title: Coordinated Activities of Multiple Myc-Dependent and Myc-Independent Biosynthetic Pathways in Hepatoblastoma

city: Pittsburgh

first: Edward

middle: V

last: Prochownik

address: 4401 Penn Ave.

department: Division of Hematology/Oncology

institute: Children’s Hospital of Pittsburgh of UPMC

summary: Hepatoblastoma (HB) is associated with aberrant activation of the b-catenin and Hippo/YAP signaling pathways. Over-expression of mutant b-catenin and YAP in mice induces HBs that express high levels of c-Myc (Myc).  In light of recent observations that Myc in unnecessary for long-term hepatocyte proliferation, we have now examined its role in HB pathogenesis using the above model. While Myc was found to be dispensable for in vivo HB initiation it was necessary to sustain rapid tumor growth. Gene expression profiling identified key molecular differences between myc+/+ (WT) and myc-/- (KO) hepatocytes and HBs that explain these behaviors. In HBs, these included both Myc-dependent and Myc-independent increases in families of transcripts encoding ribosomal proteins, non-structural factors affecting ribosome assembly and function and enzymes catalyzing glycolysis, lipid bio-synthesis and fatty acid b-oxidation. Myc-independent metabolic changes associated with HBs included dramatic reductions in mitochondrial mass and oxidative function and increases in ATP content and pyruvate dehydrogenase activity. Myc-dependent metabolic changes included higher levels of neutral lipid and acetyl-CoA in WT tumors. The latter correlated with higher histone H3 acetylation. Collectively, our results indicate that Myc’s role in HB pathogenesis is to impose mutually dependent changes in gene expression and metabolic re-programming that are unattainable in non-transformed cells and that cooperate to maximize tumor growth.

overall_design: 4 individual sets each of Myc WT and KO hepatocytes, and 5 individual sets each of Myc WT and KO Hepatoblastoma

first: Huabo

last: Wang


title: Increased Wnt and Notch signaling: A clue to the renal disease in Schimke immuno-osseous dysplasia? [RNA-Seq]

status: Public on Oct 31 2016

city: Vancouver

first: Cornelius

middle: F.

last: Boerkoel

state: British Columbia

address: 950 West 28th Avenue

department: Medical Genetics

country: Canada

institute: University of British Columbia

type: Expression profiling by high throughput sequencing

summary: Schimke immuno-osseous dysplasia (SIOD) is a multisystemic disorder caused by biallelic mutations in SWI/SNF-related matrix associated actin-dependent regulator of chromatin, subfamily A-like protein 1 (SMARCAL1). Changes in gene expression appear to underlie the immunodeficiency and arteriosclerosis of SIOD; therefore, we hypothesized that SMARCAL1 deficiency alters renal gene expression to cause the focal segmental glomerulosclerosis (FSGS) of SIOD. We tested this hypothesis by transcriptome analysis and quantitative reverse transcription PCR (qRT-PCR) of an SIOD patient kidney, a genetic screen and immunofluorescence. These showed increased expression of genes in the Wnt and Notch signaling pathways in an SIOD patient kidney, interaction of Marcal1 with genes encoding components of the Wnt and Notch signaling pathways, and increased levels of unphosphorylated b-catenin and Notch1 intracellular domain (NICD) in the glomeruli of SIOD patient kidneys. Given that increased Wnt and Notch activity are established causes of FSGS, we hypothesize that SMARCAL1 deficiency increases the activity of one or both of these pathways to cause the renal disease of most SIOD patients.

overall_design: Comparison of mRNA levels between the kidney tissue of a Schimke immuno-osseous dysplasia (SIOD) patient and an unaffected control

first: Marie

last: Morimoto

middle: F


title: RNA-seq of Procr expressing mouse vascular endothelial cells

city: Shanghai

first: Qing Cissy

last: Yu

address: 320 Yue Yang Road

department: Institute of Biochemistry and Cell Biology

country: China

institute: Shanghai Institute of Biological Sciences

summary: We have used RNA-seq to examine RNA differential expression between Procr+ and Procr- vascular endothelial cells in mouse mammary gland

overall_design: Examine RNA differential expression among subsets of freshly sorted mouse mammary gland vascular endothelal cells

first: Qing

middle: C

first: Yi

middle: A

last: Zeng


title: TET-dependent regulation of retrotransposable elements in mouse embryonic stem cells

status: Public on Oct 28 2016

city: London

first: Miguel

middle: R

last: Branco

address: 4 Newark Street

country: United Kingdom

institute: Blizard Institute

type: Non-coding RNA profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: TET-dependent regulation of retrotransposable elements in mouse embryonic stem cells [small RNA-seq]

summary: TET enzymes oxidise DNA methylation as part of an active demethylation pathway. Despite extensive research into the role of TETs in genome regulation, little is known about their effect on transposable elements (TEs), which make up nearly half of the mouse and human genomes. Epigenetic mechanisms controlling TEs have the potential to affect their mobility and to drive the co-adoption of TEs for the benefit of the host. We have performed a detailed investigation of the role of TET enzymes in the regulation of TEs in mouse embryonic stem cells (ESCs). We found that TET1 and TET2 bind multiple TE classes that harbour a variety of epigenetic signatures indicative of different functional roles. Namely, TETs co-bind with pluripotency factors to enhancer-like TEs that interact with highly expressed genes in ESCs, whose expression is partly maintained by the demethylating action of TET2. TETs and 5-hydroxymethylcytosine are also strongly enriched at the 5’ UTR of full-length, evolutionarily young LINE1 elements, a pattern that is conserved in human embryonic stem cells. TET depletion leads to a marked increase in DNA methylation levels at LINE1s, but surprisingly their expression is stably maintained through additional TET-dependent activities. Specifically, we find that TET1 recruits the SIN3A co-repressive complex to LINE1s, ensuring their repression upon TET-driven hypomethylation. This dual nature of TET action may reflect the evolutionary battle between TEs and the host. Our data implicate TET enzymes in the evolutionary dynamics of TEs, both in the context of exaptation processes and of retrotransposition control.

overall_design: TET1 or TET2 were depleted in embryonic stem cells by shRNA, using a non-targeting sequence (shScr) as a control. RNA was extracted to generate rRNA-depleted RNA-seq libraries (5 replicates of each sample) and small RNA-seq libraries (2 replicates of each sample).

first: Lorenzo

last: de la Rica

first: Ozgen

last: Deniz

first: Kevin

last: Cheng

first: Christopher

last: Todd

first: Cristina

last: Cruz

first: Jon

last: Houseley


title: Transient RNA-DNA Hybrids Are Required for Efficient Double-Strand Break Repair

city: Canberra

first: Tamas

last: Fischer

state: ACT

address: Building 131, Garran Rd

department: The John Curtin School of Medical Research

country: Australia

institute: The Australian National University

type: Expression profiling by genome tiling array


title: Single cell RNA sequencing analysis of bacterial lipoprotein-induced polyploid macrophages.

city: Freiburg

first: Sagar

address: Hugstetter Straße 55

department: Department of Internal Medicine II

country: Germany

institute: University Medical Center Freiburg

summary: Granulomas are immune cell aggregates formed in response to persistent inflammatory stimuli. Granuloma macrophage subsets are diverse and carry varying copy numbers of their genomic information. The molecular programs that control the differentiation of such macrophage populations in response to a chronic stimulus, though critical for disease outcome, have not been defined. In this study, we performed scRNA-Seq experiments to gain insights into the transcriptional regulation of polyploid macrophage differentiation in response to chronically persistent inflammatory stimuli.

overall_design: scRNA-Seq was performed on FACS-sorted 2c and >4c DNA content polyploid macrophages after six days of bacterial lipoprotein, FSL-1 treatment of  bone marrow-derived macrophage precursors. 2c DNA content macrophages treated with M-CSF alone were used as controls. CEL-Seq2 protocol was used for single cell sequencing (Hashimshony et al. 2016).

last: Sagar

first: Dominic

last: Grün

first: Antigoni

last: Triantafyllopoulou

first: Andreas

last: Diefenbach


title: Local regulation of gene expression by lncRNA promoters, transcription, and splicing

city: Stanford

first: Jesse

last: Engreitz

state: CA

address: 240 Pasteur Drive

country: USA

institute: Stanford University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Mammalian genomes are pervasively transcribed to produce thousands of spliced long noncoding RNAs (lncRNAs), whose functions remain poorly understood. Because recent evidence has implicated several specific lncRNA loci in the local regulation of gene expression, we sought to determine whether such local regulation is a property of many lncRNA loci. We used genetic manipulations to dissect 12 genomic loci that produce lncRNAs and found that 5 of these loci influence the expression of a neighboring gene in cis. Surprisingly, however, none of these effects required the specific lncRNA transcripts themselves and instead involved general processes associated with their production, including enhancer-like activity of gene promoters, the process of transcription, and the splicing of the transcript. Interestingly, such effects are not limited to lncRNA loci: we found similar effects on local gene expression at 4 of 6 protein-coding loci. These results demonstrate that ‘crosstalk’ among neighboring genes is a prevalent phenomenon that can involve multiple mechanisms and cis regulatory signals, including a novel role for RNA splice sites. These mechanisms may coordinate the expression of neighboring genes and explain the function and evolution of some genomic loci that produce lncRNAs.

overall_design: We developed a genetic approach based on classical cis-trans tests to distinguish between (i) primary effects on the expression of nearby genes resulting from direct local functions of the lncRNA locus and (ii) secondary effects on nearby genes resulting from indirect downstream consequences of the lncRNA acting elsewhere in the cell. We generated clonal cell lines carrying heterozygous genetic modifications at lncRNA loci and compared the expression of nearby genes within 1 megabase on the cis and trans alleles (i.e., on the modified and unmodified homologous chromosomes) in the same cells. Changes in neighboring gene expression that involve only the cis allele likely result from local functions, while changes that involve both the cis and trans alleles likely result as downstream effects of non-local functions. We performed genetic modifications in 129/Castaneus F1 hybrid mouse embryonic stem cells (mESCs) that contain ~1 polymorphic site every 140 basepairs (bp), enabling us to distinguish the two alleles using RNA sequencing, and we checked for consistency between knockouts on each genetic background to control for potential haplotype-specific effects. We initially characterized allele-specific gene expression using RNA sequencing combined with hybrid selection, and we further characterized a subset of clones in selected loci using global run-on sequencing (GRO-seq), chromatin immunoprecipitation (ChIP-Seq), and ATAC-Seq.

middle: M

first: Jenna

middle: E

last: Haines

first: Elizabeth

last: Perez

first: Glen

last: Munson

first: Jenny

last: Chen

first: Michael

last: Kane

first: Patrick

last: McDonel

first: Mitchell

last: Guttman

first: Eric

middle: S

last: Lander


title: TET-dependent regulation of retrotransposable elements in mouse embryonic stem cells [RNA-seq]

first: Miguel

last: Branco

first: Lorenzo

last: de la Rica

first: Ozgen

last: Deniz

first: Kevin

last: Cheng

first: Christopher

last: Todd


title: Extensive cryptic splicing upon loss of RBM17 and TDP43 in neurodegeneration models

city: Houston

first: Zhandong

last: Liu

state: TEXAS

address: 1250 Moursund St., STE NR-1325

institute: Baylor College of Medicine

summary: Translating ribosome affinity purification technology was used to isolate mRNAs from cerebellar Purkinje neurons from control (Pcp2-BacTrap; Rbm17 f/+) and mutant (Pcp2-BacTRAP; Pcp2-Cre; Rbm17 f/-) mice.

