title: DNA methylation Landscape of body size variation in sheep

city: Beijing

first: Jiaxue

last: Cao

state: Beijing

address: Yuanmingyuan West Road 2#

institute: Institute of Animal Sciences, Chinese Academy of Agricultural Sciences

summary: Examination the DNA methylation statues of the main subpopulation of Chinese Mongolian sheep. A high quality methylome of Chinese Mongolian sheep was obtained, and established a list of DMRs potentially association with sheep body size

overall_design:
Blood DNA methylation level of main Chinese Mongolian sheep was generated by deep sequencing.
Subpopulation (breed) of Chinese Mongolian sheep:
UQ: Ujumqin sheep
Tan: Tan sheep
StH: Small-tailed-Han sheep
Hu: Hu sheep

first: Caihong

last: Wei

first: Hongping

last: Zhang

first: Lixin

last: Du


title: Multi-omics approach to study global changes in a triclosan mutant strain of Acinetobacter baumannii ATCC 17978.

status: Public on Sep 28 2016

city: Winnipeg

first: Manu

middle: Kumar

last: Singh

state: Manitoba

address: 45 Chancellors circle, 412 Buller

department: Microbiology

country: Canada

institute: University of Manitoba

type: Expression profiling by high throughput sequencing

summary: Acinetobacter baumannii AB042, a triclosan-resistant mutant, was examined for modulated gene expression using whole genome sequencing, transcriptomics, and proteomics in order to understand the mechanism of triclosan-resistance as well as its impact on A. Baumannii.

overall_design: A triclosan mutant (AB042) was isolated by culturing A. baumannii ATCC 17978 in increasing concentrations of triclosan.

first: Dinesh

middle: M

last: Fernando

first: Patrick

last: Chong

first: Victor

last: Spicer

first: Mark

last: Unger

first: Peter

last: Loewen

first: Garrett

last: Westmacott

first: Ayush

last: Kumar


title: DAI Senses Influenza A Virus Genomic RNA and Activates RIPK3-Dependent Cell Death

status: Public on Sep 27 2016

city: Tarrytown

first: Asiel

middle: Arturo

last: Benitez

state: New York

address: 777 Old Saw Mill River Rd, 92-516A

department: Immunology & Inflammation

country: USA

institute: Regeneron Pharmaceuticals, Inc

summary: 293T were transfected with plasmids expressing DNA-dependent activator of IFN-regulatory factors (DAI) or retinoic acid-inducible gene 1 (RIG-I). Transfected cells were subsequently infected with influenza A/Puerto Rico/8/34 virus for 12 hours. Cell extract was subjected to FLAG Ab beads, washed, and retained. RNA was sequenced using the Illumina TruSeq Stranded Total RNA Library kit. The input sample represents total RNA from vector-infected cells.

sample_organism: Influenza A virus (A/Puerto Rico/8/1934(H1N1))

overall_design: Examination of viral RNA production. Samples include 293T fibroblasts transfected with pcDNA FLAG-based plasmids expressing DAI or RIG-I.

first: Roshan

middle: R

last: Thapa

first: Justin

middle: P

last: Ingram

first: Siddharth

last: Balachandran

first: Jason

last: Upton

middle: A

first: Benjamin

last: tenOever


title: ERBB3 and NGFR mark distinct skeletal muscle progenitor cells in human development enabling enrichment and maturation of hPSC muscle

city: Los Angeles

first: Ascia

last: Eskin

state: California

address: 695 Charles Young Drive South  Gonda 5554

department: Human Genetics

institute: UCLA

summary: Abstract: Human pluripotent stem cells (hPSCs) can be directed to differentiate into skeletal muscle progenitor cells (SMPCs). However, the myogenic potential of hPSC-SMPCs compared to human fetal or adult satellite cells (Scs) remains unclear.  This study demonstrates hPSC-SMPCs derived by commonly used protocols are functionally less mature than freshly-isolated human fetal or adult Scs.  We utilized RNA-SEQ of human fetal Scs to identify differentially expressed genes including NGFR, ERBB3, which enriched for MYOD+ or PAX7+ cells.  Furthermore, inhibition of TGFβ (TGFβi) improved hPSC-muscle maturation in three independent lines as measured by TEM and expression of myosins. Engraftment of CRISPR/Cas9-corrected Duchenne Muscular Dystrophy (DMD) hiPSC-SMPC subpopulations treated with TGFβi in vivo, increased dystrophin-positive fibers to levels of engrafted cultured fetal Scs in mdx mouse models of DMD.  This work provides the first characterization of the developmental status of hPSC-SMPCs and identifies candidates to enable robust myogenic activity in vitro and in vivo.

overall_design: Profiled transcriptomes of uncultured fetal Scs, cultured fetal muscle cells, and differentiated fetal myotubes in comparison to day 50 NCAM+ hPSC-SMPCs and SMPC-derived myotubes by RNA-SEQ.

first: Michael

last: Hicks


title: What’s a SNP between friends: the influence of single nucleotide polymorphisms on Clostridium difficile strain CD630 virulence

city: Paris

first: Monot

last: Marc

address: 25, rue du docteur roux

department: Genomes and Genetics

country: France

institute: Institut Pasteur

summary: Isogenic, toxin B (tcdB) mutants of two independently isolated erythromycin-sensitive derivatives (630E and 630Δerm) of the Clostridium difficile strain CD630 have previously been shown to behave differently in the hamster model of infection.  Those based on strain 630E failed to cause disease, whereas those based on 630Δerm did.  Here we show that whilst 630Δerm and its derivatives behave in a comparable way to the parental strain CD630 in terms of growth rate, motility, sporulation, toxin production and virulence, strain 630E and its derivatives do not.  They grow more slowly, achieve lower final cell densities, exhibit a reduced capacity for spore formation, express lower levels of toxin and are less virulent in the hamster model.  Using Next Generation Sequencing, a total of three SNPs were found that were in both CD630 and 630Δerm. In addition to these, 630Δerm had eight unique SNPs compared to CD630 and 630E, while 630E had 11 SNPs not found in the other two strains.  The strain-specific SNPs most likely arose during the repeated subculture experiments undertaken to isolate these ermB deletion strains.  The relatively large number of mutations present meant that the identification of those SNPs responsible for the altered properties of 630E was not possible.  Allelic exchange was used to correct three mutational changes in 630E, but with essentially no effect on phenotype.  These were a 150 bp inversion in the promoter region of a flagella operon, the truncation of CD630_12740 (topoisomerase I), and the correction of a SNP that results in the fusion of two components of a glucose phosphor-transferase-system.  To complete the analysis we performed RNAseq, comparing the transcriptome of the three strains at three different time points. The finding corroborated the many differences between the strains, but also highlighted that one SNP cannot necessarily be attributed to one particular expression pattern or even phenotype. In conclusion 630Δerm more accurately mirrors the behaviour of the parental strain CD630, hence if genetic-based studies with C. difficile strain CD630 are necessary, then the use of strain 630∆erm should be favoured over strain 630E.  At a fundamental level, our data underlines the importance of effective strain curation and the need to genome re-sequence master seed banks wherever possible.

overall_design: Total RNA was extracted from 2 independent biological replicates of 630, 630∆erm and 630E C. difficile strains at 3 time points (18 samples).

first: Bruno

last: Dupuy

first: Marc

last: Monot


title: Mammary Tumor Associated RNAs impact tumor cell proliferation, invasion and migration

city: Dunedin

first: Sarah

middle: D

last: Diermeier

address: 710 Cumberland Street

department: Biochemistry

country: New Zealand

institute: University of Otago

summary: Recent genome-wide studies revealed that only 2% of the human genome encodes for mRNAs that are translated into proteins while as much as 80% of the genome can be transcribed. Of these non-coding transcripts, long non-coding RNAs (lncRNAs) represent the largest and most diverse class, comprising almost 16,000 currently annotated transcripts in human and 10,000 in mouse. Here, we investigated the role of lncRNAs in mammary tumors by performing RNA-Seq on tumor sections and organoids derived from MMTV-PyMT and MMTV-Neu-NDL mice. We identified several hundred long non-coding transcripts that were over-expressed compared to the normal mammary epithelium. Among these potentially oncogenic lncRNAs we prioritized a subset as Mammary Tumor Associated RNAs (MaTARs) and determined their human counterparts, hMaTARs. To functionally validate the role of MaTARs, we performed antisense knockdown and observed reduced cell proliferation, invasion and/or organoid branching in a cancer-specific context. Assessing the expression of hMaTARs in human breast tumors revealed that 19 hMaTARs are significantly up-regulated and many of these correlate with breast cancer subtype and/or hormone receptor status, indicating potential clinical relevance.

overall_design: 20 RNA-Seq-datasets. Mammary tumors and organoids derived from MMTV-PyMT, MMTV-Neu-NDL and MMTV-Cre;Flox-Neo-Neu-NT were compared to normal wild type mammary gland organoids.

first: Kung-Chi

last: Chang

first: David

middle: L

last: Spector


title: Expression profiles in Caenorhabditis elegans mutants lacking an intestinally expressed microRNA mir-60 that promote adaptive response against chronic oxidative stress

city: Camperdown

first: Masaomi

last: Kato

state: NSW

address: Missenden Road

country: Australia

institute: Centenary Institute, The University of Sydney

summary: Recent revelations into microRNA function suggest that microRNAs serve as a key player in a robust adaptive response against stress in animals through their fine-tuning capability in gene expression. However, it remains largely unclear how a microRNA-modulated downstream mechanism contributes to the process of homeostatic adaptation. Here we show that loss of an intestinally expressed microRNA gene mir-60 in the nematode C. elegans promotes adaptive response against oxidative stress; animals lacking mir-60 dramatically extend lifespan under a mild and long-term oxidative stress condition, while they do not increase resistance against a strong and transient oxidative stress exposure. We found that canonical stress responsive factors, such as DAF-16/FOXO, are dispensable for mir-60 loss to enhance oxidative stress resistance. Gene expression profiles revealed that genes encoding lysosomal proteases and those involved in the xenobiotic metabolism and pathogen defense response are up-regulated by the mir-60 loss. Detailed genetic studies and computational microRNA target prediction suggest that endocytosis components and a bZip transcription factor gene zip-10, which functions in innate immune response, are directly modulated by miR-60 in the intestine. Our findings suggest that the mir-60 loss facilitates adaptive response against chronic oxidative stress by ensuring the maintenance of cellular homeostasis.

overall_design: To identify genes that respond to the mir-60 loss, RNA expression profiles were examined between the mir-60 loss mutant (mir-60(n4947)) and its control animals using the high-throughput sequencing technology. In this study, we used spe-9(hc88), a temperature-sensitive sterile strain, which has been shown in previous studies to have a lifespan similar to wild-type and widely used in gene expression studies to reduce the effect of RNA contamination from younger progenies. Both spe-9 single and mir-60;spe-9 double mutant animals were cultured at a restrictive temperature 23.5 °C, and treated with paraquat 5 mM during adulthood for chronic oxidative stress. Total RNAs were purified at the following time points: Day 0 young adult for both spe-9 and mir-60;spe-9 (just before paraquat exposure); Day 7 for both spe-9 and mir-60;spe-9 (50% survival time for spe-9); Day 10 for mir-60;spe-9 (50% survival time for mir-60;spe-9). For Day 0 controls, total RNAs were isolated twice independently for biological replicates. cDNA libraries were made for these 7 samples with indexed adapters using TruSeq Stranded mRNA Sample Prep Kit (Illumina), and sequenced on 2 lanes of flow cells on the HiSeq 2000/2500 platform, eventually providing 14 sequencing samples.


