title: Cell-autonomous transformation of Lgr5-positive intestinal stem cells into gastric stem cells upon loss of transcription factor Cdx2

city: Utrecht

first: Lennart

last: Kester

address: Uppsalalaan 8

institute: Hubrecht Institute

summary: Stomach and intestinal adult epithelia harbor stem cells that are responsible for their continuous regeneration. Stomach and intestinal stem cells differ in their differentiation program and in the gene repertoire that they express. We show that single adult Lgr5-positive stem cells, isolated from 3D cultured small intestinal organoids, require Cdx2 to maintain their intestinal identity and are converted cell-autonomously into stomach-pyloric stem cells in the absence of this transcription factor.

overall_design: In order to obtain Cdx2null intestinal stem cells carrying the Lgr5-EGFP marker, 5-6 days old small intestinal organoids generated from Cdx2-/fl/Lgr5-EGFP-Ires-CreERT2 mice were incubated with 1 µM of 4-hydroxytamoxifen in intestinal culture medium for 16h to activate the Cre recombinase. Controls were 4-hydroxytamoxifen-untreated small intestinal (Control SI) and stomach (Control Sto) organoids issued from mice with the same genotype. The organoids were dissociated and sorted for EGFPhi. Cdx2null, Control SI and Control Sto clonal organoids were generated and expanded from Lgr5-EGFPhi single cells in stomach specific culture medium (ENRWfg) and RNA was isolated for RNA-Seq analysis. Cdx2+ Stomach (Sto) organoids were generated by infection of the wild type stomach organoids with lentiviral stock expressing Cdx2. They were cultured in stomach medium (ENRWfg) and RNA was isolated for RNA-Seq analysis

first: Salvatore

last: Simmini

first: Monika

last: Bialecka

first: Meritxell

last: Huch

first: Marc

last: van de Wetering

first: Toshiro

last: Sato

first: Felix

last: Beck

last: van Oudenaarden

first: Hans

last: Clevers

first: Jacqueline

last: Deschamps


title: Lotus Flower-Bud Transcriptome or Gene expression

status: Public on Dec 08 2014

city: Shanghai

first: Weiwei

last: Zhang

address: No.3888, Chenhua Road, Songjiang District

department: Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences

country: China

institute: Shanghai Chenshan Botanical Garden

type: Expression profiling by high throughput sequencing

summary: Flower-lotus with many attractive floral characteristics has been studied and discussed the most. These characteristics are used as the standards of the classification in most cases, and always attracted the attention of lotus breeders on improvement program because of associating with ornamental and economic values of lotus. However, molecular mechanisms underlying the formation of these attractive floral features still remain largely unknown. Transcriptome sequencing technique has been established as an efficient approach for gene discovery and expression pattern identification. For some plants, a lot of important genes involved in plant critical metabolisms have been successfully identified by this technique. In the study, mass sequence data obtained from the deep sequencing of a mixed flower-bud cDNA pool from three individuals of N. nucifera provide a platform to comprehensively understand the processes of flower formation and development at the molecular level, and will greatly facilitate the genetic improvement of ornamental characteristics and the directive molecular breeding for lotus in the future.

overall_design: A mixed cDNA pool from young flower-buds (35-40mm in length) of three accessions of N. nucifera were used for deep sequencing using 454 GS-FLX Titanium.

first: Daike

last: Tian


title: Tissue-resident macrophage enhancer landscapes are shaped by the local microenvironment [ChIP-seq]

status: Public on Dec 05 2014

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Macrophages are hematopoietic cells critical for innate immune defense, but also control organ homeostasis in a tissue-specific manner. Tissue-resident macrophages, therefore, provide a well-defined model to study the impact of ontogeny and microenvironment on chromatin state. Here, we profile the dynamics of four histone modifications across seven tissue-resident macrophage populations, as well as monocytes and neutrophils. We identify 12,743 macrophage-specific enhancers and establish that tissue-resident macrophages have distinct enhancer landscapes. Our work suggests that a combination of tissue and lineage-specific transcription factors form the regulatory networks controlling chromatin specification in tissue-resident macrophages. The environment has the capacity to alter the chromatin landscape of macrophages derived from transplanted adult bone marrow in vivo and even differentiated macrophages are reprogramed when transferred into a new tissue. Altogether, these data provide a comprehensive view of macrophage regulation and highlight the importance of microenvironment along with pioneer factors in orchestrating macrophage identity and plasticity.

overall_design: indicated cells were cross-linked and sorted, then ChIP-seq was performed with the indicated antibody. For chimera samples - CD45.2 mice were irradiated, bone marrow from CD45.1 mice was then transplanted. 4 months later, CD45.1 macrophages were isolated from the indicated tissues, and ChIP-seq was performed.


title: Global methylation alterations in Dnmt3aKO derived malignancies

city: Houston

first: Margaret

last: Goodell

state: TX

address: One Baylor Plaza, N1030

country: USA

institute: Baylor College of Medicine

type: Methylation profiling by high throughput sequencing

summary: To test the long-term effects of lack of Dnmt3a on mouse HSCs, we established a cohort of lethally irradiated mice transplanted with Dnmt3a-KO or WT HSC control cells. Dnmt3a deletion in purified HSCs transplanted alone leads to an array of hematologic disorders that models the spectrum of disorders seen in human malignancies. We investigated DNA methylation alterations in disease and control mice by RRBS. We generated an average of 23.81 million reads per sample (18.97 - 31.67 million) of which an average of 18.07 million could be mapped to the mm9 genome (2.78 - 26.42 million). We achieved an average CpG coverage depth of 31.79-fold (8.09 - 47.44-fold) and average bisulfite conversion efficiency of 99.91% (99.87 - 99.95%).

overall_design: Reduced representation bisulfite sequencing of cells using Illumina HiSeq 2000 and 2500

first: Benjamin

last: Rodriguez

first: Wei

last: Li


title: Deep sequencing of microRNA present in ejaculated bull spermatozoa

status: Public on Dec 10 2014

city: Clemson

first: Scott

middle: L

last: Pratt

state: SC

address: 138 Poole Ag Center

institute: Clemson University

type: Non-coding RNA profiling by high throughput sequencing

summary: The objectives of our study were to identify microRNA (miRNA) present in bovine sperm.

overall_design: Angus bulls (n=6) were assigned to treatments of either toxic or non-toxic fescue seed diets. Semen was collected and subjected to RNA isolation, enriched for miRNA. Three samples from each treatment group were chosen based on RNA quality and pooled for deep sequencing.

first: Heather

middle: M

last: Stowe


title: Comparison of tamoxifen and letrozole response in mammary preneoplasia of ER and aromatase over-expressing mice defines an immune-associated gene signature linked to tamoxifen resistance

status: Public on Dec 04 2014

city: Cheonan

first: Keunsoo

last: Kang

state: Chungnam

address: Dandae-ro 119

department: Microbiology

country: South Korea

institute: Dankook University

summary: To investigate response or resistance to endocrine therapy, mice with targeted over-expression of Esr1 or CYP19A1 to mammary epithelial cells were employed, representing two direct pathophysiological interventions in estrogen pathway signaling. Both Esr1 and CYP19A1 over-expressing mice responded to letrozole with reduced HAN prevalence and decreased mammary epithelial cell proliferation. CYP19A1 over-expressing mice were tamoxifen-sensitive but Esr1 over-expressing mice were tamoxifen-resistant. Increased ER expression occurred with tamoxifen resistance but no consistent changes in progesterone receptor, pSTAT3, pSTAT5, cyclin D1 or cyclin E levels in association with response or resistance was found. RNA-seq was employed to seek a transcriptome predictive of tamoxifen resistance using these models and a second tamoxifen-resistant model, BRCA1 deficient/Trp53 haploinsufficient mice. Sixty-eight genes associated with immune system processing were upregulated in tamoxifen-resistant Esr1 and Brca1 deficient mice whereas genes related to aromatic compound metabolic process were upregulated in tamoxifen-sensitive CYP19A1 mice. Interferon Regulatory Factor 7 was identified as a key transcription factor regulating these 68 immune processing genes. Two loci encoding novel transcripts with high homology to human IGLL1 were uniquely upregulated in the tamoxifen-resistant models. Letrozole proved to be a successful alternative to tamoxifen. Further study of transcriptional changes associated with tamoxifen resistance including immune-related genes could expand our mechanistic understanding and lead to biomarkers predictive of escape or response to endocrine therapies.

overall_design: Single- and paired-end mRNA-seq with WT, Esr1 over-expressing (CERM, tetracycline-operator(tet-op)-Esr1MMTV-rtTA), CYP19A1 over-expressing (AROM, tet-op-CYP19A1MMTV-rtTA) and Brca1 KO  (BRCA, Brca1fl11/fl11/MMTV-Cre/p53+/- ) mice

first: Priscilla

last: Furth


title: Identification of differentially expressed microRNAs from a male sterile Ponkan mandarin (Citrus reticulata Blanco) and its fertile wild type by small RNA and degradome sequencing

city: Wu Han

first: Yan-ni

last: Fang

address: shizi mountain street

institute: Huazhong Agricultural University

summary: High-throughput small RNA and degradome sequencing were performed to identify a large number of miRNAs and their targets. Differential expression of several miRNAs reveals that miRNA regulatory network was closely linked to gametophyte development and male sterility in Ponkan mandarin. The expression profiles of miR156 and miR167 as well as their targets demonstrated their contribution in male sterility in the Ponkan seedless type. This study provides valuable information for better understanding of miRNAs network in plant anther development and lays a foundation to future research on male sterility in citrus and even other species.

overall_design: small RNA and degradome sequencing of seedy ‘Egan No.1’ and its male sterile and seedless mutant ‘Qianyang seedless’

first: Yan-Ni

first: Wen-Ming

last: Qiu

first: Yao

last: Wang

first: Xiao-Meng

last: Wu

first: Wen-Wu

last: Guo

first: Qiang

last: Xu


title: Complex in vivo RNA-seq analysis  reveal reprogramming of Yersinia from virulent to persistent mode during infection [RNA-seq]

city: Umea

first: Kemal

last: Avican

address: Building 6L

department: Department of Molecular Biology

country: Sweden

institute: Umea University

summary: We recently found that Yersinia pseudotuberculosis can be used as a model of persistent bacterial infections. We performed in vivo RNA-seq of bacteria in small cecal tissue biopsies at early and persistent stages of infection to determine strategies associated with persistence. Comprehensive analysis of mixed RNA populations from infected tissues revealed that Y. pseudotuberculosis undergoes transcriptional reprogramming with drastic down-regulation of T3SS virulence genes during persistence when the pathogen resides within the cecum. At the persistent stage, the expression pattern in many respects resembles the pattern seen in vitro at 26oC, with for example up-regulation of flagellar genes and invA. These findings are expected to have impact on future rationales to identify suitable bacterial targets for new antibiotics. Other genes that are up-regulated during persistence are genes involved in anaerobiosis, chemotaxis, and protection against oxidative and acidic stress, which indicates the influence of different environmental cues. We found that the Crp/CsrA/RovA regulatory cascades influence the pattern of bacterial gene expression during persistence. Furthermore, arcA, fnr, frdA, and wrbA play critical roles in persistence. Our findings suggest a model for the life cycle of this enteropathogen with reprogramming from a virulent to an adapted phenotype capable of persisting and spreading by fecal shedding.