overall_design: RNA isolation was performed when animals were four-weeks-old (n=3 animals per genotype). Using NuGEN Ovation RNA-Seq System v2, purified double-stranded cDNA was generated from 10 ng of total RNA and amplified using both 3’ poly (A) selection and random priming. 2 µg of each sample was sheared using the Covaris S2 focused-ultrasonicator following the manufacturer’s protocol to obtain a final library with insert size of 400 bp. The sheared samples were quantified using the NanoDrop ND-1000 spectrophotometer and Invitrogen Qubit 2.0 DNA quantitation assay. The fragment sizes were confirmed on the Agilent Bioanalyzer to verify proper shearing. A double-stranded DNA library was produced using Illumina TruSeq DNA library preparation system and the sequencing was run on a HiSeq 2500 system.

first: Huda

middle: Y

last: Zoghbi


title: ChIP-sequencing in stage 10.5 Xenopus laevis embryos

city: Nijmegen

first: Simon

last: van Heeringen

address: Geert Grooteplein 28

department: Molecular Developmental Biology

country: Netherlands

institute: Radboud University

summary: Epigenomic profiling (H3K4me1, H3K4me3, H3K36me3, p300 and RNA Polymerase II) of Xenopus laevis stage 10.5 embryos.

overall_design:
ChIP-seq of H3K4me1, H3K4me3, H3K36me3, p300 and RNA Polymerase II in duplicate.
BAM processed data files (a format not accepted by GEO) were generated for H3K4me1, H3K36me3, RNAPII samples.

middle: J

first: Sarita

last: Paranjpe

first: Gert-Jan

last: Veenstra


title: RNA-sequencing of subcellular fractions in mouse embryonic stem cells

first: Jesse

last: Engreitz

summary: We examined the subcellular localization of long noncoding RNAs (lncRNAs) in mouse embryonic stem cells.

overall_design: We performed cellular fractionation in V6.5 male mouse embryonic stem cells to isolate chromatin-associated, soluble nuclear, and cytoplasmic RNA, and sequenced total and polyadenylated RNA.


title: Identification of Sin3B regulated genes in HSCs

city: New York

first: David

last: Cantor

state: New York

address: 550 First Avenue

institute: NYU School of Medicine

summary: We report differences in gene expression between WT and Sin3B KO HSCs.

overall_design: RNA profiles from WT and Sin3B KO HSCs were generated in duplicate.

first: Gregory

last: David


title: Comparative miRNome analysis of bovine sera and exosomes revealing their distinct advantages in studying cattle health

city: Edmonton

first: Guanxiang

last: Liang

state: Alberta

address: 410 Agriculture/Forestry Centre

institute: University of Alberta

summary: Recently, extra-cellular components, such as serum and exosome, attract more and more attention as biomarker candidates for mammalian health. However, the contribution of different blood components to the signature of respective microRNAs (miRNAs) remains unknown, especially in cattle. In this study we aimed to investigate the miRNAs from bovine sera and exosomes, and to provide insights into their future applications. Blood collected from four healthy dairy cows were used for this study. The sera and exosomes RNAs were extracted using two commonly used commercial kits (Norgen and Invitrogen total RNA isolation kit), respectively. Sera showed higher complexity of miRNome consisting of 328 miRNAs, while significantly less miRNAs (260, p = 0.001) were detected in exosomes. The profile of total detected miRNAs in sera and exosomes was different, while exosomes represented about 78% of total miRNAs expressed in sera, suggesting that exosomes are the major miRNAs carriers in bovine sera. There were 24 and 3 miRNAs (RPM > 5) that exclusively expressed in sera and exosomes, respectively. In addition, 12 miRNAs were differentially expressed between sera and exosomes (FDR < 0.05). Moreover, functional analysis showed that uniquely and highly expressed miRNAs in sera targeted functions of diseases and disorders, while the functions of those in exosomes were enriched in tissue development and lipid metabolism. Our results provide evidence that bovine sera and exosomes miRNomes are different with regarding to miRNA numbers, types and expressions. Based on their distinct profiles, miRNAs from sera and exosomes may reflect different aspects of physiological and pathological conditions in cattle. The functional analysis suggest that sera may be preferable for the purpose of detecting inflammation in cattle, while exosomes may be a better choice for monitoring the status of muscle development and lipid metabolism.

overall_design: Four blood samples were collected from four healthy dairy cattle, and sera were isolated. Using serum and exosome RNA extraction kits to extract the sera and exosomes total RNA, and the microRNA expression was profiled.

first: Ke

last: Zhao


title: An interaction with Ewing's sarcoma breakpoint protein EWS defines the subset of ETS factors rearranged in prostate cancer

city: Bloomington

first: Vivekananda

last: Kedage

state: IN

address: 1001 E. third Street

institute: Indiana University

summary: ERG activates prostate cancer specific gene expression program by recruiting RNA binding protein EWS to ETS-AP1 and GGAA microsatellite enhancers

overall_design: ChIP-Seq of transcription factor ERG and its co-activator EWS

first: Nagarathinam

last: Selvaraj

first: Justin

last: Budka

first: Travis

last: Jerde

first: Peter

last: Hollenhorst


title: An interaction with Ewing's sarcoma breakpoint protein EWS defines the specific oncogenic mechanism of ETS factors rearranged in prostate cancer

summary: ERG activates prostate cancer specific gene expression program by recuriting RNA binding protein EWS

overall_design: RNA-seq of polyA selected RNA from RWPE1 cells expressing either empty vector, ERG-WT, ERG-WT with EWS shRNA, and ERG-P436A


title: The RNA-binding landscape of RBM10 and its role in alternative splicing regulation in models of mouse early development

status: Public on Oct 29 2016

city: Edinburgh

first: Julie

last: Rodor

address: Western General Hospital

department: MRC Human Genetics Unit

institute: University of Edinburgh

summary: Mutations in the RNA-binding protein, RBM10, result in a human syndromic form of cleft palate, termed TARP syndrome. A role for RBM10 in alternative splicing regulation has been previously demonstrated in human cell lines. To uncover the cellular functions of RBM10 in a cell line that is relevant to the phenotype observed in TARP syndrome, we used iCLIP to identify its endogenous RNA targets in a mouse embryonic mandibular cell line. We observed that RBM10 binds to pre-mRNAs with significant enrichment in intronic regions, in agreement with a role for this protein in pre-mRNA splicing. In addition to protein-coding transcripts, RBM10 also binds to a variety of cellular RNAs, including non-coding RNAs, such as spliceosomal small nuclear RNAs, U2 and U12. RNA-seq was used to investigate changes in gene expression and alternative splicing in RBM10 KO mouse mandibular cells and also in mouse ES cells. We uncovered a role for RBM10 in the regulation of alternative splicing of common transcripts in both cell lines but also identified cell-type specific events. Importantly, those pre-mRNAs that display changes in alternative splicing also contain RBM10 iCLIP tags, suggesting a direct role of RBM10 in these events. Finally, we show that depletion of RBM10 in mouse ES cells leads to proliferation defects and to gross alterations in their differentiation potential. These results demonstrate a role for RBM10 in the regulation of alternative splicing in two cell models of mouse early development and suggests that mutations in RBM10 could lead to splicing changes that affect normal palate development and cause human disease.

overall_design:
We carried out the iCLIP-seq of endogenous mouse RBM10 protein in 4 independent replicates in a mouse mandibular MEPA (Mouse Embryonic Pharyngeal Arch) cell line. For each replicate, we included a control iCLIP corresponding to an IP with rabbit IgG. Reads were mapped to the mouse genome (mm9) and we deduced the crosslink nucleotide counts for each genomic position.
We performed RNA-Seq on polyA+ RNA isolated from RBM10 Knockout in md MEPA and ES cells.
RBM10 KO md MEPA cells were obtained using CRIPR/Cas9 approach. We extracted RNAs from 4 independent RBM10 KO md cell lines (KO1 and KO2 with deletion in exon 3 and KO3 and KO4 with deletion in exon 9) and from WT md MEPA cells (Cont) in triplicates.
RBM10 KO ES cell line, that correspond to the male gene trap cell line Rbm10Gt(CSI176)Byg, was obtained from Baygenomics. We also obtained the parental cell line E14Tg2a.4 from Baygenomics. RNAs were extracted from RBM10 KO and Cont ES cells in triplicates.

last: FitzPatrick

first: Eduardo

last: Eyras

first: Javier

last: Cáceres


title: Human tracheobronchial epithelial (HTBE) cell transcriptome response to infection with H1N1, H3N2, and H5N1 influenza virus.

status: Public on Oct 27 2016

city: La Jolla

first: Max

last: Chang

address: 9500 Gilman Drive

institute: University of California, San Diego

summary: Human tracheobronchial epithelial (HTBE) cells are considered to serve as a good correlate of influenza virus infection in the human respiratory tract. mRNA-Seq analysis was used to profile the cellular transcriptome of HTBE cells at multiple time points in response to infection with influenza A/California/04/09 (H1N1), A/Wyoming/03/03 (H3N2), and A/Vietnam/1203/04 (H5N1) HALo virus. The Influenza A/Vietnam/1203/04 (H5N1) HALo mutant virus is an attenuated H5N1 virus generated from wild-type Influenza A/Vietnam/1203/04 (H5N1) virus as described in Steel, J., et al. J Virol. 2009 Feb; 83(4):1742-53.

overall_design: Human tracheobronchial epithelial (HTBE) cells that have been isolated from normal donor airway epithelial tissue were infected with influenza A/California/04/09 (H1N1), A/Wyoming/03/03 (H3N2), and A/Vietnam/1203/04 (H5N1) HALo virus at an MOI of 5. H3N2- and H5N1-infected samples and time-matched mock-infected samples were collected in duplicates at 3, 6, 12, and 18 hrs post infection for mRNA-Seq analysis. Sample from H1N1-infected cells and mock controls were collected at 3, 6, 12, 18, and 24 hrs.

first: Matthew

last: Urbanowski

first: Megan

last: Shaw

first: Sven

last: Heinz

first: Chris

last: Benner

first: Lars

last: Pache

first: Randy

last: Albrecht

first: Adolfo

last: Garcia-Sastre


title: Splinted Ligation Adapter Tagging, a novel library preparation for whole genome bisulphite sequencing

city: Uppsala

first: Jessica

last: Nordlund

address: Academic Hospital, Entrance 70, 3rd floor

department: Medical Sciences

country: Sweden

institute: Uppsala University

type: Methylation profiling by high throughput sequencing

summary: Library preparation for whole genome bisulphite sequencing (WGBS) is challenging due to side effects of the bisulphite treatment, which leads to extensive DNA damage. Recently, a new generation of methods for bisulphite sequencing library preparation have been devised. They are based on initial bisulphite treatment of the DNA, followed by adaptor tagging of single stranded DNA fragments, and enable WGBS using low quantities of input DNA. In this study, we present a novel approach for quick and cost effective WGBS library preparation that is based on splinted adaptor tagging (SPLAT) of bisulphite-converted single-stranded DNA. Moreover, we validate SPLAT against three commercially available WGBS library preparation techniques, two of which are based on bisulphite treatment prior to adaptor tagging and one is a conventional WGBS method.

overall_design: WGBS libraries were prepared with DNA from human lymphoblastoid cell line NA10860 and the ALL cell line REH

first: Amanda

last: Raine

first: Erika

last: Manlig

first: Per

last: Wahlberg

first: Ann-Christine

last: Syvänen


first: Tamas

last: Fischer

summary:
RNA-DNA hybrids are a major internal cause of DNA damage within cells, and their degradation by RNAse H enzymes is important for maintaining genomic stability.
Here, we identified an unexpected role for RNA-DNA hybrids and RNase H enzymes in DNA repair.
Using a site-specific DNA double-stranded break (DSB) system in Schizosaccharomyces pombe, we showed that RNA-DNA hybrids form as part of the homologous recombination (HR)-mediated DSB repair process
and RNase H enzymes are essential for their degradation and efficient completion of DNA repair.
Deleting RNase H stabilizes RNA-DNA hybrids around DSB sites and strongly impairs recruitment of the ssDNA-binding RPA complex.
In contrast, overexpressing RNase H1 destabilizes these hybrids, leading to excessive strand resection and RPA recruitment, and to severe loss of repeat regions around DSBs.
Our study challenges the existing model of HR-mediated DSB repair, and reveals a surprising role for RNA-DNA hybrids in maintaining genomic stability.