title: Differential expression profiling of Ustilaginoidea virens in resistant and susceptible rice varieties during early infection

first: Wenxian

last: Sun

address: 2 West Yuanmingyuan Rd., Haidian District

country: China

institute: China Agricultural University

summary: To understand pathogenicity and in planta transcriptional reprogramming, expression profiles of U. virens during infection of the resistant and susceptible cultivars were analyzed using RNA-seq data. Predicted host-pathogen interaction database (PHI-base) genes that are probably involved in host-pathogen interactions were found to be significantly enriched in fungal differential expressed genes from both rice genotypes, indicating their potential roles in pathogenicity of U.virens. Our results also indicate that genes for secreted proteins and secondary metabolism are highly enriched in the transcriptome during early infection of susceptible cultivars. GO enrichment analysis suggest that bilogical processes required for successful infection of U. virens are greatly suppressed in the resistant cultivars.

overall_design: Oryza sativa L. spp. indica cultivars IR28 (resistant) and LYP9 (susceptible) were used in our experiments. Rice panicles were inoculated with a mixture of conidial and hyphal fragments of U. virens P1 strain. Total RNA was isolated from in vitro cultures and from inoculated rice panicles using RNApure RNA isolation kit according to the manufacturer’s instruction. Total RNA from three biological replicates at each time point (6 h.p.i., 24 h.p.i. and 48 h.p.i.) were combined and used for library construction. Each library had an insert size of ~200 bp. The reads of 49 bp (for in planta expression profiling) or 100 bp (for transcriptome analysis of in vitro cultures) sequences were generated via Illumina HiSeq2000 at BGI.

first: Kang

last: Zhang


title: Divergent expression and metabolic functions of human glucuronosyltransferases through alternative splicing

city: Québec

first: Chantal

last: Guillemette

state: Québec

address: 2705 blvd Laurier

department: Faculty of Pharmacy

institute: Laval University

summary:
Purpose: Maintenance of cellular homeostasis and xenobiotics detoxification relies on the glucuronidation pathway mediated by 19 human UDP-glucuronosyltransferase enzymes (UGTs) encoded by 10 highly homologous genes. Recent evidence suggests that alternative splicing largely expands the human UGT transcriptome.
Results: we establish the quantitative portrait of the UGT transcriptome in major metabolic organs and characterize cellular functions of selected alternative UGT isoforms with novel in-frame sequences. Targeted RNA sequencing uncovered that AS significantly shapes the UGT transcriptome, with variants quantitatively representing up to 35% and 60% UGT transcripts in normal and tumoral tissues respectively. Novel distinctive in-frame sequences were present in 20% alternative transcripts, which potentially encode UGT isoforms with distinct structural and functional features.
Conclusions: This work exposes the important quantitative and biological significance of alternative UGT expression likely creating unparalleled protein diversity evolving from enzymes to regulators of cell metabolism.

overall_design: normal and tumoral metabolic tissues by targeted RNA next-generation sequencing; Total RNA was extracted from liver, kidney, intestine and colon from multiple human donors. RNA-sequencing was conducted with a Illumina HiSeq 2500 system

first: Alan

last: Tourancheau

first: Michèle

last: Rouleau

first: Arnaud

last: Droit


title: Gene expression profiling of planarian heads or cephalic ganglia after inhibition of Hedgehog signaling pathway genes by RNAi

city: Cambridge

first: Peter

middle: W

last: Reddien

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

summary: Hedgehog signaling is critical for vertebrate central nervous system (CNS) development, but its role in CNS biology in other organisms is poorly characterized. In the planarian Schmidtea mediterranea, hedgehog (hh) is expressed in medial cephalic ganglia neurons, suggesting a possible role in CNS maintenance or regeneration. We performed RNA sequencing of planarian brain tissue following RNAi of hh and the gene encoding its receptor, patched (ptc). We identified two misregulated genes, intermediate filament-1 (if-1) and calamari (cali), that are expressed in a previously unidentified non-neural CNS cell type. These cells expressed orthologs of astrocyte-associated genes involved in neurotransmitter uptake and metabolism, and extended processes enveloping regions of high synapse concentration. We conclude these are glia-like cells (GLCs). Planarian GLCs exist in two compartments with gene expression programs distinguished by Hh signaling. Planarian GLCs and their regulation by Hedgehog signaling present a novel tractable system for dissection of glia biology.

overall_design: Polyadenylated RNA isolated from dissected cephalic ganglia tissue from planarians following RNAi of a control gene (2 replicates), hedgehog (2 replicates), or patched (2 replicates). Polyadenylated RNA isolated from whole head fragments used as tissue specificity control (2 replicates).

first: Irving

middle: E

last: Wang

first: Sylvain

last: Lapan

first: M

last: Scimone


title: RNA-seq of human peripheral blood mononuclear cells

city: New York

first: Chenyi

last: Xue

state: NY

institute: Columbia University

summary: Inflammatory cytokine responses to activation of innate immunity differ between individuals, yet the genomic and transcriptomic determinants of inflammatory responsiveness are not well understood. We hypothesized that mRNA and lincRNA expression is modulated in disease-relevant tissues in humans in vivo during inflammation, and differs between individuals with divergent evoked inflammatory responses. In the Genetics of Evoked Response to Niacin and Endotoxemia (GENE) Study, we performed an inpatient endotoxin challenge (1ng/kg LPS) in healthy humans. We selected individuals in the top (high-responders) and bottom (low-responders) extremes for inflammatory responses, and applied RNASeq to peripheral blood mononuclear cells (PBMC, n=15) before and after LPS administration. At baseline, there were limited differences in gene expression by sex or race. Further, only a small number of genes differed between high and low responders at baseline. Post-LPS, there were clear differences in the magnitude of the transcriptional response between high and low responders, with a far greater number of genes differentially expressed post-LPS in high responders, consistent with the clinical response. We also found a number of differentially expressed long intergenic non-coding RNAs (lincRNAs) post-LPS. We show that differences in gene expression may drive differences in clinical inflammatory response, and that differentially expressed genes and lincRNAs represent novel candidates for modulation of immune and metabolic responses in acute and chronic diseases.

overall_design: Peripheral blood mononuclear cells (PBMCs) from 15 healthy subjects were sequenced by Illumina HiSeq 2000 with poly-A selection

first: Jane

last: Ferguson


title: Global mapping of binding sites for Nrf2 identifies novel targets in cell survival response through ChIP-Seq profiling and network analysis

city: Baltimore

first: Shyam

last: Biswal

state: MD

address: 615 N. Wolfe St.

department: Environmental Health Sciences

institute: Johns Hopkins Bloomberg School of Public Health

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The Nrf2 (nuclear factor E2 p45-related factor 2) transcription factor responds to diverse oxidative and electrophilic environmental stresses by circumventing repression by Keap1, translocating to the nucleus, and activating cytoprotective genes. Nrf2 responses provide protection against chemical carcinogenesis, chronic inflammation, neurodegeneration, emphysema, asthma and sepsis in murine models. Nrf2 regulates the expression of a plethora of genes that detoxify oxidants and electrophiles and repair or remove damaged macromolecules, such as through proteasomal processing. However, many direct targets of Nrf2 remain undefined. Here, mouse embryonic fibroblasts (MEF) with either constitutive nuclear accumulation (Keap1−/−) or depletion (Nrf2−/−) of Nrf2 were utilized to perform chromatin-immunoprecipitation with parallel sequencing (ChIP-Seq) and global transcription profiling. This unique Nrf2 ChIP-Seq dataset is highly enriched for Nrf2-binding motifs. Integrating ChIP-Seq and microarray analyses, we identified 645 basal and 654 inducible direct targets of Nrf2, with 244 genes at the intersection. Modulated pathways in stress response and cell proliferation distinguish the inducible and basal programs. Results were confirmed in an in vivo stress model of cigarette smoke-exposed mice. This study reveals global circuitry of the Nrf2 stress response emphasizing Nrf2 as a central node in cell survival response.

overall_design: We performed a ChIP-Seq experiment with Keap1−/− MEFs, in which Nrf2 is protected from ubiquitination and degradation, constitutively activating the expression of Nrf2 target genes. We generated two DNA libraries using two Nrf2-specific antibodies (one monoclonal and one polyclonal). A third control library contains the input DNA.

first: Wyeth

last: Wasserman

first: Elodie

last: Portales-Casamar

middle: J

last: Arenillas


title: Study of primary transcriptional changes induced by EDS1/PAD4 in Arabidopsis using an estradiol-inducible system

city: Cologne

first: Barbara

last: Kracher

address: Carl-von-Linné-Weg 10

department: Plant-Microbe Interactions

country: Germany

institute: Max Planck Institute for Plant Breeding Research

summary: Arabidopsis Enhanced Disease Susceptibility 1 (EDS1) and its direct partner Phytoalexin Deficient 4 (PAD4) are required for both basal resistance against virulent pathogens and innate immune responses mediated by all tested TIR (Toll-Interleukin-1 Receptors) type nucleotide-binding/leucine-rich-repeat (NLR) receptors. Using transgenic Arabidopsis plants in Col-0 eds1-2 pad4-1 background conditionally expressing PAD4 and constitutively expressing EDS1 (ED-P4E1), an EDS1/PAD4 immune response can be triggered by estradiol treatment and can induce expression of defense-related genes and lead to enhanced basal resistance. In order to capture primary transcriptional changes in response to EDS1/PAD4, we performed RNA-seq gene expression analysis in ED-P4E1 plants after estradiol or mock treatment at three time points: 6, 12 and 24 h.

overall_design: We used transgenic Arabidopsis plants expressing PAD4 under the control of an estradiol-inducible promoter and EDS1 driven by CaMV 35S promoter in an eds1-2 pad4-1 mutant background (named ED-P4E1). The ED-P4E1 plants were grown at 22ºC for 4 weeks, and then were spray-treated with either 10 uM estradiol plus 0.01% silwet-L77 or 0.2% DMSO (in water) plus 0.01% silwet-L77 as mock control. Samples were collected at 6, 12 and 24h after treatment. For each condition, three replicates were obtained.

first: Haitao

last: Cui

last: Parker


title: Uridylation-mediated RNA quality control pathway in mammalian cytoplasm [CLIP-Seq]

city: Prague 4

first: Josef

last: Pasulka

address: Vídeňská 1083

country: Czech Republic

institute: Institute of Molecular Genetics of the ASCR, v. v. i.

