title: Loss of Function Mutations in ETS2 Repressor Factor (ERF) Reveal a Balance Between Positive and Negative ETS Factors Controlling Prostate Oncogenesis [VCaP RNA-Seq]

overall_design: VCaP cells were infected with lentivirus 1:  Tet-inducible shERG,  followed by lentivirus 2:  shERF or shNT, and selected with two different antibiotics.  Subsequently, cells were treated with 100ng/mL doxycycline vs vehicle, 1nM DHT x 16h vs vehicle, or both vs vehicle.  For each condition, 3 sets of equal numbers of cells were plated and then processed independently.


title: WT Pik3ca2X basal cell expression profile

status: Public on Jun 06 2017

city: Seattle

first: Slobodan

last: Beronja

state: WA

address: 1100 Fairview Ave. N

department: Human Biology

country: USA

institute: Fred Hutchinson Cancer Research Center

type: Expression profiling by high throughput sequencing

summary: WT Pik3caH1047R/H1047R basal cell RNASeq

overall_design: RNASeq of a6 integrin high basal cells from E18.5 WT and Pik3caH1047R/H1047R mouse epidermis.

first: Zhe

last: Ying


title: Analysis by RNAseq of the transcriptome of different stage of skin carcinogenesis induced by topical application of DMBA/TPA

status: Public on Jun 07 2017

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

summary: Total RNA extracted from biopsies of healthy skin, papilloma, SCC Tumor and of 2 cell lines isolated from these tumors were purified using miRNeasy minikit (Qiagen). RNA libraries were then generated with the NEB next small library prep set for SOLID (New England Biolabs) and sequenced on the Applied Biosystems SOLiD 5500 wildfire system following the manufacturer's instructions.

overall_design: 1 sample of Healthy skin (S), two samples of 2 distinct papilloma (P1 and P2), 1 tumor sample (T), 1 sample of  non tumorigenic mSCC-20 cells and 1 sample highly tumlorigenic SCC cells  (mSCC-38)

first: G

last: Ponzio

first: N

last: Nottet

first: B

last: Mari

first: K

first: P

last: Barbry

first: R

last: Rezzonico


title: Loss of Function Mutations in ETS2 Repressor Factor (ERF) Reveal a Balance Between Positive and Negative ETS Factors Controlling Prostate Oncogenesis [Organoids RNA-Seq]

status: Public on Jun 08 2017

city: New York

first: Rohit

last: Bose

address: 1275 York Ave

institute: Memorial Sloan Kettering Cancer Center

summary: Half of prostate cancers are caused by a gene-fusion that enables androgens to drive expression of the normally silent ETS transcription factor ERG in luminal prostate cells1-4.  Recent prostate cancer genomic landscape studies5-10 have reported rare but recurrent point mutations in the ETS repressor ERF11.  Here we show these ERF mutations cause decreased protein stability and ERF mutant tumours are mostly exclusive from those with ERG fusions.  ERF loss recapitulates the morphologic and phenotypic features of ERG gain in primary mouse prostate tissue, including expansion of the androgen receptor (AR) transcriptional repertoire, and ERF has tumour suppressor activity in the same genetic background of PTEN loss that yields oncogenic activity by ERG.  Furthermore, in a human prostate cancer model of ERG gain and wild-type ERF, ChIP-seq studies indicate that ERG inhibits the ability of ERF to bind DNA at consensus ETS sites.  Consistent with a competition model, ERF loss rescues ERG-positive prostate cancer cells from ERG dependency. Collectively, these data provide evidence that the oncogenicity of ERG is mediated, in part, by displacement of ERF and raise the larger question of whether other gain-of-function oncogenic transcription factors might also inactivate endogenous tumour suppressors.

overall_design: Murine Pten+/+ prostates were infected with shNT or shErf lentivirus, selected with antibiotics and 2 rounds of FACS.  For each condition, 2 sets of equal numbers of cells were plated and then processed for RNA extraction and RNA-seq independently.