overall_design:
Inducible Double Strand Break (DSB) system. 6 samples, all in duplicates (12 samples alltogether)
Insert sequence file (DSB.system.insert.txt); modified S. pombe genome sequence (Schizosaccharomyces_pombe.ASM294v2.29.dna.genome.modified_DSBsystem03032016.fa), and modified S. pombe annotation file (Schizosaccharomyces_pombe.ASM294v2.29.dna.genome.modified_DSBsystem03032016.bed)

first: Corina

last: Ohle

first: Rafael

last: Tesorero

first: Géza

last: Schermann

first: Nikolay

last: Dobrev

first: Irmgard

last: Sinning

first: Tamás


title: Snai2 and Snai3 transcriptionally regulate cellular fitness and functionality of T cell lineages through distinct gene programs

city: Saskatoon

first: Peter

middle: Dion

last: Pioli

state: SK

address: 107 Wiggins Rd

department: Biochemistry, Microbiology and Immunology

institute: University of Saskatchewan

summary: T lymphocytes are essential contributors to the adaptive immune system and consist of multiple lineages that serve various effector and regulatory roles.  As such, precise control of gene expression is essential to the proper development and function of these cells.  Previously, we identified Snai2 and Snai3 as being essential regulators of immune tolerance partly due to the impaired function of CD4+ regulatory T cells in Snai2/3 conditional double knockout mice.  Here we extend those previous findings using a bone marrow transplantation model to provide an environmentally unbiased view of the molecular changes imparted onto various T lymphocyte populations once Snai2 and Snai3 are deleted.  The data presented here demonstrate that Snai2 and Snai3 transcriptionally regulate the cellular fitness and functionality of not only CD4+ regulatory T cells but effector CD8α+ and CD4+ conventional T cells as well.  This is achieved through the modulation of gene sets unique to each cell type and includes transcriptional targets relevant to the survival and function of each T cell lineage.  As such, Snai2 and Snai3 are essential regulators of T cell immunobiology.

overall_design: GFP- CD3e+ CD8a+ CD4-, GFP- CD3e+ CD8a- CD4+ CD25- and GFP- CD3e+ CD8a- CD4+ CD25+ T cells were isolated from spleens of UBC-GFP mice transplanted with WT or cDKO lineage-depleted donor bone marrow following lethal irradiation of recipient mice.  RNA-seq was performed on 3-4 biological replicates from each genotype for all T cell populations analyzed.

middle: D

first: Sarah

middle: K

last: Whiteside

first: Janis

last: Weis

first: John

middle: H


title: Lysine-specific demethylase 1 target genes in brown adipocytes

first: Dominica

last: Willmann

address: Breisacherstr. 66

institute: Uniklinik-Freiburg


title: Lysine-specific demethylase 1 targets in brown adipocytes [ChIP-seq]

summary:
The aim of this study is to identify the Lsd1 genome binding profile in brown adipocytes.
Purpose: The aim of this study is to identify the Lsd1 genome binding profile in brown adipocytes.
Methods: Libraries were prepared from Lsd1-immunoprecipitated DNA according to standard methods. ChIP-seq libraries were sequenced using a HiSeq 2000 (Illumina) and mapped to the mm10 reference genome using bowtie 2 (Langmead et al., 2009). Data were further analysed using the peak finding algorithm MACS 1.41 (Zhang et al., 2008) using input as control. All peaks with FDR greater than 0.3 % were excluded from further analysis. The uniquely mapped reads were used to generate the genome-wide intensity profiles, which were visualized using the IGV genome browser (Thorvaldsdottir et al., 2012).
Results: HOMER (Heinz et al., 2010) was used to annotate peaks, to calculate overlaps between different peak files, and for motif searches. The genomic features (promoter, exon, intron, 3’ UTR, and intergenic regions) were defined and calculated using Refseq and HOMER. Genes annotated by HOMER were further used for a pathway analysis in WebGestalt (Heinz et al., 2010; Wang et al., 2013). ChIP-seq analysis revealed that Lsd1 was located at the promoter of 11735 genes.

overall_design: Lsd1 binding profile in brown adipocytes; Primary brown adipocytes were differentiated for 10 days in adipogenic medium. Cells were fixed for 5 min at room temperature according to Arrigoni et al. 2015

first: Delphine

last: Duteil

first: Laura

last: Arrigoni

first: Roland

last: Schüle


title: Transcriptomic profile of several temperate Cluster N actinobacteriophages during various stages of growth.

first: Travis

last: Mavrich

state: Pennsylvania

address: 4249 Fifth Avenue

department: Biological Sciences

institute: University of Pittsburgh

summary: The goal of this sequencing project was to measure transcription levels of several Cluster N actinobacteriophages during different stages of their lifecycle, including lysogeny, early infection (30 minutes), and late infection (2 hours 30 minutes), in order to study which genes contribute to superinfection exclusion.

sample_organism:
Mycolicibacterium smegmatis MC2 155
Mycobacterium phage Charlie
Mycobacterium phage Redi
Mycobacterium phage Butters
Mycobacterium phage MichelleMyBell
Mycobacterium phage Xerxes
Mycobacterium phage Panchino
Mycobacterium phage Xeno
Mycobacterium phage Phrann

overall_design: Total RNA was isolated from cultures grown in log phase, depleted of rRNA and prepared for sequencing using a strand-specific library kit during lysogeny, early infection (30 minutes), and late infection (2 hours 30 minutes) of phages Butters, Charlie, MichelleMyBell, Panchino, Phrann, Redi, Xeno, and Xerxes A total of twelve different RNA samples were prepared

first: Graham

last: Hatfull

first: Rebekah

last: Dedrick

middle: N

first: Daniel

last: Russell

first: Rebecca

last: Garlena


title: Determination of Lsd1 function in brown adipose tissue by global transcriptome analysis [RNA-seq]

summary: To investigate the role of Lsd1 in BAT, we crossed mice harboring conditional Lsd1 alleles (Zhu et al., 2014) with the Ucp1-Cre deleter strain (Turpin et al., 2014), which results in Cre-mediated loss of Lsd1 selectively in brown adipocytes. Transciptome analysis of BAT obtained from control and knock-out mice revealed 3322 genes differentially expressed between Lsd1 knock-out and control mice at 10 weeks of age (p-value<10-2).

overall_design:
We selectively knocked-out Lsd1 in brown adipose tissue by crossing Lsd1 floxed mice to Ucp1-Cre mice. RNA from BAT of 10 week.old control (Lsd1 floxed mice) and knock-out mice was extracted with trizol according to the manufacturer protocol. RNA samples were sequenced by the standard Illumina protocol to create raw sequence files (.fastq files). We annotated these reads to the mm10 build of the mouse genome using TopHat version 2. The aligned reads were counted with the homer software (analyze RNA) and DEG’s were identified using EdgeR and DESeq version 1.8.3.
LSD1 binding profile in fat cells - samples and experiments will continue to be added to this study over the course of the project.

first: Milica

last: Tosic


title: RNA-seq analysis of S. pneumoniae Pn-STP (PhpP) mutants

city: Columbus

first: Vijay

last: Pancholi

state: OH

address: 420W 12th Ave, TMRF-288

department: Pathology

institute: Ohio State University

summary: We report the mRNA expression profile of Streptococcus pneumoniae Type 2 D39 strain-derived mutant lacking the phpP gene encoding eukaryote-type ser/thr phosphatase .

overall_design: Measuring transcriptome profiling in D39ΔphpP mutants vs D39-WT pneumococcus wild-type strain


title: Single-cell RNA Sequencing Uncovers A Close Relationship Between Differentiating Dopamine and Subthalamic Nucleus Neuronal Lineages

city: Stockholm

first: Nigel

last: Kee

address: Nobels vag 3

institute: LICR Stockholm

summary: Stem cell engineering and grafting of mesencephalic dopamine (mesDA) neurons provides a promising strategy for brain repair in Parkinson’s disease (PD). However, essential refinement of differentiation protocols will require deeper interrogation of mesDA neuron lineage development. Here we studied neuronal development at the transcriptome-wide expression level by single-cell RNA sequencing of cells expressing the mesDA neuron transcription factor determinant Lmx1a. This approach resolved the differentiation of mesDA and neighboring neuronal lineages and revealed a remarkably close relationship between developing mesDA and subthalamic nucleus (STN) neurons. The combined ablation of Lmx1a and Lmx1b in mice disrupted both STN and mesDA neural development, while a distinct transcription factor set defined progenitors developing into STN neurons. Importantly, markers previously used to guide stem cell engineering into human mesDA neurons are shared between the two lineages. These results have important implications for stem cell engineering into mesDA neurons for cell replacement therapy in PD.

overall_design: Single-cell Smart-seq2 rna-sequencing of E10.5 to E13.5 developing ventral midbrain cells

first: Thomas

last: Perlmann


title: RBM25 is a global splicing factor promoting inclusion of alternatively spliced exons

status: Public on Oct 26 2016

first: Or

last: Gozani

address: 371 Serra Mall

department: Biology

summary: The goal of this study was to determine the role of RBM25 in pre-mRNA splicing and examine whether lysine 77 contributes to this function.

overall_design: We examined mRNA transcript level and splicing events in 293T cells in two experiments. First is CRISPR/Cas9 depletion of RBM25 vs control sgRNA. Second is over-expression of GFP, RBM25 or RBM25 K77R mutant.

first: Scott

last: Carlson

first: Cameron

last: Soulette

first: Ze

last: Yang

first: Joshua

last: Elias

first: Angela

last: Brooks


title: RNA-sequencing profiles of e12.5 transcriptomes in WT and Itgb1-/- mouse pituitaries.

first: Michal

last: Krawczyk

address: 9500 Gilman Dr

department: Ophthalmology

institute: UCSD

summary: The goal of the study was to understand how integrin beta1 expressed in epithelial cells directs developmental angiogenesis. Integrin beta1 was deleted specifically in the pituitary glands of embryonic mice. RNA was isolated from knockout and WT control pituitaries dissected at e12.5, one day prior to the initiation of developmental angiogenesis.

overall_design: RNA from the e12.5 pituitaries of 3 WT and 2 KO littermate embryos was profiled.

first: Kathleen

last: Scully

first: Daria

last: Merkurjev

first: Michael

middle: G

last: Rosenfeld


title: Overexpression of PHF8 promotes an EMT-related gene signature in MCF10A cells

city: Iowa City

first: Noah

last: Butler

state: IA

address: 4-350 BSB, 51 Newton Road

department: Department of Microbiology and Immunology

institute: University of Iowa

summary: PHF8 exerts distinct functions in different types of cancer. However, the mechanisms underlying its specific functions in each case remain obscure. To establish whether overexpression of PHF8 regulates the TGF-β induced the epithelial-mesenchymal transition (EMT), we treated MCF10A-Mock (control) and MCF10A-PHF8wt (overexpressing wild-type PHF8) cells with TGF-β1 for 0, 24, 48 and 72 hours and performed RNA-seq in biological duplicates. Our data indicated that EMT gene signatures were significantly enriched in MCF10A-PHF8 cells with TGF-β1 treatment at all time points, strongly indicating that PHF8 overexpression induces a sustained EMT signaling program.