summary: Uridylation of various cellular RNA species at the 3’ end has been generally linked to RNA degradation. Uridylated pre-miRNAs in mammals and uridylated mRNAs in fission yeast are targeted by the 3′ to 5′ exoribonuclease DIS3L2. In humans, DIS3L2 mutations have been associated with Perlman syndrome development and Wilms tumor susceptibility. In this work, we employ crosslinking in vivo and immunoprecipitation (CLIP) method to assess the RNA binding capacity of human DIS3L2 on a genome-wide scale. Our study uncovers a broad spectrum of uridylated RNAs in human cytoplasm, which include mature as well as aberrant forms of coding and noncoding RNAs, such as rRNAs, snRNAs, snoRNAs, tRNAs and pre-miRNAs. Most importantly, we have identified that a fraction of Pol II transcription start-site associated transcripts are exported to cytoplasm, where they are targeted by the TUT-DIS3L2 pathway. Moreover, this pathway appears to mainly target RNA regions that form stable secondary structures. Our findings imply the role of DIS3L2 and oligouridylation in general RNA quality control of most, if not all RNA classes.

overall_design: CLIP-seq of total RNA in DIS3L2 D391N mutant (3 replicates)

first: Stepanka

last: Vanacova

first: Dmytro

last: Ustianenko


title: Investigation of the effect of succinate and dimethyl malonate on murine bone-marrow derived macrophages (BMDMs) treated with or without LPS

first: Mukund

last: Varma

address: 415 Main Street

institute: Broad Institute

summary: We aim to further elucidate the effect of succinate and the succinate dehydrogenase inhibtor, dimethyl malonate, on macrophages treated with LPS. Specifically we want to deepen our understanding of how these reagents influence both LPS-induced IL-1B and IL-10.

overall_design: BMDMs were either left untreated or treated with succinate or dimethyl malonate for 3 h prior to treatment with or without LPS for 4 or 48 h.

first: Evanna

last: Mills

first: Luke

last: O'Neill

first: Bihua

last: Li

first: Ramnik

last: Xavier

first: Isabel

last: Latorre


title: TUT-DIS3L2 is a mammalian surveillance pathway for aberrant structured non-coding RNAs.

summary: Uridylation of various cellular RNA species at the 3' end has been generally linked to RNA degradation. In mammals, uridylated pre-let-7 miRNAs and mRNAs are targeted by the 3' to 5' exoribonuclease DIS3L2. Mutations in DIS3L2 have been associated with Perlman syndrome and with Wilms tumor susceptibility. Using in vivo cross-linking and immunoprecipitation (CLIP) method, we discovered the DIS3L2-dependent cytoplasmic uridylome of human cells. We found a broad spectrum of uridylated RNAs including rRNAs, snRNAs, snoRNAs, tRNAs, vault, 7SL, Y RNAs, mRNAs, lncRNAs, and transcripts from pseudogenes. The unifying features of most of these identified RNAs are aberrant processing and the presence of stable secondary structures. Most importantly, we demonstrate that uridylation mediates DIS3L2 degradation of short RNA polymerase II-derived RNAs. Our findings establish the role of DIS3L2 and oligouridylation as the cytoplasmic quality control for highly structured ncRNAs.

overall_design: CLIP-seq and RNA-seq data for DIS3L2 dysfunctional mutant


title: Integrated RNA-seq and sRNA-seq analysis reveals miRNA effects on secondary metabolism in Solanum tuberosum L

city: Lanzhou

first: Yan

last: Qiao

state: Gansu Province

address: No. 1 Yingmen village, Anning District

department: College of Agronomy

institute: Gansu Agricultural University

type: Non-coding RNA profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Uridylation-mediated RNA quality control pathway in mammalian cytoplasm [RNA-Seq]

overall_design: RNAseq of total RNA in DIS3L2 D391N mutant (3 replicates) and empty HEK293 cells (3 replicates)


title: Gene expression profiling of AR deletion in prostate luminal cells

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

summary: Benign prostatic hyperplasia (BPH) is a common urological disease that adversely affects quality of life among elderly males, but its etiology remains poorly understood. We show that the expression of the androgen receptor (AR) is decreased in the luminal epithelial cells of human BPH specimens and is inversely correlated with the degree of regional prostatic inflammation.

overall_design: To identify the extracellular signaling that promotes epithelial proliferation, we performed RNA sequencing of FACS-isolated prostate luminal cells from tamoxifen-treated control and K8-AR mice (with knockout of androgen receptor).

first: Boyu

last: Zhang

first: Yiqun

first: Li

last: Xin


title: Single Novel single cell assay reveals progressive lymphoid defect in aging multipotent hematopoietic progenitors cell RNA-seq reveals LMPP clonal dynamics in aging.

city: Bar Harbor

first: Jennifer

last: Trowbridge

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

summary: Declining immune function with age is associated with reduced lymphoid output of hematopoietic stem cells (HSCs). Currently, there is poor understanding of the dynamic changes with age in the heterogeneous multipotent hematopoietic progenitor cell compartment, which regulates output of differentiated lymphoid cells. In this study, we observed progressive and specific loss of lymphoid-primed multipotent progenitor cells (LMPP/MPP4) as young animals began to age. Single cell RNA-seq revealed a concomitant increase in cycling of these progenitors with loss of a lymphoid priming signature. To interrogate functional multipotency of single cells, we developed a novel, feeder-free in vitro assay to concurrently assess lymphoid and myeloid potential. This assay revealed altered clonal composition of the LMPP/MPP4 compartment with aging, where progenitors with B cell and macrophage-restricted potential are lost while functionally multipotent progenitors are preserved. These results pinpoint an age and cellular compartment to focus further interrogation of the drivers of lymphoid cell loss with aging.

overall_design: Examination of single cell RNA-seq transcriptomes in LMPP isolated from the bone marrow of 4mo and 14mo wild-type C57BL/6J female mice

first: Sneha

last: Borikar

first: Lauren

last: Kuffler

first: Vivek

last: Phillip


title: Identification of a Transcription Factor that Promotes Spermatogonial Stem Cell Establishment

city: La Jolla

first: Kun

address: 9500 Gilman Drive

institute: UCSD

summary: Spermatogonial stem cells (SSCs) are critical for maintaining spermatogenesis throughout adult life. Little is known about how SSCs are first generated. Here, we report the identification of a transcription factor—RHOX10—that promotes the initial establishment of SSCs. We were led to this discovery because we found that conditional loss of a large X-linked gene cluster comprised of 33 related homeobox genes, including Rhox10, causes defects predicted if SSCs fail to be generated or maintained. Remarkably, KO of only Rhox10 elicits SSC-related defects indistinguishable from KO of the entire gene cluster. Using a battery of approaches, including single cell-RNAseq analysis, we determined that loss of Rhox10 causes accumulation of undifferentiated germ cells—Pro-spermatogonia (ProSG)—at a time when they normally would form SSCs. The identification of a transcription factor that drives the initial generation of SSCs has potential therapeutic applications for infertility.

overall_design: Single cell RNA-seq analysis of ID4-positive testicular cells from Wildtype and Rhox10 knockout mice (Postnatal day 3 and 7)

first: Hye-Won

last: Song

first: Blue

middle: B

last: Lake

first: Miles

middle: F

last: Wilkinson


title: Differential expression of Staphylococcus equorum grown alone and in the presence of fungi

city: Medord

first: Benjamin

last: Wolfe

address: 200 Boston Ave.

institute: Tufts University

summary:
A specific interaction between the mold Scopulariopsis and S. equorum shifts the composition of the Staphylococcus community from dominance by a strong competitor, S. xylosus, to dominance by a weak competitor, S. equorum. To better understand specific genes and pathways involved with Scopulariopsis stimulation of S. equorum, we used RNA-seq to identify CDS that were up- and down-regulated in the genome of S. equorum in the presence and absence of the mold Scopulariopsis. We compared the effect of Scopulariopsis on the S. equorum transcriptome to the effect of Penicillium on the S. equorum transcriptome to determine why Scopulariopsis had such strong growth promotion effects relative to Penicillium.
In the presence of both molds, Methionine biosynthesis and uptake pathways are strongly down-regulated, while Thiamine biosynthesis is up-regulated, suggesting that bacterial-fungal interactions alter the availability of free amino acids and nutrients in cheese environment for both partners. In the presence of Scopulariopsis only, there is a decrease in expression of genes involved with iron acquisition and the production of siderophores, notably the staphyloferrin B operon.

overall_design: Staphylococcus equorum was grown on cheese medium alone or with one of two fungal neighbors - a Penicillium spp. or a Scopulariopsis spp.


title: Keratinocytes contribute intrinsically to psoriasis upon loss of Tnip1 function

status: Public on Sep 26 2016

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

summary: To increase our understanding of psoriasis, we utilized RNA-seq to assay the transcriptomes of skin samples from 3 Tnip1+/+ and 3 Tnip1-/- mice that were treated for two days with imiquimod (IMQ) and performed cross-species analyses with human transcriptome data derived from psoriasis patients and healthy subjects (GSE54456). Intriguingly, the vast majority of genes deregulated in Tnip1-/- mice correlated with their human counterparts, substantiating the interpretation that gene deregulation in Tnip1-/- mice reflects a psoriasis-specific pattern rather than being the consequence of an overall exaggerated inflammatory skin response. Together, the data demonstrate that loss of Tnip1 function leads to genetic susceptibility against IMQ, akin to human disease. As expected, gene ontology (GO) analysis highlighted gene sets known to be affected in psoriasis, such as epidermal development, immune/ defense response, proteolysis and response to wounding.

overall_design: Skin samples from 3 Tnip1+/+ and 3 Tnip1-/- mice that were treated for two days with imiquimod (IMQ)

first: S

middle: K

last: Ippagunta

first: R

last: Gangwar

first: D

first: P

last: Vogel

last: Pelletier

last: Gingras

first: V

last: Redecke

first: H

last: Häcker


title: Single Novel single cell assay reveals progressive lymphoid   defect in aging multipotent hematopoietic progenitors  Cell RNA-seq reveals LMPP clonal dynamics in aging.

overall_design: Examination of RNA-seq transcriptome in 3 cell types isolated from the bone marrow of wild-type C57Bl/6J female mice


title: Efficient derivation of microglia-like cells from human pluripotent stem cells

first: Julien

last: Muffat

address: 9 Cambridge center

institute: Whitehead Institute

summary: Microglia-like cells and neural cells were generated from several hES and hIPS lines. As subset was characterized by RNA seq and compared to expression profiles of published primary and induced samples. ABSTRACT: Microglia, the only lifelong resident immune cells of the central nervous system (CNS), are highly specialized macrophages which have been recognized to play a crucial role in neurodegenerative diseases such as Alzheimer’s, Parkinson’s and Adrenoleukodystrophy (ALD). However, in contrast to other cell types of the human CNS, bona fide microglia have not yet been derived from cultured human pluripotent stem cells. Here we establish a robust and efficient protocol for the rapid production of microglia-like cells from human embryonic stem (ES) and induced pluripotent stem (iPS) cells that uses defined serum-free culture conditions. These in vitro pluripotent stem cell-derived microglia-like cells (termed pMGLs) faithfully recapitulate the expected ontogeny and characteristics of their in vivo counterparts and resemble primary fetal human and mouse microglia. We generated these cells from multiple disease-specific cell lines, and find that pMGLs derived from MeCP2 mutant hES cells are smaller than their isogenic controls. We further describe a culture platform to study integration and live behavior of pMGLs in organotypic 3D-cultures. This modular differentiation system allows the study of microglia in highly defined conditions, as they mature in response to developmentally relevant cues, and provides a framework to study the long-term interaction of microglia residing in a tissue-like environment.

overall_design: Individual donors/genetic backgrounds. Dataset inlcudes 4 differentiated neural progenitor biological replicates (NPC1-4), 2 primary fetal microglia samples as reference, 5 induced microglia samples grown in basal medium (pMGL1-5), 3 induced microglia samples grown in neural conditioned medium (pMGL1-3+NCM)

first: Rudolf

last: Jaenisch


city: Marseille

first: Laurent

last: Fasano

address: Parc Scientifique de Luminy

institute: CNRS-AMU

summary: TSHZ3, which encodes a zinc-finger transcription factor, was recently positioned as a hub gene in a module of genes with the highest expression in the developing human neocortex, but its functions remained unknown. Here, we identify TSHZ3 as the critical region for a syndrome associated with heterozygous deletions at 19q12q13.11, which includes autism spectrum disorder (ASD). In Tshz3 null mice, differentially expressed genes include layer-specific markers of cerebral cortical projection neurons (CPNs) and their human orthologues are strongly associated with ASD. Furthermore, heterozygous Tshz3-deficient mice show functional changes at synapses established by CPNs and exhibit core ASD-like behavioral abnormalities. These findings reveal essential roles for Tshz3 in CPN development and function, whose alterations can account for ASD in the newly-defined TSHZ3 deletion syndrome.

overall_design:
Three independent replicates, each containing cortices from 3-4 embryos from multiple litters, were prepared from wild-type and Tshz3 mutant neocortex at E18.5.