first: Charles

middle: L

last: Sawyers


title: Analysis of CAL165 cells transcriptome using RNASeq

summary: Total RNA extracted from the head and neck cell line CAL165 were purified using miRNeasy minikit (Qiagen). RNA libraries were then generated with the NEB next small library prep set for SOLID (New England Biolabs) and sequenced on the Applied Biosystems SOLiD 5500 wildfire system following the manufacturer's instructions.

overall_design: 1 sample of CAL165


title: Geometry-dependent functional changes in iPSC-derived cardiomyocytes

city: Cambridge

first: Adam

middle: Ezra

last: Cohen

state: MA

address: 12 Oxford Street

department: Chemistry and Chem. Biol.

institute: Harvard University

summary: Human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CM) are a promising platform for cardiac studies in vitro, and possibly for tissue repair in humans. However, hiPSC-CM cells tend to retain morphology, metabolism, patterns of gene expression, and electrophysiology similar to that of embryonic cardiomyocytes.  We grew hiPSC-CM in patterned islands of different sizes and shapes, and measured the effect of island geometry on action potential waveform and calcium dynamics using optical recordings of voltage and calcium from 970 islands of different sizes.  hiPSC-CM in larger islands showed electrical and calcium dynamics indicative of greater functional maturity. We then compared transcriptional signatures of the small and large islands against a developmental time course of cardiac differentiation. Although island size had little effect on expression of most genes whose levels differed between hiPSC-CM and adult primary CM, we identified a subset of genes for which island size drove the majority (58%) of the changes associated with functional maturation. Finally, we patterned hiPSC-CM on islands with a variety of shapes to probe the relative contributions of soluble factors, electrical coupling, and direct cell-cell contacts to the functional maturation. Collectively, our data show that optical electrophysiology is a powerful tool for assaying hiPSC-CM maturation, and that island size powerfully drives activation of a subset of genes involved in cardiac maturation.

overall_design: Examination of geometrical effects on the functional changes of hiPSC-derived cardiomyocytes

first: Christopher

middle: A

last: Werley

first: Miao-Ping

last: Chien

first: Jellert

last: Gaublomme

first: Karthik

last: Shekhar

first: Aviv

last: Regev

middle: E


title: Ethylene signaling is important for isoflavonoid mediated resistance to Rhizoctonia solani in roots of Medicago truncatula

city: Floreat

first: Jonathan

middle: P

last: Anderson

state: Western Australia

address: 147 Underwood Avenue

country: Australia

institute: CSIRO

summary: The root-infecting necrotrophic fungal pathogen Rhizoctonia solani causes significant disease to all the world’s major food crops. As a model for pathogenesis of legumes we have examined the interaction of R. solani AG8 with Medicago truncatula. RNAseq analysis of the moderately resistant M. truncatula accession A17 and highly susceptible sickle (skl) mutant (defective in ethylene sensing) identified major transcriptional reprogramming early in A17. Responses specific to A17 included components of ethylene signalling, numerous class IX ERF transcription factor family members, reactive oxygen species metabolism and consistent up-regulation of the isoflavonoid biosynthesis pathway. Mass-spectrometry revealed accumulation of the isoflavonoid related compounds liquiritigenin, formononetin, medicarpin and biochanin A in A17. Over-expression of an isoflavone synthase (IFS) in M. truncatula roots increased isoflavonoid accumulation and resistance to R. solani. Addition of exogenous medicarpin suggested this phytoalexin may be one of several isoflavonoids required to contribute to resistance to R. solani. Together these results provide evidence for the role of ethylene-mediated accumulation of isoflavonoids during defence against root pathogens in legumes.

overall_design: Root tissue of moderately resistant wild type and highly susceptible mutant lines of Medicago truncatula responding to infection from Rhizoctona solani at two time points. Each time point contains mock treated and R. solani inoculated samples. All samples in triplicate, sequenced with strand specific illumina paired end RNA sequencing.


