed and gene expression profiles were compared between controls and conditional knockouts.

overall_design: Examination of gene expression in Otp-lineage neurons in two mouse groups.

first: Hsiang-Chih

last: Lu

first: Ying-Wooi

last: Wan

first: Zhandong

last: Liu

first: Huda

middle: Y

last: Zoghbi


title: Transcriptome analysis of mouse lung epithelial cells

first: Gordon

last: Smyth

summary: Mouse lung epithelial subpopulations (alveolar type 2, basal and airway luminal cells) freshly dissociated from mouse lung and trachea were isolated by FACS. RNA-seq gene expression profiling was used to determine gene signature from each population.

overall_design: Cells were isolated from the small airway (SA) and large airway (LA) of 6 mouse lungs

first: Yunshun

last: Chen

first: Clare

last: Weeden

first: Marie-Liesse

last: Asselin-Labat


title: Improved growth of Clostridium thermocellum AG553 via medium supplementation with formate and strain evolution

city: Oak Ridge

first: Dawn

middle: Marie

last: Klingeman

state: TN

address: 1 Bethel Valley Rd building 15056 Rm 366  MS 6038

department: Biosciences Division

institute: Oak Ridge National Lab

summary: Strain AG553 was successfully constructed to eliminate side product formation during fermentation increasing the ethanol yield. Though ethanol yields were higher, the growth rate of the organism was significantly impaired. In order to improve growth rate, the organism was evolved and formate was added to the growth media. Both strategies successfully improved growth rate, but the mechanisms for that improved growth rate were still not understood. In order to get a better understanding of the mechanisms for improved growth, a proteomics and transcriptomics study of three strains: wild type, the unevolved AG553, and a representative evolved strain AG601 was completed with and without the addition of formate in the growth media.

overall_design: There were three strains, with and without formate in quadruplicates. 24 samples in total were analyzed

first: Beth

last: Papanek

first: Adam

last: Guss

first: Steven

last: Brown

first: Punita

last: Manga


title: Multilayered control of alternative splicing regulatory networks by transcription factors

first: Ulrich

last: Braunschweig

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

overall_design: Refer to individual Series


title: ChIP-seq of histone methylation marks in YB5 cells

first: Takahiro

last: Sato

summary: ChIP-seq of H3K4me2, H3K9me2, and H3K27me3 was performed in YB5 cells to determine the impact of baseline histone methylation patterns on gene reactivation by epigenetic therapy

overall_design: Biological duplicates were performed for a total of 8 samples. For peak calling, duplicates were merged and MACS2 (H3K4me2) or SICER (H3K9me2 or H3K27me3) was used to determine significant peaks compared to Input

first: Matteo

last: Cesaroni

first: Shoghag

last: Panjarian

first: Anthony

last: Tran

first: Jozef

last: Madzo

first: Yasuyuki

last: Okamoto

first: Hanghang

last: Zhang

first: Xiaowei

first: Jaroslav

last: Jelinek


title: RNA-seq of YB5 and MCF7 treated with different doses of decitabine

summary: RNA-seq was performed after YB5 cells were treated with 1uM decitabine, and MCF7 cells were treated with 100nM decitabine

overall_design: Biological triplicates were performed for a total of 6 samples. Fold change of each gene was calculated by comparing change in expression after inhibitor treatment to expression in the control samples from GSE73966 for YB5, and GSE74036 for MCF7. These control samples have been re-accessioned here for convenient access to the entire study.

last: Chen

first: Jean-Pierre

last: Issa


title: Gene expression analysis of Lgr5/Tspan8 expressing cells in the adult mammary gland

city: Roseworthy

first: Ruijie

last: Liu

state: South Australia

address: Mudla Wirra Rd

institute: the university of Adelaide

summary:
Purpose: The aim of this study is to identify genes that are differentially expressed in the different basal cell populations defined by Lgr5 and Tspan8 (T8) expression from adult mouse mammary glands.

Methods: Total RNA was extracted from sorted basal populations defined by Lgr5 and Tspan8 expression from the mammary glands of 10-week-old Lgr5-GFP-IRES-creERT2 female mice. Total RNA (50 ng) for each of the two biological replicates was used to generate libraries for whole-transcriptome analysis following Illumina's TruSeq RNA v2 sample preparation protocol. Libraries were sequenced on an Illumina HiSeq 2000 at the Australian Genome Research Facility (AGRF), Melbourne. At least 20 million 100 bp single-end reads were obtained for each sample. Reads were aligned to the mouse genome mm10 using Rsubread version 1.8.0. The number of reads overlapping each Entrez gene was counted using RefSeq gene annotation and featureCounts. Filtering and normalization used the edgeR package. Genes were filtered as unexpressed if their count per million (CPM) was less than 0.5 in fewer than 2 samples. Compositional differences between libraries were normalized using the trimmed mean of M-values (TMM) method. Differential expression was analyzed using the limma package. Counts were transformed to log2-CPM values with associated precision weights using voom. Differential expression was assessed using moderated t-statistics. Genes were considered to be differentially expressed if they achieved a false discovery rate of 5% and a fold-change in excess of 2.

overall_design: Total RNA was extracted and purified from each sample (Lgr5-T8hi, Lgr5+T8-, Lgr5-T8-, Lgr5+T8hi ) and their transcriptomes analysed by RNA-Seq.

first: Nai

last: Fu

first: Cynthia

first: Geoffrey

last: Lindeman

first: Jane

last: Visvader


title: Eomes related gene regulation in Definitive Endoderm (ChIP-seq)

status: Public on Jan 30 2017

city: Headington

first: Damien

last: Downes

state: Oxfordshire

address: John Radcliffe Hospital

department: MRC Weatherall Institute of Medicine

country: United Kingdom

institute: The University of Oxford

summary: Precisely co-ordinated activation of lineage specific transcription factors direct cell fate decisions during mouse early development. The T-box transcription factor Eomes is dynamically expressed during mouse gastrulation and is a key regulator of the anterior visceral endoderm (AVE), cardiac mesoderm and definitive endoderm (DE) lineages. The cis-acting regulatory elements that direct spatiotemporally restricted Eomes expression domains have yet to be elucidated. To understand transcriptional regulation of Eomes in Definitive Endoderm open chromatin data was generated by ATAC-seq and histone modifications identified by ChIP-seq. Interactions at the Eomes locus and the loci of two related transcription factors Foxa2 and Lhx1, was also determined by NG Capture-C.

overall_design: ChIP-seq of Histone 3 Lysine 4 Trimethylation (H3K4me3) in Definitive Endoderm (3 replicates)

first: Matthew

last: Gosden

first: Claire

last: Simon


title: Eomes related gene regulation in Definitive Endoderm (NG Capture-C)

overall_design: NG Capture-C combines 3C library preparation with oligonucleotide capture for the desired viewpoint restriction fragments. The method was applied to biological triplicates of embryonic stem cells, definitive endoderm cells, and erythroid cells capturing either promoter or enhancer elements.


title: Effect of Estrogen Receptor Beta Ligand on Gene Expression in Liver

city: Memphis

first: Daniel

middle: Lee

last: Johnson

state: Tennessee

address: 71 S Manassas

department: Molecular Informatics Core

institute: UTHSC

summary: C57BL/6 male mice were fed with normal diet or high fat diet and treated with vehicle or 30 mg/kg/day s.c. of ER-beta ligand, B-LGND2. Genes differentially expressed by H.F.D. and B-LGND2 are represented in this RNA-Sequencing data

overall_design: n=3/group. Liver. Mice were fed and treated as indicated above for 9 weeks. Liver was collected, RNA isolated, and expression of genes was measured by RNA-Sequencing.

first: Ramesh

last: Narayanan


title: Changes in chromatin accessibility assocaiated with CD8 T cell responses to viral infections

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

summary: The goal of this study was to identify the molecular programming using ATAC-seq of CD8 T cells responding to different viral infections.  Mice were infected with either LCMV Armstrong to model an acute infection or LCMV Clone-13 to model a chronic infection.  At various time points following infection, virus-specific CD8 T cells were purified and ATAC-seq performed.  These data identify the changes in chromatin accessibility associated with acute infections and the establishment of functional memory versus those accessibility changes associated with chronic infection.

overall_design: ATAC-seq time course on CD8 T cells following either LCMV Armstrong and Clone13 infection.

first: C

first: J

middle: M

last: Boss


title: Eomes related gene regulation in Definitive Endoderm


title: RNA-Seq of Xenopus tail regeneration

city: Stanford

first: Jessica

middle: Kay

last: Chang

state: CA

address: 300 Pasteur Drive, Alway Building M311

department: Genetics

institute: Stanford University

summary: In contrast to humans, many amphibians are able to rapidly and completely regenerate complex tissues, including complete appendages. Following tail amputation, Xenopus tropicalis tadpoles quickly regenerate muscle, spinal cord, cartilage, vasculature and skin, all properly patterned in three dimensions. To better understand the molecular basis of this regenerative competence, we performed a transcriptional analysis of regeneration using RNA-Seq. We profiled the transcriptome at 6 timepoints during tail regeneration, and used clustering analysis to identify biological processes that are prioritized during different transitions in the regeneration process. Our work expands significantly on previous expression analyses of tail regeneration. We are able to refine the windows during which many key biological signaling processes act, including embryonic patterning signals, immune responses, bioelectrical signaling and apoptosis. By including multiple timepoints within the first 24 hours post-amputation, we have also identified new processes that are highly prioritized early in regeneration, including axonogenesis, chemotaxis, and RNA metabolism. Our work provides a deep database for researchers interested in appendage regeneration, and highlights new avenues for further study.

overall_design:
Whole tail (WT) samples were obtained from an an initial amputation.  Immediately thereafter, a second amputation was performed on the cut tadpole to obtain 0 hour time point samples.  The 0 hpa time point samples the tissue directly adjacent to the initial cut site.  Regenerating tail samples collected up to 72 hpa.
Expression profiling of six time points in tadpole tail regeneration were sequenced in duplicate via Illumina HiSeq.

first: Andrea

last: Wills

first: Julie

last: Baker


title: DNA methylation heterogeneity in Ewing sarcoma defines an epigenetic disease spectrum underlying a genetically homogeneous developmental cancer.