overall_design: Examination of Y. pseudotuberculosis expression in two mouse cecal tissue at early and at persistent infection. Also pure bacterial cultures two at 26C and two 37C. Additionally, the bacterial content of cecal tissue during infections and before infection were analyzed with read mapping on 16SMicrobial NCBI database with non-rRNA-depleted reads.

first: Maria

last: Fällman


title: Gene profile of Wt and miR-155-/- Tfh cells

status: Public on Dec 09 2014

city: Salt lake city

first: Ryan

last: O'Connell

state: UT

address: 15 N Medical Dr East

department: Pathology

institute: University of Utah

summary: Differential gene expression profile of Tfh and non-Tfh cells from both Wt and miR-155-/- mice spleens.

overall_design: Wt and miR-155-/- mice were immunized with OVA. 8 days post immunization, CD4+CXCR+PD1+ Tfh cells and CD4+CXCR5-PD1- non Tfh cells were sorted from mice spleens for analyses.

first: Ruozhen

last: Hu


title: Endothelial Cells Control Pancreatic Cell Fate at Defined Stages through EGFL7 Signaling

city: New York

first: Der-I

last: Kao

state: NY

address: 1300 York Ave

institute: Weill Cornell Medical College

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Tissue-resident macrophage enhancer landscapes are shaped by the local microenvironment

first: Ido

last: Amit


title: Complex in vivo RNA-seq analysis reveal reprogramming of Yersinia from virulent to persistent mode during infection

platform_organism:
Yersinia pseudotuberculosis
Yersinia pseudotuberculosis YPIII


title: RNA profiling of PDX1+ pancreatic progenitors before or after co-culture with different types of cells

summary: Analysis of gene expression of Pdx-EGFP1+ pancreatic progenitors before or after co-culture at mRNA level. The hypothesis tested in the study was that the overall gene expression in Pdx1-EGFP+ does not alter after co-culture with endothelial cells. The result supported our hypothesis.

overall_design:
Total RNA isolated from Pdx1-EGFP+ progenitors from the Pdx1-EGFP HUES8 cell-derived pancreatic progenitor population before (none) and after co-culture (AKT-HUVEC, MPEC, or BJ)
Fig 2d in publication.

first: Shuibing

last: Chen


title: The extraembryonic serosa is a frontier epithelium providing the insect egg with a full-range innate immune response

city: Leiden

first: Chris

last: Jacobs

state: Zuid-Holland

address: Sylviusweg 72

department: Institute of Biology

country: Netherlands

institute: Leiden University

summary: Drosophila larvae and adults possess a potent innate immune response, but the response of their eggs is particularly poor. Here we show that eggs of the beetle Tribolium castaneum, in contrast, possess a full range of immune defence mechanisms, based on complete transcriptome comparisons of naïve, sterilely injured, and bacterially challenged eggs. Upon infection, we find massive upregulation of AMPs and differential regulation of 375 other genes including both IMD and Toll signalling components. Importantly, we show that this extensive response depends on the serosa, an extraembryonic epithelium enveloping yolk and embryo. When we delete the serosa using Tc-zen1 RNAi, none of the AMPs and merely 57 other genes are differentially regulated upon infection. Furthermore, unchallenged eggs reveal serosa-biased expression of several bacterial recognition genes. Thus, the serosa is an immune competent frontier epithelium, and its loss in higher flies might account for the poor immune response of Drosophila eggs.

overall_design: Three different types of eggs were analysed. Wildtype eggs, eggs of which the mother was injected with a control dsRNA, and eggs without a serosa of which the mothers were injected with Tc-zen1 dsRNA. These three egg-types were subjected to three treatments, untreated (naïve), pricked with a sterile needle (sterile injury) and pricked with a mix of E.coli and M.luteus. This resulted in 9 samples which were all collected three times resulting in a total of 27 samples.

first: CGC

first: H

middle: P

last: Spaink

first: Maurijn

last: van der Zee


title: Paternal diet defines offspring chromatin state and intergenerational obesity.

city: Badalona

first: Tanya

last: Vavouri

state: BARCELONA

address: Ctra de Can Ruti, Cami de les Escoles, s/n

country: Spain

institute: Josep Carreras Leukemia Research Institute

summary: The global rise in obesity has revitalized a search to understand genetic, and in particular, epigenetic factors underlying the disease. We present a Drosophila model of paternal-diet-induced Inter-Generational Metabolic Reprogramming (IGMR) and identify genes required for its encoding in offspring. Intriguingly, we find that as little as two days of dietary intervention in fathers elicits obesity in offspring. Paternal sugar acts as a physiological suppressor of variegation, de-silencing chromatin state-defined transcriptional units in both mature sperm and in offspring embryos. We identify requirements for H3K9/K27me3 dependent reprogramming of metabolic genes in two distinct germline and zygotic windows. Critically, we find evidence that a similar system regulates obesity-susceptibility and phenotype variation in mice and humans. The findings provide insight into the mechanisms underlying intergenerational metabolic reprogramming and carry profound implications for our understanding of phenotypic variation and evolution.

overall_design: RNA-seq on Drosophila embryos and sperm samples fed medium and high sugar.

first: Anita

last: Öst

first: Adelheid

last: Lempradl

first: Eduard

last: Casas

first: Melanie

last: Weigert

first: Theo

last: Tiko

first: Merdin

last: Deniz

first: Lorena

last: Pantano

first: Ulrike

last: Boenisch

first: Pavel

last: Itskov

first: Marlon

last: Stoeckius

first: Marius

last: Ruf

first: Nikolaus

last: Rajewsky

first: Gunter

last: Reuter

first: Nicola

last: Iovino

first: Carlos

last: Ribeiro

first: Mattias

last: Alenius

first: Steffen

last: Heyne

first: John

middle: A

last: Pospisilik


title: Convergent Sense/Antisense Transcription At Intragenic Super-Enhancers Targets AID-initiated Genomic Instability

city: Boston

first: Feilong

last: Meng

state: MA

address: 300 Longwood Ave

department: PCMM

institute: Boston Children's Hospital

summary: Activation-induced cytidine deaminase (AID) initiates both somatic hypermutation (SHM) for antibody affinity maturation and DNA breakage for antibody class switch recombination (CSR) via transcription-dependent cytidine deamination of single stranded DNA targets. While largely specific for immunglobulin genes, AID also acts on a limited set of off-targets, generating oncogenic translocations and mutations that contribute to B cell lymphoma. How AID is recruited to off-targets has been a long-standing mystery. Based on deep GRO-Seq studies of mouse and human B lineage cells activated for CSR or SHM, we report that most robust AID off-target translocations occur within highly focal regions of target genes in which sense and antisense transcription converge. Moreover, we found that such AID-targeting "convergent" transcription arises from antisense transcription that emanates from Super-Enhancers within sense transcribed gene bodies. Our findings provide a mechanistic explanation for AID off-targeting to a small subset of mostly lineage-specific genes in activated B cells.

overall_design: We performed GRO-Seq and H3K27Ac ChIP-Seq with different B lineage cell types and MEF cells to find the signatures associated with AID targeting.

first: Fredrick

middle: W

last: Alt


title: Environment Drives Selection and Function of Enhancers Controlling Tissue-Specific Macrophage Identities

city: Québec

first: David

last: Gosselin

state: Quebec

address: CRCHUL - 2705 Boulevard Laurier, Bloc T - 2-34

department: Molecular Medicine

country: Canada

institute: Université Laval

summary: Macrophages reside in essentially all tissues of the body and play key roles in innate and adaptive immune responses. Distinct populations of tissue macrophages also acquire context-specific functions that are important for normal tissue homeostasis. To investigate mechanisms responsible for tissue-specific functions, we analyzed the transcriptomes and enhancer landscapes of brain microglia and resident macrophages of the peritoneal cavity. In addition, we exploited natural genetic variation as a genome-wide “mutagenesis” strategy to identify DNA recognition motifs for transcription factors that promote common or subset-specific binding of the macrophage lineage-determining factor PU.1. We find that distinct tissue environments drive divergent programs of gene expression by differentially activating a common enhancer repertoire and by inducing the expression of divergent secondary transcription factors that collaborate with PU.1 to establish tissue-specific enhancers. These findings provide insights into molecular mechanisms by which tissue environment influences macrophage phenotypes that are likely to be broadly applicable to other cell types.

overall_design: Chromatin marks H3K4me2, H3K27Ac, and transcription factors PU.1 were assessed by ChIP-Seq and RNA-Seq were used to measure gene expression in 5 different macrophage subtypes.

first: Christopher

middle: K

last: Glass


title: Tissue-resident macrophage enhancer landscapes are shaped by the local microenvironment [ATAC-seq]

first: Ido

last: Amit

overall_design: 7 tissue-resident macrophage populations were isolated, as well as monocytes and neutrophils, and ATAC-seq (Assay for transposase-accessible chromatin using sequencing) was performed. Experiment was done in duplicates for all but Kupffer cells.


title: Deconstructing the dynamic transcriptional program of pluripotent stem cells.

city: Baltimore

first: Patrick

last: Cahan

state: MD

address: 733 North Broadway, MRB 653

department: ICE and Biomedical Engineering

institute: Johns Hopkins University School of Medicine

summary: Pluripotent stem cells (PSCs) are capable of dynamic interconversion between distinct substates, but the regulatory circuits specifying these states and enabling transitions between them are not well understood. We set out to address this issue and map the landscape of gene expression variability in PSCs by single-cell expression profiling of PSCs under different chemical and genetic perturbations. We find that signaling factors and developmental regulators show highly variable expression in PSCs, with expression states for some variable genes heritable through multiple cell divisions. Expression variability and population heterogeneity can be influenced by perturbation of signaling pathways and chromatin regulators. Strikingly, either removal of mature miRNAs or pharmacologic blockage of external signaling pathways drives PSCs into a low-noise ground state characterized by a reconfigured pluripotency regulatory network, increased self-renewal efficiency, and a distinct chromatin state, an effect mediated by the action of opposing miRNA families on the c-myc / Lin28 / let-7 axis. These findings illuminate the causes of transcriptional heterogeneity in PSCs and their consequences for cellular decision-making.

overall_design: Single-cell RNA-Seq on 183 individual v6.5 mouse embryonic stem cells (mESCs) cultured in serum+LIF media, 94 v6.5 mESCs cultured in 2i+LIF media ('ground state' conditions), and 84 Dgcr8 -/- mESCs (constructed in a v6.5 background), that lack mature miRNAs due to knockout of a miRNA processing factor, cultured in serum+LIF. ChIP-Seq for RNA polymerase II, H3K4me3, H3K27me3, H3K27ac, H3K9me3, and H3K36me3 on the three populations of mESCs profiled by single-cell RNA-Seq. Single-cell RNA-Seq on 54 individual nestin-positive neural precursor cells derived from v6.5 mESCs.

first: Roshan

last: Kumar


title: Deficiency in glucose transporter 12 results in heart failure and a diabetic phenotype in zebrafish

city: Bad Nauheim

first: Rubén

last: Marín-Juez

address: Ludwigstrasse 43

country: Germany

institute: Max Planck Institute

summary: Cardiomyopathies-associated metabolic pathologies (e.g. T2D and insulin resistance) are a leading cause of mortality. It is known that the association between the pathologies works in both directions, where heart failure can lead to metabolic derangements such as insulin resistance. This intricate crosstalk exemplifies the importance of a fine coordination between one of the most energy demanding organs and an equilibrated carbohydrate metabolism. In this light, to assist in the understanding of the role of insulin regulated glucose transporters and the development of cardiomyopathies, we set out to study GLUT12. GLUT12 is a novel insulin regulated GLUT expressed in the main insulin sensitive tissues such as cardiac and skeletal muscle and adipose tissue. This study investigates the role of GLUT12 in heart failure and diabetes by developing a model for glut12 deficiency in zebrafish.