Caubit et al., TSHZ3 deletion causes an autism syndrome and defects in cortical projection neurons. Nat. Genet ###, xxx-yyy (2016).

first: Xavier

last: Caubit

first: Emeric

last: Dubois

first: Ahmed

last: Fatmi

first: Dany

last: Severac


title: A single-cell transcriptomic map of the human and mouse pancreas reveals inter- and intra-cell population structure

first: Adrian

last: Veres

state: Massachusetts

address: 7 Divinity Ave

institute: Harvard University

summary: While the function of the mammalian pancreas hinges on complex interactions of distinct cell types, gene expression profiles have primarily been described with bulk mixtures of cells. Here, we invoked inDrop, a droplet-based single-cell RNA-Seq method, to determine the transcriptomes of over 12,000 individual pancreatic cells from four human donors and two strains of mice. Cells could be divided into 15 clusters that matched previously characterized cell types: all endocrine cell types, including rare ghrelin-expressing epsilon-cells, exocrine cell types, vascular cells, Schwann cells, quiescent and activated pancreatic stellate cells, and four types of immune cells. We detected subpopulations of ductal cells with distinct expression profiles, and validated their existence with immuno-histochemistry stains. Moreover, among human beta-cells, we detected heterogeneity in the regulation of genes relating to functional maturation and levels of ER-stress. Finally, we deconvolve bulk gene expression samples using single-cell RNA-Seq to detect disease associated differential expression. Thus, our cross-species dataset provides a resource for the discovery of novel cell type-specific and cell type-restricted transcription factors, signaling receptors, and medically-relevant genes.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Single-cell RNA sequencing of pancreatic islets from 4 human donors and 2 mice strains.

first: Maayan

last: Baron


title: Ovarian transcriptome associated with reproductive senescence in the long-living Ames dwarf mice

city: Orlando

first: Augusto

last: Schneider

state: FL

address: 6900 Lake Nona Blvd

department: Burnett School of Biomedical Sciences

institute: University of Central Florida

summary: The aim of the current work was to evaluate the ovarian transcriptome in Ames dwarf (df/df) mice. df/df mice have a delayed ovarian aging compared to normal (N) mice. Although a high number of genes were differentially expressed during aging of N mice, only a small fraction of these changed with aging in df/df mice. These alterations involved more than 500 categorized biological processes. The majority of these biological processes, including inflammatory/immune responses, were up-regulated with aging in N mice, while old df/df mice were characterized by down-regulation of these same processes in comparison to age matched N mice. However, biological processes related to DNA damage and repairing were commonly down-regulated with aging in both genotypes. In conclusion, delayed ovarian aging in long-living df/df mice was associated with reduced expression of genes related to the inflammatory and immune responses.

overall_design:
Ovarian mRNA profile of 6 and 22 month old Ames dwarf (df/df) and Normal (N/df) female mice. Twenty mice were used in this study, for each age/genotype 5 ovarian samples were processed.
PRJNA327085; SRP077508

first: Scot

last: Matkovic

first: Tatiana

last: Saccon

first: Berta

last: Victoria

first: Lina

last: Spinel

first: Andrzej

last: Bartke

first: Pawel

last: Golusinski

first: Michal

last: Masternak


title: Airway epithelial cells from smokers treated with myo-inositol or placebo

city: Boston

first: Adam

middle: C

last: Gower

address: 72 East Concord Street, E632

department: Department of Medicine

institute: Boston University School of Medicine

summary: Samples were obtained as part of a randomized, double blind, placebo-controlled, phase IIb study to determine the effects of myo-inositol in smokers with bronchial dysplasia.  Smokers with greater than 1 site of dysplasia identified by autofluorescence bronchoscopy-directed biopsy were randomly assigned to receive oral placebo or myo-inositol, 9 g once/day for two weeks and then twice/day for 6 months.  Cytologically normal airway epithelial cells were obtained via bronchoscopy from the right or left mainstem bronchus at baseline and 6 months post-treatment with myo-inositol or placebo from 69 study participants (n=138 samples).  The RNA from these samples was isolated and used to prepare libraries for mRNA sequencing.  Subjects were classified by response according to their change in dysplasia rate after 6-months.  Among subjects with a complete response in the myo-inositol arm, there was a significant decrease in a gene expression signature reflective of PI3K activation.

overall_design: Cytologically normal bronchial airway cells were profiled by mRNA-Seq from 69 phase IIb study participants with bronchial dysplasia before and after 6 months of treatment with oral placebo or myo-inositol.

first: Yaron

last: Gesthalter

first: Jennifer

last: Beane

first: Marc

last: Lenburg

first: Avrum

last: Spira


title: Gene expression level of Aspergillus fumigatus CEA17_ΔakuBKU80 at three different stages

city: Paris

first: Rachel

last: Legendre

address: 28, rue du docteur Roux

department: Research and Resource Center for Scientific Informatics

institute: Institut Pasteur

summary: We report the gene expression level of Aspergillus fumigatus CEA17_ΔakuBKU80 strain in dormant conidia, in swollen conidia (after 4h of culture in Glucose 3%, Yeast Exrtract 1% liquid medium) and in germinated conidia (after 8h of culture in Glucose 3%, Yeast Extract 1% liquid medium after construction of an RNAseq library.

overall_design: Three different samples have been analyzed including 3 replicates each.

first: Isabelle

last: Mouyna

first: Odile

last: Sismeiro

first: Marie-Agnès

last: Dillies

first: Bernd

last: Jagla


title: BCL6-centric reorganization of the genome during B cell affinity maturation

first: David

last: Soong

address: 1305 York Avenue

institute: Weill Cornell Medical College

summary: During the humoral immune response mature B-cells undergo a dramatic change in phenotype to enable antibody affinity maturation in germinal centers (GCs).  Here, we observe for the first time that these phenotypic changes are accompanied by large-scale reorganization of the genomic architecture that encodes the GCB-cell transcriptional program.  The coordinate expression of genes that specify the GCB-cell phenotype – most prominently, BCL6 – is achieved through a non-random, multilayered, chromatin reorganization process involving i) increased promoter connectivity, ii) formation of higher-order enhancer networks, iii) 5’ to 3’ gene looping, and iv) merging of gene neighborhoods that share active epigenetic marks.  These cell-specific events are closely linked to binding of GC transcription factors and the structural proteins CTCF and cohesin.  The gene encoding the GC master regulator, BCL6, is an anchor point for the formation of GC-specific gene and enhancer loops on chromosome 3. Furthermore, through CRISPR-mediated knockout we demonstrate that a putative locus control region upstream of Bcl6 is required for GCB-cell formation in mice. Thus, architectural reorganization of phenotype-driving gene sets, including assembly of cell type-specific promoter and enhancer networks, may be key to controlling tissue-specific gene expression programs.

overall_design: We performed replicate HiC experiments in primary human mature naïve B cells and germinal center B cells purified from tonsils of healthy individuals to examine three-dimensional organization of the B cell genome. We performed RNAseq to measure gene expression in the same specimens.

first: Karen

last: Bunting

first: Rajat

last: Singh

first: Yanwen

last: Jiang

first: Wendy

last: Beguelin

last: Poloway

first: Brandon

last: Swed

first: Katerina

last: Hatzi

first: William

last: Reisacher

first: Matt

last: Teater

first: Olivier

last: Elemento

first: Ari

last: Melnick


title: MCF10A H-Ras RNA-Seq

first: Carol

last: Prives

address: 1212 Amsterdam Ave

department: Biological Sciences

institute: Columbia University

summary:
Paired-end sequencing of Vector and H-Ras expressing cell lines: p53-del and WT-p53
We found that activated forms of H-Ras and PIK3CA oncogene lead to repression of p63, a p53 family member. They also lead to induction of EMT, a cancer-related process.
Our results suggest that, through Ras regulation of p63, this oncogene can drive mammary epithelial cells towards greater invasive ability.

overall_design: 4 samples analyzed with 3 replicates each, control samples for each H-Ras line are the Vector cell line created at the same time

first: Kathryn

last: Yoh

first: Kausik

last: Regunath

first: Seung-Min

last: Lee

first: Ron

last: Prywes


title: RNA-sequencing of B-ALL cell lines, REH treated with LNA GapmeRs against four lncRNAs

city: Ghent

first: Farzaneh

last: Ghazavi

address: De Pintelaan 185

department: Center of medical genetics

country: Belgium

institute: Gent university hospital

summary: Overwhelming evidence indicates that long non-coding RNAs have essential roles in tumorigenesis. Nevertheless, their expression and role in pediatric B-cell precursor acute lymphoblastic leukemia has not been extensively explored. Here, we conducted a comprehensive analysis of the long non-coding RNA transcriptome in ETV6/RUNX1 positive BCP-ALL, one of the most frequent subtypes of pediatric leukemia. An ETV6/RUNX1 expression signature was established, consisting of 596 lncRNAs (434 up and 162 down) using expression analysis of a series of primary patient samples. Subsequently, RNA sequencing from BCP-ALL cell lines and shRNA-mediated silencing of ETV6/RUNX1, illustrated that lnc-NKX2-3-1, lnc-TIMM21-5, lnc-ASTN1-1 and lnc-RTN4R-1 are bona fide ETV6/RUNX1 targets and could serve as novel biomarkers of this prevalent subtype of human leukemia.

overall_design: REH cell lines were treated with LNA GapmeRs. Cells were collected 72h after treatment. This was performed for 3 replicates. RNA-sequencing was performed on these samples.

first: Wouter

last: Van Loocke

first: Pieter

last: Van Vlierberghe

first: Barbara

last: De Moerloose

first: Tim

last: Lammens

first: Yves

last: Benoit

first: Frank

last: Speleman


title: Two outer membrane proteins contribute to Caulobacter crescentus cellular fitness by preventing intracellular S-layer protein accumulation

city: Livermore

first: K.