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

type: Methylation profiling by high throughput sequencing

summary: We performed reduced representation bisulfite seqeuncing (RRBS) and ChIP-seq of histone modification marks on three Ewing sarcoma tumor samples, and we quantified epigenetic heterogeneity on three levels. First, we identified a Ewing sarcoma specific hypomethylation signature at EWS-FLI1 regulated enhancers, showing that epigenetic enhancer reprogramming is a defining feature of Ewing sarcoma. Second, inter-individual DNA methylation differences in Ewing sarcoma samples identified a continuous disease spectrum with two dimensions: the strength of the EWS-FLI1 regulatory signature and the balance of mesenchymal versus stem cell regulatory signatures. Third, we observed substantial epigenetic heterogeneity within individual tumors. In summary, our study provides a comprehensive assessment of epigenetic heterogeneity in Ewing sarcoma, highlighting its importance as a source of variability for genetically homogeneous tumors.

overall_design: Reduced representation bisulfite seqeuncing (RRBS) and ChIP-seq of histone modification marks on three Ewing sarcoma tumor samples with an untreated (input) sample serving as the sample-specific control for peak calling.


title: Transcriptome of EMT induced MCF10A cells by TGFb treatment or SNAIL S6A expression.

city: Charlestown

first: Robert

last: Morris

address: 149 13th Street

institute: Mass. General Hospital Cancer Center

summary: EMT, Epithelial to mesenchymal transition is a developmental biology process associated with migration, known to be involved in cancer metastasis. To study this process, we used the breast epithelial cell line MCF10A that enter in EMT after treatment with the cytokine TGFB or by expression of EMT transcriptor factor SNAIL.

overall_design: mRNA profiles of MCF10A cells treated for 1 or 6 days with TGFb (done in duplicate), and mRNA profiles of Snail inducible line, MCF10A-SNAIl, induced for 1 or 6 days.

first: Comaills

last: Valentine

first: Shyamala

last: Maheswaran

first: David

last: Ting

first: Srinjoy

last: Sil


title: Transcription facilitated genome-wide recruitment of topoisomerase I and DNA gyrase

city: Bangalore

first: Valakunja

last: Nagaraja

state: Karnataka

address: C V Raman Avenue

department: Department of Microbiology and Cell Biology

country: India

institute: Indian Institute of Science (IISc)

summary: Genome-wide distribution of topoisomerase I and DNA gyrase is directed by transcription induced supercoiling

sample_organism:
Mycobacterium tuberculosis H37Rv
Mycobacterium tuberculosis H37Ra

overall_design: Mtb H37Rv cells were ChIP-ed with either anti-TopoI or anti-gyrA antibodies. Mtb H37Ra cells were ChIP-ed with anti-TopoI or anti-gyrA antibodies, or mock ChIP-ed (no antibody).

first: W

last: Ahmed

last: Sala

first: S

last: Hegde

first: R

last: Jha

middle: T

last: Cole

first: V


title: ZBTB33 (Kaiso) Differentially Regulates Cell Cycle Through cyclin D1 and cyclin E1 in a Cell Specific Manner [RNA-seq]

city: Salt Lake City

first: Bethany

last: Buck-Koehntop

state: Utah

department: Chemistry

institute: University of Utah

summary: The emerging correlation between aberrant DNA methylation patterns leading to transcriptional responses that promote and progress many cancers has prompted an interest in discerning the associated regulatory mechanisms. ZBTB33 (also known as Kaiso) is a specialized transcription factor that selectively recognizes mCpG-containing sites as well as a sequence-specific DNA target (termed the KBS) utilizing three Cys2His2 zinc fingers. Increasing reports link ZBTB33 overexpression and transcriptional activities with metastatic potential and poor prognosis, though the specific cellular consequences appear to be dependent on disease phenotype. There is currently little mechanistic insight into how various cellular phenotypes are then able to harness the transcriptional capabilities of ZBTB33 to differentially promote and progress the disease state. Here we have mechanistically interrogated the cell cycle responses mediated by the transcriptional activities of ZBTB33 in two different cell lines. Utilizing a series of ZBTB33 depletion and overexpression studies, we have determined that in HeLa cells ZBTB33 directly occupies the promoter regions of cyclin D1 and cyclin E1 in a KBS and methyl-specific manner, respectively, inducing increased proliferation by promoting RB1 hyper-phosphorylation, allowing for E2F transcriptional activity that coordinates an accelerated G1- to S-phase transition. Conversely, in HEK293 cells ZBTB33 indirectly regulates Cyclin E abundance resulting in reduced RB1 phosphorylation, decreased E2F activity and a decelerated transition through G1-phase. Thus, we have identified a novel mechanism by which ZBTB33 directly mediates the highly coordinated cyclin D1/cyclin E1/RB1/E2F signaling pathway controlling the passage through the G1-phase restriction point and accelerating cellular proliferation in a cancer cell line.

overall_design: Determination of cellular and transcriptional consequences for ZBTB33 depletion in HeLa cells.

first: Tommy

last: Terooatea


title: Next Generation Sequencing Facilitates Quantitative Analysis of FOXP3-YFP-Cre and FOXP3-YFP-Cre/USP21-floxp/floxp Treg Cells Transcriptomes

status: Public on Jan 29 2017

city: Shanghai

first: Bin

last: Li

address: 320 Yueyang Road, Xuhui District,

institute: Institut Pasteur of Shanghai, CAS

summary: Regulatory T (Treg) cells harbor immune suppressive capacity and are crucial for the maintenance of peripheral tolerance. Treg cells are considered to be heterogenic, where compromised FOXP3 expression results in the generation of exTreg cells. Here we report that the E3 deubiquitinase USP21 prevents the depletion of FOXP3 protein and restricts tissue-resident exTreg cell generation. Mice lacking USP21 in Treg cells display immune disorders characterized by spontaneous T cell activation and excessive T helper type 1 (Th1) skewing. USP21 stabilizes FOXP3 protein by mediating its deubiquitination and therefore helps to maintain the expression of Treg signature genes. Moreover, at inflamed loci, tissue-resident USP21-deficient Treg cells display a Th1-like effector phenotype. Therefore, we demonstrate how USP21 controls the identity of tissue-resident Treg cells by preventing FOXP3 loss.

overall_design: We purified CD4+CD25hiYFP+ Treg cells from spleens and LNs of Foxp3-YFP-Cre mice or FOXP3-YFP-Cre/USP21-floxp/floxp mice and performed RNA-seq experiments subsequently. mRNA profiles were further analyzed and compared according to standard protocols.

first: Yangyang


title: ZBTB33 (Kaiso) Differentially Regulates Cell Cycle Through cyclin D1 and cyclin E1 in a Cell Specific Manner


title: Transcriptomic response induced by iron limitation in the cyanobacteria Synechococcus sp. PCC 7002 (BMB04)

city: Geneva

first: Sonia

last: Blanco-Ameijeiras

state: GE

address: 66 Boulevard Carl Vogt

department: F.-A. Forel Institute

country: Switzerland

institute: University of Geneva

summary: In this study, we characterized the homeostasis of the marine cyanobacteria Synechococcus sp. PCC7002 (BMB04) growing in chemically characterized synthetic seawater with three different levels of iron limitation representative of the modern ocean. Using transcriptomic approach, we identified the sequence of physiological responses to increasing Fe limitation. Our results showed an increase in the number of dysregulated genes and in the complexity of the response to increasing Fe limitation. Genes involved in photosynthesis were strongly down-regulated under MiFeL, while membrane transporters were up-regulated. Genes involved in regulation of energy metabolism responded under strong Fe limitation, while fine metabolic regulation of co-factors expression and activation of specific cellular mechanisms to minimize oxidative stress were only observed under severe Fe limitation. Additionally, our results demonstrate the limitations in the construct of the bioreporter BMB04 that hamper its application in areas of the ocean strongly Fe limited.

overall_design: Twelve samples were analyzed. Three levels of Fe limitation were tested (0.41, 0.04 and 0.003 nM inorganic Fe), each biological triplicates. The control was Fe repleted (10.9 nM inorganic Fe), in biological replicates as well.