overall_design: mRNA profiles of MCF10A-Mock (control) and MCF10A-PHF8 with TGF-β1 treatment for 0, 24, 48 and 72 hours were generated by RNA-seq, in duplicate, using HiSeq2500 instrument.

first: Peng

last: Shao

first: Hank

last: Qi


title: Comprehensive transcriptome analysis of phytohormone pathway genes and miRNAs in ABA initiated strawberry receptacle ripening

city: Hangzhou

first: Dongdong

last: Li

state: Zhejiang

address: Yuhangtang Road

department: Food Science and Nutrition

institute: Zhejiang University

summary: We used Illumina sequencing to investigate the global transcriptomic expression of hormonal pathway genes in ABA initiated strawberry receptacle ripening. Expression profiles of hormone synthetic and signaling genes further demonstrated the positive roles of ABA and GA, and the negative role of auxin in receptacle ripening. We also evaluated the transcript profiling of ethylene and JA pathway genes, and the results suggested that both ethylene and JA participated in receptacle ripening. Furthermore, two novel miRNAs and three conserved miRNAs were identified and validated to target genes in ABA and auxin pathways, respectively. Our analyses reveal the molecular mechanism of hormonal regulation during strawberry receptacle ripening. The data also provide an abundant of genetic information for molecular manipulation on non-climacteric fruit ripening.

overall_design: Sample 1: CK0 (Strawberry fruit two weeks after athesis treated with water, set as day 0); Sample 2: CK5 (fruit treated with water on day 5); Sample 3: CK8 (fruit treated with water on day 8); Sample 4: ABA5 (fruit treated with ABA on day 5); Sample 5: ABA8 (fruit treated with ABA on day 5); Sample 6: NDGA5 (fruit treated with water on day 5); Sample 7: NDGA8 (fruit treated with NDGA on day 8).

first: Zisheng

last: Luo


title: Tracing Enhancer Networks using Epigenetic Traits (TENET)

city: Los Angeles

first: Suhn

last: Rhie

address: 1450 Biggy Street NRT 3504

department: Biochemistry and Molecular Medicine

institute: University of Southern California

summary: Although technological advances now allow increased tumor profiling, a detailed understanding of the mechanisms leading to the development of different cancers remains elusive. Our approach towards understanding the molecular events that lead to cancer is to characterize changes in transcriptional regulatory networks between normal and tumor tissue. Because enhancer activity is thought to be critical in regulating cell fate decisions, we have focused our studies on distal regulatory elements and transcription factors that bind to these elements. Using DNA methylation data, we identified more than 25,000 enhancers that are differentially activated in breast, prostate, and kidney tumor tissues, as compared to normal tissues. We then developed an analytical approach called TENET (Tracing Enhancer Networks using Epigenetic Traits) that correlates DNA methylation levels at enhancers with gene expression to identify more than 800,000 genome-wide links from enhancers to genes and from genes to enhancers. We found more than 1,200 transcription factors to be involved in these tumor-specific enhancer networks. We further characterized several transcription factors linked to a large number of enhancers in each tumor type, including GATA3 in non-basal breast tumors, HOXC6 and DLX1 in prostate tumors, and ZNF395 in kidney tumors. We showed that HOXC6 and DLX1 are associated with different clusters of prostate tumor-specific enhancers and confer distinct transcriptomic changes upon knockdown in C42B prostate cancer cells. We also discovered de novo motifs enriched in enhancers linked to ZNF395 in kidney tumors. Our studies characterized tumor-specific enhancers and revealed key transcription factors involved in enhancer networks for specific tumor types and subgroups. Our findings, which include a large set of identified enhancers and transcription factors linked to those enhancers in breast, prostate, and kidney cancers, will facilitate understanding of enhancer networks and mechanisms leading to the development of these cancers.

overall_design:
Examination of FAIRE and ChIP assays in prostate and breast epithelial cells.
RNA-seq assays in C42B, prostate cancer cell line after knocking down of TFs (HOXC6, DLX1).

first: Yu

last: Guo

first: YuGyoung

last: Tak

first: Peggy

last: Farnham


title: Gene expression of collecting duct carcinoma of the kidney

status: Public on Oct 25 2016

city: Buffalo

first: Jianmin

last: Wang

state: NY

address: Elm and Carlton Streets

department: Bioinformatics and Biostatistics

institute: Roswell Park Comprehensive Cancer Center

summary: The genetic landscape and molecular features of collecting duct carcinoma (CDC) of the kidney remain largely unknown. Herein, we performed whole exome sequencing (WES) and transcriptome sequencing (RNASeq) on 7 CDC samples (CDC1 -7). Among the 7 samples, 4 samples with matched non-tumor tissue were used for copy number analysis by SNP array data. No recurrent somatic SNVs were observed except for MLL, which was found to be mutated (p.V297I and p.F407C) in 2 samples. We identified somatic SNVs in 14 other cancer census genes including: ATM, CREBBP, PRDM1, CBFB, FBXW7, IKZF1, KDR, KRAS, NACA, NF2, NUP98, SS18, TP53, and ZNF521. SNP array data identified a CDKN2A homozygous deletion in 3 samples and SNV analysis showed a non-sense mutation of the CDKN2A gene with unknown somatic status. To estimate the recurrent rate of CDKN2A abnormalities, we performed FISH screening of additional samples and confirmed the frequent loss (62.5%) of CDKN2A expression. Since cisplatin based therapy is the common treatment option for CDC, we investigated the expression of solute carrier (SLC) family transporters and found 45% alteration. In addition, SLC7A11 (cystine transporter, xCT), a cisplatin resistance associated gene, was found to be overexpressed in 4 out of 5 (80%) cases of CDC tumors tested, as compared to matched non-tumor tissue. In summary, our study provides a comprehensive genomic analysis of CDC and identifies potential pathways suitable for targeted therapies.

overall_design:
Paired tumor and normal samples from 7 patients
------------------------------------
The author states that the CDC5 normal sample is unavailable: CDC samples are rare and for CDC5, we don't have a matched normal

first: Antonios

last: Papanicolau-Sengos

first: Sreenivasulu

last: Chintala

first: Roberto

last: Pili


title: Targeting and Regulation of Epstein-Barr Virus Origin of DNA Replication by MicroRNA Hsa-miR-155

city: Taipei

first: Yu-Chan

last: Chao

state: Taiwan

address: 128 Academia Road, Section 2, Nankang

department: Institute of Molecular Biology

country: Taiwan

institute: Academia Sinica

summary: MicroRNAs (miRNAs) are a class of small RNA molecules previously known to function as post-transcriptional regulators in multiple cellular processes. Here, we show that a human cellular miRNA, hsa-miR-155, can regulate the latent replication origin (oriP) of Epstein-Barr virus (EBV) by competing with Epstein-Barr nuclear antigen 1 (EBNA-1) for direct binding to the dyad symmetry (DS) sequence on the oriP, and thus regulate the function of the DNA replication origin. When this direct binding was abolished by introducing a mutation into the hsa-miR-155 or DS sequence, replication resumed. Furthermore, endogenous hsa-miR-155 could target specifically to the EBV genomic replication origin in EBV type I-latently infected cells and regulate the viral DNA replication. Our discovery represents a hitherto undiscovered and important function of miRNA for the control of DNA replication, and demonstrates a probable mechanism of how this can be achieved using the latent replication origin of EBV.

overall_design: In this sequencing, miR-155, miR-3117 and miR-control (based on miR-67) were used to evaluate the targeting sequence in DS element of EBV.

first: Yueh-Lung

last: Wu

first: Carol

middle: P

first: Tzu-Chien

last: Kao

first: Paul

middle: W

last: Hsu

first: Chih-Hsuan

last: Tsai

first: Chien-Hsien

last: Lee

first: Hsuan

last: Tung

first: Sung-Chan

last: Wei

first: Catherine

last: Liu


title: CD133+ vs. CD133- cells in GBML8, a primary glioblastoma tumorsphere culture

first: Igor

last: Dolgalev

address: 550 1st Ave

institute: NYU Grossman School of Medicine

summary: CD133+ and CD133- cells were FACS islated from GBML8 cells to find gene signatures upregulated in cancer stem cells

overall_design: After surface immuno staining, CD133+ and CD133- cells were FACS isolated and subjected to RNA isolation. Experiment represent averaged data of 2 independent FACS isolations.

first: Dimitris

last: Placantonakis

first: Nermin

last: Bayin


title: ChIP-seq analysis of  oligodendrocytes treated with demyelinating compound lysolecithin

city: Xiamen

first: Ying

last: Chen

state: Fujian Provinee

address: XiangAn Nan Road

department: School of Life Sciences

institute: Xiamen University

summary: We performed a series of ChIP-Seq analysis, and demonstrated that Olig2 and its downstream target Gpr17 were the key factors functioning in demyelination process. During demyelination, Olig2 was significantly up-regulated, and Gpr17 was the top ranking Olig2 transcriptional target.

overall_design: ChIP-Seq analysis to examine the H3K27Ac and Olig2 recruitment to genome in oligdendrocytes

first: Zhimin

last: Ou


title: Impact of miRNA Levels, Target-Site Complementarity and Cooperativity on ceRNA-Regulated Gene Expression

city: South San Francisco

first: Vikram

last: Agarwal

address: 1130 Veterans Blvd

institute: Calico Life Sciences

summary: Expression changes of competitive endogenous RNAs (ceRNAs) have been proposed to influence microRNA (miRNA) activity and thereby regulate other transcripts that contain miRNA binding sites. Here, we find that although miRNA levels define the extent of repression, they do not affect the magnitude of the ceRNA expression change required to observe derepression. Canonical 6-nt sites, which typically mediate modest repression, can nonetheless compete for miRNA binding, with potency ~20% of that observed for canonical 8-nt sites. Sites with extensive additional complementarity can be even more potent, but this occurs predominantly through miRNA degradation rather than competition. Cooperative binding of closely spaced sites for different miRNAs can also increase potency. These results provide quantitative insights into the stoichiometric relationship between miRNA and target abundance, target-site spacing and affinity requirements for ceRNA-mediated gene regulation and specify the unusual circumstances in which ceRNA-mediated gene regulation might be observed.

overall_design: Sixty-four mRNA profiles were generated of 1) primary hepatocytes of mice expressing variable levels of a recombinant Adenovirus expressing the transcript of AldolaseA (Ad-AldoA), containing sites matching miR-122, let-7, miR-192, miR-194 or a mutated site (no site) or 2) embryonic stem (ES) cells that were transfected with a Tet-inducible dual-color reporter construct expressing enhanced yellow fluorescent protein (eYFP) and mCherry that contains zero (0s) or three (3s) 8 nt miRNA seed matches for miR-293 or miR-92 in the 3′ UTR. ES cells were sorted with a FACSAria IIIu flow cytometer into three bins based on their eYFP fluorescence intensity. All samples were sequenced in duplicates by an Illumina HiSeq 2500. Library preparation and sequencing were performed by Fasteris SA (Switzerland) or by the Functional Genomics Centre Zürich (FGCZ). Three small RNA profiles or either primary hepatocytes or embryonic stem cells were also generated by Solexa sequencing.

first: Rémy

last: Denzler

first: Sean

last: McGeary

first: Alexandra

last: Title

first: David

last: Bartel

first: Markus

last: Stoffel


title: H3K4me1 ChIP-seq in murine pre-B cells

first: Salvatore

last: Loguercio

state: California

address: 10550 North Torrey Pines Rd

department: MB

institute: TSRI

summary: H3K4me1 binding in murine pre-B cells detected by ChIP-seq.

overall_design: For the ChIP-seq, input and immunoprecipitated DNA was given to the TSRI Next Generation Sequencing Core (the Scripps Research Institute, La Jolla, CA, US), where it was prepared for massively parallel sequencing on Illumina HiSeq2000.