middle: Wesley

last: Overton

state: CA

address: 7000 East Avenue

department: Biosciences and Biotechnology Division

institute: Lawrence Livermore National Laboratory

summary: Caulobacter crescentus is unique in that it has two homologous, seemingly redundant outer membrane proteins, RsaFa and RsaFb, that, together with other components, form a type I protein translocation pathway for S-layer export. RsaFa and RsaFb are required to prevent intracellular accumulation and aggregation of the S-layer protein RsaA; deletion of RsaFa and RsaFb led to a general growth defect and lowered cellular fitness. We show that loss of both RsaFa and RsaFb led to accumulation of insoluble RsaA in the cytoplasm, which in turn caused upregulation of a number of genes involved in protein mis-folding and degradation pathways. These findings provide new insight into the requirement for RsaFa and RsaFb in cellular fitness and tolerance to antimicrobial agents and further our understanding of the S-layer export mechanism on both the transcriptional and translational levels in C. crescentus.

overall_design: RNA-seq of biological triplicate samples of Caulobacter crescentus NA1000 wild type, single RsaFa mutant, single RsaFb mutant, double RsaFa/RsaFb mutant, and triple RsaFa/RsaFb/RsaA mutant

first: K

first: Yongqin

last: Jiao


title: RNA-sequencing of two the B-ALL cell lines, REH and 697

overall_design: RNA-sequencing data was generated  in two B-ALL cell lines REH and 697.


title: Dino-dependent gene expression signature in MEFs

city: Stanford

first: Adam

last: Schmitt

address: 269 Campus Drive

department: Department of Dermatology

institute: Stanford University

summary: Genetically modified Dino mice were generated with loxP sites flanking the mouse Dino gene. We set out to identify the set of genes regulated by Dino in DNA damaged mouse embryonic fibroblasts using 3' sequencing. Early passage Dino+/+ or Dino loxP/loxP MEFs were treated with 0.2ug/mL doxorubicin prior to addition of Trizol and RNA isolation.

overall_design: We examined gene expression by 3seq in early passage Dino_+/+ and Dino_lox/lox MEFs treated with 0.2ug/mL doxorubicin or vehicle alone for 8 hours.

first: Ying

last: Shen

first: Howard

last: Chang


title: Unique long non-coding RNA expression signature in ETV6/RUNX1-driven B-cell precursor acute lymphoblastic leukemia

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

overall_design: Refer to individual Series


title: lncRNA DINO ChIRPseq in DNA damaged U2OS cells

summary: Examine the chormatin localization of DINO in DNA damaged human U2OS cells using DINO ChIRP-seq.

overall_design: DINO is a DNA damage induced long noncoding RNA required for the transactivation of several p53-regulated genes. We examined the chormatin localization of DINO in DNA damaged human U2OS cells in order to determine whether DINO regulated gene expression by interacting with gene regulatory elements. We performed ChIRP with two independed probe sets (even and odd) according to previously published methods (Chu et al. 2011) . RNAse treated chromatin controls identify we utilized to confirm that DINO ChIRP recovery of DNA was indeed RNA dependent and not the result of direct DNA interaction by the probes.


title: Base J represses genes at the end of polycistronic gene clusters in Leishmania major by promoting RNAP II termination [small RNA-seq]

city: Athens

first: David

last: Reynolds

state: Georgia

address: 120 E Green St

department: Biochemistry and Molecular Biology

institute: University of Georgia

summary: Base J and H3.V promote RNA Polymerase (RNAP) II termination within polycistronic gene clusters in the kinetoplastid species Trypanosoma brucei. Although base J has been shown to promote RNAP II termination in the related kinetoplastid species Leishmania major and Leishmania tarentolae, the role of H3.V was unclear. The effect of acute J loss on mRNA transcript abundance was also unknown. We find here that H3.V does not promote transcription termination in Leishmania major, but loss of H3.V does reduce J levels. The J loss in H3.V knockout cells is not enough to result in a termination defect, which we show is due to a threshold level of J that is sufficient to promote termination. Loss of J beyond that threshold results in termination defects. Further, the decreased J in H3.V knockout cells allowed greater reduction of J by dimethyloxalylglycine (DMOG), which inhibits J synthesis, compared to wild type cells treated with DMOG, and resulted in stronger defects in RNAP II termination and cell growth. By mRNA-seq we see largely upregulation of genes near the ends of gene clusters following J loss, indicating that J represses genes near termination sites. These findings reveal a conserved role of J in promoting termination prior to the end of polycistronic gene clusters in kinetoplastid parasites and suggest that the essential nature of J is related to its role in repressing genes by promoting termination.

overall_design:
The role of base J and H3.V in promoting RNA Polymerase II transcription termination was assessed by small RNA-seq, mRNA-seq, and strand-specific RT-PCR. Wild type cells were compared to H3.V knockout cells and to WT and H3.V knockout cells treated with dimethyloxalylglycine (DMOG) to reduce base J.
This Series represents small RNA-seq samples.

first: Robert

last: Sabatini

first: Laura

last: Cliffe

first: Nicolai

last: Siegel

first: Britta

last: Anderson

first: Stephen

last: Beverley

first: Brigitte

middle: T

last: Hofmeister

last: Schmitz


title: Initial seeding of the embryonic thymus by an immune-restricted lympho-myeloid progenitor independently of Notch signaling

city: Oxford

first: Claus

last: Nerlov

address: John Radcliffe Hospital, University of Oxford

department: MRC Molecular Haematology Unit

country: United Kingdom

institute: Weatheral Institute of Molecular Medicine

summary: Gene expression analysis of purified thymopoiesis-initiating progenitors/early thymic progenitors, lymphoid primed multipotent progenitors (LMPP) and hematopoietic stem/progenitor cells from E11.5, E12.5, E13.5 embryos, neonatal (1 week old) and adult (8 weeks old) mice

overall_design: Differentially expressed genes analysis

first: S

last: Luc

first: T

last: Luis

last: Thongjuea

first: Sten

last: Jacobsen


title: H3K27ac ChIP-Seq in REH and 697

first: Farzaneh

last: Ghazavi

summary: H3K27ac ChIP-Seq data of the B-ALL cell lines REH and 697 were obtained to find active regions in the genome and to correlate that with expression profiling  of lncRNAs in these cell lines.

overall_design: ChIP-sequencing data was generated for H3K27ac in two B-ALL cell lines REH and 697.

first: Wouter

last: Van Loocke

first: Pieter

last: Van Vlierberghe

first: Barbara

last: De Moerloose

first: Tim

last: Lammens

first: Yves

last: Benoit

first: Frank

last: Speleman


title: Micro RNAs in pluripotent human stem cells

city: Turku

first: Riikka

last: Lund

address: Tykistökatu 6

country: Finland

institute: Turku Centre for Biotechnology, University of Turku

summary: The goal of this study was to analyze the miRNA profiles of pluripotent embryonic stem cell lines.

overall_design: Analysis of miRNA profiles and pluripotency factors in hESCs.

first: Nelly

last: Rahkonen


title: ATAC-Seq on DNA damaged human fibroblasts

first: Adam

last: Schmitt

summary: The goal of this experiment was to determine the role of the lncRNA DINO in the DNA damage response in regulating transcription factor occupancy of human fibroblasts. DINO, an inducible long noncoding in respose to DNA damage, is required for cell cycle arrest and induction of several p53 regulated genes. We hypothesized that ATACseq in DINO-depleted cells may uncover a role for DINO in transcription factor recruitment to p53 responsive genes following DNA damage.

overall_design: We examined chromatin accessibility in human fibroblasts in response to DNA damage with 0.2ug/mL doxorubicin for 12 hours or untreated controls (vehicle). 24 hours prior to treatement with doxorubicin, cells were transfected with 100nM  antisense oligonucleotides targetting DINO (DINO ASO 1 or DINO ASO2) or control antisense oligonucleotide using RNAimax transfection reagent. Following doxorubicin, 50,000 cells were isolated for each replicate and processed according to the standard ATACseq protocol (Buenrostro et al. 2013).

first: Ying

last: Shen

first: Howard

last: Chang


title: RNA-seq analysis of LPS induced RIPK1 kinase dependent gene expression changes in  CD11b+ myeloid bone marrow cells

status: Public on Sep 25 2016

first: Alexei

last: Degterev

address: 37 tyler street

summary: We used RNA-seq as a method of next generation sequencing (NGS) to identify RIPK1 dependent inflammatory mediators and pathways in LPS injected mice.

overall_design: Mice were divided intro 3 groups - control (n=2), LPS (n=2) and LPS/Nec-1 (n=2). BM cells were isolated by FACS as described for qPCR analysis. Total RNAs were isolated using Qiagen RNeasy kit according to the manufacturer’s protocol

first: Malek

last: Najjar


title: Developing a Novel Two-Dimensional Culture System to Enrich Human Prostate Luminal Progenitors That Can Function as a Cell of Origin for Prostate Cancer

city: Changsha

first: Dingxiao

last: Zhang

state: Hunan

address: Yuelushan

department: School of BioMedical Sciences

institute: Hunan University

summary: Elucidating the cell of origin of cancer has great significance in stratifying patients into appropriate treatment groups and for developing novel targeted therapies. Early studies demonstrate that only stem-like basal cells in the normal human prostate (NHP) can function as the cell of origin for prostate cancer (PCa). Here, we show that the organoids derived from bulkNHPluminal cells can also be tumorigenically transformed. We further show that the WIT medium, which is used to culture human mammary epithelial progenitor cells, when combined with the ROCK inhibitor, can readily propagate a population of progenitor-like cells from the primary NHP luminal cell isolates. Such functionally defined luminal progenitors can be transformed by distinct sets of genetic perturbations (i.e., AR+AKT/ERG or c-MYC+PTEN knockout) to form tumor glands. Genome-wide RNA-Seq analysis of freshly purified unperturbed human benign prostatic basal and luminal cells and culture-expanded lineage specific stem/progenitor populations reveals that the luminal progenitors possess a distinct gene expression profile that is greatly enriched in advanced, castration-resistant, and metastatic PCa, and it associates with poor patient survival. The ability of the simple two-dimensional culture system reported herein to greatly enrichNHPprogenitor-like cells should facilitate biological and biochemical studies as well as high-throughput screening in these cells and in progenitor-like PCa cells.

overall_design: Human total RNA profiles of HPCa167N benign prostatic bulk epithelial cells and freshly purified basal and luminal populations cultured primarily in WIT and PrEGM media by deep RNA-seq.

first: Kevin

last: Lin

first: Yue

last: Lu

first: Dean

middle: G

last: Tang


title: Genome-wide maps of DNA methylation in zebrafish larvae through MeDIP-sequencing after benzo[a]pyrene exposure

city: LA

first: Li

last: Qinqun

state: LA

address: 421 HongCao Rd., Building 63, 2nd floor

department: TS

institute: Kangchen

type: Methylation profiling by high throughput sequencing

summary: In this research, we used  MeDIP-sequencing technology to detect genome-wide methylation changes in benzo[a]pyrene(BaP)-exposed zebrafish larvae. We identified differentially methylated genes are associated with many diseases, including development of brain, and central nervous system.This high-throughput sequencing could help us to understand new mechanisms of BaP toxicity.

overall_design: Examination of different methylation in zebrafish larvae after BaP exposure.