title: Mosquito-borne diseases and Omics: Tissue-restricted expression and alternative splicing revealed by transcriptome profiling of Anopheles stephensi

city: Bangalore

first: T.S. Keshava

last: Prasad

state: Please select one below:

address: 7th floor, Discoverer block, ITPL

country: India

institute: Institute of bioinformatics

summary: Malaria is as one of the most debilitating mosquito-borne global health burdens. While much of the malaria and mosquito-borne disease attention have focused on Africa, South East Asia accounts for a sizable portion of the malaria global burden. Moreover, about 50% of the Asian malaria incidence and deaths have been from India. The completion of genome sequence of Anopheles stephensi, a major malaria vector in Asia, offers new opportunities for global health innovation, not to mention for progress in deciphering the vectorial ability of this mosquito species at a molecular level. Moving forward, tissue-based expression profiling would be the next obvious step in understanding gene functions of Anopheles stephensi. We report here the first study, to the best of our knowledge, on transcriptomic profile of four important organs of an adult female Anopheles stephensi mosquito (midgut, Malpighian tubules, fat body and ovary). In all, we identified over 21,000 transcripts corresponding to more than 12,000 gene loci from these four tissues. This study provides the tissue-based expression profiles of majority of annotated transcripts in Anopheles stephensi genome, and the dynamics of alternative splicing in these tissues. Understanding the transcript expression and gene function at the tissue level would immensely help in enhancing our knowledge of this important vector and decipher the putative role of these tissues. This knowledge might in turn provide the basis of selection of candidates for future studies on vectorial ability and novel molecular targets to intercept malaria transmission.

overall_design: Transcriptome analysis of four An.stephensi tissues from female adult mosquitoes indexed and analyzed as technical replicates on two lanes of Illumina HiScanSQ. Reference - PRJNA253267

first: Sreelakshmi

middle: K

last: Sreenivasamurthy

first: Anil

last: Madugundu

first: Gourav

last: Dey

first: Ajeet

last: Mohanty

first: Manish

last: Kumar

last: Wang

first: Ashwani

first: Akhilesh

last: Pandey

first: T

middle: S


title: Widespread changes in nucleosome accessibility without changes in nucleosome occupancy during a rapid transcriptional induction

city: Boston

first: Michael

last: Tolstorukov

address: 185 Cambridge Street

department: Molecular Biology

institute: Massachusetts General Hospital

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Activation of transcription requires alteration of chromatin by complexes that increase the accessibility of nucleosomal DNA. Removing nucleosomes from regulatory sequences has been proposed to play a significant role in activation. We tested whether changes in nucleosome occupancy occurred on the set of genes that are activated by the unfolded protein response (UPR). We observed no decrease in occupancy on most promoters, gene bodies, and enhancers. Instead there was an increase in the accessibility of nucleosomes, as measured by MNase digestion and by ATAC-seq, that did not result from removal of the nucleosome. Thus changes in nucleosome accessibility predominate over changes in nucleosome occupancy during rapid transcriptional induction during the UPR.

overall_design: Time series of nucleosome occupancy, MNase-seq, ATAC-seq, H3K27ac, RNAseq and Pol2 profiles for UPR-induced S2 cells.

first: Britta

last: Mueller

first: Jakub

last: Mieczkowski

first: Sharmistha

last: Kundu

first: Peggy

first: Ruslan

last: Sadreyev

middle: Y

first: Robert

last: Kingston


title: AK144841 in Cutaneous Squamous Cell Carcinoma (cSCC)

first: Kevin

last: Lebrigand

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Analysis of hypertranscription in E13.5 mouse primordial germ cells

city: London

first: Michelle

last: Percharde

address: Du Cane Road

department: Imperial College London

country: United Kingdom

institute: MRC Laboratory of Medical Sciences

summary: During embryonic development, large-scale reprogramming occurs in primordial germ cells (PGCs) at the level of both DNA demethylation and histone modifications. While much is known about epigenetic changes, it still remains unclear how this chromatin state impacts the transcriptome and development of the germline.    We have used cell-number normalised (CNN) RNA-seq to document the striking upregulation of the germ cell transcriptome at E13.5 compared to neighboring somatic cells of the embryonic gonad. We provide a novel, genome-wide analysis of hypertranscription during development, documenting the global amplification of the majority of the E13.5 PGC transcriptome. Upregulated transcripts in PGCs include those for ribosome biogenesis, translation and chromatin remodelling, as well as all transposable element families. These data reveal the significant hyperactivity of the germ cell transcriptome.