overall_design: 6 samples in total were analyzed. 3 replicates from control samples (injected with contol MO) and 3 replicates from glut12 morphant samples (injected with glut12 splice MO). In each sample 10 embryos were pooled.

first: Vanesa

last: Jiménez-Amilburu

first: Susanne

last: Jong-Raadsen

first: Jeroen

last: Bakkers

first: Herman

last: Spaink


title: Uridylation by TUT4 and TUT7 marks mRNA for degradation

city: Seoul

first: Hyeshik

last: Chang

state: South Korea

address: Building 203 Room 525, School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu

department: School of Biological Sciences

institute: Seoul National University


title: Identification of Hfq bound RNA by co-immunoprecipitation and RNA-sequencing

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

institute: ZB MED - Information Centre for Life Sciences

summary: Co-immunoprecipitation with endogenous Hfq3xFlag in exponential, stationary, non-induced and virulence induced conditions, followed by RNA-sequencing, revealed 1697 mRNAs and 208 ncRNAs associated with Hfq. We identified 56 new ncRNAs and validated 3 Hfq-dependent trans sRNAs on by Northern blot analysis. Interestingly, 55% of the ncRNAs were encoded antisense to a protein coding sequence. Abundance of 4 asRNAs and their corresponding target mRNAs was altered upon hfq, indicating a substantial influence of Hfq on asRNA-target interactions.

overall_design: 8 cDNA libraries were sequenced. A. tumefaciens hfq3xFlag and hfqWT (control) strains were grown to stationary and exponential growth phase and under non-induced and virulence induced conditions.

first: Philip

last: Möller

first: Aaron

last: Overlöper

first: Tuan-Nan

last: Wen

first: Cynthia

last: Sharma

first: Erh-Min

last: Lai

first: Franz

last: Narberhaus


title: Asymmetric nucleosomes flank promoters in the budding yeast genome

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

summary: Nucleosomes in active chromatin are dynamic, but whether they have distinct structural conformations is unknown. To identify nucleosomes with alternative structures genome-wide, we used H4S47C-anchored cleavage mapping, which revealed that nucleosomes at 5% of budding yeast nucleosome positions have asymmetric histone-DNA interactions. These asymmetric interactions are enriched at nucleosome positions that flank promoters. Micrococcal nuclease (MNase) sequence-based profiles of asymmetric nucleosome positions revealed a corresponding asymmetry in MNase protection near the dyad axis, suggesting that the loss of DNA contacts around H4S47 is accompanied by protection of the DNA from MNase. Chromatin immunoprecipitation mapping of selected nucleosome remodelers indicated that asymmetric nucleosomes are bound by the RSC chromatin remodeling complex, which is required for maintaining nucleosomes at asymmetric positions. These results imply that the asymmetric nucleosome-RSC complex is a metastable intermediate representing partial unwrapping and protection of nucleosomal DNA on one side of the dyad axis during chromatin remodeling.

overall_design: We have analyzed the chromatin landscape of the yeast genome using paired-end MNase-seq and the chromatin binding of yeast remodelers Swr1, Ino80 and RSC at base-pair resolution using native chromatin immunoprecipitation followed by sequencing (N-ChIP-seq).

first: Srinivas

last: Ramachandran

first: Gabriel

last: Zentner

first: Steven


title: B cell super-enhancers and regulatory clusters recruit AID tumorigenic activity

city: Bethesda

first: Marei

last: Dose

address: 9000 Rockville Pk

institute: National Institutes of Health

summary: The antibody gene mutator AID promiscuously damages oncogenes and B cell identity genes leading to chromosomal translocations and tumorigenesis. Why non-immunoglobulin loci are susceptible to AID activity is unknown. Here we study AID-mediated lesions in the context of nuclear architecture and the B cell regulome. We show that AID targets are not randomly distributed across the genome, but are predominantly clustered within super-enhancers. Unexpectedly, in these domains AID deaminates highly active promoters and eRNA+ enhancers interconnected in some instances over megabases of linear chromatin. Using genome editing we demonstrate that 3D-linked targets cooperate to recruit AID-mediated breaks. Furthermore, a comparison of hypermutation in mouse B cells, AID-induced kataegis in human lymphomas, and translocations in MEFs reveals that AID damages different genes in different cell types. Yet, in all cases, the targets are predominantly associated with topological complex, highly transcribed super-enhancers, demonstrating that these compartments are key mediators of AID recruitment.

overall_design: Examination of AID activity in human cells via Single Nucleotide Variant discovery in H3K4me3 ChIP-seq data from 26 MSH2-/-; AIDtg; UGItg, 18 AICDA-/- and 2 unmodified RAMOS clonal populations.  Examination of PolII mediated long-range interactions via Chia-PET of RAMOS cells (2 sample).  Identification of super-enhancers from H3K27Ac ChIP-Seq data from activated B cells (3 replicates and 1 input control) and RAMOS cells (1 sample and 1 input control), 2 preparations of naive and 2 of germinal center (GC) B cells from human tonsilectomy samples.  Mapping of regulatory elements in RAMOS based on H3K4me1 (1 sample) and Nipbl (2 replicates) ChIP-Seq.  RNA expression analyses of activated B cells from 3 WT and 3 Il4raU/U mice and RAMOS cells (3 replicates).  Mapping of long-range interactions by 4C in activated B cells from a WT and an Il4raU/U mouse with the IL4ra and Il21r locus, respectively, as a viewpoint.  Mapping of Super-Enhancers in activated B cells from Il4raU/U and WT control mice (2 samples).

first: Jason

last: Qian

first: Qiao

last: Wang

first: Nathanael

last: Pruett

first: Kyong-Rim

last: Kieffer-Kwon

first: Wolfgang

last: Resch

first: Genqing

last: Liang

first: Zhonghui

last: Tang

first: Ewy

last: Mathe

first: Christopher

last: Benner

first: Wendy

last: Dubois

first: Steevenson

last: Nelson

first: Laura

last: Vian

first: Thiago

middle: Y

last: Oliveira

first: Mila

last: Jankovic

first: Ofir

last: Hakim

first: Anna

last: Gazumyan

first: Rushad

last: Pavri

first: Parirokh

last: Awasthi

first: Bin

last: Song

first: Geng

last: Liu

first: Longyun

last: Chen

first: Shida

last: Zhu

first: Lionel

last: Feigenbaum

first: Louis

last: Staudt

first: Cornelis

last: Murre

first: Yijun

last: Ruan

first: Davide

middle: F

last: Robbiani

first: Qiang

last: Pan-Hammarstrom

first: Michel

middle: C

last: Nussenzweig

first: Rafael

last: Casellas


title: The exon junction complex is required for definition and excision of neighboring introns in Drosophila

city: Vienna

first: Dominik

last: Handler

address: Dr. Bohr-Gasse 3

country: Austria

institute: IMBA-Institute of Molecular Biotechnology of Austrian Academy of Sciences

summary: Splicing of pre-mRNAs results in the deposition of the exon junction complex (EJC) upstream of exon-exon boundaries. The EJC plays crucial post-splicing roles in export, translation, localization and nonsense-mediated decay of mRNAs. It also aids faithful splicing of pre-mRNAs containing large introns, albeit via an unknown mechanism. Here, we show that the core EJC plus the accessory factors RnpS1 and Acinus aid in definition and efficient splicing of neighboring introns. This requires prior deposition of the EJC in close proximity either from an upstream or downstream splicing event. If present in isolation, EJC-dependent introns are splicing-defective also in wildtype cells. Interestingly, the most affected intron belongs to the piwi locus, which explains the reported transposon de-silencing in EJC-depleted Drosophila ovaries. We propose that the dependency of splicing on the EJC is exploited as a means to control the temporal order of splicing events. Our observations provide a powerful basis to dissect the molecular events that underlie the role of the EJC in splicing.

overall_design: Analysis of splicing defects in 3 knockdowns (siGFP [control], siACN, siTSU) in Drosohpila OSCs. PolyA RNA (biological duplicates) and total-RNA was sequenced on a Illumina HiSeq2000 in PE50 mode.

first: Rippei

last: Hayashi

first: David

last: Ish-Horowicz

first: Julius

last: Brennecke


title: Uridylation by TUT4 and TUT7 marks mRNA for degradation [TAIL-Seq]

first: Hyeshik

last: Chang

summary: Uridylation occurs pervasively on mRNAs in mammals, yet its mechanism and significance remain unknown. Here we identify TUT4 and TUT7 (also known as ZCCHC11 and ZCCHC6, respectively) as the enzymes that uridylate mRNAs. Uridylation readily occurs on deadenylated mRNAs that are not associated with poly(A) binding protein (PABPC1) in cells. Consistently, purified TUT4 and TUT7 (TUT4/7) selectively uridylate RNAs with short A tails (< ~25 nt) while PABPC1 antagonizes uridylation of polyadenylated mRNAs in vitro. In cells depleted of TUT4/7, the vast majority of mRNAs lose the U tails, and their half-lives are extended. Suppression of mRNA decay factors leads to the accumulation of uridylated mRNAs. In line with this, microRNA induces uridylation of its targets, and TUT4/7 is required for enhanced decay of microRNA targets. Our study explains the mechanism underlying selective uridylation of deadenylated mRNAs, and demonstrates a fundamental role of the U tail as a molecular mark for global mRNA decay.

overall_design:
Thirteen separate sets of TAIL-seq experiments were performed. Each set includes a negative control for transfection, immunoprecipitation, or knockout cell generation. Experimental samples were treated with various conditions including siRNA transfection, transdominant negative protein expression, TALEN-based gene knockout, or immunoprecipitation.