first: Claudia

last: Cosio

first: Christel

middle: S

last: Hassler


title: Loss of Snf5 and the formation of an aberrant SWI/SNF complex

city: Smithville

first: Solomon

last: Hailu

state: Tx

address: Park road 1c

department: Epigenetics and Molecular Carcinogenesis

institute: MD Anderson Cancer Center

summary: Aberrant forms of the SWI/SNF chromatin remodeling complex are associated with human disease.  Loss of the Snf5 subunit of SWI/SNF is a driver mutation in pediatric rhabdoid cancers and forms aberrant sub-complexes that are not well characterized. We determined the effects of loss of Snf5 on the composition, nucleosome binding, recruitment and remodeling activities of yeast SWI/SNF.  The Snf5 subunit interacts with the ATPase domain of Snf2 and forms a submodule consisting of Snf5, Swp82 and Taf14 as shown by mapping SWI/SNF subunit interactions by crosslinking-mass spectrometry and subunit deletion followed by immunoaffinity chromatography. Snf5 promoted binding of the Snf2 ATPase domain to nucleosomal DNA, enhanced its catalytic activity and facilitated nucleosome remodeling. Snf5 was required for acidic transcription factors to recruit SWI/SNF to chromatin.  RNA-seq analysis suggested that both the recruitment and catalytic functions mediated by Snf5 are required for SWI/SNF regulation of gene expression.

overall_design: Determining the effects of loss of Snf5 on the composition, nucleosome binding, recruitment, remodeling activities and gene expression profile of yeast SWI/SNF

middle: G

first: Payel

last: Sen

first: Arjan

last: Hada

first: Mekonnen

last: Lemma Dechassa

first: Jim

last: Persinger

first: Jie

last: Luo

first: Jeff

last: Ranish

first: Blaine

last: Bartholomew


title: Gene expression signature of Runx1Δ/Δ lin- sca- kit+ CD105- CD16/32+ CD150+ (XMP) progenitors

city: Hamburg

first: Kira

last: Behrens

address: Martinistrasse 52

institute: Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology

summary: FLT3-ITD mutations are found in 30% of acute myeloid leukemia (AML) and portend a poor prognosis. Patient AML samples with FLT3-ITD express high levels of RUNX1, a transcription factor with known tumor-suppressor function. Using an inducible system, we demonstrate that RUNX1 cooperates with FLT3-ITD to trigger AML and that RUNX1 expression as well as its Tyr-phosphorylation is necessary for both initiation and maintenance of leukemogenesis. Inactivating RUNX1 in tumors released the differentiation block and downregulated genes controlling ribosome biogenesis. We identified Hhex as a direct target of RUNX1 and FLT3-ITD stimulation and confirmed high HHEX expression levels in FLT3-ITD AMLs. Importantly, HHEX could replace RUNX1 in AML induction with FLT3-ITD. These results establish and elucidate the unanticipated oncogenic function of RUNX1 in AML.

overall_design: Blasts were isolated from the bone marrow of leukemic mice, FACS-sorted, totalRNA extracted and sequenced

first: Malik

last: Alawi

first: Carol

last: Stocking


title: Sox9 transcriptionally regulates Wnt signaling in intestinal epithelium stem cells under hypomethylated crypts in diabetic state (ChIP-Seq)

city: Guang-Zhou

first: Can-Ze

last: Huang

address: 107 Yan-Jiang Xi-Road

institute: Sun Yat-Sen Memorial Hospital

summary: Mammalian  intestinal epithelium stem cells (IESCs) and their daughter cells require the participation of DNA methylation and the transcription factor Sox9 for proliferation and differentiation. Combining methylated DNA immunoprecipitation with microarray hybridization, we demonstrate that hypomethylation in promoter participates in the aberrant formation of crypts in diabetic db/db mice through ectopic Wnt signaling. More importantly, increased expression of Sox9 is accompanied by the loss of methylation in its promoter in IESCs. Using ChIP-seq analysis for Sox9 in IESCs, we demonstrate that Sox9 primarily targets the enhancers of Wnt signaling pathway-related genes. Sox9 is not only predominately acting as a transcriptional activator at proximal enhancer but also as a potential transcriptional inhibitor at distant enhancer. Lack of Sox9 transcriptional activation in specific repressors of Wnt signaling pathway results in loss of intrinsic inhibitory action and ultimately produces over-activation of this pathway in diabetes mellitus.

overall_design: A total of three samples are included in the experiment for ChIP-seq analysis, in which one is experimental group from pooled cohorts of four diabetic mice, one is control group from pooled cohorts of five controls and one is the input sample. The db/db diabetic mice were maintained under a 12 h light/12 h dark cycle in a specific pathogen-free animal facility. The experiments were conducted using 16-week-old male homozygous mice, which were maintained for 8 weeks with hyperglycemia (blood glucose level ≥ 16.7 mmol/l) prior to euthanasia. Identical genetic background BKS littermates were used as the control group.

first: Ji-Hao

last: Xu

first: Wa

last: Zhong

first: Zhong-Sheng

last: Xia

first: Si-Yi

last: Wang

first: Di

last: Cheng

first: Jie-Yao

first: Ting-Feng

last: Wu

first: Qi-Kui

last: Chen

first: Tao

last: Yu


title: The evolutionary capacitor HSP90 buffers the regulatory effects of mammalian endogenous retroviruses.

city: Freiburg

first: Barbara

last: Hummel

address: Stübeweg 51

institute: Max Planck Institute of Immunobiology and Epigenetics

summary: The molecular chaperone heat shock protein 90 (HSP90) is thought to buffer genetic variation uncoupling phenotypic outcome from individual genotypes. HSP90 thus acts as an evolutionary capacitor by facilitating an accumulation of natural genetic variation. The molecular mechanism underlying the buffering ability is unclear, and HSP90-contingent genetic variation maps both to coding and non-coding parts of the genome. Our genome-wide data indicate that a compromised chaperoning activity of HSP90 causes derepression of endogenous retroviruses (ERVs) in mouse somatic cells. This results in an upregulation of host genes located in the neighborhood of pre-existing ERVs insertion sites. We provide genetic and biochemical evidence that HSP90 cooperates with KAP1/ SETDB1 histone methyltranferase pathway to repress ERVs. Individual mouse strains have unique integration sites of ERVs in their genomes. Consequently distinct genes are responsive to HSP90 inhibitor in different mouse strains depending on the position of the genes vis-à-vis strain-specific ERV insertion sites. Since ERVs have been exapted to drive novel transcriptional networks during mammalian evolution, HSP90 may have acted as a capacitor by buffering variation caused by ERV in non-coding regions of the genome. Our studies provide the first molecular framework by which HSP90 can mitigate genetic variation in gene-regulatory regions affecting gene expression and phenotypes.

overall_design: We have performed RNA-seq in mouse embryonic stem cells, neuronal progenitor cells and bone-marrow-derived macrophages treated with NVP-AUY922 in triplicates.

first: Erik

last: Hansen

first: Aneliya

last: Yoveva

first: Fernando

last: Aprile-Garcia

first: Rebecca

last: Hussong

first: Ritwick

last: Sawarkar


title: Operon mRNAs are organized into ORF-centric structures that predict translation efficiency

city: San Francisco

first: Yan

last: Zhang

address: 600 16th Street

institute: UC San Francisco

summary: Bacterial mRNAs are organized into operons consisting of discrete open reading frames (ORFs) in a single polycistronic mRNA. Individual ORFs on the mRNA are differentially translated, with rates varying as much as 100-fold. The signals controlling differential translation are poorly understood. Our genome-wide mRNA secondary structure analysis indicated that operonic mRNAs are comprised of ORF-wide units of secondary structure that vary across ORF boundaries such that adjacent ORFs on the same mRNA molecule are structurally distinct. ORF translation rate is strongly correlated with its mRNA structure in vivo, and correlation persists, albeit in a reduced form, with its structure when translation is inhibited and with that of in vitro refolded mRNA. These data suggests that intrinsic ORF mRNA structure encodes a rough blueprint for translation efficiency. This structure is then amplified by translation, in a self-reinforcing loop, to provide the structure that ultimately specifies the translation of each ORF.

overall_design: mRNA-seq and ribosome profiling of E. coli MG1655 (wild-type) cells at 37°C and DMS-seq of in vivo modified mRNA from wild-type cells, kasugamycin-treated or untreated ΔgcvB cells, as well as in vitro modified mRNA refolded at 37°C or denatured at 95°C. Reads from replicates of the same experiment were pooled in wiggle files.

first: David

middle: H

last: Burkhardt

first: Silvi

last: Rouskin

first: Gene-Wei

last: Li

first: Jonathan

last: Weissman

first: Carol

last: Gross


title: LSD1 promotes oncogenesis via H3K9 demethylation-mediated cell cycle gene expression and cellular senescence inhibition

city: San Antonio

first: Zhenqing

last: Ye

state: TX

address: 8403 Floyd Curl Dr

department: 6Department of Population Health Sciences

institute: UT Health San Antonio

summary: Histone H3 lysine-9 methylation (H3K9me) is essential for retinoblastoma protein (RB)-mediated heterochromatin formation, epigenetic silencing of S-phase genes and permanent cell cycle arrest or cellular senescence. Besides as an H3K4me demethylase, lysine-specific demethylase 1 (LSD1) has also been shown to promote H3K9 demethylation. However, it is unclear whether LSD1 plays any roles in regulating cell cycle entry and senescence. Here we demonstrate that genetic depletion or pharmacological inhibition of LSD1 triggers G1 arrest and cellular senescence. Genome-wide chromatin immunoprecipitation-sequencing (ChIP-seq) analysis reveal that the binding sites of LSD1 significantly overlaps with those bound by the S-phase gene transcription factor E2F1. Gene ontology (GO) analysis demonstrates that a large portion of E2F1 and LSD1 co-targeted genes are involved in cell cycle and proliferation. Further analyses show that depletion of LSD1 not only inhibits expression of the LSD1-E2F1 co-target genes, but also decreases the level of H3K9me2, but not H3K4me2 in those loci. Furthermore, the enzymatic activity of LSD1 is essential for H3K9me2 demethylation at cell cycle gene loci. Notably, co-treatment of chemotherapeutic agent camptothecin (CPT) enhanced LSD1 inhibitor-induced senescence and growth inhibition of cancer cells in vitro and in mice. Our data reveal LSD1 as a molecular rheostat regulating selective H3K9 demethylation at cell cycle gene loci, thereby representing a key event in oncogenesis and a viable target for cancer therapy.