first: Ann

last: Feeney


title: Transcriptomic profiling of cardiac remodeling in high phosphate exposed cardiomyoblasts

city: Coimbatore

first: Manivannan

last: Jeganathan

state: Tamilnadu

address: Maruthamalai Road

department: Environmental Sciences

country: India

institute: Bharathiar University

summary: Cardiovascular disease (CVD) in chronic kidney disease (CKD) is characterized by vascular calcification and cardiac remodeling. CKD induced cardiac hypertrophy precedes cardiac fibrosis and is associated with left ventricular dysfunction. Elevated phosphate concentration due to renal failure is known to be involved in cardiac remodeling.

overall_design: Transcriptomic analysis of differentially expressed genes in H9c2 cardiomyoblasts treated with high phosphate by RNA-Seq and pathway analysis.

first: Jeganathan

last: Manivannan

first: Manjunath

last: Prashanth

first: Manickaraj

last: Shairam


title: Comprehensive analysis of microRNA signature of mouse pancreatic acini identifies over-expression of miR-21-3p in acute pancreatitis.

city: Minneapolis

first: Anne

last: Sarver

state: MN

address: 420 Delaware St. MMC 195, S.E Minneapolis, MN-55455

department: Surgery

institute: University of Minnesota

summary: In the current study, we characterized the global miRNA expression profile in mouse pancreatic acinar cells during acute pancreatitis using next-generation RNA-Sequencing. We identified 330 known and 6 novel miRNAs being expressed in mouse pancreatic acinar cells. At basal state, miR-148a-3p, miR-375-3p, miR-217-5p, miR-216a-5p were among the most abundantly expressed whereas miR-24-5p and miR-421-3p were least abundant. Treatment of acinar cells with supra-maximal caerulein or bile acid induced numerous changes in miRNA expression levels. In particular, we observed significant upregulation of miR-21-3p in these experiments, which was further, confirmed using mouse models of acute pancreatitis. In summary, this is the first comprehensive analysis of miRNA expression in healthy mouse pancreatic acinar cells and how this expression signature changes in acute pancreatitis.

overall_design: 5 treatment groups with 3 samples per group: control (no drug), Caerulein 100 nM (pathological dose),  Caerulein 100 pM (physiological dose),  TLC-S 62.5 uM, TLC-S 250 uM

first: Ajay

last: Dixit

first: Zuobiao

last: Yuan

first: John

last: George

first: Usman

last: Barlass

first: Hassam

last: Cheema

first: Archana

last: Sareen

first: Sulagna

last: Banerjee

first: Vikas

last: Dudeja

first: Rajinder

last: Dawra

first: Subbaya

last: Subramanian

first: Ashok

last: Saluja


title: Transcriptional profiling of newly generated dentate granule cells using TU-tagging reveals pattern shifts in gene expression during circuit integration

city: Brockport

first: Rongkun

last: Shen

address: 350 New Campus Dr

institute: SUNY Brockport

summary: We sequenced total 10 virus infected mouse hippocampus: 3 samples of lentivirus infected, 4 samples of 1st batch retrovirus infected as batch A, and 3 samples as batch B retrovirus infected.

overall_design: Examination of mRNA levels using TU-tagging approach that differ the newborn neurons from mature neurons.

first: Christina

last: Chatzi

first: Gina

last: Zhang

first: Gary

middle: L

last: Westbrook

first: Richard

last: Goodman


title: Pan-cancer transcriptomic analysis associates long non-coding RNAs with key mutational driver events

city: Gothenburg

first: Arghavan

last: Ashouri

address: Medicinaregatan 9A

department: Medical Biochemistry and Cell Biology

institute: University of Gothenburg

summary: To identify genes regulated by NFE2L2 (Nrf2), we selected a lung cancer cell line (A549) in which NFE2L2 is normally active. Three transfections using siRNAs targeting NFE2L2 and four control transfections using two different negative control siRNAs were done. As a result, we found several genes up or down regulated in response to NFE2L2 inactivation in these cells.

overall_design: A549 cells were cultured, and 250,000 cells were transfected with Lipofectamine RNAiMAX reagent containing 5 nmol siRNA particles in a 6-well plate. Three transfections with siRNAs targeting NFE2L2 were performed, using three independent duplexes, while four control transfections were done using two different control duplexes, in addition to one mock (Lipofectamine only) transfection. RNA was prepared using the RNeasy Mini kit. 8 strand-specific total RNA-seq libraries were generated on an Illumina NextSeq 500. Between 50.5 and 60.6 million reads were obtained per sample. Reads were aligned to hg19 genome, at an alignment rate exceeding 94.4% for all samples.

first: Volkan

middle: I

last: Sayin

first: Jimmy

last: Van den Eynden

first: Simranjit

middle: X

last: Singh

first: Thales

last: Papagiannakopoulos

first: Erik

last: Larsson


title: Modeling the ESR1 tyrosine 537 mutation with CRISPR-Cas9 for mechanistic studies and evaluation of therapeutic approaches for metastatic breast cancer [RNA-Seq]

city: London

first: Van

middle: Thuy Mai

last: Nguyen

address: 237 Fulham Rd, Chester Beatty Laboratories, third floor

department: Cancer Biology

institute: Institute of cancer research

summary: Estrogen receptor-α (ERα) is an important driver of breast cancer and is the target for hormonal therapies, anti-estrogens and drugs that limit estrogen biosynthesis (aromatase inhibitors). Mutations in the ESR1 gene identified in metastatic breast cancer provide a potential mechanism for acquired resistance to hormone therapies. We have used CRISPR-Cas9 mediated genome editing in the MCF-7 breast cancer cell line, generating MCF-7-Y537S. MCF-7-Y537S cells encode a wild-type (tyrosine 537) and a mutant (serine 537) allele. Growth of the line is estrogen-independent and expression of ERα target genes is elevated in the absence of estrogen. ER ChIP-seq was carried out to map global ERα binding sites in the presence and absence of estrogen. RNA-seq following estrogen treatment was used for gene expression analysis. We show that expression of ER target genes and ER recruitment to ER binding regions is similar in MCF-7 and MCF-7-Y537S cells, except that ER recruitment to DNA and expression of ER target genes is frequently elevated in the absence of estrogen.

overall_design: Hormone depleted MCF7 Luc or Y537S cells were treated with 10nM E2 or ethanol, as vehicle control, for 8 hours, with 3 replicates (2 replicates for Y537S + E2). RNA-seq was carried out using Illumina Hiseq 2500.

first: Simak

last: Ali

first: Alison

last: Harrod


title: Modeling the ESR1 tyrosine 537 mutation with CRISPR-Cas9 for mechanistic studies and evaluation of therapeutic approaches for metastatic breast cancer

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

overall_design: Refer to individual Series


title: RNA sequencing of hiPSC derived neural crest populations from Familial Dysautonomia patients

city: New York

first: Lorenz

last: Studer

department: Developmental Biology

institute: Memorial Sloan Kettering Cancer Center

summary: We have generated expression profiles of induced pluripotent stem cells (iPSCs) and iPSC-derived neural crest populations from Familial Dysautonomia patients.  These profiles were compared to a normal iPSC line that does not harbor the IKBKAP mutation.

overall_design: All cell types were differentiated from patient derived iPSCs.  Bulk iPSCs were harvested for RNA and the neural crest populations were sorted on day 18 for p75/HNK1 before RNA isolation.

first: Nadja

last: Zeltner


title: Study on miRNA expression pattern in Aging Mouse Hippocampal Neurons

city: DAEGU

first: keetae

last: kim

address: 333 TECHNO0 JUNGANG-DAERO

department: NEW BIOLOGY

country: South Korea

institute: DGIST

summary: Mouse hippocampal microRNA

overall_design: 3 samples

first: Chand

last: Mohammed

first: Keetae

last: Kim


title: Multiparameter functional diversity of human C2H2 zinc finger proteins [RNA-Seq]

city: Montreal

first: Hamed

last: Najafabadi

state: QC

address: 740 Dr. Penfield Avenue, Room 7202

department: Human Genetics

institute: McGill University

summary: C2H2 zinc finger proteins represent the largest and most enigmatic class of human transcription factors. Their C2H2 arrays are highly variable, indicating that most will have unique DNA binding motifs. However, most of the binding motifs have not been directly determined. We have determined the binding sites and motifs of 119 C2H2 zinc finger proteins and the expression pattern of 80 cell lines overexpressing C2H2 zinc finger proteins in order to study the role of C2H2 zinc finger proteins in gene regulation.

overall_design: We expressed GFP-tagged C2H2-ZF proteins in stable transgenic HEK293 cells. Total RNA was isolated using Trizol and sequencing libraries were constructed using TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold or TruSeq RNA Library Preparation Kit v2.

first: Frank

last: Schmitges

first: Ernest

last: Radovani

first: Jack

last: Greenblatt

first: Timothy

middle: R

last: Hughes


title: LKB1 loss links the serine metabolic network to DNA methylation and tumourigenesis [RNA-seq]

status: Public on Oct 24 2016

city: Cambridge

first: Rahul

last: Karnik

state: MA

address: 419 Broadway

summary: Intermediary metabolism generates substrates for covalent modification of chromatin, enabling potential coupling of metabolic states and epigenetic control. Here, we identify such a network as a major component of oncogenic transformation downstream of the LKB1 tumour suppressor. LKB1 encodes a serine-threonine kinase that integrates nutrient availability, metabolism and growth, however the mechanisms for LKB1-dependent tumour suppression remain elusive. By developing genetically engineered mouse and primary epithelial cell models and employing transcriptional, proteomics, and metabolic analyses, we find that oncogenic cooperation between LKB1 loss and KRAS activation, alterations commonly coinciding in human cancer, is fueled by pronounced mTOR-dependent induction of the serine-glycine-one carbon network coupled to S-adenosylmethionine generation. In concert, DNA methyltransferases (DNMT1, DNMT3A) are upregulated, leading to elevation in genomic 5-methylcytosine levels, with particular enrichment at retrotransposon elements, associated with silencing of retrotransposon transcription. Correspondingly, LKB1 deficiency renders cells highly sensitive to inhibition of serine biosynthesis and DNA methylation in vitro and in vivo. Thus, we define a hypermetabolic state resulting from LKB1 loss and KRAS activation that fuels changes in the epigenetic landscape. This state is critically required for the tumourigenic program of LKB1-mutant cells, suggesting novel points of therapeutic intervention in defined patient subsets.

overall_design: RNA-sequencing was performed using total RNA isolated from 2 independent murine pancreatic ductal cell lines from KRASG12D/+ (K) or KRASG12D/+;LKB1-/- (KL) genotypes or from the two independent KL lines transduced with full length LKB1 cDNA (rescue). RNAseq libraries were prepared using standard Illumina protocols and sequencing was performed in the Illumina HiSeq 2500 instrument. Data was processed using a standard RNA-seq pipeline that used Tophat2 to align the reads to mm9, and the Cufflinks suite8 to calculate differential expression.

first: Nabeel

last: Bardeesy

first: Alexander

last: Meissner


title: LKB1 loss links the serine metabolic network to DNA methylation and tumourigenesis [bisulfite-seq]

overall_design: Whole genome bisulfite sequencing profiles were generated for 2 independent murine pancreatic ductal cell lines from KRASG12D/+ (K) or KRASG12D/+;LKB1-/- (KL) mice.