first: Dongxu

last: Gao

first: Xiangming

last: Wang


title: Diverse Patterns of N6-methyladenosine mRNA Methylation in Porcine Liver of Postnatal Development Stages

city: Chengdu

first: Shen

last: He

address: wenjiang, huimin road 211

department: College of Animal Science and Technology

institute: Sichuan Agricultural University

summary: We profile transcriptome-wide m6A in porcine liver of three developmental stages: newborn, suckling and adult. Approximately one-third of the transcribed genes are modified by m6A, with a frequency of 1.47 to 1.56 m6A peaks per mRNA. m6A was distributed predominantly around stop codon. Consensus motif sequence ‘RRm6ACH’ has been observed in most m6A peaks. A negative correlation rate (average Pearson’s r = -0.450) was found between m6A methylation level and gene expression. Gene ontology analysis of transcripts persistently modified in three stages showed m6A modified genes relevant to critical functions, including regulation of growth and development, regulation of metabolic process and protein catabolic process. Genes with higher m6A methylation and lower expression of one certain stage are associated with the biological processes required for or unique to this stage. These results will provide a source for identifying adenosine methylation modified mRNA of porcine liver and extended our knowledge of the role of m6A in development and growth of mammalian organ.

overall_design: Transcriptome-wide search for m6A methylation in porcine liver at three developmental stages using the MeRIP-Seq technique

first: Hong

first: Mengnan

first: Mingzhou

last: Li


title: Quantitative predictions of protein interactions with long non-coding RNAs

status: Public on Sep 24 2016

city: Pasadena

first: Mario

last: Blanco

address: 1200 E California Blvd

institute: Caltech

summary: Computational Approach to define binding sites on lncRNAs validated with eCLIP data

overall_design: Using Global Score performances, we investigated protein interactions with Xist lncRNA, the master regulator of X chromosome inactivation. We validated our calculations by means of enhanced individual nucleotide CLIP (eCLIP)

first: Gian

last: Tartaglia


title: Analysis of polysomal enrichment and depletion of mRNA in untreated and TGF-beta treated MCF-10A and MCF7 cells

city: Houston

first: Arindam

last: Chaudhury

address: One Baylor Plaza / MS BCM335

department: Molecular Physiology and Biophysics

institute: Baylor College of Medicine

summary: We have performed sucrose-gradient-based isolation of polysomal fractions from untreated and TGF-beta treated MCF-10A and MCF7 cells, subjected these fractions to RNA-seq, and also sequenced total mRNA from each cell line in the treated and untreated condition

overall_design: Examination of two different cell types in a treated and untreated state

first: Joel

last: Neilson


title: Biceps femoris muscle transcriptome in pure and crossbred Iberian pigs at birth

city: Madrid

first: Cristina

last: Ovilo

address: Ctra Coruña km 7.5

country: Spain

institute: INIA-CSIC

summary: Iberian ham production includes both purebred (IB) and Duroc-crossbred (IBxDU) Iberian pigs, which show important differences in meat quality and production traits, such as muscle growth and fatness. This experiment was conducted to investigate gene expression differences, transcriptional regulation and genetic polymorphisms that could be associated with the observed phenotypic differences between IB and IBxDU pigs. Nine IB and 10 IBxDU pigs were slaughtered at birth. Morphometric measures and blood samples were obtained and samples from Biceps femoris muscle were employed for compositional and transcriptome analysis by RNA-Seq technology. Phenotypic differences were evident at this early age, including greater body size and weight in IBxDU and greater Biceps femoris intramuscular fat and plasma cholesterol content in IB newborns. We detected 150 differentially expressed genes between IB and IBxDU neonates (p < 0.01 and Fold-Change > 1. 5). Several were related to adipose and muscle tissues development (DLK1, FGF21 or UBC). The functional interpretation of the transcriptomic differences revealed enrichment of functions and pathways related to lipid metabolism in IB and to cellular and muscle growth in IBxDU. Protein catabolism, cholesterol biosynthesis and immune system were functions enriched in both genotypes. We identified transcription factors potentially affecting the observed gene expression differences. Some of them have known functions on adipogenesis (CEBPA, EGRs), lipid metabolism (PPARGC1B) and myogenesis (FOXOs, MEF2D, MYOD1), which suggest a key role in the meat quality differences existing between IB and IBxDU hams. We also identified several polymorphisms showing differential segregation between IB and IBxDU pigs. Among them, non-synonymous variants were detected in several transcription factors as PPARGC1B gene, which could be associated to altered gene function. Taken together, these results provide information about candidate genes, metabolic pathways and genetic polymorphisms potentially involved in phenotypic differences between IB and IBxDU associated to meat quality and production traits.

overall_design: In total 12 biceps femoris samples were analyzed, 6 coming from purebred Iberian male newborns and 6 coming from crossbred male newborns (IberianxDuroc)

last: Óvilo

first: Miriam

last: Ayuso


title: Dissecting the clonal nature of allelic expression in somatic cells by single-cell RNA-seq

city: Stockholm

first: Daniel

last: Ramsköld

address: Nobels väg 3

country: Sweden

institute: Karolinska Institutet

summary: Cellular heterogeneity can emerge from the expression of only one parental allele, however it has remained unknown to what degree patterns of random monoallelic expression of autosomal genes (aRME) are mitotically inherited (clonal) or stochastic (dynamic) in somatic cells. Here, we resolved this by applying allele-sensitive single-cell RNA-seq on primary mouse fibroblasts and in vivo human T-cells to simultaneously investigate clonal and dynamic aRME. Dynamic aRME affected a considerable portion of the transcriptome, with levels dependent on the cell’s transcriptional activity, but clonal aRME was surprisingly scarce (<1% of genes) and affected mainly lowly expressed genes. Consequently, the overwhelming portion of aRME occurs transiently and is scattered throughout somatic populations rather than, as previously hypothesized, confined to spatially restricted patches of clonally related cells.

overall_design: Cells were collected from in vitro clonal expansions, or from tissue or blood, to study the effect of relatedness and cell size on allele-specific expression

first: Björn

last: Reinius

first: Jeff

last: Mold

first: Rickard

last: Sandberg


title: S-adenosyl-methionine treatment selectively block liver cancer cell lines transformation and invasiveness by alterations of cancer- and invasion specific transcriptome and methylome (Bisulfite-Seq)

status: Public on Sep 23 2016

city: BeiJing

first: Wang

last: Yan

address: 16# LinCui Road

institute: Institute of Psychology

summary: S-adenosyl methionine (SAM) is a ubiquitous methyl donor that was reported to have chemo- protective activity against liver cancer, however the molecular footprint of SAM has been unknown. We show here that SAM selectively inhibits growth, transformation and invasiveness of hepatocellular carcinoma cell lines but not normal primary liver cells. Analysis of the transcriptome of SAM treated and untreated cancer cell lines HepG2 and SKHep1 and primary liver cells reveals pathways involved in cancer and metastasis that are upregulated in cancer cells and silenced by SAM. Analysis of the methylome using bisulfite mapping of captured promoters and enhancers reveals that SAM hyper-methylates and silences genes in pathways of growth and metastasis that are activated in liver cancer cells. Depletion of two SAM silencing targets similarly reduces cellular transformation and invasiveness. Taken together these data provide a molecular foundation for SAM as an anticancer agent.

overall_design: DNA from control and SAM treated 3 cell lines: HepG2, Skhep1 and NorHep was captured using  SeqCap Epi CpGiant Enrichment Kit and sequenced

first: Moshe

last: Syzf


title: S-adenosyl-methionine treatment selectively block liver cancer cell lines transformation and invasiveness by alterations of cancer- and invasion specific transcriptome and methylome (RNA-Seq)

overall_design: RNA from control and SAM treated 3 cell lines: HepG2, Skhep1 and NorHep was sequenced


title: UMI-4C for quantitative and targeted chromosomal contact profiling

city: Rehovot

first: Lilach

last: Gilboa

address: 234 Herzl Street,

department: Biological Regulation

country: Israel

institute: Weizmann Institute of Science

summary: We developed a targeted chromosome conformation capture (4C) approach that uses unique molecular identifiers (UMI) to derive high complexity quantitative chromosome contact profiles with controlled signal to noise ratios. We demonstrate that the method improves the sensitivity and specificity for detection of long-range chromosomal interactions, and that it allows the design of interaction screens with predictable statistical power. UMI-4C robustly quantifies contact intensity changes between cell types and conditions, opening the way toward incorporation of long-range interactions in quantitative models of gene regulation.

overall_design: We constructed UMI-4C profiles of 5 different genomic loci (viewpoints) in one cell line under four different conditions, and two larval tissues, in order to study the 3D chromatin contact maps of these selected loci. The coordinates for these viewpoints are: BaitB1 chrX:1609904;  BaitB2 chrX:1619649; BaitX1 chrX:158064; BaitX2 chrX:1829722; BaitX3 chrX:1945463


title: MEF2C regulates cortical inhibitory and excitatory synapses and behaviors relevant to neurodevelopmental disorders

city: Charleston

first: Christopher

last: Cowan

state: SC

address: 173 Ashley Ave, BSB 403

department: Neurosiences; Psychiatry

institute: Medical University of South Carolina

summary: Numerous genetic variants associated with MEF2C are linked to autism, intellectual disability (ID) and schizophrenia (SCZ) – a heterogeneous collection of neurodevelopmental disorders with unclear pathophysiology. MEF2C is highly expressed in developing cortical excitatory neurons, but its role in their development remains unclear. We show here that conditional embryonic deletion of Mef2c in cortical and hippocampal excitatory neurons (Emx1-lineage) produces a dramatic reduction in cortical network activity in vivo, due in part to a dramatic increase in inhibitory and a decrease in excitatory synaptic transmission. In addition, we find that MEF2C regulates E/I synapse density predominantly as a cell-autonomous, transcriptional repressor. Analysis of differential gene expression in Mef2c mutant cortex identified a significant overlap with numerous synapse- and autism-linked genes, and the Mef2c mutant mice displayed numerous behaviors reminiscent of autism, ID and SCZ, suggesting that perturbing MEF2C function in neocortex can produce autistic- and ID-like behaviors in mice.

overall_design: We carried out RNA-sequencing (RNA-seq) of somatosensory cortical tissue from control (Mef2cfl/fl) or Mef2c cKO (Mef2cfl/fl; Emx1-Cre) adult male mice. For the RNA-seq, three indipendent replicates were used for the mouse tissues.

first: Adam

last: Harrington

first: Aram

last: Raissi

first: Stefano

last: Berto

first: Gemma

last: Molinaro

first: Genevieve

last: Konopka


title: S-adenosyl-methionine treatment selectively block liver cancer cell lines transformation and invasiveness by alterations of cancer- and invasion specific transcriptome and methylome