overall_design: Examination of 2 LSD1 and E2F1 in cell lines

first: Yu

last: Zhao

first: Wang

last: Liguo

first: Huang

last: Haojie

first: Yundong

last: He


title: Transcriptome profiling of adult cardiac tissue of control versus overfed female sheep prenatally treated with bisphenol A

city: Ann Arbor

first: Richard

middle: C

last: McEachin

state: United States

address: 2800 Plymouth Road

department: DCM&B

institute: University of Michigan

summary: Developmental programming is the concept that environmental factors during fetal growth can alter development, metabolism and physiology of an organism, thus diseases can be programmed by intrauterine influences. The fetal origin of health and disease hypothesis has received strong support from experimental studies in animals including livestock species.  Using a sheep model, it has been shown that developmental changes of ewe offspring may be susceptible to maternal pregnancy bisphenol A (BPA) treatment. For example, prenatally BPA treated female offspring tended to have reduced birth weight. In this study we sought to identify gene expression differences in ewe offspring as a result of maternal pregnancy BPA treatment on a control or high-caloried diet. Samples of heart tissues were collected during the second breeding season, allowing us to examine gene expression changes in ewes prenatally treated with BPA and maturing under the different diets.

overall_design: Pregnant ewes were randomized to two groups and then treated with bisphenol A+vehicle or vehicle alone. Their female offspring were assigned randomly to either a control-fed or over-fed group. This division of each of the treatment groups by feeding assignment created four groups: control, prenatal BPA-treated (BPA), overfed control (obese) and overfed prenatal BPA-treated (ObBPA). Four biological replicates were sequenced for each of the four groups using mRNA-seq.

first: Lada

last: Koneva


title: Expression data from control and WHSC1 siRNA treated PC3 cells

first: Ni

state: Shanghai

address: 320 Yueyang Road, Shanghai, 200025 P.R. China

institute: Institute of Health Sciences, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences

summary: We conduct transcriptome comparison of control and WHSC1 depleted PC3 cells to gain genomic insights on the biological processes that WHSC1 is involved in prostate cancer cells. More than 2000 known genes were found changed in the WHSC1 depleted cells. Ingenuity Pathway Analysis (IPA) and Gene Set Enrichment Analysis (GSEA) show that the most prominent altered pathways in the WHSC1 depleted cells are related to regulation of actin-based motility, mTOR signaling pathway.

overall_design: Genome-wide expression profiling of PC-3 cells transiently transduced with control siRNA in comparison to two independent siRNAs against WHSC1 and total RNA was isolated 72 hours later. Each is tested in duplicate.

first: Jun

last: Qin


title: The gray phenotype in the human fungal pathogen Candida tropicalis

city: Beijing

first: guanghua

last: huang

address: NO.1 West Beichen Road, Chaoyang District

institute: Institute of Microbiology

summary: Phenotypic plasticity, the ability to switch between different morphological types, plays critical roles in environmental adaptation, leading to infections, and allowing for sexual reproduction in pathogenic Candida species. Candida tropicalis, which is both an emerging human fungal pathogen and an environmental fungus, can switch between two heritable cell types termed white and opaque. In this study, we report the discovery of a novel phenotype in C. tropicalis, named the gray phenotype. Similar to Candida albicans and Candida dubliniensis, white, gray, and opaque cell types of C. tropicalis also form a tristable switching system, where gray cells are relatively small and elongated. In C. tropicalis, gray cells exhibit intermediate levels of mating competency and virulence in a mouse systemic infection model compared to the white and opaque cell types, express a set of cell type-enriched genes, and exhibit both common and species-specific biological features. The key regulators of white-opaque transitions, Wor1 and Efg1, are not required for the gray phenotype. A comparative study of the gray phenotypes in C. tropicalis, C. albicans, and C. dubliniensis provides clues to explain the species differences in terms of virulence, ecological niches, and prevalence among these three species.

overall_design: total RNA profiles of 2 days old white, gray and opaque cell types

first: Guanghua

last: Huang

first: Yulong


title: Gene expression profiles in 786-O cells in response to glucose starvation

city: Houston

first: Jiexin

address: 1515 Holcombe Blvd

department: Bioinformatics & Computational Biology

institute: UT MD Anderson Cancer Center

summary: To understand gene expression profiling in glucose starvation, we treated 786-O cells with and without glucose, and then subjected to next generation sequencing.

overall_design: RNA profiling of 786-O cells in two conditions

first: Boyi

last: Gan


title: HOXB13 ChIP seq in G401 cells

city: Los Angeles

first: Paul-Joseph

middle: P

last: Aspuria

state: California

address: 8400 Beverly Blvd.

department: Women's Cancer Program

institute: Cedars-Sinai Medical Center

summary: We report the ChIP-seq analysis of HOXB13, H3K27Ac, H3K27me3, H3K4me3, and RNA POL II in G401 rhabdoid tumor of the kidney cells.

overall_design: Examination of HOXB13 binding in G401 cells

first: Paul

last: Labhart

first: Sandra

last: Orsulic


title: Next-Generation Sequencing identified piRNA profiles in healthy and Alzheimer’s-affected human brain

status: Public on Jan 28 2017

city: Rourkela

first: Dr. Bibekanand

last: Mallick

state: Odisha

address: NIT Rourkela

department: Department of Life Science

institute: National Institute of Technology

type: Non-coding RNA profiling by high throughput sequencing

summary: To investigate the presence of piRNAs and their potential functions in human brain and neurodegenerations, we performed the genomic profiling in Healthy Brain (HB) sample as well as Alzheimer-affected brain (AD) sample by adopting Next-Gen small RNA sequencing technology. Using deep sequencing of small RNAs, we identified an extensive catalogue of 564 and 451 mature piRNAs in HB and AD respectively. The piRNAs from each sample exhibited varied length distribution between 26-32 nts and are originated from different genomic locations. We found 149 piRNAs to be differentially expressed in Alzheimer’s disease which comprises of 146 up-regulated and 3 down-regulated piRNAs. Ours is the first study that reported the presence of piRNAs in healthy as well as Alzheimer’s disease-affected human brain. The extensive catalogue of human piRNAs detected in this study provides a useful resource for decrypting the involvement of piRNAs in neurological functions as well as neurodegenerations.

overall_design: Total RNA isolated from healthy human and Alzheimer’s disease brain using modified guanidine thiocyanate technique was used for library preparation as prescribed by Illumina Truseq small RNA library protocol. The small RNA sequencing was performed on Illumina NextSeq 500.

first: Jyoti

last: Roy

first: Bibekanand


title: Eomes related gene regulation in Definitive Endoderm (ATAC-seq)

city: Headington

first: Damien

last: Downes

address: John Radcliffe Hospital

institute: The University of Oxford

summary: Precisely co-ordinated activation of lineage specific transcription factors direct cell fate decisions during mouse early development. The T-box transcription factor Eomes is dynamically expressed during mouse gastrulation and is a key regulator of the anterior visceral endoderm (AVE), cardiac mesoderm and definitive endoderm (DE) lineages. The cis-acting regulatory elements that direct spatiotemporally restricted Eomes expression domains have yet to be elucidated. To understand transcriptional regulation of Eomes in Definitive Endoderm open chromatin data was generated by ATAC-seq and histone modifications identified by ChIP-seq. Interactions at the Eomes locus and the loci of two related transcription factors Foxa2 and Lhx1, was also determined by NG Capture-C.

overall_design: ATAC-seq of Definitive Endoderm (3 replicates), Embryonic Stem Cells (3 replicates)

middle: J

first: Matthew

last: Gosden

first: Claire

last: Simon


title: Transcriptome-wide response to synthetic chromatin protein PcTF

city: Tempe

first: Karmella

last: Haynes

state: Arizona

address: 501 E Tyler Mall, Box 9709

department: SBHSE

institute: Arizona State University

summary: The goal of this study was to identify genes that become upregulated in response to a synthetic transcription factor, PcTF. PcTF contains a conserved H3K27me3-binding chromodomain expressed in-frame with an mCherry fluorescent tag and a VP64 activation domain. Therefore, we expected genes with H3K27me3-associated promoters to become upregulated upon PcTF expression. We observed that hundreds of genes became up or downregulated.