overall_design: 3 replicates each of E13.5 male or female PGCs and 3 replicates each of male of female soma were used to generate RNA-seq library samples (12 samples total)

first: Priscilla

last: Wong

first: Miguel

last: Ramalho-Santos


title: Tcrd rearrangement redirects a processive Tcra recombination program to expand the Tcra repertoire

city: Durham

first: Zachary

last: Carico

state: North Carolina

address: 207 Research Drive

department: Immunology

institute: Duke University

summary: The Tcra-Tcrd locus undergoes Tcrd rearrangement in DN thymocytes followed by primary and secondary Tcra rearrangements in DP thymocytes. Here we reveal the mechanisms underpinning combinatorial diversity in the Tcra repertoire. We show that V-alpha and J-alpha segments on individual Tcra alleles are used in stepwise and coordinated proximal-to-distal progressions during primary and secondary rearrangements, substantially constraining combinatorial diversity. Notably, Tcrd recombination in DN thymocytes diversifies the Tcra repertoire by truncating the V-alpha array to permit otherwise disfavored V-J combinations. Such diversification is important, because Trav1-Traj33+ mucosa-associated invariant T cells are depleted when Tcrd rearrangement is impaired. Our results reveal an important biological advantage conferred by the nested organization of Tcrd and Tcra gene segments.

overall_design: High-throughput sequencing was used to analyze Tcra repertoire from transcripts purified from sorted DP thymocytes from groups of 1 to 4 mice bearing either wild-type or genetically modified Tcra alleles. Higher-order chromatin structure of wild-type and HYa Tcra alleles in DP thymocytes was analyzed using 4C-seq from 5 viewpoints.

middle: M

first: Kingshuk

last: Roy Choudhury

first: Baojun

last: Zhang

first: Yuan

last: Zhuang

last: Krangel


title: Primate Primordial Germ Cells Acquire Transplantation Potential by Carnegie Stage 23

city: Haining

first: Wanlu

last: Liu

state: Zhejiang

address: 718 East Haizhou Rd.,

department: Zhejiang University - University of Edinburgh Institute

country: China

institute: Zhejiang University

summary: Primordial germ cells (PGCs) are the earliest embryonic progenitors in the germline. Correct formation of PGCs is critical to reproductive health as an adult. Recent work has shown that primate PGCs can be differentiated from pluripotent stem cells; however, a bioassay that supports their identity as transplantable germ cells has not been reported. Here, we adopted a xenotransplantation assay by transplanting single-cell suspensions of human and nonhuman primate embryonic Macaca mulatta (rhesus macaque) testes containing PGCs into the seminiferous tubules of adult busulfan-treated nude mice. We discovered that both human and nonhuman primate embryonic testis are xenotransplantable, generating colonies while not generating tumors. Taken together, this work provides two critical references (molecular and functional) for defining transplantable primate PGCs. These results provide a blueprint for differentiating pluripotent stem cells to transplantable PGC-like cells in a species that is amenable to transplantation and fertility studies.

sample_organism:
Macaca mulatta
Homo sapiens

overall_design: 10 mRNAseq for Rhesus Macaque

first: Chen

last: Di


title: Transcriptional profiling of WT and XBP1 Mutant Larvae

status: Public on Jun 05 2017

first: Hyung Don

last: Ryoo

state: NY

address: 550 First Avenue, MSB 497

department: Cell Biology

institute: NYU School of Medicine

summary:
the purpose of the study is to compare the gene expression profile of WT vs. XBP1 Mutant Drosophila Larvae
Methods: RNA sequencing was performed from 2nd instar Larvae of WT and XBP1 Mutant flies
Results: Across the 4 samples, there was an average of 51 million mapped reads per sample with an average unique mapping rate of 83%.  Using an adjusted p-value cutoff of 0.05, 154 genes were calculated to be differentially expressed.
Conclusions: XBP1 affects gene expression profiling in drosophila larvae