The 'README-TAIL-seq.txt' include detailed information about structure of seq entries in FASTQ files and of processed data for 3' end modifications.

first: Jaechul

last: Lim

first: Minju

last: Ha

first: V

middle: N

last: Kim


title: Uridylation by TUT4 and TUT7 marks mRNA for degradation [RNA-Seq]

overall_design: HeLa cells were knocked down of control or TUT4/7, then total RNAs were prepared for RNA-seq on 0, 1, 2, 4h after actinomycin D treatment. The whole processes of experiments were repeated two times.


title: The human nuclear exosome targeting complex is loaded onto newly synthesized RNA to direct early ribonucleolysis

status: Public on Dec 03 2014

city: Aarhus

first: Peter

last: Andersen

state: Denmark

address: Universitetsbyen 83

department: MBG

country: Denmark

institute: Aarhus University

summary:
Individual-nucleotide resolution UV-crosslinking and immunoprecipitation (iCLIP) followed by high-throughput sequencing of RBM7-associated transcripts.
Note: these data relate to Figure 1, 2, 3, 4, 5 and 6 in Lubas, Andersen et al., Cell Reports 2014

overall_design: RBM7-associated transcripts

first: Michal

last: Lubas

middle: R

first: Aleks

last: Schein

first: Andrzej

last: Dziembowski

first: Grzegorz

last: Kudla

first: Torben

middle: H

last: Jensen


title: The relative importance of DNA methylation and Dnmt2-mediated epigenetic regulation on Wolbachia densities and cytoplasmic incompatibility

city: Nashville

first: Daniel

last: LePage

state: TN

address: U7214 MRBIII 465 21st Ave S

institute: Vanderbilt University

summary: Wolbachia pipientis is a worldwide bacterial parasite of arthropods that infects host germline cells and manipulates host reproduction to increase the ratio of infected females, the transmitting sex of the bacteria. The most common reproductive manipulation, cytoplasmic incompatibility (CI), is expressed as embryonic death in crosses between infected males and uninfected females. Specifically, Wolbachia modify developing sperm in the testes by unknown means to cause a post-fertilization disruption of the sperm chromatin that incapacitates the first mitosis of the embryo. As these Wolbachia-induced changes are stable, reversible, and affect the host cell cycle machinery including DNA replication and chromosome segregation, we hypothesized that the host methylation pathway is targeted for modulation during cytoplasmic incompatibility because it accounts for all of these traits. Here we show that infection of the testes is associated with a 55% increase of host DNA methylation in Drosophila melanogaster, but methylation of the paternal genome does not correlate with penetrance of CI. Overexpression and knock out of the Drosophila DNA methyltransferase Dnmt2 neither induces nor increases cytoplasmic incompatibility. Instead, overexpression decreases Wolbachia titers in host testes by approximately 17%, leading to a similar reduction in CI levels. Finally, strength of CI induced by several different strains of Wolbachia does not correlate with levels of DNA methylation in the host testes. We conclude that DNA methylation mediated by Drosophila's only known methyltransferase is not required for the transgenerational sperm modification that causes CI.

overall_design: Genomic DNA was extracted from pooled samples of Drosophila melanogaster adult testes. One sample from Wolbachia-infected males and one from uninfected males. Bisulfite sequencing was used to determine whether Wolbachia infection affects host DNA methylation in the testes.

first: Kristin

last: Jernigan

first: Seth

last: Bordenstein


title: RNA profiling of two endothelial cells (MPEC and AKT-HUVEC) and one human fibroblast line (BJ)

first: Der-I

last: Kao

summary: Analysis of overall gene expression in endothelial cells, MPEC and AKT-HUVEC, comparing to a human fibroblast line, BJ. We are looking for the highly abundant genes in endothelial cells comparing to fibroblasts.

overall_design:
Total RNA isolated from MPEC, AKT-HUVEC and BJ
Fig 3b in publication.

first: Shuibing

last: Chen


title: Apoptotic caspases prevent the induction of type I interferons by mitochondrial DNA

city: New Haven

first: Christian

last: Harman

state: Connecticut

address: 300 Cedar Street, The Anlyan Center

department: Genetics/Immunobiology

institute: Yale University

summary:
RNA sequencing of wild-type or Interferon Alpha receptor 1 Knockout MEF cells treated with DMSO or the Caspase Inhibitor Q-VD-OPh.

The mechanism by which cells undergo death determines whether dying cells trigger inflammatory responses or remain immunologically silent. Mitochondria play a central role in the induction of cell death, as well as in immune signaling pathways. Here, we identify of a mechanism by which mitochondria and downstream pro-apoptotic caspases regulate the activation of antiviral immunity. In the absence of active caspases, mitochondrial outer membrane permeabilization by Bax and Bak results in the expression of type I interferons (IFNs). This induction is mediated by mitochondrial DNA-dependent activation of the cGAS/STING pathway and results in the establishment of a potent state of viral resistance. Our results show that mitochondria have the capacity to simultaneously expose a cell-intrinsic inducer of the IFN response, and to inactivate this response in a caspase-dependent manner. This mechanism provides a dual control, which determines whether mitochondria initiate an immunologically silent or a pro-inflammatory type of cell death.

In order to determine whether the pharmacological inhibition of caspases could activate the type I interferon response, we treated WT MEFs with the caspase inhibitor Q-VD-OPH. The inhibitor induced an increased expression of ISGs, which was dependent on type I IFN receptor (IFNAR1) signaling.

overall_design: RNA was extracted from duplicate samples and libraries generated for sequencing using the directional RNA-Seq library prep at the Yale Center for Genome Analysis. Libraries were sequenced using a Hiseq2500 sequencer to generate 76bp single-end reads. Duplicate samples were analyzed for each condition.

first: Richard

last: Flavell

first: Anthony

last: Rongvaux


title: ChIP-seq for IRF7

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

institute: Weizmann Institute of Science

summary: We performed ChiP-Seq for IRF7 in GM-CSF induced bone-marrow cells.

overall_design: IRF7 ChIP-Seq in myeloid cells

first: Ronnie

last: Blecher-Gonen


title: Spinal cord injury (RNA sequencing data)

summary: We investigated the gene expression profile of monocyte-derived macrophages and microglia following spinal cord injury. Moreover, we investigated the gene expression profole of M-CSF induced macrophages and new-born derived microglia following TGFb1 treatment.

overall_design:
monocyte-derived macrophages and microglia following spinal cord injury
M-CSF induced macrophages and new-born derived microglia following TGFb1 treatment


title: Expression Profiling E. Coli Evolved on Glucose Minimal Media

city: La Jolla

first: Bernhard

last: Palsson

state: CA

address: 9500 Gilman Dr.

department: Bioengineering

institute: UCSD

summary: mRNA sequencing was performed on E. coli evolved at 37C on M9 Minimal Media with Glucose

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: Growth of evolved E. coli was characterized under the same conditions as the evolution and compared to the wild type parent strain

first: Ryan

last: LaCroix

first: Troy

middle: E

last: Sandberg

first: Edward

middle: J

last: O’Brien

first: Jose

last: Utrilla

first: Ali

last: Ebrahim

first: Gabriela

middle: I

last: Guzman

last: Szubin

middle: O

first: Adam

last: Feist


title: The essential Schizosaccharomyces pombe Pfh1 DNA helicase promotes fork movement past G-quadruplex motifs to prevent DNA damage

city: Umeå

first: Nasim

last: Sabouri

address: Linnaeus väg

department: Medical Biochemistry and Biophysics

institute: Umeå University

summary:
Background
G-quadruplexes (G4s) are stable non-canonical DNA secondary structures consisting of stacked arrays of four guanines, each held together by Hoogsteen hydrogen bonds. Sequences with the ability to form these structures in vitro, G4 motifs, are found throughout bacterial and eukaryotic genomes. The budding yeast Pif1 DNA helicase, as well as several bacterial Pif1 family helicases, unwind G4 structures robustly in vitro and suppress G4-induced DNA damage in S. cerevisiae in vivo.
Results
We determined the genomic distribution and evolutionary conservation of G4 motifs in four fission yeast species and investigated the relationship between G4 motifs and Pfh1, the sole S. pombe Pif1 family helicase. Using chromatin immunoprecipitation combined with deep sequencing, we found that many G4 motifs in the S. pombe genome were associated with Pfh1. Cells depleted of Pfh1 had increased fork pausing and DNA damage near G4 motifs, as indicated by high DNA polymerase occupancy and phosphorylated histone H2A, respectively. In general, G4 motifs were underrepresented in genes. However, Pfh1-associated G4 motifs were located on the transcribed strand of highly transcribed genes significantly more often than expected, suggesting that Pfh1 has a function in replication or transcription at these sites.
Conclusions
In the absence of functional Pfh1, unresolved G4 structures cause fork pausing and DNA damage of the sort associated with human tumors.

overall_design: Examination of Pfh1 association, Cdc20 association in Pfh1-expressed and Pfh1-depleted cells and gamma-H2A association in Pfh1-expressed and Pfh1-depleted cells. Two replicates were performed.  Input DNA was used as control.

first: John

last: Capra

first: Virginia

last: Zakian


title: Hairpin Capture of DNA End Structures reveals chromosomal DNA end structure with single nucleotide resolution

city: St. Louis

first: Jacqueline

last: Payton

state: MO

address: 660 S. Euclid Ave

department: Pathology and Immunology

institute: Washington University School of Medicine

summary: The structure of broken DNA ends is a critical determinant of the pathway used for DNA double strand break (DSB) repair.  Here, we develop an approach, hairpin capture of DNA end structures (HCoDES), which elucidates chromosomal DNA end structures at single nucleotide resolution.  HCoDES defines structures of physiologic DSBs generated by the RAG endonuclease, as well as those generated by nucleases widely used for genome editing.  Analysis of G1-phase cells deficient in H2AX or 53BP1 reveals DNA ends that are frequently resected to form long single-stranded overhangs that can be repaired by mutagenic pathways.  In addition to 3’ overhangs, many of these DNA ends unexpectedly form long 5’ single-stranded overhangs.  The divergence in DNA end structures resolved by HCoDES suggests that H2AX and 53BP1 may have distinct activities in end protection.  Thus, the high-resolution end structures obtained by HCoDES identify new features of DNA end processing during DSB repair.

overall_design: Single stranded DNA ligation of genomic DNA isolated from G1 arrested LigaseIV-/-, LigaseIV-/- 53BP1-/- and LigaseIV-/- H2AX-/- Abelson pre-B cells harboring site specific DSBs generated by the RAG recombinase, Cas9 endonuclease or Zinc Finger Endonuclease.

first: Barry

last: Sleckman

first: Yanjiao

last: Zhou

first: Yair

last: Dorsett


title: mRNASeq  of Nitrosomonas europaea and Nitrobacter winogradskyi

city: Corvallis

first: Luis

last: Sayavedra-Soto

state: OR

address: Cordley Hall 2082

department: Botany and Plant Pathology

institute: Oregon State University

summary: N.europaea and  N. winogradskyi were grown singly and in co-culture in chemostat to probe for transcriptome diffrences between the two growth conditions.

sample_organism:
Nitrobacter winogradskyi
Nitrosomonas europaea

overall_design: The comparison was done in chemostats. Single cultures maintained with 60 mM ammonium or nitrate, as appropiate, were compared to co-culture maintained with 60 mM ammonium.

last: Perez

first: Alex

last: Buchanan

first: Brett

last: Mellbye

first: Rebecca

last: Ferrrel

first: Jeff

last: Chang

first: Frank

last: Chaplen

first: Peter

last: Bottomley


title: DNA binding activities of the C-clamp

city: Irvine

first: Michael

last: Zeller

state: California

department: Computer Science

institute: University of California, Irvine

summary: Investigated the DNA binding specificity of the C-clamp of dnTCF1E

overall_design: Used a doxycycline inducible system to investigate the role of the C-clamp in the genome-wide binding of dnTCF1E.  Induced dnTCF1EWT and dnTCF1Emut (C-clamp mutant that is null for C-clamp DNA binding) over 2 time points (2 hours and 9 hours).  A 0 hour (no doxycycline, uninduced) control was also included.