overall_design: Total RNA was extracted from PcTF-transfected U-2 OS, K562, or SK-N-SH cells, or from a stable U-2 OS cell line that carried a dox-inducible transgene that expressed either full-length PcTF or a truncated "delta-TF" peptide that lacked the histone-binding domain.


title: Macrophage transcriptional profile identifies lipid catabolic pathways that can be therapeutically targeted after spinal cord injury

city: Miami

first: Jae

middle: K.

last: Lee

state: FL

address: 1095 NW 14th Terrace

institute: University of Miami Miller School of Medicine

summary: We used the RiboTag method to obtain macrophage-specific mRNA directly from injured spinal cord and performed RNA sequencing to investigate the translational profiles. Our data show that macrophages at 3 days after SCI are enriched in genes related to cell migration and cytokine signaling. However, at 7 days, lipid catabolism represents the main biological process, and we identify canonical nuclear receptor pathways as potential mediators of lipid catabolism in macrophages.

overall_design: RNA-seq of macrophages from 3 and 7 days post contusive spinal cord injury.

first: Yunjiao

last: Zhu

first: Kirill

last: Lyapichev

first: Do Hun

first: Dario

last: Motti

first: Nicole

last: Ferraro

first: Y

last: Zhang

first: Stephanie

middle: L

last: Yahn

first: Cynthia

last: Soderblom

first: Ji

last: Zha

first: John

middle: R

last: Bethea

first: Kara

last: Spiller

first: Vance

last: Lemmon


title: Using RNA-seq to examine the oncogenic function of RUNX1 in AML

first: Kira

last: Behrens

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

overall_design: Refer to individual Series


title: Analysis of Thermosynechococcus elongatus BP1 response to co-cultivation with Meiothermus ruber strain A

status: Public on Jan 27 2017

city: Richland

first: Ryan

middle: Scott

last: McClure

state: Washington

address: 902 Battelle Boulevard

institute: Pacific Northwest National Laboratory

summary: The transcriptional response of the cyanobacteria T. elongatus to co-cultiavation with a heterotrophic partner M. ruber was examined under three varying light levels and three varying oxygen levels.

overall_design: Three light levels were examined: low (197 µmol photons m-2 sec-1), mid (1190 µmol photons m-2 sec-1), and high (1995 µmol photons m-2 sec-1) all with oxygen at at a partial pressure of 0 .  Three oxygen levels were also examined: low (partial pressure of oxygen=0), mid (partial pressure of oxygen=0.3) and high (partial pressure of oxygen=0.6) all at a light level of 197 µmol photons m-2 sec-1.  T. elongatus was examined both axenically and with a hetertrophic partner of each of these six conditions.  The high light condition overlaps with the low oxygen condition for both axenic and co-culture experiments

first: Hans

last: Bernstein

first: Meng

last: Markillie


title: Gene expression analysis of murine FLT3ITD induced acute leukemias

first: Malik

last: Alawi

first: Carol

last: Stocking


title: PRRSV counteracts type I interferon-induced antiviral state

city: Shanghai

first: Gai

middle: Ni

last: Ma

address: ziyue road

institute: Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science Shanghai, CHINA

summary: Porcine reproductive and respiratory syndrome (PRRS) is an economically important  disease with a significant impact on the pig industry. It is caused by PRRS virus  (PRRSV), which predominantly infects and replicates in porcine pulmonary alveolar  macrophages (PAMs), providing a useful in vitro model for understanding the host  immune response to PRRSV infection. We pretreated PAMs with porcine IFN-α to  induce an antiviral state within the cells and subsequently infected them with highly  pathogenic (HP)-PRRSV. Changes in global gene expression in IFN-α-pretreated  PAMs in response to HP-PRRSV infection were determined by RNA-sequence  analysis. A total of 346 differentially expressed genes (DEGs) were transcriptionally upregulated  by porcine IFN-α. Among these up-regulated DEGs, 93 showed significantly  attenuated expression levels in response to HP-PRRSV infection. These attenuated  DEGs were remarkably enriched in immune-response-related terms, such as 'RIG-Ilike  receptor signaling pathway', 'Response to virus', and 'Response to stimulus'.  Notably, expression levels of 93.8% (15/16) of antiviral genes (such as PKR, OAS1,  IFIT1(ISG56) and ISG15), and genes encoding retinoic-acid-inducible gene-I protein  (LOC100737466(DDX58), a cytoplasmic viral RNA sensor), interferon regulatory factor  7 (IRF7, a key transcriptional regulator of type I IFN-dependent immune response),  signal transducer and activator of transcription 1 (LOC100738308(STAT1), a  transcription factor for IFN-stimulated genes), and tumor necrosis factor-related  apoptosis-inducing ligand (TNFSF10, a cytokine initiating proapoptotic signaling  cascades) were significantly attenuated by HP-PRRSV infection. These results suggest  that HP-PRRSV can counteract the type I IFN-induced antiviral state by interfering with  the expression of genes involved in the host-defense response.

overall_design: Highly pathogenic porcine reproductive and respiratory syndrome virus counteracts type I interferon-induced antiviral state by interfering with the expression of hostdefense genes

first: Gaini

first: Zhiyong

first: Ke

last: Liu

first: Jianchao

last: Wei

first: Beibei

last: Li

first: Donghua

last: Shao


title: The effect of Abl kinases on non-small cell carcinoma global transcriptome

city: Durha

first: Jing Jin

last: Gu

state: NC

address: 308 Research Dr.

department: Pharmacology and Cancer Biology

institute: Duke University

summary: To gain insight into the signaling pathway(s) required for ABL1/ABL2-dependent non-small cell carcinoma cells metastasis

overall_design: Samples were analyzed by pair of either control versus ABL Kinase inhibitor GNF5, Or using scrambled shRNA versus ABL1/ABL2-specific shRNAs.

first: Jing

first: Ann

last: Pendergast


title: Subepithelial telocytes are an indispensable source of Wnt ligands supporting intestinal crypts

city: Philadelphia

first: Michal

last: Shoshkes-Carmel

state: PA

address: 3400 Civic Center Blvd, 12-161

institute: University of Pennsylvania

summary: We successfully sequenced and annotated Foxl1 positive and Foxl1 negative mouse intestine mesenchymal cells ( triplicate for each group). We also report that Foxl1 positive cells express molecules of key signaling pathways such as Wnt, BMP,Shh, Tgfb and NFkB.

overall_design: Foxl1 positive and Foxl1 negative sorted mouse intestine mesenchymal cells from three Foxl1Cre;Rosa-YFP or Foxl1Cre;Rosa-mTmG  mice were sequenced.

first: Kirk

last: Wangensteen

first: Yue

last: Wang

first: Beata

last: Toth

first: Shalev

last: Itzkovitz

first: Ayano

last: Kondo

first: Efi

middle: E

last: Massasa

first: Klaus

last: Kaestner


title: Critical role of the transcription factors IRF1 and BATF in preparing the chromatin landscape during Type 1 regulatory cell differentiation [RNA-seq]

city: Cincinnati

first: Emily

last: Miraldi

state: Ohio

address: 3333 Burnet Avenue, MLC 7038

department: Immunobiology and Biomedical Informatics

institute: Cincinnati Children's Hospital Medical Center

summary: Type 1 regulatory T (Tr1) cells are induced by interleukin-27 (IL-27) and have critical roles in the control of autoimmunity and resolution of inflammation. Here, we show that the transcription factors IRF1 and BATF are induced early during treatment with IL-27 and are required for the differentiation and function of Tr1 cells in vitro and in vivo. Epigenetic and transcriptional analyses reveal that both transcription factors influence chromatin accessibility and expression of genes required for Tr1 cell function. IRF1 and BATF deficiencies uniquely alter the chromatin landscape, suggesting that these factors serve a pioneering function during Tr1 cell differentiation.

overall_design: Transcriptinal analysis of IL27-induced of WT, Irf1 KO, and Batf KO cells

first: Katarzyna

last: Karwacz

first: Aviv

last: Regev

first: Bonneau

last: Richard

first: Vijay

last: Kuchroo


title: Critical role of the transcription factors IRF1 and BATF in preparing the chromatin landscape during Type 1 regulatory cell differentiation


title: ZBTB33 (Kaiso) Differentially Regulates Cell Cycle Through cyclin D1 and cyclin E1 in a Cell Specific Manner [BiSulfite-seq]

city: Salt Lake City

first: Bethany

last: Buck-Koehntop

institute: University of Utah

summary: The emerging correlation between aberrant DNA methylation patterns leading to transcriptional responses that promote and progress many cancers has prompted an interest in discerning the associated regulatory mechanisms. ZBTB33 (also known as Kaiso) is a specialized transcription factor that selectively recognizes mCpG-containing sites as well as a sequence-specific DNA target (termed the KBS) utilizing three Cys2His2 zinc fingers. Increasing reports link ZBTB33 overexpression and transcriptional activities with metastatic potential and poor prognosis, though the specific cellular consequences appear to be dependent on disease phenotype. There is currently little mechanistic insight into how various cellular phenotypes are then able to harness the transcriptional capabilities of ZBTB33 to differentially promote and progress the disease state. Here we have mechanistically interrogated the cell cycle responses mediated by the transcriptional activities of ZBTB33 in two different cell lines. Utilizing a series of ZBTB33 depletion and overexpression studies, we have determined that in HeLa cells ZBTB33 directly occupies the promoter regions of cyclin D1 and cyclin E1 in a KBS and methyl-specific manner, respectively, inducing increased proliferation by promoting RB1 hyper-phosphorylation, allowing for E2F transcriptional activity that coordinates an accelerated G1- to S-phase transition. Conversely, in HEK293 cells ZBTB33 indirectly regulates Cyclin E abundance resulting in reduced RB1 phosphorylation, decreased E2F activity and a decelerated transition through G1-phase. Thus, we have identified a novel mechanism by which ZBTB33 directly mediates the highly coordinated cyclin D1/cyclin E1/RB1/E2F signaling pathway controlling the passage through the G1-phase restriction point and accelerating cellular proliferation in a cancer cell line.