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

overall_design: Refer to individual Series


title: Editing DNA methylation in the mammalian genome

city: New York

first: Xuebing

last: Wu

address: 630 West 168th Street

department: Medicine/Systems Biology

institute: Columbia University

summary: Mammalian DNA methylation is a critical epigenetic mechanism orchestrating gene expression networks in many biological processes. However, investigation of the functions of specific methylation events remains challenging. Here, we demonstrate that fusion of Tet1 or Dnmt3a with a catalytically inactive Cas9 (dCas9) enables targeted DNA methylation editing. Targeting of the dCas9-Tet1 or -Dnmt3a fusion protein to methylated or unmethylated promoter sequences caused activation or silencing, respectively, of an endogenous reporter. Targeted demethylation of the BDNF promoter IV or the MyoD distal enhancer by dCas9-Tet1 induced BDNF expression in post-mitotic neurons or activated MyoD facilitating reprogramming of fibroblasts into myoblasts, respectively. Targeted de novo methylation of a CTCF loop anchor site by dCas9-Dnmt3a blocked CTCF binding and interfered with DNA looping, causing altered gene expression in the neighboring loop. Finally, we show that these tools can edit DNA methylation in mice demonstrating their wide utility for functional studies of epigenetic regulation.

overall_design: dCas9-Dnmt3a ChIP-seq in V6.5 mouse ES cells expressing dCas9-Dnmt3a and guide RNAs targeting two different locus. Controls: 1) cells expressing dCas9-Dnmt3a and a scrambled guide RNA, 2) cells expressing dCas9-Dnmt3 only, and 3) wildtype cells without dCas9-Dnmt3a or guide RNA.

first: X-Shawn

last: Liu

first: Xiong

last: Ji


title: RNA-Seq analysis of the cystic fibrosis rat small intestine

city: Kansas City

first: Robert

last: De Lisle

state: KS

address: 3901 Rainbow Blvd

department: Anatomy & Cell Biology

institute: Univ Kansas Med Ctr

summary: Background: A recently developed animal model of the genetic disease is the cystic fibrosis (CF) rat, which similar to other animal models of CF exhibits a lethal intestinal phenotype. To begin characterizing the CF rat intestinal phenotype, we investigated global gene expression in the CF rat small intestine. Methods: Total RNA was extracted from full thickness of the entire small intestines of wild type (WT) and CF rats just before weaning. Results: There were 890 genes with significantly different expression levels (1.2-fold cutoff) comparing CF to wild type (WT), including 485 genes increased and 405 decreased in the CF intestine. The major pathways associated with these changes were inflammation, lipid metabolism, cytochrome P450-mediated degradative pathways, and cell growth/death. Comparison of the rat RNA-Seq dataset to earlier microarray analysis using a CFTR knockout mouse showed significant overlap with the CF rat small intestine. Conclusions: The small intestine of the new CF rat model exhibits numerous alterations in gene expression similar to other animal models of CF which indicate this will be an additional new model to study the gut effects CF.

overall_design: RNA-Seq between WT and CF rat intestine

first: Jennifer

last: Knapp


title: Candidate genes and pathways downstream of PAX8 involved in ovarian high-grade serous carcinoma

city: Naples

first: Stella

last: Zannini

address: Via Pansini 5

country: Italy

institute: CNR IEOS

summary: Our goal was to identify candidate genes and pathways regulated by PAX8 that could be additional targets for the therapy of ovarian carcinoma. To reach this aim, we have determined the molecular profiles of ovarian cancer cells and in parallel of Fallopian tube epithelial cells by mean of a silencing approach followed by an RNA-seq analysis

overall_design: Comparison of the transcriptome in normal Fallopian tube secretory epithelial cells and ovarian cancer cells with and without PAX8 silencing

first: T

last: de Cristofaro

last: Di Palma

first: A

last: Soriano

last: Monticelli

first: O

last: Affinito

first: S

last: Cocozza

first: M


title: Temporal regulation of dUTP biosynthesis limits uracil incorporation during early DNA replication

city: Aurora

first: Jay

middle: R.

last: Hesselberth

state: CO

department: Biochemistry and Molecular Gentetics

institute: University of Colorado School of Medicine

summary: Antimetabolite chemotherapies increase uracil levels in DNA, and thus identification of factors that influence the uracil content in DNA may have implications for understanding uracil-mediated chromosomal instability. We previously showed in the budding yeast Saccharomyces cerevisiae that uracil content in DNA correlates with replication timing, where the earliest and latest replicating regions are depleted in uracil. Here, we manipulated nucleotide biosynthesis enzymes in budding yeast to determine whether the pattern of uracil incorporation could be altered. In strains with high levels of uracil incorporation, deletion of dCMP deaminase (Dcd1) accelerated uracil incorporation at early-firing origins, likely due to rapid dTTP pool depletion. In contrast, increasing the activity of ribonucleotide reductase, which is required for the synthesis of all dNTPs via ribonucleotide diphosphates, lead to dUTP and dTTP pool equilibration and a concomitant increase in uracil content throughout the genome. These data suggest that uracil availability and the dUTP:dTTP ratio are temporally regulated during S phase and govern uracil incorporation into the genome. Therapeutic manipulation of nucleotide biosynthesis in human cells to either increase the dUTP pool or deplete the dTTP pool in early S phase may therefore improve the efficacy of antimetabolite chemotherapies.

overall_design: 4 single read sequencing runs. All using post-digest Excision-seq to measure uracil depletion in dut1-1 ung1∆, dut1-1 ung1∆ dcd1∆, and dut1-1 ung1∆ sml1∆ yeast

first: D

middle: S

last: Bryan


title: A Widespread Impact on Small RNAs and Gene Networks in Rice msp1/ostdl1a Mutants, Partners with Key Roles in Anther Development

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

summary:
Dissection of the genetic pathways and mechanisms by which anther development occurs in grasses is crucial for both a basic understanding of plant development and for traits of agronomic importance like male sterility. In rice, MULTIPLE SPOROCYTES1 (MSP1), a leucine-rich-repeat receptor kinase, play an important role in anther development by limiting the number of sporocytes. OsTDL1a (a TPD1-like gene in rice) encodes a small protein which acts as a cofactor of MSP1 in the same regulatory pathway. In this study, we analyzed small RNA and mRNA changes in different stages of spikelets from wildtype rice, and from msp1 and ostdl1a mutants. Analysis across different stages of rice spikelets of the small RNA data identified miRNAs demonstrating differential abundances. miR2275 was depleted in the two rice mutants; this miRNA is specifically enriched in anthers and functions to trigger the production of 24-nt phased secondary siRNAs (phasiRNAs) from PHAS loci. We observed that the 24-nt phasiRNAs as well as their precursor PHAS mRNAs were also depleted in the two mutants. Based on comparisons of transcript levels across the spikelet stages and mutants, we identified 22 transcription factors as candidates to have roles specific to anther development, potentially acting downstream of the OsTDL1a-MSP1 pathway. An analysis of co-expression identified three Argonaute-encoding genes (OsAGO1d, OsAGO2b, and OsAGO18) that accumulate transcripts coordinately with phasiRNAs, suggesting a functional relationship. By mRNA in situ analysis, we demonstrated a strong correlation between the spatiotemporal pattern of accumulation of these OsAGO transcripts with previously-published phasiRNA accumulation patterns from maize.
Raw files for smallRNA-Seq were not provided by submitter.

overall_design: Genome-wide small RNA and mRNA profiling was done by Illumina TruSeq sample preparation followed by high-throughput sequencing with the Illumina HiSeq 2000 platform.

first: Qili

last: Fei

first: Li

last: Yang

first: Wanqi

last: Liang

first: Dabing

last: Zhang


title: Histone H3K36M mutation impairs mesenchymal differentiation and drives sarcoma development [ChIP-Seq]

city: Madison

first: Peter

last: Lewis

state: Wisconsin

address: 330 N Orchard Street

department: Department of Biomolecular Chemistry

institute: University of Wisconsin-Madison

summary: The goal of this study is to understand the genome-wide alterations in chromatin landscapy induced by a histone mutation (H3.3 K36M) derived from chondroblastomas

overall_design: Examination of 2 different histone modifications in 2 cell types.

first: Chao

last: Lu

first: Siddhant

middle: U

last: Jain


title: Histone H3K36M mutation impairs mesenchymal differentiation and drives sarcoma development [RNA-Seq]


title: Long noncoding RNA related-competing endogenous RNAs in retinal pigment epithelial cells induced by clusterin

status: Public on Sep 22 2016

city: Beijing

first: zi

last: ye

address: FuXing Road 28

institute: PLA General Hospital

summary: long noncoding RNAs (lncRNAs) play crucial roles in regulating gene expression by acting as competing endogenous RNAs (ceRNAs).

overall_design: Based on high throughput sequencing data of RPE cells treated by clusterin or not, we first identified differentially expressed mRNAs, lncRNAs and miRNAs. Then, we constructed an lncRNA-mRNA-miRNA network (ceRNA network) based on bioinformatic database miRanda and microRNA (miRNA) targets database miRTarBase.

first: Zi

last: Ye

first: Zhaohui

last: Li

first: Shouzhi

last: He


title: Sequencing analysis for 5hmC pull-down DNA

city: Tokyo

first: Mayumi

last: Oda

address: 35 Shinanomachi, Shinjuku

department: School of Medicine

country: Japan

institute: Keio University

summary: The gene body regions of cardiomyocyte-specific genes in cardiomyocytes are hypomethylated. We confirmed that the DNA methylation in gene body regions were demethylated during development. We speculated that the demethylation of gene body regions in cardiomyocyte-specific genes might be associated with active demethylation by Tet oxidation.To explore 5hmC distribution in cells and tissues, we performed 5hmC-specific chemical labeling-mediated pull-down DNA sequencing (hMe-Seal)(Song 2011 Nat genet, PMID:21151123). We found that the 5hmC in gene body regions are associated with demethylation, but not exclusively, and also with transcriptional activity. We concluded that gene body DNA hypomethylation in cardiomyocyte specific genes were mediated by oxidative demethylation.

overall_design: Genomic DNA from ESC and heart and liver tissues from different developmental periods was used for the analysis.

first: Shunichi

last: Wakabayashi


title: RNA-Seq analyses of liver samples in mice fed ad libitum or subject to a 24 hr fast

city: Bethesda

first: Haiming

last: Cao

address: 9000 Rockville Pike

department: NHLBI

institute: NIH

summary: To systemically identify long non-coding RNAs (lncRNAs) regulating energy metabolism, we performed transcriptome analyses to simultaneously profile mRNAs and lncRNAs in key metabolic organs in mice under pathophysiologically representative metabolic conditions by using a microarray platform (Mouse LncRNA Array V2.0, Arraystar). This microarray platform has been thoroughly evaluated for detecting mRNAs, but to further confirm its accuracy in detecting lncRNA expression at a genome-wide level, we performed RNA-seq for the same ad libitum and fasting liver samples used for the microarray. For those differentially expressed lncRNAs (fasting vs ad libitum) identified by microarray, 93.4% could be detected by RNA-seq and the Pearson correlation between microarray and RNA-seq of expression changes for these lncRNAs is 0.71.

overall_design: Examination of livers from four mice fed ad libitum and four mice subject to a 24 hr fast

first: Ling

first: Ping

first: Wenjing

first: Xiangbo

last: Ruan

first: Kurtis

last: Kiesewetter

first: Jun

last: Zhu


title: RNA-seq analysis of livers of mice fed a high fat diet with and without administration of an inhibitor of the ileal bile acid uptake transporter ASBT

city: Atlanta

first: Astrid

last: Kosters

address: 1760 Haygood Drive

institute: Emory University

summary: The study was designed to determine the effect of inhibition of ileal bile acid uptake on hepatic gene expression in high fat diet induced hepatic steatosis in mice

overall_design: RNA-seq profiling was performed on liver tissues of mice fed a chow diet, a high-fat diet plus 0.2% (w/w) cholesterol (HFD), and the HFD plus the ASBT-inhibitor SC-435 (0.006%), for 16 weeks.