first: Nate

last: Hoverter

first: Pierre

last: Baldi

first: Marian

middle: L

last: Waterman


title: The DNMT1 associated lncRNA Dali is an epigenetic regulator of neural differentiation [4]

city: Oxford

first: Vladislava

last: Chalei

address: Sherrington building, Parks road

department: MRC FUnctional Genomics Unit, Department of Physiology, Anatomy and Genetics

country: United Kingdom

institute: University of Oxford

summary: Many intergenic long noncoding RNA (lncRNA) loci regulate the expression of adjacent protein coding genes. Less clear is whether intergenic lncRNAs commonly regulate transcription by modulating chromatin at genomically distant loci. Here, we report both genomically local and distal RNA-dependent roles of Dali, a conserved central nervous system expressed intergenic lncRNA. Dali is transcribed downstream of the Pou3f3 transcription factor gene and its depletion disrupts the differentiation of neuroblastoma cells. Locally, Dali transcript regulates transcription of the Pou3f3 locus. Distally, it preferentially targets active promoters and regulates expression of neural differentiation genes, in part through physical association with the POU3F3 protein. Dali interacts with the DNMT1 DNA methyltransferase in mouse and human and regulates DNA methylation status of CpG island-associated promoters in trans. These results demonstrate, for the first time, that a single intergenic lncRNA controls the activity and methylation of genomically distal regulatory elements to modulate large-scale transcriptional programmes.

overall_design:
The genome-wide binding profile of Dali was determined using Capture Hybridisation Analysis of RNA Targets (CHART)-Seq technique (Simon et al, Proc Natl Acad Sci U S A 108: 20497-20502, 2011) in N2A cells. Following the CHART-seq protocol, we used RNase H elution to recover genomic DNA associated with endogenous Dali transcripts. We identified Dali binding sites in comparison both to an input DNA sample from N2A cells and to DNA recovered using the control E.coli LacZ oligonucleotide.
Please note that n2a_input, n2a_LacZ data was published previously [GSE52571]

first: Stephen

last: Sansom

first: Lesheng

last: Kong

first: Sheena

last: Lee

first: Juan

last: Montiel

first: Keith

last: Vance

first: Chris

last: Ponting


title: Regulation of σK activity and function by SpoIIID during Clostridium difficile sporulation

status: Public on Dec 02 2014

city: Burlington

first: Julie

last: Dragon

state: VT

address: 95 Carrigan Dr

department: MMG

institute: UNIVERSITY OF VERMONT & ST AGRIC COLLEGE

summary:
Purpose: A goal of this study was to identify genes induced in the mother cell during Clostridium difficile sporulation (specifically in a σE-, σK-, and SpoIIID-dependent manner).
Methods: Whole genome RNA sequencing was performed on wildtype, sigE-, sigK- and spoIIID- C. difficile strains (strain 630 background; JIR8094 = parent strain), and the transcriptional profiles of the different mutants during growth on 70:30 agar plates were determined using an Illumina MiSeq1000.
Results: This analysis identified 200 genes whose expression is collectively activated by sporulation sigma factors: 159 were σF-dependent, 162 were σE-dependent, 28 were σG-dependent, and 36 were σK-dependent. A total of 254 genes were identified as requiring Spo0A for their expression when sporulation was induced on the 70:30 plates.
Conclusions: These results provide the first genome-wide transcriptional analysis of genes whose expression is induced by specific sporulation sigma factors in the Clostridia and highlight that diverse mechanisms regulate sporulation sigma factor activity in the Firmicutes. For example, in contrast with the B. subtilis sporulation pathway, C. difficile σE was not required to fully activate σG, and σG was not required to activate σK.

overall_design: Wildtype, sigE-, sigK- and spoIIID- strains were streaked onto 70:30 plates in triplicate, and sporulation was induced. RNA from the three biological replicate samples was harvested, DNAse-I treated, and ribosomally depleted using Ribo-Zero kits. This RNA was transformed into cDNA, and the resulting libraries were subjected to paired end sequencing using an Illumina HiSeq 1000.

first: Keyan

last: Pishdadian

first: Aimee

last: Shen


title: A common cell state in Triple Negative Breast Cancers represents a druggable vulnerability

first: Sebastian

middle: M

last: Nijman

address: Lazarettgasse 14

institute: Research Center for Molecular Medicine

summary: A basal (MDAMB468) and luminal (ZR75-1) cell line were treated with DMSO or PKC412 for 6h

overall_design: 2 DMSO and 3 PKC412 treated samples for each cell line

first: Markus

last: Muellner


title: The DNMT1 associated lncRNA Dali is an epigenetic regulator of neural differentiation

type:
Expression profiling by array
Other

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

overall_design: Refer to individual Series


title: The oncogenic microRNA hsa-mir-155-5p targets the transcription factor ELK3 and links it to the hypoxia response and the Hypoxia Inducible Factor HIF1α

city: Illkirch

first: Tao

last: YE

address: 1 rue Laurent Fries

country: France

institute: IGBMC (CNRS/INSERM/UDS)

summary: The molecular response to hypoxia is a critical cellular process implicated in cancer, and a target for drug development. The activity of the major player, HIF1α, is regulated at different levels, including the transcriptional level by the Ets factor ELK3. The molecular mechanisms of this intimate transcriptional connection remain largely unknown. Whilst investigating global ELK3-chromatin interactions, we uncovered an unexpected connection that involves the microRNA hsa-miR-155-5p, a hypoxia-inducible oncomir that targets HIF1α. One of the ELK3 chromatin binding sites, detected by Chromatin Immuno-Precipitation Sequencing (ChIP-seq) of normal Human Umbilical Vein Endothelial Cells (HUVEC), is located at the transcription start site of the MIR155HG genes that expresses hsa-miR-155-5p. We confirmed that ELK3 binds to this promoter by ChIP and QPCR. We showed that ELK3 and hsa-miR-155-5p form a double-negative regulatory loop. ELK3 depletion induced hsa-miR-155-5p expression, and hsa-miR-155-5p expression decreased ELK3 expression at the RNA level through a conserved target sequence in its 3’-UTR. We further showed that the activities of hsa-miR-155-5p and ELK3 are functionally linked. Pathway analysis indicates that both factors are implicated in related processes, including cancer and angiogenesis. hsa-miR-155-5p expression and ELK3 depletion have similar effects on expression of known ELK3 target genes, and in-vitro angiogenesis and wound closure. Bioinformatic analysis of cancer RNA-seq data shows that hsa-miR-155-5p and ELK3 expression are significantly anti-correlated, as would be expected from hsa-miR-155-5p targeting ELK3 RNA. Hypoxia (0% oxygen) down-regulates ELK3 mRNA in a microRNA and hsa-miR-155-5p dependent manner. These results tie ELK3 into the hypoxia response pathway through an oncogenic microRNA and into a circuit implicated in the dynamics of the hypoxic response. This crosstalk could be important in the development of new treatments for a range of pathologies.

overall_design: Examination of ELK3 DNA interactions in HUVEC cells under normal oxygen conditions

first: E

middle: D

last: Robertson

first: Christine

last: Wasylyk

last: Ye

first: Alain

last: Jung

first: Bohdan


title: In vitro differentiation of human low threshold mechanoreceptive (LTMR) neurons from embryonic stem cells

city: Heidelberg

first: Katrin

last: Schrenk-Siemens

address: Im Neuenheimer Feld 366

department: Institute of Pharmacology

institute: University Heidelberg

summary: Human embryonic stem cells were differentiated into peripheral sensory neurons via the intermediate generation of neural crest like cell (NCC). Using various markers we identified these cells as LTMR. We then analyzed there complete transcriptional profile in comparison to the intermediate neural crest like cells.

overall_design: mRNA expression data of human ESC-derived sensory neuron clusters (10-20 cells) and human ESC-derived neural crest like cells (~100 cells) was generated by illumina deep sequencing

first: Hagen

last: Wende

first: Jan

last: Siemens


title: The genetic architecture of the genome-wide transcriptional response to ER stress in the mouse

city: Ithaca

first: Clement

last: Chow

state: NY

address: 227 Biotech Bldg

institute: Cornell University

summary: Endoplasmic reticulum (ER) stress occurs when misfolded proteins accumulate in the ER. The cellular response to ER stress involves complex transcriptional and translational changes, important to the survival of the cell. ER stress is a primary cause and a modifier of many human diseases. A first step to understanding how the ER stress response impacts human disease is to determine how the transcriptional response to ER stress varies among individuals. The genetic diversity of the eight mouse Collaborative Cross (CC) founder strains allowed us to determine how genetic variation impacts the ER stress transcriptional response. We used tunicamycin, a drug commonly used to induce ER stress, to elicit an ER stress response in mouse embryonic fibroblasts (MEFs) derived from the CC founder strains and measured their transcriptional responses. We identified hundreds of genes that differed in response to ER stress across these genetically diverse strains. Strikingly, inflammatory response genes differed most between strains; major canonical ER stress response genes showed relatively invariant responses across strains. To uncover the genetic architecture underlying these strain differences in ER stress response, we measured the transcriptional response to ER stress in MEFs derived from a subset of F1 crosses between the CC founder strains. We found a unique layer of regulatory variation that is only detectable under ER stress conditions. Over 80% of the regulatory variation under ER stress derives from cis-regulatory differences. This is the first study to characterize the genetic variation in ER stress transcriptional response in the laboratory mouse. Our findings indicate that the ER stress transcriptional response is highly variable among strains and arises from genetic variation in individual downstream response genes, rather than major signaling transcription factors. These results have important implications for understanding how genetic variation impacts the ER stress response, an important component of many human diseases.

overall_design: We investigated the genetic variation in ER stress transcriptional response in mouse embryonic fibroblasts (MEFs) across eight mouse strains: A/J, C57BL/6J, 129S1Sv/ImJ, NOD/ShiLtJ, NZO/H1LtJ, CAST/EiJ, PWK/PhJ, and WSB/EiJ. MEFs from each strain were treated with a control DMSO or ER stress-inducing drug, Tunicamycin (TM). To identify the genetic architecture underlying this genetic variation, MEFs from F1 strains were also studied. MEFs from the following F1s were evaluated: C57BL/6J X CAST/EiJ, C57BL/6J X 129S1Sv/ImJ, C57BL/6J X NOD/ShiLtJ, C57BL/6J X NZO/H1LtJ, and C57BL/6J X WSB/EiJ. Again F1 MEFS were treated with either DMSO or TM. There are two or three replicates for each sample.