overall_design: Determination of global methylation patterns in HeLa cells.

first: Tommy

middle: W

last: Terooatea

middle: A


title: RNA-Seq analysis of E.coli, under multiple growth conditions

city: AUSTIN

first: Mehmet

middle: Umut

last: Caglar

state: Texas

address: 2500 Speedway, A4800

department: Integrative Biology

institute: UNIVERSITY OF TEXAS AUSTIN

summary: The goal of the study is to obtain rna concentrations of E.coli under different growth conditions including growth phase carbon source and salt stresses of Mg+2 and Na+

overall_design: Mostly triple replicates of 152 samples with a time span of 2 weeks corresponding to exponential stationary and late-stationary phases, low base and high Mg+2 levels, base and high Na+ levels, and four carbon sources; glucose gluconate lactate glycerol. The reference condition to be glucose as carbon source, with 5 mM Na+ and 0.8 mM Mg2+.

middle: U

first: John

last: Houser

first: Craig

last: Barnhart

first: Daniel

last: Boutz

first: Sean

middle: M

last: Carroll

first: Aurko

last: Dasgupta

first: Christopher

last: Marx

first: Edward

last: Marcotte

first: Jeffrey

last: Barrick

first: Claus

middle: O

last: Wilke


title: The endfeetome, a astroglial translatome of the neurovascular unit

city: PARIS

first: Stephane

last: Le Crom

address: 46 rue Ulm

department: Genomic Core Facility

country: France

institute: IBENS

summary: We aimed to identify astroglial transcripts preferentially translated in the neurovascular unit. The translatome of whole astrocytes extracted following the bacTRAP protocol was compared to a translatome of astrocyte perivascular endfeet.

overall_design: BAC array purification of astroglial translatome in whole astrocytes and in the neurovascular unit

first: Anne-Cecile

last: Boulay

first: Bruno

last: Saubamea

first: Nicolas

last: Adam

first: Sandrine

last: Perrin

first: Corinne

last: Blugeon

first: Mathieu

last: Banin

first: Leïla

last: Bastianelli

first: Martine

last: Cohen-Salmon


title: Critical role of the transcription factors IRF1 and BATF in preparing the chromatin landscape during Type 1 regulatory cell differentiation [ATAC-seq]

first: Emily

last: Miraldi

overall_design: Chromatin accessibility (ATAC-seq) analysis of IL27-induced CD4 cells (WT, IRF1 KO, AHR KO, MAF KO, and BATF KO)

first: Katarzyna

last: Karwacz

first: Maria

last: Pokrovskii

first: R

last: Bonneau

first: D

last: Littman

first: Vijay

last: Kuchroo


title: Expression and Splicing of ABC and SLC Transporters in the Blood-Brain Barrier

status: Public on Jan 26 2017

city: Columbus

first: Amy

last: Hite

state: OH - Ohio

address: 1800 Cannon Drive 250 Lincoln Tower

department: Biomedical Informatics

institute: The Ohio State University

summary: The low permeability and high selectivity of the blood vessels of the brain and central nervous system (CNS) characterize the blood-brain barrier (BBB).  Tight junctions, a lack of fenestrations, and low rates of transcytosis in the endothelial cells of the vasculature prevent passive diffusion of most molecules other than water, gases and some lipid soluble molecules (Obermeier, Daneman, & Ransohoff, 2013).  Any additional nutrients must be transported across the barrier with the help of transporter proteins.  Two protein families account for most transporters.  ABC transporters use ATP to power primary-active transport to move molecules across the BBB against an electrochemical gradient, frequently excluding drugs from entering the brain.  Some SLC transporters facilitate transport of solutes along an electrochemical gradient, while others permit secondary-active transport by coupling the flow of a solute traveling down the electrochemical gradient to power another solute against its electrochemical gradient.  Brain microvessel endothelial cells (BMEC) from human cerebral cortex were enriched through a homogenization and centrifugation procedure.  Two BMEC and two tissue were sequenced with paired-end reads on a SOLiD 5500 Wildfire.  Raw data was aligned using LifeScope Genomic Analysis, gene expression determined through Cufflinks, and splice junctions identified by aligning to a custom database of known to known and known to novel junctions.  We found numerous examples of transporters with enriched expression in the isolated BMECs compared to whole brain tissue.  In total, 131 transporter genes or pseudogenes (109 SLC, 22 ABC) are enriched at least 1.25 fold in BMEC enriched samples, and 57 of these are enriched over 2-fold (50 SLC, 7 ABC).  Thirteen genes were found to have at least twice as many counts in BMEC enriched samples than in whole tissue for at least one alternative splice junction.  Inversely, 23 genes were found to have at least one alternative splice junction with half as many counts in BMEC enriched samples than in whole tissue.

overall_design: We sequenced 2 brain tissue samples and 2 matched brain microvessel endothelial cells.  Barcoded libraries were sequenced across 5 lanes of a SOLiD wildfire.

first: Wolfgang

last: Sadee

first: Adam

last: Suhy

first: Audrey

last: Papp

last: Webb

first: Ethan

last: Geier

first: Kathleen

last: Giacomini


title: Alternative splicing in Col-0 and sc35-scl mutant in Arabidopsis tlianaha

first: Qing

middle: qing

last: Yan

address: 300 Feng Lin Road

institute: Yuda Fang

summary: Serine/arginine-rich (SR) proteins are important splicing factors which play significant roles in spliceosome assembly and splicing regulation. However, little is known regarding their biological functions in plants. Here, we analyzed the phenotypes of mutants upon depleting different subfamilies of Arabidopsis SR proteins. We found that loss of the functions of SC35 and SC35-like (SCL) proteins cause pleiotropic changes in plant morphology and development, including serrated leaves, late flowering, shorter roots and abnormal silique phyllotaxy. Using RNA-seq, we found that SC35 and SCL proteins play roles in the pre-mRNA splicing. Motif analysis revealed that SC35 and SCL proteins preferentially bind to a specific RNA sequence containing the AGAAGA motif. In addition, the transcriptions of a subset of genes are affected by the deletion of SC35 and SCL proteins which interact with NRPB4, a specific subunit of RNA polymerase II. The splicing of FLOWERING LOCUS C (FLC) intron1 and transcription of FLC were significantly regulated by SC35 and SCL proteins to control Arabidopsis flowering. Therefore, our findings provide mechanistic insight into the functions of plant SC35 and SCL proteins in the regulation of splicing and transcription to maintain the proper expression of genes and development.

overall_design: Total mRNA profiles of 12-day wild type (Col-0) and sc35-scl were generated by RNA sequencing.

first: Qingqing

first: Xi

last: Xia

first: Zhenfei

last: Sun


title: A role of RPA in replication coupled nucleosome assembly

last: Li

address: No.5 Yiheyuan Road Haidian District

department: School of Life Science

institute: Peking University

summary: Chromatin replication requires tight coordination of nucleosome assembly machinery with DNA replication machinery. While significant progress has been made in characterizing histone chaperones in this process, the mechanism of whereby nucleosome assembly couples with DNA replication remains largely unknown. Here we show that replication protein A (RPA), a single-stranded DNA (ssDNA) binding protein that is essential for DNA replication provides a binding platform for H3-H4 deposition by histone chaperons and is required for nucleosome formation on nascent chromatin. RPA binds free histone H3-H4 but not nucleosomal histones, and a RPA coated ssDNA stimulates assembly of H3-H4 onto double strand DNA in vitro. RPA mutant with reduced H3-H4 binding exhibits synthetic genetic interaction with mutations at key factors involved in replication-coupled (RC) nucleosome assembly, and are defective in assembly of replicating DNA into nucleosomes in cells. These results reveal a novel function for RPA in nucleosome assembly and a mechanism whereby nucleosome assembly is coordinated with DNA replication.

overall_design: To thoroughly compare nucleosome formation on nascent chromatin between wild type and RPA mutant cells, we mapped nucleosomes and genomic DNA in wild type, rfa1-A88P and rtt109∆ cells at G1 and early S phase. Two independent biological repeats were performed for each sample.

first: Shaofeng

last: Liu

first: Zhiyun

last: Xu

first: He

last: Leng

first: Pu

last: Zheng

first: Jiayi

last: Yang

first: Kaifu

last: Chen

first: Jianxun

last: Feng


title: Next Generation Sequencing Facilitates Quantitative Analysis of miRNA

city: beijing

first: zhengqin

last: rong

address: Chaoqian Rd,Changping Science Park of Zhongguancun Science Park

institute: hornortech

summary: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare miRNA expressions of pear in two different conditions.