title: Protection against maternal infection-associated fetal growth restriction: proof-of-concept with a microbial-derived immunomodulator

city: Subiaco

first: Anthony

last: Bosco

state: WA

address: 100 Roberts Road

institute: Telethon Kids Institute

summary: Infection-associated inflammatory stress during pregnancy is the most common cause of fetal growth restriction. Treatment strategies for protection of at-risk mothers are limited. Employing mouse models, we demonstrate that oral treatment during pregnancy with a microbial-derived immunomodulator (OM85), markedly reduces risk for fetal loss/growth restriction resulting from maternal challenge with bacterial LPS or influenza. Focusing on LPS exposure, we demonstrate that the key molecular indices of maternal inflammatory stress (RANTES, MIP-1a, CCL2, KC, G-CSF) in gestational tissues/serum, are abrogated by OM85 pretreatment. Systems-level analyses of RNASeq data revealed that OM85 pretreatment selectively tunes LPS-induced activation in maternal gestational tissues for attenuated expression of TNF-, IL1-, and IFNg- driven proinflammatory networks, without constraining Type1-IFN-associated networks central to first-line anti-microbial defense. This study suggests that broad-spectrum protection-of-pregnancy against infection-associated inflammatory stress, without compromising capacity for efficient pathogen eradication, represents an achievable therapeutic goal.

overall_design: Mice were exposed to four treatment conditions (sham control, OM85 pretreatment, LPS challenge, or OM85 pretreatment followed by LPS challenge). Gene expression patterns were profiled in two different tissues (uterus and decidua). There were six animals in each experimental group.

first: Anya

middle: C

last: Jones

first: Jean-Francois

last: Lauzon-Joset

first: Deborah

last: Strickland


title: RNA-Seq of Kidney Glomeruli from Type 2 diabetic (db/db) and non-diabetic mice

city: Houston

first: Shawn

middle: Samson

last: Badal

state: TX

address: 2121 W. Holcombe Blvd

department: Nephrology

institute: MD Anderson Cancer Center

summary: We investigated the gene expression profiles of RNA isolated from kidney glomeruli from aged, 25 week old type-2 diabetic (db/db) and non-diabetic mice.

overall_design: In order to investigate the consequences of hyperglycemia on the pathogenesis and progression of diabetic nephropathy Kidney glomeruli from 3 diabetic and 3 non-diabetic, control mice were isolated and RNA purified for RNA-Seq analysis on the Illumina HiSeq 2000. The goal of the project was to generate comprehensive list of noncoding RNA genes differentially regulated between the two conditions in order to identify novel targets for further study.

first: Farhad

last: Danesh

middle: S

first: Jianyin

last: Long


title: AZ1366: An inhibitor of tankyrase and the canonical Wnt pathway that limits the persistence of non-small cell lung cancer cells following EGFR inhibition

city: Cleveland

first: Jihye

state: Ohio

address: 9500 Euclid Ave.

department: Quantitative Health Sciences

institute: Cleveland Clinic

summary: EGFR-mut NSCLC lines show differential suceptibility to inhibition of tankyrase in the presence of EGFR inhibitors

overall_design: NSCLC cells were treated in quadruplicate with gefitinib, AZ1366 (tankyrase inhibitor) or a combination thereof

first: Hannah

middle: A

last: Scarborough

first: Barbara

last: Helfrich

first: Matias

last: Casas-Selves

first: Alwin

last: Schuller

first: Shaun

middle: E

last: Grosskurth

first: Aik-Choon

last: Tan

first: Daniel

last: Chan

first: Zhiyong

last: Zhang

first: Vadym

last: Vadym Zaberezhnyy

first: Paul

last: Bunn

first: James

last: DeGregori


title: In-phase oscillation of global regulons is orchestrated by a pole-specific organizer

city: Lausanne

first: Johann

last: Mignolet

address: Biophore Quartier UNIL-SORGE

department: DMF

country: Switzerland

institute: UNIL

summary: Cell fate determination in the asymmetric bacterium Caulobacter crescentus (Caulobacter) is triggered by the localization of the developmental regulator SpmX to the old (stalked) cell pole during the G1-S transition. While SpmX is required to localize and activate the cell fate-determining kinase DivJ at the stalked pole in Caulobacter, it is also required for organelle (stalk) positioning in the cousin Asticaccaulis. We unearth the conserved s54-dependent transcriptional activator regulator TacA as global regulator in Caulobacter whose activation by phosphorylation is indirectly down-regulated by SpmX. Using a combination of forward genetics and cytological screening we uncover a previously uncharacterized and polarized component (SpmY) of the TacA phosphorylation control system, and we show that the SpmY function and localization is conserved. Thus, we demonstrate that SpmX organizes a site-specific, ancestral and multi-functional regulatory hub whose function includes the coordinated control of two co-oscillating global transcriptional regulators, CtrA and TacA.

overall_design: Examination of 2 transcription factors occupancy in WT and two mutant backgrounds + assessment of synthetic lethal and viable genes in WT and one null-allele background

first: Balaganesh

last: Janakiraman

first: Sharath

last: Narayanan

first: Patrick

last: Viollier

first: Sunish

last: Radhakrishnan


title: Amino acid catabolism fuels microalgal lipogenesis

city: Singapore

first: Lina

last: Yao

address: 5 Science Drive 2

department: Department of Microbiology and Immunology

country: Singapore

institute: National University of Singapore

summary: Microalgal lipid, a feasible substrate for biofuel, is typically accumulated during the stationary growth phase. Generating strains which trigger lipogenesis from the exponential growth phase will enhance lipid productivity, reduce cost of biofuel production. We characterized a lipid-rich microalgal mutant, Dunaliella tertiolecta, which exhibited a six-fold enhancement of neutral lipids production in the exponential growth phase with marginal compromise on growth (4%). Using transcriptomics and metabolomics, regulatory mechanisms of the mutant were uncovered.

overall_design: Characterization of a lipid-rich mutant using transcriptomics and metabolomics.

first: Tin

first: Yuan

last: Lee


title: Genome wide map of  long noncoding RNA Tug1 binding sites in cultured mouse podocytes

first: Shawn

last: Badal

summary: We generated a genome wide map of instances where the long noncoding RNA, Tug1, binds to DNA in cultured mouse podocytes under normal glucose conditions using Chromatin-RNA Precipitation coupled with high throughput sequencing (ChIRP-Seq)

overall_design: 48 alternating (even, odd) biotynilated probes were designed to span the full length of Tug1 RNA. Chromatin was prepared from gluteraldehyde crosslinked nuclei from early passage podocytes. Chromatin extracts were duplicated with either even or odd probes. Duplicate samples for Input DNA, Even pulldown (PD) and Odd PD DNA was purified following incubation and supplied for Illumina sequencing by ArrayStar (Rockville, MD).

first: Farhad

last: Danesh

first: Jianyin

last: Long


title: Developmental gene expression of Hymenochirus boettgeri

city: Ulsan

first: Taejoon

last: Kwon

address: 50 Unist-gil

department: Department of Biomedical Engineering

institute: Ulsan National Institute of Science and Technology

summary: RNA-seq experiments to construct Hymenochirus bettgeri transcripts

overall_design: Collect mRNA from whole eggs/embryos/tadpoles, with poly-A enrichment method

first: K

last: Miller

first: R

last: Heald

first: A

last: Session

first: D

last: Rokhsar


title: RNA sequencing analysis of human podocytes reveals glucocorticoid regulated gene networks targeting non-immune pathways

city: Bristol

first: Lulu

last: Jiang

state: State...

address: Academic Renal Unit,Dorothy Hodgkin Building,Whitson Street

department: School of Clinical Sciences

institute: University of Bristol

summary: To understand the nature of glucocorticoids targeting non-immune cell function, we generate RNA sequencing data from 3 human podocyte cell lines derived from 3 kidney transplant donors and identify the genes that are significantly regulated in dexamethasone-treated podocytes compared to vehicle-treated cells.Our results represent a significant step forward in the genome-wide characterization of the molecular effects of glucocorticoids on human podocytes. The resource generated in this study is important for understanding the targeting of non-immune cell function by glucocorticoids and also for designing more specific podocyte-targeted agents for MCN therapy.

overall_design: Transcriptome profiles of human podocytes treated with vehicle and dexamethasone were generated by RNA-sequencing using Illumina HiSeq 2500

first: Charlie

last: Hindmarch

first: Mark

last: Rogers

first: Christy

last: Waterfall

first: Jane

last: Coghill

first: Peter

last: Mathieson

first: Gavin

last: Welsh


title: RNA-seq of brain mural cells and microvascular fragments

city: Uppsala

first: L.

last: He

address: Dag Hammarskjölds Väg 20

institute: Uppsala University

summary:
Purpose: Pericytes, the mural cells of blood microvessels, have come into focus as regulators of microvascular development and function, but due to paucity of defining markers, the identification and functional characterization of PC remain problematic, and reported data are often controversial. Here, we used a new approach for the isolation of mural cell from mouse brain in combination with RNA-sequencing (RNA-seq) and previously published vascular transcriptome data to assemble a state-of-the-art catalogue of brain mural cell-enriched gene transcripts.
Methods: We isolated double positive cells from the brain of Pdgfrb-eGFP/NG2-DsRed transgenic mice using FACS. Cells were lysed, RNA extracted and sequenced with next-generation sequencing (NGS). For comparison, we also determined the transcriptome of brain microvascular fragments (containing both endothelial cells and mural cells) isolated by mechanical tissue disintegration, collagenase digestion and immune-panning using anti-CD31 antibodies coupled to magnetic beads. The reads were aligned to the Ensembl mouse gene assembly (NCBIM37) using Tophat2 software (version 2.0.4). The duplicated reads were removed using the picard tool (version 1.92). To identify the genes significantly enriched in the pericyte samples as compared with microvascular samples, statistical tests were performed using the Cufflinks tool (version 2.2.1)
Results: The result showed that mRNA transcripts representing 856 different genes were enriched more than two-fold in FACS isolated Pdgfrb-eGFP/NG2-DsRed double positive cells compared with whole microvascular fragments (False Discovery Rate < 0.05)

overall_design: The RNA from three FACS sorted brain mural cell samples and three whole brain microvascular samples isolated from three animals were processed and sequenced on the Illumina HiSeq 2500 platform in the sequencing facility in Uppsala University.

first: Christer

last: Betsholtz


title: Chemical Enhancement of Direct Cardiac Reprogramming In Vitro and In Vivo

city: Louisville

first: Tamer

middle: M

last: Mohamed

state: KY

address: 580 S. Preston St., Baxter II Bldg., Room 122

department: Cardiology

institute: University of Louisville

summary: Reprogramming of cardiac fibroblasts into induced cardiomyocyte-like cells (iCMs) in situ represents a promising strategy for cardiac regeneration.  A combination of three cardiac transcription factors, Gata4, Mef2c and Tbx5 (GMT), can convert fibroblasts into iCMs, albeit with low efficiency in vitro. Here, we screened 5,500 compounds in primary cardiac fibroblasts and found that a combination of the transforming growth factor (TGF)-β inhibitor SB431542 and the WNT inhibitor XAV939 increased reprogramming efficiency eight-fold when added to GMT-overexpressing cardiac fibroblasts. The small-molecules also enhanced the speed and the quality of cell conversion, as we observed beating cells as early as 1 week after reprogramming compared to 6–8 weeks with GMT alone. In vivo, mice exposed to GMT, SB431542, and XAV939 for 2 weeks after myocardial infarction showed significantly improved reprogramming and cardiac function compared to those exposed to only GMT. Human cardiac reprogramming was similarly enhanced upon TGF-b and WNT inhibition and was achieved most efficiently with GMT plus Myocardin. Thus, TGF-β and WNT inhibitors jointly enhance GMT-induced direct cardiac reprogramming from cardiac fibroblasts in vitro and in vivo and provide a more robust platform for cardiac regeneration.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Examine RNA expression profile in iCMs (mouse in vitro, mouse in vivo and human in vitro)

first: Deepak

last: Srivastava


title: FOXA and master transcription factors recruit Mediator and Cohesin to the core transcriptional regulatory circuitry of cancer cells

city: Quebec

first: Steve

last: Bilodeau

state: Quebec

address: 2260 boul. Henri-Bourassa

institute: Centre de recherche du CHU de Québec-Université Laval

summary: The Mediator and Cohesin complexes control the cellular transcriptional program. However, it is not well understood how they are recruited to regulatory regions. Our study shows that the core transcriptional regulatory circuitry of cancer cells is essential to recruit Mediator, Cohesin and NIPBL to enhancer and promoter regions of actively transcribed genes in cancer cells.