first: Andrew

middle: G

last: Clark


title: Prolonged growth of a clinical S. aureus strain selects for a stable SCV and Full genomic characterization of the development in a clinical Staphylococcus aureus strain of a stable Small Colony Variant cell-type

city: Adelaide

first: Long

last: Bui

state: South Australia

address: North Terrace Campus

department: Microbiology

country: Australia

institute: University of Adelaide

summary:
We have observed that for a number of S. aureus strains as they switch to a SCV lifestyle there is the formation of an extracellular matrix. We focused our analysis on one strain, WCH-SK2. For bacterial survival in the host, the combination of low nutrients and the prolonged timeframe forms a stress that selects for a specific cell-type from the population. In this context, we used steady-state growth conditions with low nutrients and a controlled low growth rate, for a prolonged time and with methylglyoxal. These conditions induced S. aureus WCH-SK2 into a stable SCV cell-type, they did not revert after sub-culturing.
Methods: Transcriptomic profiles of wild-type (WT) and SCV were generated in continuous culture in the presence of stress (high and low level of methylglyoxal).
Results: Analysis revealed these cells possessed a metabolic and surface profile that was different from previously described SCVs or biofilm cells. The extracellular matrix was protein and extracellular DNA; but not polysaccharide. The SCV cells induced expression of certain surface proteins (such as Ebh) and lantibiotic synthesis while down-regulating factors that stimulates immune response (leucocidin, capsule, carotenoid). We also studied further their genetic characteristics. They possessed an increased viability in the presence of antibiotics compared to their non-SCV form. Their stability implied there had been genetic changes, we determined the whole genome sequence of WCH-SK2 and its stable SCV forms at a single base resolution, employing Single Molecular Real-Time (SMRT) sequencing that also enables the methylome to be determined. The genetic features of this isolate have been identified; the SCCmec type, the pathogenicity and genetic islands and virulence factors. The comparison has identified a set of genetic changes that occurred in the stable SCV form; most notably to the global regulator MgrA and the phosphoserine phosphatase RsbU (part of the regulatory pathway of the sigma factor SigB). There was a shift in the methylation across the genome.
Conclusions: Our data reveal a cell heterogeneity within a S. aureus population and using conditions that resemble long-term survival in the host has identified a previously unnoticed S. aureus cell-type, with a distinctive metabolic and molecular profile. The results from this study represent a unique identification of a suite of epigenetic, genetic and transcriptional factors that are implicated in the switch in S. aureus to its persistent SCV form

overall_design: Total RNA of WT (batch culture) and SCV formed in high level of methylglyoxal  (0.031%) at day 55 and SCV formed at low level of methylglyoxal (0.0078%) at day 30 of continuous culture. DNA genomic of WT and stable SCV formed in high level of methylglyoxal (0.031%)

first: Stephen

last: Kidd


title: Novel selective regulation of hematopoietic progenitor self-renewal, survival and proliferation by estrogens has therapeutic potential in myeloproliferative neoplasms

city: Madrid

first: Simón

last: Méndez-Ferrer

address: Calle Melchor Fernández Almagro, 3

institute: CNIC

summary: Estrogens are potential regulators of the hematopoietic stem cell (HSC) niche and have effects on mature hematopoietic cells; however, whether estrogen signaling directly regulates normal and malignant HSC remains unclear. We demonstrate differential expression and specific roles of estrogen receptors (ER) in hematopoietic progenitors. ERa activation in short-term HSC and multipotent progenitors induced apoptosis. In contrast, the selective ER modulator (SERM) tamoxifen induced proliferation of quiescent long-term HSC, altered their self-renewal signature and compromised hematopoietic reconstitution following myelotoxic stress. Treatment with tamoxifen alone abolished hematopoietic progenitor expansion induced by JAK2V617F by restoring normal levels of apoptosis, blocked JAK2V617F-induced myeloproliferative neoplasm in vivo, and sensitized MLL-AF9+ leukemias to chemotherapy. Tamoxifen showed selective effects on mutant cells compared to normal ones, and had only a minor impact on steady-state hematopoiesis in disease-free animals. These results uncover specific regulation of hematopoietic progenitors by estrogens and potential anti-leukemic properties of SERM

overall_design: LT-HSCs, ST-HSCs and MPPs sorted from the bone marrow of mice treated with tamoxifen or vehicle (3 biological replicates per group)

first: Abel

last: Sánchez-Aguilera


title: Genome-wide analyses reveal DNA methylation in the central nucleus of the amygdala is linked to anxious temperament in young primates

city: Madison

first: Reid

last: Alisch

state: WI

address: 6001 Research Park Blvd.

department: Department of Psychiatry

institute: University of Wisconsin School of Medicine

summary: We used reduced representation bisulfite sequencing to profiled 5-methylcytosine in the Ce of rhesus monkeys (N = 23) fully phenotyped for anxious temperament (AT) and identified 5,489 CpG sites (1,363 genes) with methylation levels predictive of individual differences in AT (FDR p-value < 0.05), including genes previously implicated in psychiatric-related disorders (e.g. GRIN1, GRM5, HTT, ADCYAP1, and SHANK3).

overall_design: Used RRBS to profile the central nucleus of the amygdala of 23 monkeys and the resulting data analyzed using anxious temperament as a continuous trait using only age as a covariate.

middle: S

first: Pankaj

last: Chopra

first: Ned

last: Kalin


title: ChIP-nexus: a novel ChIP-exo protocol for improved detection of in vivo transcription factor binding footprints

city: Kansas City

first: Julia

last: Zeitlinger

institute: Stowers Institute for Medical Research

summary: Understanding how eukaryotic enhancers are bound and regulated by specific combinations of transcription factors is still a major challenge. To better map transcription factor binding genome-wide at nucleotide resolution in vivo, we have developed a robust ChIP-exo protocol called ChIP-nexus (chromatin immunoprecipitation experiments with nucleotide resolution through exonuclease, unique barcode and single ligation), which utilizes an efficient DNA self-circularization step during library preparation. Application of ChIP-nexus to four proteins—human TBP, Drosophila NFkB, Twist and Max—showed that it outperformed existing ChIP protocols in resolution and specificity, pinpointed relevant binding sites within enhancers containing multiple binding motifs, and allowed for the analysis of in vivo binding specificities. Notably, we show that Max frequently interacted with DNA sequences next to its motif, and that this binding pattern correlated with local DNA-sequence features such as DNA shape. ChIP-nexus will be broadly applicable to the study of in vivo transcription factor binding specificity and its relationship to cis-regulatory changes in humans and model organisms.

sample_organism:
Drosophila melanogaster
Homo sapiens

platform_organism:
Drosophila melanogaster
Homo sapiens

overall_design: ChIP-nexus was performed against Dorsal (Drosophila melanogaster embryos), Twist (Drosophila melanogaster embryos), Max (Drosophila melanogaster S2 cells), Myc (Drosophila melanogaster S2 cells), and TBP (Human K562 cells)

first: Qiye

last: He

first: Jeff

last: Johnston


title: Genome-wide profiling of short fragment-enriched RNA in HeLa cells subjected to exosome depletion by RNAi

status: Public on Dec 01 2014

city: Aarhus

first: Peter

last: Andersen

address: Universitetsbyen 83

institute: Aarhus University

summary:
To assay the effect of depletion of the RNA exosome on RNAs shorter than the standard length captured by RNA-seq (>200 nt), we created RNA-seq libraries using fragmented RNA and a linker-ligation-based protocol that does not deplete RNAs shorter than 200 nt.
Note: these data relate to Figure 6E in Lubas, Andersen et al., Cell Reports 2014 (accepted)

overall_design:
These samples constitute RNA-seq libraries prepared to enrich for short RNA fragments such as snRNA and snoRNAs. Three different HeLa cell RNAi experiments were used to generate the RNA samples applied in the library construction: control transfected, hRRP40-depleted and triple-depleted of the known RNA exosome-associated ribonucleases (DIS3, DIS3L and hRRP6 knock-down). By these means the data offers reveal RNA exosome substrates via their up-regulation in the respective knock-downs

NOTE: The 'Figure6E_RNAseq_DataTable_PlottedValues.txt' was generated from total 5 samples, with two additional published samples [SRP031620] and provided to better allow readers to fully replicate the analyses presented in the publication.

first: Lubas

last: Michal

first: Andersen

middle: P

last: Refsing

first: Schein

last: Aleks

first: Dziembowski

last: Andrzej

first: Kudla

last: Grzegorz

first: Jense

middle: T

last: Heick


title: Gene Expression and Exon Splicing Change Analysis of Mouse N2A Cell Transcriptome upon Polypyrimidine tract-binding protein depletion (II)

city: Los Angeles

first: Areum

last: Han

address: 6577 MacDonald Research Lab. 675 Charles E. Young Dr. South

institute: UCLA

summary:
Purpose: Splicing factors regulate splice site choices in pre-mRNA and determine final exon set in mRNA. To understand mechanisms of splicing regulation, it is important to identify and characterize exon targets of splicing factors. Recently, development of RNA-seq technology enables researchers to investigate exon splicing profiles as well as gene expression profiles in transcriptome-wide. The goal of this study is to investigate transcriptome changes by splicing factors, Polypyrimidine Tract Binding proteins (PTB). In this study, we analyzed exon and gene expression changes followed by Ptbp1, Ptbp2, and both Ptbp1 & Ptbp2 knock down.
Methods: The knockdown experiment was performed in mouse neuroblastoma (N2A) cells. Total RNA was collected from cells and further treated with DNase I to avoid DNA contamination. RNA-seq libraries were constructed in a strand specific way using dUTP and Uracil-Specific Excision Reagent enzyme. The libraries were subjected to 100bp paired-end sequencing (Illumina HiSeq2000 platform).

overall_design: Poly(A)-mRNA and exon profiles of N2A mouse blastoma cells in four samples: shRNA transfection control, single knock down of ptbp1, single knock down of ptbp2, double knock down of ptbp1 and ptbp2. RNA-seq libraries were generated in strand specific way using dUTP and USER enzyme and sequenced using Illumina HiSeq2000.


title: Molecular Effects of Doxycycline Treatment on Pterygium from Caucasian Patients as Revealed by Massive Transcriptome Sequencing

city: Logroño

first: Ignacio

last: Larrayoz

state: Please Select

address: C\ Piqueras 98, Ed CIBIR

department: Oncology Area

institute: CIBIR

summary: Genes were identified which modified their expression in a dose-dependent manner upon exposure to doxycycline. The more represented cellular pathways included all mitochondrial genes, the endoplasmic reticulum stress response, integrins and extracellular matrix components, and growth factors.

overall_design: Examination of 4 different doses of doxycycline in three human pterygium samples.

first: Alfredo

last: Martinez


title: Deep sequencing and analysis of small RNAs from Nt-Xanthi and CMV delta 2b-infected Nt-Xanthi

city: Beijing

first: Zhao

last: Jian-Hua

address: Datun road

institute: Chinese Academy of Sciences

summary: To investigate if CMV infection might affect the accumulation of sat-like RNAs, sRNA isolated from Nt-Xanthi and Nt-Xanthi infected with SD-CMVdeltasatRNA were sequenced.

overall_design: sRNA sequencing was employed to identify the different of the sRNA between Nt-Xanthi and Nt-Xanthi infected with SD-CMVdeltasatRNA

first: Jian-Hua

last: Zhao

first: Yuan-Yuan

last: Fang

first: Ming-Bo

last: Wang

first: Hui-Shan

last: Guo


title: Simultaneous sequencing of oxidized methylcytosines produced by TET/JBP proteins in Coprinopsis cinerea [CMS-seq]

first: Lukas

last: Chavez

address: Im Neuenheimer Feld 280

institute: German Cancer Research Center (DKFZ)

summary: TET/JBP enzymes oxidize 5-methylpyrimidines in DNA. In mammals, the oxidized methylcytosines (oxi-mC) function as epigenetic marks and likely intermediates in DNA demethylation. Here we present a novel diglucosylation-based method to simultaneously map 5hmC, 5fC and 5caC at near base-pair resolution, and verify the results using independent methods. We have used the method to map the distribution of oxi-mC across the genome of Coprinopsis cinerea, a basidiomycete that encodes 47 TET/JBP paralogs in a new class of DNA transposons. Like 5-methylcytosine (5mC) residues from which they are derived, oxi-mC modifications are enriched at centromeres, TET/JBP transposons, and multicopy paralogous genes that are not expressed, but rarely mark genes whose expression changes between two developmental stages. Our study provides evidence for the emergence of an epigenetic regulatory system through recruitment of selfish elements in a eukaryotic lineage, and describes a method to map all three different species of oxi-mC simultaneously.

overall_design:
Anti-CMS data has been generated for two biological replicates where one biological replicate has three technical replicates and the other biological replicate has two technical replicaltes. For each biologial replicate one Input replicate has been generated.
based on sodium bisulfite-mediated conversion of 5hmC to cytosine-5-methylenesulfonate (CMS); CMS-containing DNA fragments are then immunoprecipitated using a CMS-specific antiserum.