sample_organism: Pyrus x bretschneideri x Pyrus pyrifolia

overall_design: Fruit mRNA profiles after 2 different parent pollination to same female parent


title: The Eph-related tyrosine kinase ligand Ephrin-B1 marks germinal center and memory precursor B cells

city: San Francisco

first: Brian

last: Laidlaw

state: CA

address: 513 Parnassus Avenue, HSE 1001

institute: University of California, San Francisco

summary: Identification of germinal center (GC) B cells is typically reliant on the use of surface activation markers that exhibit a wide range of expression. Here we identify Ephrin-B1, a ligand for Eph-related receptor tyrosine kinases, as a specific marker of mature GC B cells. The number of Ephrin-B1+ GC B cells increases during the course of an immune response with Ephrin-B1+ GC B cells displaying elevated levels of Bcl6, S1pr2, and Aicda relative to their Ephrin-B1– counterparts. We further identified a small proportion of recently dividing, somatically mutated Ephrin-B1+ GC B cells that have begun to downregulate Bcl6 and S1pr2 and express markers associated with memory B cells such as CD38 and EBI2. Transcriptional analysis indicates that these cells are developmentally related to memory B cells, and likely represent a population of GC memory precursor (PreMem) B cells. GC PreMem cells display enhanced survival relative to bulk GC B cells, localize near the edge of the GC and are predominantly found within the light zone. These findings offer insight into the significant heterogeneity that exists within the GC B cell population and provide tools to further dissect signals regulating the differentiation of GC B cells.

overall_design: 8 samples- 3 groups (VenusPos, 3 replicates; VenusNeg, 3 replicates; Mem, 2 replicates)

first: Timothy

middle: H

last: Schmidt

first: Jesse

last: Green

first: Christopher

middle: D

last: Allen

first: Takaharu

last: Okada

first: Jason

middle: G

last: Cyster


title: Human embryonic stem cells do not change their X-inactivation status during differentiation [RNA-Seq]

first: Kathrin

last: Plath

address: 615 Charles E. Young Drive South

institute: UCLA

summary: Female human ESC-lines can carry active X-chromosomes (Xa) or an XIST-RNA-coated inactive X-chromosome (XiXIST+). Additionally, many ESC lines have abnormal X-chromosomeinactivation (XCI)-states where the Xi no longer expresses XIST-RNA and has transcriptionally active regions (eroded Xi=Xe). The fate of each XCI-state upon differentiation is unclear because individual lines often contain a mixture of XCI-states. Here, we established homogeneous XiXa, XeXa, and XaXa ESC-lines. Employing RNA-FISH, RNA-sequencing and DNA methylation analyses, we found that these lines were unable to initiate XIST-expression and X-chromosome-wide silencing upon differentiation indicating that the ESC XCI-state is maintained in differentiated cells. Consequently, differentiated XeXa and XaXa cells displayed higher levels of X-linked gene-expression than XiXa cells. Although global transcriptional compensation between X-chromosomes and autosomes is not required for female ESC-differentiation, the degree of X-chromosome-silencing influences differentiation efficiencies. Our data suggest that the XiXIST+Xa state is inherent to human ESCs and that all other XCI-states, including XaXa, are abnormal and arise during ESC-derivation or maintenance.

overall_design: RNA-seq was used to measure the expression state of X-linked and autosomal genes in undifferentiated human embryonic stem cells with different X-chromosome states and their differentiated cells.

first: Sanjeet

last: Patel

first: Giancarlo

last: Bonora

first: Rachel

last: Kim

first: Constantinos

last: Chronis

first: Anna

last: Sahakyan

first: Justin

last: Langerman

first: Sorel

last: Fitz-Gibbon

first: Liudmilla

last: Rubbi

first: Rhys

last: Skelton

first: Reza

last: Ardehali

first: Matteo

last: Pelligrini

first: Bill

last: Lowry

first: Amander

last: Clark


title: Gene expression profile of M. smegmatis expressing RbpA truncations

city: New York

first: Michael

middle: S

last: Glickman

state: NY

address: 408 East 69th street, Z1531

department: Immunology

institute: Memorial Sloan Kettering Cancer Center

summary: We report the gene expression profile of strains expressing domain truncations of the essential mycobacterial transcriptional activator RbpA

overall_design: Triplicate RNA samples of wildtype (MGM6232), RbpACD-BL-SID(MGM6234), and RbpABL-SID(MGM6236) were prepared from logathrimically growing cells

first: James

last: Bean

first: Allison

last: Fay


title: A genome-wide RNAi screen identifies genes and networks governing hematopoietic stem cell development

city: La Jolla

first: Tianxu

last: Han

address: 9500 Gilman Dr

institute: UCSD

summary: We report a functional genome-wide RNAi screen to identify genes required for embryonic stem cell (ESC) differentiation to hematopoietic stem/progenitor cells (HSPC) in vitro, and report the discovery of novel genes important for differentiation to the endothelial–hematopoietic transition and subsequently to HSPC specification. iHoxB4 ESCs were transduced with a library of shRNAs targeting >15,000 genes, and were differentiated towards hematopoietic stem and progenitor cells by forcing HoxB4 expression in the cells. Five cell populations were isolated on differentiation days 6 and 20. Differentiated mesodermal/endothelium cell population D6F (Ssea1–Flkl+Cxcr4–), endodermal cell population D6C (Ssea1–Flkl–Cxcr4+), D20LS (Lin–Sca1+c-Kit–), D20LK (Lin–Sca1–c-Kit+), and D20LSK (Lin–Sca1+c-Kit+) cells were purified by FACS. Transduced iHoxB4 cells were analyzed as undifferentiated control cells. The experiment was performed three times independently. High-throughput sequencing and bioinformatics analysis identified twelve groups of shRNA target genes implicated in ESC to HSPC development, including a group of 351 novel genes that appear to be required for HSPC specification. As proof of concept in vivo, four genes in this group, Ap2a1, Mettl22, Lrsam1, and Hal, were selected for validation and were confirmed to be essential for HSPC development in zebrafish and for maintenance of human HSCs. Taken together, our results not only identify a number of novel regulatory genes and pathways throughout HSPC development but also serve as a potentially valuable resource for directed differentiation of therapy-grade HSPCs from human pluripotent stem cells.

overall_design: A total of 18 samples from three replicates were sequenced and analyzed. Sample ESC serves as control.

first: Tariq

last: Rana


title: MerR and ChrR mediate blue light induced photo-oxidative stress response at the transcriptional level in Vibrio cholerae

city: Ann Arbor

first: mehmet

last: tardu

state: MI

address: 930 N University Ave

institute: University of Michigan

summary: Blue light (BL) is a major environmental factor that affects the physiology, behavior, and infectivity of bacteria as it contributes to the generation of reactive oxygen species (ROS) while increasing photo-oxidative stress in cells. However, precise photo-oxidative response mechanism in non-phototrophic bacteria is yet to be elucidated. In this study, we investigated the effect of BL in Vibrio cholerae by using genetics and transcriptome profiling. Genome-wide analysis revealed that transcription of 6.3% of V. cholerae genes were regulated by BL. We further showed that BL enhances ROS production, which is generated through the oxidative phosphorylation. To understand signaling mechanisms, we generated several knockouts and analyzed their transcriptome under BL exposure. Studies with a double-knockout confirm an anti-sigma factor (ChrR) and putative metalloregulatory-like protein (MerR) are responsible for the genome-wide regulation to BL response in V. cholerae. Collectively, these results demonstrate that MerR-like proteins, in addition to ChrR, are required for V. cholerae to mount an appropriate response against photo-oxidative stress induced by BL. Outside its natural host, V. cholerae can survive for extended periods in natural aquatic environments. Therefore, the regulation of light response for V. cholerae may be a critical cellular process for its survival in these environments.

sample_organism: Vibrio cholerae O1 biovar El Tor str. N16961

overall_design: mRNA profiles of wild type (WT), ΔChrR, ΔChrRΔMerR  and Δcry1Δcry2Δphr mutant V.cholerae cells were generated by deep sequencing, in duplicate, using Illumina MiSeq platform.

first: Mehmet

last: Tardu

first: Ibrahim

last: Kavakli


title: Human embryonic stem cells do not change their X-inactivation status during differentiation

city: Los Angeles

first: Kathrin

last: Plath

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

overall_design: Refer to individual Series


title: Systematic mapping of RNA-chromatin interactions in vivo

first: Marcelo

last: Rivas

address: 9500 Gilman Drive, MC 0412

department: Bioengineering

institute: University of California San Diego

summary: RNA molecules can attach to chromatin and thus provide a type of epigenomic information. It remains difficult to know what RNAs are associated with chromatin and where are the genomic target loci of these RNAs. Here, we present MARGI (Mapping RNA-genome interactions), a technology to massively reveal native RNA-chromatin interactions from unperturbed cells. The gist of this technology is to ligate chromatin-associated RNA (caRNA) with their target genomic sequence by proximity ligation, forming RNA-DNA chimeric sequences, which are converted to sequencing library for paired-end sequencing. Using MARGI, we produced RNA-genome interaction maps for human embryonic stem (ES) cells and HEK cells. MARGI revealed hundreds of chromatin-associated RNAs (caRNA), including previously known XIST, SNHG1, NEAT1, and MALAT1, as well as each caRNA's genomic interaction loci. Using a cross-species experiment, we estimated that approximately 2.2% of MARGI identified interactions are false positives. MARGI data suggested that 80-95% of interactions are proximal, where a caRNA is connected to its nearby genomic regions, 1-2% are distal, and 5-15% are inter-chromosomal. The majority of TSSs are associated with distal or inter-chromosomal caRNAs. ChIP-seq reported H3K27ac and H3K4me3 levels are positively correlated while H3K9me is negatively correlated with MARGI reported RNA attachment levels. The MARGI technology should facilitate revealing novel RNA functions and epigenomic events.