overall_design: ChIP-seq analysis of Mediator (MED1), Cohesin (SMC1A) and NIPBL  in HEPG2, A549 and MCF7 cells. The analysis also includes ChIP-Seq data for the transcription factor ERa in MCF7 cells treated with estradiol.

first: Michèle

last: Fournier

first: Gaëlle

last: Bourriquen

first: Fabien

last: Lamaze

first: Éric


title: Modeling the ESR1 tyrosine 537 mutation with CRISPR-Cas9 for mechanistic studies and evaluation of therapeutic approaches for metastatic breast cancer [ChIP-Seq]

first: Van

last: Nguyen

summary: Estrogen receptor-α (ERα) is an important driver of breast cancer and is the target for hormonal therapies, anti-estrogens and drugs that limit estrogen biosynthesis (aromatase inhibitors). Mutations in the ESR1 gene identified in metastatic breast cancer provide a potential mechanism for acquired resistance to hormone therapies. We have used CRISPR-Cas9 mediated genome editing in the MCF-7 breast cancer cell line, generating MCF-7-Y537S. MCF-7-Y537S cells encode a wild-type (tyrosine 537) and a mutant (serine 537) allele. Growth of the line is estrogen-independent and expression of ERα target genes is elevated in the absence of estrogen. ER ChIP-seq was carried out to map global ERα binding sites in the presence and absence of estrogen. RNA-seq following estrogen treatment was used for gene expression analysis. We show that expression of ER target genes and ER recruitment to ER binding regions is similar in MCF-7 and MCF-7-Y537S cells, except that ER recruitment to DNA and expression of ER target genes is frequently elevated in the absence of estrogen

overall_design: Hormone depleted MCF-7 LUC /Y537S mutant cells were treated with estrogen (10nM) or ETOH as vehicle control for 45 mins. Erα Chip-seq was performed using Illumnia methodology

first: Simak

last: Ali

first: Alison

last: Harrod

middle: T

first: Luca

last: Magnani


title: Developmental gene expression of Xenopus laevis J strain

first: Taejoon

last: Kwon

overall_design: Refer to individual Series


title: Developmental gene expression of Xenopus laevis J strain [stage]

summary: Comprehensive RNA-seq experiments to measure the expression of homoeologs across different developmental stages, as a part of the Xenopus laevis genome project. This work is funded by Agency Japanese Ministry of Education, Culture, Sports, Science and Technology (MEXT; "Genome Science" Grant ID 221S0002).

overall_design: Collect mRNA from whole embryos; two clutches were used (Taira dataset for one pair, Ueno dataset for the other pair)

first: Shuji

last: Takahashi

first: Yutaka

last: Suzuki

first: Atsushi

last: Toyoda

first: Naoto

last: Ueno

first: Masanori

last: Taira


title: Tissue gene expression of Xenopus laevis J strain [tissue]

summary: Comprehensive RNA-seq experiments to measure the expression of homoeologs across different tissues, as a part of the Xenopus laevis genome project. This work is funded by Agency Japanese Ministry of Education, Culture, Sports, Science and Technology (MEXT; "Genome Science" Grant ID 221S0002).

overall_design: Collect mRNA from whole tissue; two female frogs were used as donors for most tissues (Taira dataset for one frog, Ueno dataset for the other frog); testis samples were collected from two male frogs (sibling of two female donors)


title: Direct regulation of alternative splicing by SMAD3 through interaction with PCBP1 is essential for the tumor-promoting role of TGF-beta

city: Bethesda

first: Ying

last: Zhang

state: Maryland

address: 37 Convent Dr., Bldg.37, Rm.2056

department: LCMB/CCR

institute: National Cancer Institute, NIH

summary:
To assess the global impact of TGF-beta on alternative splicing, we conducted RNA-seq of total RNAs isolated from various lines of HeLa cells that were generated for this study and treated without or with TGF-beta and EGF.
Using rMAT tool from the RNA-Seq data and annotation of transcripts in GTF format, we identified differential alternative splicing events between untreated and treated cell lines.
Our study shows that the TGF-beta-mediated alternative splicing affects the protein products of a large number of genes enriched in pathways critical for EMT, cykeskeleton organization, and adherens junction signaling.  PCBP1 was required for the most, if not all, alternative splicing events detected.

overall_design: SRA accession number: SRP061634, BioProject ID PRJNA290799.  RNAs from Hela cells were treated with TGF-β and EGF, in triplicates and sequenced on HiSeq2000 with 2 samples pooled into one lane with Illumina TruSeq v3 chemistry.


title: ABA is required for plant acclimation to a combination of salt and heat stress

city: Denton

first: Rajeev

middle: K.

last: Azad

state: Texas

address: 1155 Union Circle #305220

institute: University of North Texas

summary: We examined changes in steady-state transcript level in leaves of Arabidopsis plants subjected to salinity, heat stress and their combination by a transcriptome analysis of leaves.

overall_design: mRNA profiles of Arabidopsis plants subjected to salinity, heat stress and their comination were generated by RNA-Seq analysis, in triplicate, using an Illumina HiSeq2000.

first: Nobuhiro

first: Elias

last: Basil

first: Eduardo

last: Blumwald

first: Ron

last: Mittler


title: LKB1 loss links the serine metabolic network to DNA methylation and tumourigenesis

first: Rahul

last: Karnik

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


title: Large-scale epigenetic reprogramming is punctuated late during the evolution of pancreatic cancer progression [RNA-Seq]

city: Guangzhou

first: Xin

last: Li

state: Guangdong

address: 132 Daxuecheng Outer Ring E Rd

department: School of Medicine

institute: Sun Yat-sen University

summary: During pancreatic cancer progression, heterogeneous subclonal populations evolve in the primary tumor that possess differing capacities to metastasize and cause patient death. However, the genetics of metastasis reflects that of the primary tumor, and PDAC driver mutations arise early. This raises the possibility than an epigenetic process could be operative late. Using an exceptional resource of paired patient samples, we found that different metastatic subclones from the same patient possessed remarkably divergent malignant properties and global epigenetic programs. Global reprogramming was targeted to thousands of large chromatin domains across the genome that collectively specified malignant divergence. This was maintained by a metabolic shift within the pentose phosphate pathway, independent of KRAS driver mutations. Analysis of paired primary and metastatic tumors from multiple patients uncovered substantial epigenetic heterogeneity in primary tumors, which resolved into a terminally reprogrammed state in metastatic lesions. This supports a model whereby driver mutations accumulate early to initiate pancreatic tumorigenesis, followed by a period of subclonal evolution that generates sufficient intra-tumor heterogeneity for selection of epigenetic programs that may increase fitness during malignant progression and metastatic spread.

overall_design: To map the epigenomic landscape of pancreatic cancer progression as it evolves within patients. RNA-Seq of 2 patients (A13 and A38). Patient A38 included local peritoneal metastasis and 2 distant metastsis (liver and lung mets), and 6AN treated and DMSO control samples. Patient A13 included 2 primary tumors and 1 distant lung metastasis. Each sample has been done with replicates.

first: Oliver

last: McDonald

first: Christine

last: Iacobuzio-Donahue

first: Andrew

last: Feinberg


title: Large-scale epigenetic reprogramming is punctuated late during the evolution of pancreatic cancer progression [ChIP-Seq]

overall_design: To map the epigenomic landscape of pancreatic cancer progression as it evolves within patients. Chip-Seq (K27Me3, K36Me3, K9Me2/3, K4Me3 and K27Ac) of 2 patients (A13 and A38) and HPDE cell line. Patient A38 included local peritoneal metastasis and 2 distant metastsis (liver and lung mets), and 6AN treated and DMSO samples for lung matastasis. Patient A13 included 2 primary tumors and 1 distant lung metastasis. Each sample has been done with replicates.


title: Large-scale epigenetic reprogramming is punctuated late during the evolution of pancreatic cancer progression [BS-Seq]

overall_design: To map the epigenomic landscape of pancreatic cancer progression as it evolves within patients.  BS-Seq of 4 patients (A13, A38, A124 and A125). Patient A38 included local peritoneal metastasis and 2 distant metastsis (liver and lung mets). Patient A13 included 2 primary tumors and 1 distant lung metastasis. Each sample has been done with replicates. Patient A124 included 2 primary tumors and 1 normal pancreas.


title: Identification of miRNA, lncRNA and mRNA-associated ceRNA networks and potential biomarker for MELAS with mitochondrial DNA A3243G mutation

status: Public on Oct 23 2016

city: Jinan

first: Wei

last: Wang

state: Shandong

address: West Wenhua Road

department: Department of Neurology

institute: Qilu Hospital, Shandong University


title: Next Generation Sequencing Facilitates Quantitative Analysis of brain Transcriptome after viral infection with ZIKV (Zika Virus)

city: MIAMI

first: Fan

last: Lai

state: FL

address: 1501 NW 10th Ave, BRB 731G

institute: University of Miami

summary:
Purpose: The goals of this study are to understand ZIKV induced immune responses in the developing brain at genome-wide level.
Methods: Total RNA was isolated from E17.5 mouse brains after viral infection at E14.5. After genomic DNA and ribosomal RNA removal, fractionated RNA were subjected to strand-specific library preparation using NEBNext Ultra RNA Library Prep Kit. Sequencing was performed on Nextseq500 (Illumina). The sequencing reads that passed quality filters were analyzed with TopHat followed by Cufflinks.
Results:  After performed Gene Ontology analyses with RNA-seq data, our results revealed a set of genes that are associated with the immune response and apoptosis pathways. Gene Set Enrichment Analysis (GSEA) further show significant enrichments on both the immune system response and apoptosis pathways. Some of these results were also verified with qRT-PCR.
Conclusions: Our results suggest that ZIKV infection triggers an aggressive immune response, which has the potential to cause exacerbation of brain damage by enhancing neuronal death and generating vascular abnormalities. Our discovery of massive neuronal death, leaky blood-brain-barrier (BBB), and astrogliosis in ZIKV infected brains is the first study to suggest that ZIKA causes extensive brain damage.

overall_design: RNA-seq of C56BL/6 mouse E17.5 brain with or without Zika virus infection.

first: Jian-fu

last: Chen

first: Qiang

last: Shao

first: Stephanie

last: Herrlinger

first: Si-Lu

last: Yang

first: Julie

last: Moore

first: Melinda

last: Brindley


title: Transcriptome profiling at neural tube closure site

city: Baton Rouge

first: J. Michael

last: Salbaum

state: LA

address: 6400 Perkins Road

department: Regulation of Gene Expression

institute: Pennington Biomedical Research Center

summary: Maternal diabetes is a teratogen that can lead to neural tube closure defects in the offspring. We therefore sought to compare gene expression profiles at the site of neural tube closure between stage-matched embryos from normal dams, and embryos from diabetic dams. Neurulation-stage mouse embryos at 8.5 days of gestation were used to prepare neural tissue at the anterior aspect of neural tube closure site 1. Tissue was procured from the open neural tube immediately anterior of the closure site, and from the closed neural tube immediately posterior to the closure site by laser microdissection. For each sample, 10 sections were pooled, total RNA was extracted, and 7 ng of total RNA were used for expression profiling by Tag sequencing using an Applied Biosystems SolidSAGE kit for library construction, and an AB SOLiD 5500 XL instrument for sequencing. Sequence reads were mapped to RefSeq RNA, and count data per gene were obtained using a modified version of the Applied Biosystems SOLiD™ SAGE™ Analysis Software.