first: Yun

last: Huang

first: Anjana

last: Rao


title: GATA Family Members as Inducers for Cellular Reprogramming to Pluripotency

first: Minjie

last: Zhang

address: 1985 Zonal Avenue

department: Department of Pharmacology and Pharmaceutical Sciences

institute: University of Southern California

summary: Members of the GATA protein family play important roles in lineage specification and transdifferentiation. Previous reports show that some members of GATA protein family also can induce pluripotency in somatic cells by substituting for the key pluripotency-associated factor Oct4. However, the mechanism that links the lineage specifying cues and activation of pluripotency remains elusive. Here, we report that all GATA family members can substitute for Oct4 to induce pluripotency. We found that all members of the GATA family can inhibit elevated ectodermal-lineage genes, which is consistent with previous reports that a balance of different lineage-specifying forces is important for restoration of pluripotency. A conserved DNA-binding domain in the C-terminal zinc finger is critical for the GATA family to induce pluripotency. Using RNA-seq and ChIP-seq we identified that the pluripotency-related gene Sall4 is a direct target of GATA family members during reprogramming, serving as a bridge linking the lineage-specific GATA family to the pluripotency circuit. Thus, the GATA family is the first family of proteins wherein all members can function as inducers of the reprogramming process that can substitute for Oct4. Our results suggest that the roles of the GATA family in reprogramming have been greatly underestimated, and that the GATA family may serve as a general mediator for cell fate conversion.

overall_design: GATA4 and GATA6 ChIP-Seq at day 6 post-induction MEFs. mRNA profiles of GATA4- and GATA6- MEFs at days 0, 2, 4, and 6 respectively. Sequencing repeated twice each sample.

first: Jian

last: Shu


title: Molecular Effects of Doxycycline Treatment on Pterygium as Revealed by Massive Transcriptome Sequencing

summary: A total of 332 genes were identified which modified their expression in a dose-dependent manner upon exposure to doxycycline. The more represented cellular pathways included all mitochondrial genes, the endoplasmic reticulum stress response, integrins and extracellular matrix components, and growth factors.

overall_design: Examination of 4 different doses of doxycycline in ten human pterygium samples.


title: RNA-seq analysis of differences in gene expression between dorsal and ventral MEC

city: Edinburgh

first: Matthew

middle: Francis

last: Nolan

state: UK

address: Hugh Robson Building

department: Centre for Integrative Physiology

institute: University of Edinburgh

summary: Neural circuits in the medial entorhinal cortex (MEC) encode an animal’s position and orientation in space. Within the MEC spatial representations, including grid and directional firing fields, have a laminar and dorsoventral organization that corresponds to a similar topography of neuronal connectivity and cellular properties. Yet, in part due to the challenges of integrating anatomical data at the resolution of cortical layers and borders, we know little about the molecular components underlying this organization. To address this we develop a new computational pipeline for high-throughput analysis and comparison of in situ hybridization (ISH) images at laminar resolution. We apply this pipeline to ISH data for over 16,000 genes in the Allen Brain Atlas and validate our analysis with RNA sequencing of MEC tissue from adult mice. We find that differential gene expression delineates the borders of the MEC with neighboring brain structures and reveals its laminar and dorsoventral organization. Our analysis identifies ion channel-, cell adhesion- and synapse-related genes as candidates for functional differentiation of MEC layers and for encoding of spatial information at different scales along the dorsoventral axis of the MEC. Our results support the hypothesis that differences in gene expression contribute to functional specialization of superficial layers of the MEC and dorsoventral organization of the scale of spatial representations.

overall_design: Examination of dorsal and ventral regions from 4 replicate samples each containing pooled data from 3-4 mice

first: Helen

last: Ramsden

first: Gulsen

last: Surmeli


title: A zebrafish model of intrahepatic cholangiocarcinoma by dual expression of hepatitis B virus X and hepatitis C virus core protein in liver

city: Taipei

first: Wangta

last: Liu

address: Academia Rd.

country: Taiwan

institute: Institute of Cellular and Organismic Biology,  Academia Sinica

summary: We sequenced mRNA from each transgenic zebrafish line including WT, HBx, HCP, and HBx+HCP.

overall_design: Examination of mRNA levels in individual line at three month of age.

first: Jen-Leih

last: Wu


title: Mapping gene regulatory networks in Drosophila eye development by large-scale transcriptome perturbations and motif inference [ChIP-Seq]

city: Marseille

first: Delphine

last: Potier

address: 27 boulevard Lei Roure

institute: CRCM

summary: Genome control is operated by transcription factors (TF) controlling their target genes by binding to promoters and enhancers. Conceptually, the interactions between TFs, their binding sites, and their functional targets are represented by gene regulatory networks (GRN). Deciphering in vivo GRNs underlying organ development in an unbiased genome-wide setting involves identifying both functional TF-gene interactions and physical TF-DNA interactions. To reverse-engineer the GRN of eye development in Drosophila, we performed RNA-seq across 72 genetic perturbations and sorted cell types, and inferred a co-expression network. Next, we derived direct TF-DNA interactions using computational motif inference, ultimately connecting 241 TFs to 5632 direct target genes through 24926 enhancers. Using this network we found network motifs, cis-regulatory codes, and new regulators of eye development. We validate the predicted target regions of Grainyhead by ChIP-seq and identify this factor as a general co-factor in the eye network, being bound to thousands of nucleosome-free regions.

overall_design: Grh ChIP-seq performed in Drosophila 3rd instar larval eye-antennal discs.

first: Kristofer

last: Davie

first: Marina

last: Naval Sánchez

first: Lotte

last: Haggen

first: Valerie

last: Christiaens

first: Stein

last: Aerts


title: Small RNAs from third instar Drosophila melanogaster males

city: Detroit

first: Victoria

last: Meller

state: Michigan

address: 5047 Gullen Mall

department: Biological Sciences

institute: Wayne State University

summary: The goal of this study was to determine if small RNAs from the 1.688 g/cm 3 satellite repeats are present in male larvae.

overall_design: The small RNA profiles of wild type male larvae and males expressing a snap back construct containing 1.688 sequence were compared.  Abundant 21 nt 1.688 RNAs were found in males expressing the snap back 1.688 g/cm 3 construct, but not in wild type males.

first: Debashish

middle: U

last: Menon


title: Simultaneous sequencing of oxidized methylcytosines produced by TET/JBP proteins in Coprinopsis cinerea

first: Lukas

last: Chavez

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

overall_design: Refer to individual Series

first: Yun

last: Huang


title: Mapping gene regulatory networks in Drosophila eye development by large-scale transcriptome perturbations and motif inference


title: Simultaneous sequencing of oxidized methylcytosines produced by TET/JBP proteins in Coprinopsis cinerea [RNA-seq]

overall_design: RNA-seq in Oidia and Hyphae (Coprinopsis cinerea).

first: Anjana

last: Rao


title: High-resolution Sox2 DNA-binding sites mapping by ChIP-exo in TSA-treated ES cells

city: Ashburn

first: Zhe

state: Virginia

address: 19700 Helix Dr.

department: Janelia Farm Research Campus

institute: Howard Hughes Medical Institute

summary: Mapping ultra-high resolution of Sox2:DNA interaction after trichostatin A (TSA) treatment would provide us with valuable new mechanistic insights into how epigenome regulates transcription factor DNA interactions in the cells.

overall_design: Embryonic stem cells were treated with 50nM TSA (Sigma: T8552) for 8 hours prior to ChIP-exo mapping.

first: Li

last: Li

first: Liu

last: Zhe


title: Functional Antagonism Between CELF and Mbnl Proteins in Cytoplasm and Nucleus [CLIP-seq]

city: Gainesville

first: Eric

last: Wang

state: FL

address: 2033 Mowry Rd

institute: University of Florida

summary: The CUG-BP and ETR-3-like factor 1 (Celf1) RNA binding protein plays an important role in heart and muscle development, and is over-expressed in the disease myotonic dystrophy.  Celf1 has known roles in regulation of RNA splicing, RNA stability, and protein translation.  To identify transcriptome-wide targets of the Celf1 protein, we performed CLIP-seq against Celf1 using the 3B1 antibody, in myoblasts, heart tissue, and muscle tissue.

overall_design: CLIP-Seq was performed against Celf1 in mouse muscle, heart, and C2C12 mouse myoblasts.

first: Amanda

last: Ward

first: Daniel

last: Treacy

first: Thomas

first: David

last: Housman

first: Tom

last: Cooper

first: Christopher

last: Burge


title: Functional Antagonism Between CELF and Mbnl Proteins in Cytoplasm and Nucleus

sample_organism:
Mus musculus
synthetic construct

platform_organism:
Mus musculus
synthetic construct


title: Transcriptome analysis of wild tobacco Nicotiana attenuata after Alternaria alternata infection

city: Kunming

first: Jinsong

last: Wu

address: Lanhei Road 132

institute: Kunming institute of Botany, the Chinese Academy of Sciences

summary: To understand the transcriptome changes of source-sink transition leaves after infection of Alternaria alternata at 1 dpi

overall_design: mRNA profiles of source-sink stransition leaves at 1 dpi/ mock 1 d were generated by deep sequencing,  using Illumina Hiseq2000.


title: Functional Antagonism Between CELF and Mbnl Proteins in Cytoplasm and Nucleus [muscle]

summary: The CUG-BP and ETR-3-like factor 1 (Celf1) RNA binding protein plays an important role in heart and muscle development, and is over-expressed in the disease myotonic dystrophy.  Celf1 has known roles in regulation of RNA splicing, RNA stability, and protein translation.  To identify transcriptome-wide targets of the Celf1 protein in heart, we performed RNA-Seq of polyA+ RNA from mice inducibly expressing Celf1 in the muscle.

overall_design: Mice were engineered to express the reverse tetracycline trans-activator (rtTA2S-M2) from the rate myosin light chain 1/3 promoter/enhancer, and an N-terminal Flag-tagged version of the LYLQ isoform of human Celf1 from a tet-inducible promoter.  Mice were fed doxycycline to induce Celf1 expression in muscle, and gastrocnemius muscles were harvested from 3 mice each at 12 hour, 24 hour, 72 hour, and 7 day time points.  To account for potential doxycycline-dependent effects, control mice were fed doxycycline for 72 hours but these mice did not contain the tet-inducible Celf1 cassette.  In total, 15 gastrocnemius samples were analyzed by RNA-Seq.


title: Transcriptional changes in dormant potato minitubers treated with 1-(alpha-ethylbenzy)-3-nitroquanidine

city: Erie

first: Michael

middle: A

last: Campbell

state: PA

address: 4205 College Drive

department: School of Science

institute: Penn State Erie

summary:
RNA was sequenced from commercially grown greenhouse minitubers treated with 10 ug of 1-(alpha-ethylbenzy)-3-nitroquanidine (NG) in DMSO and followed for four, and seven days post treatment.
Control tubers were injected with DMSO alone. Sequence reads were mapped to the potato genome (PGSC_DM_v3_2.1.11) and transcript abundance was determined using Cuffdiff v 2.02.

overall_design: Minitubers were injected with DMSO (control) or 10 ug of NG and then trancript changes were examined at on, four, and seven days after exposure.