first: Anuradha

last: Rao

first: Jamie

last: Mells

first: Wujuan

first: Kenneth

last: Setchell

first: Angelica

last: Amanso

first: Grace

last: Wynn

first: Tianlei

last: Xu

first: Brad

last: Keller

first: Hong

last: Yin

first: Sophia

last: Banton

first: Dean

last: Jones

first: Hao

last: Wu

first: Paul

last: Dawson

first: Saul

last: Karpen


title: Capture of Associated Targets on Chromatin (CATCH) Links Long-Distance Chromatin Looping to Transcriptional Coordination

city: Chicago

first: Hari

last: Singhal

state: IL

address: 929 E 57th St

department: Ben May Department for Cancer Research

institute: University of Chicago

summary: We describe here a sensitive and novel method of identifying endogenous DNA-DNA interactions.  Capture of Associated Targets on CHromatin (CATCH) uses efficient capture and enrichment of specific genomic loci of interest through hybridization and subsequent purification via complementary biotinylated oligonucleotide.  The CATCH assay requires no enzymatic digestion or ligation, requires little starting material, provides high quality data, has excellent reproducibility and is completed in less than 24 hours.  Efficacy is demonstrated through capture of three disparate loci, which demonstrate unique subsets of long-distance chromatin interactions enriched for both enhancer marks and estrogen receptor binding sites.  In each experiment, CATCH-seq peaks representing long-distance chromatin interactions were centered near the TSS of genes, and critically, the genes identified as physically interacting are shown to be transcriptionally co-expressed. These interactions could potentially create transcriptional hubs for the regulation of gene expression programs.

overall_design: There are 7 bedgraph files; two are “control” samples; sets of samples were pulled from the same chromosome.

first: Ryan

last: Bourgo

first: Geoffrey

last: Greene


title: Analysis of differential gene expression in Drosophila dIME4 null mutants

city: Nottingham

first: Nigel

middle: P

last: Mongan

address: University Park

department: Biodiscovery Institute

institute: University of Nottingham


title: Quantifying variation within the bacterial species E. coli

city: La Jolla

first: Jonathan

last: Monk

state: California

address: 9226A Regents Rd

institute: UCSD

summary: Escherichia coli strains are widely used in academic and applied research as well as in biotechnology for production of various compounds. Despite its status as a model organism, strain-specific differences and their underlying contributing factors are still not well characterized. These differences have a major impact on cell physiology and for the applied purposes of synthetic biology, metabolic engineering, and process design. In this study, strain-specific differences are quantified in seven widely-used applied biotechnology strains of E. coli (BL21, C, Crooks, DH5a, K-12 MG1655, K-12 W3110, and W) using genomics, phenomics, transcriptomics and genome-scale modelling to guide the choice of strain for a given product. Even given the genetic similarity of the strains, mMetabolic physiology and gene expression varied widely with downstream implications for productivity, product yield, and titre. Further, these differences can be linked to differential regulatory structure. Analysing high flux reactions and the expression levels of their encoding genes revealed a quantitative link between these sets and show that often, these sets are correlated with strain-specific caveats. Integrated modelling also revealed that certain strains are better suited to produce a given compound or express a desired construct considering native expression states of pathways that enable high-production phenotypes. The result of this study is a resource comparing strains in an important model species and a general strategy for choosing a host strain or chassis selection for applied biotechnology.

sample_organism: Escherichia coli str. K-12 substr. W3110

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

overall_design: 7 different strains of E. coli were grown in glucose M9 minimal media aerobically and anaerobically.  Their gene expression was measured using RNAseq on an Illumina HiSeq2000

first: Monk

last: Jonathan

first: Feist

last: Adam


title: Global analyses of RNA G-quadruplexes

city: Cambridge

first: Junjie

last: Guo

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute

summary: In vitro, some RNAs can form stable four-stranded structures known as G-quadruplexes. Although RNA G-quadruplex structures have been implicated in post-transcriptional gene regulation and diseases, direct evidence for quadruplex formation in cells has been lacking. Here, we developed a suite of methods that identify RNAs with quadruplex-forming ability and measure their folding state in living cells. Applying these methods to mammalian cell lines, the budding yeast S. cerevisiae and several bacteria, we characterized the folding landscapes of RNA G-quadruplexes in these species.

sample_organism:
Pseudomonas putida
Escherichia coli
Saccharomyces cerevisiae
Homo sapiens
Mus musculus
Parasynechococcus marenigrum WH 8102

overall_design: RT-stop profiling of untreated, DMS- or NAI-treated RNA samples from 6 species

first: David

last: Bartel


title: Genome-wide expression profile in Fh1-competent vs Fh1-deficient mouse kidney cells

first: Chandra

last: Chilamakuri

address: Robinson Way

institute: Cancer Research UK Cambridge Institute

summary: Comparison of the transcriptome of immortalised mouse kidney epithelial cells either wt for Fh1 or Fh1-deficient. The cells were isolated from kidneys of P5 mouse(see Frezza et al, Nature 2011). Briefly, Fh1_fl (flox) are wt for Fh1 (floxed cassette not excised), clone 1 and clone 19 are two different Fh1-deificent clones (floxed cassette excised) and Rec are clone 19 with reconstituted Fh1 expression from exogenous plasmid.

overall_design: Examination of gene transciption in 4 cell types.

first: Vincent

last: Zecchini

first: Chistian

last: Frezza


title: Genome-wide expression profile in FH-deficient vs FH-competent cells


title: Genome-wide binding sites for Arabidopsis REPLUMLESS

city: NORWICH

first: Robert

last: Sablowski

state: Norfolk

address: The John Innes Centre

department: CDB

institute: JIC

summary: The Arabidopsis thaliana REPLUMLESS gene (RPL), also known as PENNYWISE (PNY) and BELLRINGER (BLR) encodes a BEL1-like TALE homeodomain (BLH) transcription factor that controls multiple aspects of meristem and floral development, including meristem maintenance, phyllotaxis, transition to flowering, stem development and floral organ patterning [1-3]. As part of a screen for genes that mediate the function of RPL in the processes above, we performed ChIP-seq to identify genome-wide RPL binding sites within inflorescence apices.     1. Byrne, M.E., Groover, A.T., Fontana, J.R., and Martienssen, R.A. (2003). Development 130, 3941-3950.  2. Roeder, A.H.K., Ferrandiz, C., and Yanofsky, M.F. (2003). Current Biology 13, 1630-1635.  3. Smith, H.M.S., and Hake, S. (2003).  Plant Cell 15, 1717-1727.

overall_design: Plants expressing GFP-tagged RPL (pRPL:RPL-GFP) were used for ChIP-seq with anti-GFP antibodies; wild-type controls (Landsberg-erecta) were used as epitope-negatve controls.

first: Stefano

last: Bencivenga


title: Analysis of differential gene expression in Drosophila dIME4 null mutants [paired-end]

summary: Methylation of mRNA at the N6 position of adenosin is known for a long time, but its function remains poorly understood. Here generated a null mutant in the catalytic subunit of the m6A mRNA methylosome, dIME4, in Drosophila to determine the impact of loss of m6A on gene expression using Illumina sequencing.

overall_design: Since dIME4 is preferentially expressed in the nervous system and dIME4 null mutants are viable, we compared gene expression and alternative splicing in wild type (2 samples) and dIME4 mutants (3 samples) with genetic background matched w control females in neuron enriched head/thorax.

first: Irmgard

last: Haussmann

first: Matthias

last: Soller


title: Gene expression following: RNAi knockdown of grappa, lilliputian, or Suppressor of Triplolethal; induction of Cyclin-dependent kinase 9 dominant negative constructs, or ectopic expression of stand still in Drosophila melanogaster.

first: Brian

last: Oliver

state: MD

address: 50 South Drive

department: LBG

institute: NIDDK, NIH

summary: We report the transcriptional profiling of Drosophila melanogaster gonadectomized adults following RNAi knockdown of grappa (gpp), lilliputian (lilli), or Suppressor of Triplolethal [Su(Tpl)], as well as induction of Dominant Negative (DN) allele of Cyclin-dependent kinase 9 (Cdk9), or ectopic expression of stand still (stil), with a three-component temperature sensitive system. We also included the transcriptional profiling of testes and ovaries of gppRNAi, lilliRNAi, and Su(Tpl)RNAi flies under permissive temperature. All data includes induced and non-induced sham controls.

overall_design: We used a three-component temperature sensitive expression system by ubiquitously expressing both Gal4 [P{tubP-GAL4}LL7 (FBti0012687)] and the temperature-sensitive Gal4 repressor, Gal80ts [P{tubP-GAL80ts}7 (FBti0027798)], in the presence of one of the Gal4 UAS responsive transgenes - gppRNAi [y1 sc* v1; P{TRiP.HMS00160}attP2 (FBst0034842)], lilliRNAi [y1 sc* v1; P{TRiP.HMS01066}attP2 (FBst0034592)], Su(Tpl)RNAi [y1 sc* v1; P{TRiP.HMS00277}attP2 (FBst0033399)]. We used the same system to express the dominant negative allele of Cdk9 with P{UASp-Cdk9DN}Ifm1 and P{UASp-Cdk9DN}Ifm1, P{UASp-Cdk9DN}Cff1 (Daniel Pauli, unpublished), and ectopically express stil with w*; P{UASp-stil+}Amm (Daniel Pauli, unpublished). Both stil and Cdk9 constructs were cloned into the expression vector (i.e., UASp) and introduced into fly third chromosome by P-element mediated transformation. The Cdk9DN has a codon substitution to encode asparagine rather than aspartic acid in position 199 (D199N) in the active site of the kinase. For the gonadectomized fly samples, we used gppRNAi, lilliRNAi, Su(Tpl)RNAi, stil ectopic over expression, Cdk9DN over expression, as well as two sham control lines, i.e., w1118 (FBst0003605) and P{UASp-lacZ} (FBtp0010276), and all flies of the above lines were reared and crossed under the same protocol. Following shifts from the permissive (20 oC) to the restrictive temperature (29 oC), we removed the gonads and collected gonadectomized flies (three per sample) for single-end 50 bp PolyA+ strand-specific RNA-seq. For all the gonad samples, we used gppRNAi, lilliRNAi, Su(Tpl)RNAi, and the control line P{UASp-lacZ}, and the files were reared at the permissive temperature only. For each gonad sample, we dissected three pairs. We followed the same library and RNA-seq pipeline for all samples. In total, 192 samples were sequenced, of which 189 samples with > 2.5 million mapped reads are reported here. 93 samples are in triplicate, 92 samples are in quadruplicate, and four samples are in duplicate. There are 96 male samples (including 16 testis) and 93 female samples (including 16 ovary). Additionally, there are time-points at 0, 24, and 48 hours post temperature shift for all non-gonad samples.

first: Haiwang

last: Yang

first: Cale

last: Whitworth

first: Daniel

last: Pauli


title: Analysis of differential gene expression in Drosophila dIME4 null mutants [single-end]

first: Nigel

last: Mongan