sample_organism:
Drosophila melanogaster
Homo sapiens

platform_organism:
Drosophila melanogaster
Homo sapiens

overall_design:
Two human cell lines were analysed: H9 and HEK. For each, we used two protocols, pxMARGI and diMARGI, having two replicates for the former and only one for the latter. Two samples from each replicate were sequenced.
Whereas pxMARGI is designed to not differentiate passive and direct interactions, diMARGI is aimed to reveal protein tethered interactions. For the former, this was achieved by a combination of formaldehyde crosslinking and complete genome fragmentation, by overnight HaeIII digestion to ensure all genomic regions including heterochromatin were fragmented before the subsequent DNA ligation step. For the second, after crosslinking with formaldehyde and DSG, the chromatin was fragmented by sonication, and only the soluble fraction was passed onto the subsequent ligation steps.

first: Bharat

last: Sridhar

last: Rivas-Astroza

first: Tri

middle: C

last: Nguyen

first: Weizhong

last: Chen

first: Zhangming

last: Yan

first: Xiaoyi

last: Cao

first: Lucie

last: Hebert

first: Sheng

last: Zhong


title: Functional characterization of open chromatin in bidirectional promoters of rice

city: Nanjing

first: Fang

last: Yuan

state: Jiangsu

address: No.1, Weigang Street, Xuanwu District, Nanjing

institute: NanJing Argricultural University

summary: Bidirectional gene pairs tend to be highly coregulated and function in similar biological   processes in eukaryotic genomes. Structural features and functional consequences of BDPs   have received considerable attention among diverse species. However, the underlying   mechanisms responsible for bidirectional transcription and coexpression of BDPs remain poorly   understood in plants. In this study, we integrated DNase-seq, RNA-seq, ChIP-seq and   nucleosome positioning data and investigated the effect of DHSs on transcription of rice BDPs.   We found that the physical localization of DHSs can affect the expression of the corresponding   genes, closer to TSS, higher expression level of genes. Most importantly, we observed that   distribution of DHS plays a significant role in regulation of transcription and coexpression of   gene pairs, which is possibly mediated by orchestrating the positioning of histone marks and   canonical nucleosomes around BPDs. Our results demonstrate that the combined actions of   chromatin structures with DHSs, which contain functional cis-elements for interaction with   transcriptional machinery, may play an important role in regulation of bidirectional   transcription or coexpression in rice BDPs. Our findings may help to enhance the understanding   of DHSs in regulation of bidirectional gene pairs.

overall_design: Examination of 6 different histone modifications in rice leaves tissue.

first: Yuan

last: Fang

first: Ximen

last: Wang

first: Lei

first: Xiucai

last: Pan

first: Yufeng

last: Wu

first: Wenli

last: Zhang


title: Human embryonic stem cells do not change their X-inactivation status during differentiation [RRBS-Seq]

overall_design: Reduced representation bisulfite sequencing was used to measure DNA methylation in human embryonic stem cells with different X-inactivation states and their differentiated daughter cells.

first: Sanjeet

last: Patel

first: Giancarlo

last: Bonora

first: Rachel

last: Kim

first: Constantinos

last: Chronis

first: Anna

last: Sahakyan

first: Justin

last: Langerman

first: Sorel

last: Fitz-Gibbon

first: Liudmilla

last: Rubbi

first: Rhys

last: Skelton

first: Reza

last: Ardehali

first: Matteo

last: Pelligrini

first: Bill

last: Lowry

first: Amander

last: Clark


title: The long intergenic non-coding RNA CCR492 functions as a let-7 competitive endogenous RNA to regulate c-Myc expression

city: Torino

first: Francesco

last: Neri

state: Italy

address: Via Nizza 52

country: Italy

institute: University of Torino

summary: The cell cycle progression through the G1 phase is a tightly regulated process mediated by the transcriptional activation of early genes in response to mitogenic stimuli, whose dysregulation often leads to tumorigenesis. We here report the discovery by RNA-seq of cell cycle regulated (CCR) long intergenic non-coding RNAs (lincRNAs), potentially involved in the control of the cell cycle progression. We identified 10 new lincRNAs whose expression was induced in response to serum treatment in mouse embryonic fibroblasts (MEF) and in Balb/c fibroblasts, comparably to early genes. By loss-of-function experiments we found that lincRNA CCR492 is required for cell cycle progression, localizes in the cell cytoplasm and contains 4 let-7 miRNA recognition elements (MREs). Mechanistically, CCR492 functions as a competing endogenous RNA (ceRNA) to antagonize the function of Let-7 microRNA, leading to the de-repression of c-Myc. Moreover, we show that ectopic expression of CCR492 along with a constitutively active H-Ras triggers cell transformation. In brief, we found a novel lincRNA that regulates c-Myc expression, is required for efficient progression of the cell cycle, and whose deregulation contributes to tumour growth.

overall_design: Expression profiling by high-throughput sequencing

first: Mara

last: Maldotti

first: Danny

last: Incarnato

first: Stefania

last: Rapelli

first: Francesca

last: Anselmi

last: Krepelova

first: Caterina

last: Parlato

first: Giulia

last: Basile

first: Raffaele

last: Calogero

first: Salvatore

last: Oliviero


title: RNAseq analysis of the N. punctiforme transcriptome during hormogonium development

status: Public on Jan 25 2017

city: Stockton

first: Douglas

last: Risser

address: 3601 Pacific Ave

department: Biology

institute: University of the Pacific

summary: Change in gene expression for wild-type Nostoc punctiforme ATCC 29133 over the time course of hormogonium development

overall_design: Total RNA from 1 biological replicate at 0,1,6,12, and 18 hours after hormogonium induction was ribodepleted, converted to cDNA, apended with adapters and sequenced in a single lane of a flow cell on an illumina HiSeq 2000 instrument


title: Transcriptome Profiling of Influenza A Virus-infected Lung Epithelial (A549) Cells with Lariciresinol-4-β-D-glucopyranoside Treatment

city: Macau

first: Beixian

last: Zhou

address: Av. Wai Long, Taipa, Macau

institute: Macau University of Science and Technology

summary: The influenza A virus is an acute contagious pathogen that affects the human respiratory system and can cause severe lung disease and even death. Lariciresinol-4-β-D-glucopyranoside is a lignan that is extracted from Isatis indigotica, which is a medicinal herb plant that was commonly applied to treat infections, the common cold, fever and inflammatory diseases. Our previous study demonstrated that lariciresinol-4-β-D-glucopyranoside possesses anti-viral and anti-inflammatory properties. However, the comprehensive and detailed mechanisms that underlie the effect of lariciresinol-4-β-D-glucopyranoside interventions against influenza virus infection remain to be elucidated. In this study, we employed high-throughput RNA sequencing (RNA-seq) to investigate the transcriptomic responses of influenza A virus-infected lung epithelial (A549) cells with lariciresinol-4-β-D-glucopyranoside treatment. The transcriptome data show that infection with influenza A virus prompted the activation of 368 genes involved in RIG-I signalling, the inflammatory response, interferonsignalling and gene expression that was not affected by lariciresinol-4-β-D-glucopyranoside treatment. Lariciresinol-4-β-D-glucopyranoside exerted its pharmacological actions on the immune system, signal transduction, cell cycle and metabolism, which may be an underlying defence mechanism against influenza virus infection. In addition, 166 differentially expressed genes (DEGs) were uniquely expressed in lariciresinol-4-β-D-glucopyranoside-treated cells, which were concentrated in the cell cycle, DNA repair, chromatin organization, gene expression and biosynthesis domains. Among them, six telomere-associated genes were up-regulated by lariciresinol-4-β-D-glucopyranoside treatment, which have been implicated in telomere regulation and stability. Collectively, we employed RNA-seq analysis to provide comprehensive insight into the mechanism of lariciresinol-4-β-D-glucopyranoside against influenza virus infection.

overall_design: We used RNA-seq technology to systematically assess the transcriptome profile of influenza A virus-infected lung epithelial (A549) cells following lariciresinol-4-β-D-glucopyranoside treatment

first: Zhihong

last: Jiang


title: RNA Sequencing Reveals Immunosuppressive Role of Anthrax Lethal Toxin in Human Lung Epithelial and Monocytic Cells

city: Ansan

first: Se Kye

last: Kim

state: GYOENGGI-DO

address: 55 Hanyangdaehak-ro

department: Molecular and Life Science

country: South Korea

institute: Hanyang University ERICA

summary: Using RNA-seq, we report here that anthrax lethal toxin (LeTx) induces immunosuppression in human lung epithelial cell line A549 and monocytic cell line U937.

overall_design: Examination of LeTx-treated A549 and U937, generated by deep sequencing on an Illumina HiSeq 2000 (101 cycles PE lane).

first: YoungGyu

last: Chai

first: Sekye