overall_design: diabetic dam - closed neural tube // diabetic dam - open neural tube // normal dam - closed neural tube // normal dam - open neural tube

first: J


title: Programs for the persistence, vigilance and control of human CD8+ lung-resident memory T cells

city: Amsterdam

first: Benjamin

last: Nota

state: Noord Holland

address: Plesmanlaan 125

department: Research Facilities

institute: Sanquin

summary: Tissue-resident memory T-cells (TRM) mediate optimal protection against respiratory infections. Little is known about human TRM. Here we characterized memory T-cells from human lungs. We identify two distinct memory T-cell populations in lung tissue. Lung TRM are poised for rapid, but restrained responsiveness by constitutive expression of genes encoding effector molecules and inhibitory regulators.  Although TRM express little T-bet and Eomesodermin, transcription factor signatures revealed that multiple drivers of effector gene expression are active in TRM, including Notch. We show that Notch is required for maintenance of the CD103+ TRM population in mouse lungs. These findings suggests that the lung tissue environment actively maintains the T-cells that protect it from infectious assault through activating the Notch surface receptor in TRM.

overall_design: From 18 mice, both CD69+ and CD69- memory T cells were taken, that were either treated with DMSO (control) or GSI, at time points 2 or 5 days.

first: Pleun

last: Hombrink

first: Christina

last: Helbig

first: Ronald

last: Backer

first: Berber

last: Piet

first: Ana

last: Oja

first: Regina

last: Stark

first: Giso

last: Brasser

first: Aldo

last: Jongejan

first: Rene

last: Jonkers

first: Onur

last: Basak

first: Hans

last: Clevers

first: Perry

last: Moerland

first: Derk

last: Amsen

last: van Lier


title: Identification of miRNA, lncRNA and mRNA-associated ceRNA networks and potential biomarker for MELAS with mitochondrial DNA A3243G mutation [sequencing]

first: Wei

last: Wang

summary: To elucidate the regulating networks of dysregulated ncRNAs in Mitochondrial myopathy, Encephalopathy, Lactic Acidosis, and Stroke-like episodes (MELAS) with m.A3243G mutation.

overall_design: The MELAS sample consisted of a muscle pool from 20 MELAS patients with m.A3243G mutation, and the Control sample consisted of a muscle pool from 20 healthy controls. LncRNA sequencing and miRNA array of muscle pools were performed by the service provider (LC Sciences). The secondary qRT-PCR validation of the most promising miRNAs and lncRNAs using individual samples were from the same group. The findings were all consistent with results from our high-throughput data.


title: Photomorphogenesis of Arabidopsis seedlings is accompanied by complex alternative splicing alterations

city: Tübingen

first: Andreas

last: Wachter

address: Auf der Morgenstelle 32

department: Center for Plant Molecular Biology

institute: University of Tübingen

summary: We analyzed transcriptome-wide gene expression and AS changes in etiolated Arabidopsis seedlings exposed to red, blue, and white light. Our study revealed that different types of light signals trigger rapid AS responses of numerous genes, including splicing factors and other functional groups. Among these candidates was RRC1, which was previously shown to function in PHYB signaling. The light signaling phenotype of an rrc1 mutant could only be complemented with the splicing variant being up-regulated upon light exposure, indicating a self-reinforcing circuit. Finally, we provide evidence that light-regulated AS can occur in a phytochrome-independent manner and is closely intertwined with the plant’s energy status.

overall_design: Analysis of alternative splicing patterns of dark-grown Arabidopsis seedlings exposed for 1 or 6 hours to white, blue, or red light, or kept in darkness; all samples in duplicates

first: Lisa

last: Hartmann

first: Philipp

last: Drewe

first: Gunnar

last: Rätsch


title: Neonatal cardiac dysfunction and transcriptome changes caused by the absence of Celf1

status: Public on Oct 22 2016

city: Portland

first: Zheng

last: Xia

state: Oregon

address: 3181 SW Sam Jackson Park Rd

institute: Oregon Health & Science University

summary: The RNA binding protein Celf1 regulates alternative splicing in the nucleus and mRNA stability and translation in the cytoplasm. Celf1 is strongly down-regulated during mouse postnatal heart development. Its re-induction in adults induced severe heart failure and reversion to fetal splicing and gene expression patterns. However, the impact of Celf1 depletion on cardiac transcriptional and posttranscriptional dynamics in neonates has not been addressed. We found that homozygous Celf1 knock-out neonates exhibited cardiac dysfunction not observed in older homozygous animals, although homozygous mice are smaller than wild type littermates throughout development. RNA-sequencing of mRNA from homozygous neonatal hearts identified a network of cell cycle genes significantly up-regulated and down-regulation of ion transport and circadian genes. Cell cycle genes are enriched for Celf1 binding sites supporting a regulatory role in mRNA stability of these transcripts. We also identified a cardiac splicing network coordinated by Celf1 depletion. Target events contain multiple Celf1 binding sites and enrichment in GU-rich motifs. Identification of direct Celf1 targets will advance our knowledge in the mechanisms behind developmental networks regulated by Celf1 and diseases where Celf1 is mis-regulated.

overall_design: RNA-seq was performed in RNA samples of cardiac ventricles at postnatal day 3 (PN3) and at postnatal day 38 (PN38) from wild type mice or Celf1 knock out mice (homozygous)

first: Jimena

last: Giudice

last: Li

first: Thomas

last: Cooper


title: Large-scale epigenetic reprogramming is punctuated late during the evolution of pancreatic cancer progression

first: Xin


title: Nuclear TIGAR mediates an epigenetic-metabolic loop via Nrf2 for cancer therapeutics resistance

city: Sacramento

first: Clifford

middle: G.

last: Tepper

state: CA

address: 4645 2nd Avenue, Room 2300A

department: Biochemistry and Molecular Medicine

institute: UC Davis School of Medicine

summary: Epigenetic and metabolic reprogrammings are implicated in cancer progression with unclear mechanisms. We report here that the histone methyltransferase NSD2 drives cancer cell and tumor resistance to therapeutics such as tamoxifen, doxorubicin, and radiation by reprogramming of glucose metabolism. NSD2 coordinately up-regulates expression of TIGAR, HK2 and G6PD and stimulates pentose phosphate pathway (PPP) production of NADPH for ROS reduction. We discover that elevated expression of TIGAR, previously characterized as a fructose-2,6-bisphosphatase, is localized in the nuclei of resistant tumor cells where it stimulates NSD2 expression and global H3K36me2 mark. Mechanistically, TIGAR interacts with the antioxidant regulator Nrf2 and facilitates chromatin assembly of Nrf2-H3K4me3 methylase MLL1 and elongating Pol-II, independent of its metabolic enzymatic activity. In human tumors, high levels of NSD2 correlate strongly with early recurrence and poor survival and are associated with nuclear-localized TIGAR. This study defines a nuclear TIGAR-mediated, epigenetic autoregulatory loop functioning in redox rebalance for resistance to tumor therapeutics.

overall_design: A total of 4 samples were analyzed in this study.  The study included two cell lines, MCF7 and the tamoxifen-resistant subline TMR. Both were were cultured in medium containing vehicle control and/or 4-hydroxytamoxifen (Tam). The untreated MCF7 and TMR cell lines served as controls for the study.

first: Hong-Wu

last: Chen

first: Junjian


title: Developmental heterogeneity of cardiac fibroblasts does not predict pathological proliferation and activation

city: los angeles

first: Sara

last: Ranjbarvaziri

state: California

address: 650 Charles E young

institute: ucla

summary: The resulting heat map shows an increased expression of ECM and ECM regulatory genes, 'activated' fibroblast genes, and cell cycle genes in the THY1+HE- sorted cells and in Tie2 and Tbx18-derived cardiac fibroblasts from TAC relative to sham

overall_design: RNA-seq of Thy1+HE- cells isolated 7 days after injury in mice that underwent sham and transaortic constriction (TAC) operations.

first: Shah

last: Ali

first: Mahmood

last: Talkhabi


title: LPA receptor activity is basal specific and coincident with early pregnancy and involution during mammary gland postnatal development

status: Public on Oct 21 2016

city: Bronx

first: Cristina

last: Montagna

address: 1301 Morris Park Avenue

institute: Albert Einstein College of Medicine

summary: During pregnancy, luminal and basal epithelial cells of the adult mammary gland proliferate and differentiate resulting in remodeling of the adult gland. While pathways that control this process have been characterized in the gland as a whole, the contribution of specific cell subtypes, in particular the basal compartment, remains largely unknown. Basal cells provide structural and contractile support, however they also orchestrate the communication between the stroma and the luminal compartment at all developmental stages. Using RNA-seq, we show that basal cells are extraordinarily transcriptionally dynamic throughout pregnancy when compared to luminal cells. We identified gene expression changes that define specific basal functions acquired during development that led to the identification of novel markers. Enrichment analysis of gene sets from 24 mouse models for breast cancer pinpoint to a potential new function for insulin-like growth factor 1 (Igf1r) in the basal epithelium during lactogenesis. We establish that β-catenin signaling is activated in basal cells during early pregnancy, and demonstrate that this activity is mediated by lysophosphatidic acid receptor 3 (Lpar3). These findings identify novel pathways active during functional maturation of the adult mammary gland.

overall_design:
We profiled a total of 47 samples for RNA-seq analysis, 3 biological repliaces from each of the 2 cell types across 8 time points (lactation day 10 basal population has 2 biological replicates)

Please note that one sample (P14_2B) was deemed an outlier and subsequently removed from further processing (i.e. 46 data columns in the processed data file).

first: Deanna

last: Acosta


title: A high-resolution binding profile of meiotic cohesin in murine spermatocytes reveals accumulation at rDNA loci

city: Dresden

first: Maciej

last: Paszkowski-Rogacz

address: Tatzberg 47/49

department: UCC / Medical Faculty and University Hospital Carl Gustav Carus

institute: Technische Universität Dresden

summary: In mammalian spermatocytes and oocytes, cohesin complexes serve several distinct functions including establishing the meiotic chromosome architecture into axes and loops, providing sister chromatid cohesion, protecting telomeres, and supporting meiotic recombination. High-resolution analysis of cohesin binding to meiotic chromosomes, however, remained to be performed, mainly because of the complexity of germ cell development and meiotic chromatin, and of the difficulty obtaining proper meiocyte populations. Here, we established a ChIP-seq approach to identify and characterize the genome-wide binding profile of cohesin specifically in murine spermatocytes. Chromatin binding of cohesin proteins SMC3, present in all cohesin complexes, and SMC1β representing the major meiotic complexes, were analyzed. Both cohesins were much reduced in coding exons as well as in 5’ and 3’ UTRs.  SMC1β cohesin binding sequences coincide in a large fraction with CACA repeats and thus with transcription factor ZSCAN4C binding sites, but also with other TF sites. We observed neither overlap with recombinase DMC1 sites nor with recombination hotspot marker PRDM9 sites. Most interestingly, meiotic cohesin is strongly enriched at 5S ribosomal RNA genes. We hypothesize a role of cohesin in the regulation of meiotic rDNA stability and/or transcription.

overall_design: SMC3 and SMC1B-LAP ChIP-Seq in murine spermatocytes

first: Cornelia

last: Wetzker

first: Frank

last: Buchholz

first: Rolf

last: Jessberger