title: Functional Antagonism Between CELF and Mbnl Proteins in Cytoplasm and Nucleus [hearts]


title: MED13cTg heart ventricles and epididymal fat

city: Dallas

first: Kedryn

middle: K

last: Baskin

state: TX

address: 6000 Harry Hines

department: Molecular Biology

institute: UT Southwestern

summary: The heart requires a continuous supply of energy but has little capacity for energy storage and thus relies on exogenous metabolic sources.  We previously showed that cardiac MED13 modulates systemic energy homeostasis in mice.  Here we sought to define the extra-cardiac tissue(s) that respond to cardiac MED13 signaling.  We show that cardiac over-expression of MED13 in transgenic (MED13cTg) mice confers a lean phenotype that is associated with increased lipid uptake, beta-oxidation and mitochondrial content in white adipose tissue (WAT) and liver.  Cardiac expression of MED13 decreases metabolic gene expression and metabolite levels in heart and liver but enhances them in WAT.  Although exhibiting increased energy expenditure in the fed state, MED13cTg mice metabolically adapt to fasting.  Furthermore, MED13cTg hearts oxidize fuel that is readily available, rendering them more efficient in the fed state.  Parabiosis experiments in which circulations of wild-type and MED13cTg mice are joined, reveal that circulating factor(s) in MED13cTg mice promote enhanced metabolism and leanness.  These findings demonstrate that MED13 acts within the heart to promote systemic energy expenditure in extra-cardiac energy depots and point to an unexplored metabolic communication system between the heart and other tissues.

overall_design: n=3 for each genotype and organ

first: Chad

last: Grueter

first: Christine

last: Kusminski

first: William

last: Holland

first: Angie

last: Bookout

first: Santosh

last: Satapati

first: Megan

last: Kong

first: Shawn

middle: C

last: Burgess

first: Craig

last: Malloy

first: Philipp

last: Scherer

middle: B

last: Newgard

first: Rhonda

last: Bassel-Duby

middle: N

last: Olson


title: Mapping gene regulatory networks in Drosophila eye development by large-scale transcriptome perturbations and motif inference. [RNA-seq]

first: Delphine

last: Potier

overall_design: RNA-seq gene expression profiling across Drosophila 3rd instar larval wild type tissues (brain, eye-antennal and wing discs), specific cell types from the eye-antennal disc, sorted by FACS, and genetic perturbations (TF mutants, TF over-expression, and TF RNAi knockdown).

first: Kristofer

last: Davie

first: Marina

last: Naval Sánchez

first: Lotte

last: Haggen

first: Valerie

last: Christiaens

first: Stein

last: Aerts


title: Sustained expression of activated beta-catenin in dermal fibroblasts causes skin fibrosis

city: Cleveland

first: Radhika

middle: Paresh

last: Atit

state: Ohio

address: 2074 Adelbert Road, Millis 316

department: Biology

institute: Case Western Reserve University

summary: Forced expression of activated beta-catenin in mouse dermal fibroblasts is sufficient to cause spontaneous, progressive skin fibrosis in vivo.  We generated triple-transgenic HoxB6CreERT/+; R26-YFP/+; CatnbΔex3/+ "activated beta-catenin" mice and double-transgenic HoxB6CreERT/+; R26-YFP/+ littermate control mice.  We induced Cre activity (resulting in expression of activated beta-catenin in triple-transgenic mutant fetuses) by administering tamoxifen to the pregnant dam at embryonic day 16.5.  The activated beta-catenin mice developed fibrotic skin, characterized by elevated collagen deposition and increased fibroblast proliferation.  We performed RNA-sequencing to profile gene expression in the dermis of control and activated beta-catenin mutant mice with established skin fibrosis at 3 weeks of age.

overall_design: Gene expression profiles were determined by paired-end sequencing (Illumina HiSeq 2500) of total RNA from the dermis of 3 activated beta-catenin and 3 littermate control mice at 3 weeks of age.


title: Ribosome Profiling in P. falciparum asexual blood stages

city: San Francisco

first: Joseph

last: DeRisi

address: 1700 4th Street

department: Biochemistry

institute: UCSF

summary: The description of the transcriptome and proteome datasets of Plasmodium falciparum, the deadliest strain of human malaria, has been a tremendous resource for the understanding of the molecular physiology of this parasite. However, the underlying translational control that links global measurements of steady-state mRNA with protein levels is not well understood. Our work bridges this disconnect by measuring translation on a whole genome scale using ribosome profiling, providing the first measurements of new protein synthesis through the asexual blood phase developmental cycle.

overall_design: Cultures corresponding to ring, early trophozoite, late trophozoite, schizont stage, merozoite were harvested for both mRNA and polysome isolation using cycloheximide to freeze ribosomes in place.

first: Florence

last: Caro

first: Vida

last: Ahyong

first: Miguel

last: Betegon


title: Direct identification of endogenous SMG6 targets and a preferred motif spanning SMG6 cleavage sites by parallel analysis of RNA ends in human cells

city: Newark

first: Pamela

middle: J

last: Green

state: DE

address: 15 Innovation Way

department: Delaware Biotechnology Institute

institute: University of Delaware

summary: In metazoans, the endoribonuclease SMG6 is thought to cleave many endogenous mRNAs targeted for nonsense-mediated mRNA decay (NMD). However, most evidence as to the identity of endogenous SMG6 substrates is indirect, and little is known about their cleavage sites. Here, we report the efficacy of an RNA degradome approach called parallel analysis of RNA ends (PARE) for identifying NMD intermediates in human cells. By specifically sequencing the 5’ ends of intermediates dependent on SMG6 and the critical NMD factor UPF1, hundreds of endogenous transcripts that are direct targets of SMG6 have been revealed. A preferred sequence motif spanning most SMG6 cleavage sites has been identified and validated by mutational analysis. For many SMG6 substrates, depletion of SMG6 leads to decapping of the RNAs. These findings provide key insights into NMD and targeting by SMG6 while also demonstrating the potential of PARE for analyzing other ribonucleases with diverse endogenous substrates.

overall_design:
Genome-wide degradome sequencing and mRNA profiling was done following the knockdown of SMG6 and UPF1.  SPARE libraries targeting a sequence motif surrounding the identified cleavage site were also deeply sequenced on an Illumina platform.
PARE is a method of degradome analysis that captures and deeply sequences the 5' monophosphorylated ends of polyadenylated RNAs (see.German 2009 Nat Protoc 4, 356-362).  C-PARE libraries capture capped, polyadenlyated RNAs by first dephosphorylating the RNA, then decapping using tobacco acid pyrophosphatase and constructing PARE libraries, and will be described in the forthcoming paper.  SPARE captures the 5' monophosphorylated ends of specific RNAs using transcript-specific primers (see Schapire 3013 Methods 64:283-291).

first: Skye

last: Schmidt

first: Patricia

last: Foley

first: Joel

last: Belesco

first: Pam


title: Elucidation of stress memory inheritance through epigenome alterations in Brassica rapa plants

city: Lethbridge

first: Igor

last: Kovalchuk

address: 4401 University Drive

institute: UofL


title: PROTEOFORMER: deep proteome coverage through ribosome profiling and MS integration

city: Ghent

first: Gerben

last: Menschaert

address: Coupure Links 653

country: Belgium

institute: Ghent University, Faculty of BioScience Engineering

summary: An increasing amount of studies integrate mRNA sequencing data into MS-based proteomics to complement the translation product search space. We present the generation of a protein synthesis-based database from deep sequencing of ribosome-protected mRNA fragments. This approach increases the overall protein identification rates with 3% and 11% (improved and new identifications) for human and mouse respectively and enables proteome-wide detection of 5’-extended proteoforms, uORF translation and near-cognate translation start sites.

overall_design: Ribosome profiling of lactimidomycin and cycloheximide treated HCT116 cells

first: G

first: P

last: Van Damme

first: J

last: Crappé

first: E

last: Ndah

first: S

last: Steyaert

first: A

last: Koch

first: D

last: Gawron


title: Elucidation of stress memory inheritance through epigenome alterations in Brassica rapa plants [RNA-seq]

summary: In the current study we have profiled changes in the transcriptome of somatic and reproductive tissues of B.rapa plants following heat shock stress exposure. For this we used Illumina GAIIx platform. We have demonstrated that the highest tissue-specific alterations in the transcriptome profile are detected in tissues that were not directly exposed to stress, namely, in the endosperm and pollen. The progeny of exposed plants also exhibited significant alterations in the gene expression as compared to progeny of control plants.

overall_design:
The transcriptome profile was assessed after heat shock treatment in the following tissues of Brassica rapa plants: parental leaves, inflorescence meristem, pollen, unfertilized ovules, 24-hour post-fertilization ovules, embryo, endosperm and leaf tissues of progeny plants.

Please note that *diff_out.tar.gz contains all the standard output produced by cuffmerge and cuffdiff and each file content/format details are provided in the 'README.txt' file

first: Bilichak

last: Andriy

first: Kovalchuk

last: Igor


title: Characterization of human CDK12 and CDK13 in the regulation of RNA processing

city: Kansas City

first: Joan

last: Conaway

institute: Stowers Institute

summary: We report the total RNA-seq results after CDK9, CDK12 and CDK13 depletion in human HCT116 cells for three days. RNA-seq was performed in cells using two non-targeting replicates and two different shRNAs for each CDK knockdown.  For each CDK knockdown, most of the differentially expressed genes were down-regulated with a very small subset of genes upregulated. Different CDK proteins control distinct subsets of genes in vivo, with CDK12 and CDK13 sharing more overlap in function compared to CDK9. Besides, CDK12 and CDK13 loss preferentially affects DNA damage response and snRNA gene expression, respectively.

overall_design: Examine the changes of mRNA expression levels after CDK9, CDK12 and CDK13 depletion.

first: Kaiwei

last: Liang

first: Xin

last: Gao

first: Ali

last: Shilatifard


title: Genome-wide analysis of transcriptome and translatome following eIF4A1 knockdown in MCF7 cells

city: Cambridge

first: Roslin

last: Russell

address: Robinson Way

institute: Cambridge Research Institute, Cancer Research UK


title: InFusion: advancing discovery of fusion genes and chimeric transcripts from RNA-seq data

city: Berlin

first: Thomas

middle: F

last: Meyer

address: Chariteplatz 1

institute: Max Planck Institute for Infection Biology

summary: Gene fusions and chimeric transcripts occur frequently in cancers and in some cases drive the development of the disease. An accurate detection of these events is crucial for cancer research and in a long-term perspective could be applied for personalized therapy. RNA-seq technology has been established as an efficient approach to investigate transcriptomes and search for gene fusions and chimeric transcripts on a genome-wide scale. A number of computational methods for the detection of gene fusions from RNA-seq data have been developed. However, recent studies demonstrate differences between commonly used approaches in terms of specificity and sensitivity. Moreover their ability to detect gene fusions on the isoform level has not been studied carefully so far. Here we propose a novel computational approach called InFusion for fusion gene detection from deep RNA sequencing data. Validation of InFusion on simulated and on several public RNA-seq datasets demonstrated better detection accuracy compared to other tools. We also performed deep RNA sequencing of two well-established prostate cancer cell lines. Using these data we showed that InFusion is capable of discovering alternatively spliced gene fusion isoforms as well as chimeric transcripts that include non-exonic regions. In addition our method can detect anti-sense transcription in the fusions by incorporating strand specificity of the sequencing library.

overall_design: Detection of fusion genes and chimeric transcripts from deep RNA-seq data

first: Konstantin

last: Okonechnikov