overall_design: Gene expression profiling during normal development of the fly


title: RNA-sequencing of  hepatocyte specific ABCA1 deletion mice

city: Ithaca

first: Praveen

last: Sethupathy

address: T7 006 Vet Research Tower

institute: Cornell University

summary: ATP binding cassette transporter A1 (ABCA1) regulates cellular cholesterol efflux. We characterized the gene expression changes following hepatocyte specific ABCA1 deletion in mice. We report that genes and pathways related to lipogenesis were downregulated in mice with hepatocyte specific ABCA1 deletion compared to floxed controls.

overall_design: mRNA profiles of C57BL/6 mice with hepatocyte specific (Albumin-Cre) ABCA1 deletion and floxed controls were generated by high throughput sequencing using the Illumina HiSeq 2500 platform.

first: John

last: Parks


title: Genes directly regulated by NF-κB in human hepatocellular carcinoma HepG2 [ChIP-seq]

city: Nanjing

first: Wei

last: Dai

state: Jiangsu

address: Sipailou 2#,Nanjing, Jiangsu Province, P. R. China

institute: Southeast University

summary: Over activation of NF-κB has close relationship with hepatitis and hepatocellular carcinoma (HCC). In this study, by manipulating NF-κB activity with its recognized activator TNFα and using ChIP-seq and RNA-seq techniques, we identified 699 NF-κB direct target genes (DTGs) in a widely used HCC cell line, HepG2, including 399 activated and 300 repressed genes. In these NF-κB DTGs, 216 genes (126 activated and 90 repressed genes) are among the current HCC gene signature. Functional annotation revealed that NF-κB DTGs in HepG2 cell are mainly related with many typical NF-κB-related biological processes, such as immune system process, response to stress, response to stimulus, defense response and signaling pathways of NF-kappa B. Some NF-κB DTGs are also involved in Hepatitis C and B pathways. The NF-κB DTGs were further confirmed by detecting the NF-κB binding and expression of 14 genes with ChIP-PCR and RT-PCR.

overall_design: ChIP-seq of NF-kB in TNFα-induced and TNFα-uninduced HepG2 cells with two biological replicates.

first: Jian

last: Wu

first: Shuyan

first: Bingjie

last: Shi

first: Xinhui

last: Xu

first: Danyang

last: Wang

first: Jinke


title: The deacetylase activity of histone deacetylase 3 is required for productive VDJ recombination and B cell development [RNA-seq]

city: Nashville

first: Scott

last: Hiebert

state: TN

address: 2220 Pierce Ave

department: Biochemistry

institute: Vanderbilt University

summary: Histone deacetylase 3 (HDAC3) is the catalytic component of NCoR/SMRT corepressor complexes that mediate the actions of transcription factors implicated in the regulation of B cell development and function. We crossed Hdac3 conditional knockout mice with Mb1-Cre knockin animals to delete Hdac3 in early progenitor B cells. The spleens of Hdac3F/-Mb1-Cre+/- mice were virtually devoid of mature B cells, and B220+CD43+ B cell progenitors accumulated within the bone marrow. Quantitative deep sequencing of the immunoglobulin heavy chain locus from B220+CD43+ populations identified a defect in VHDJH recombination with a severe reduction in productive rearrangements, which directly corresponded to the loss of pre-B cells from Hdac3D/- bone marrow. For Hdac3D/- B cells that did show productive VDJ rearrangement, there was significant skewing toward the incorporation of proximal VH gene segments and a corresponding reduction in distal VH gene segment usage. While transcriptional effects within these loci were modest, Hdac3D/- progenitor cells displayed global changes in chromatin structure that likely hindered effective distal V-DJ recombination. Re-introduction of wild type Hdac3 restored normal B cell development, whereas an Hdac3 point mutant lacking deacetylase activity failed to complement this defect. Thus, the deacetylase activity of Hdac3 is required for the generation of mature B cells.

overall_design: Bone marrow was isolated from Hdac3+/+Mb1cre+/- or Hdac3F/-Mb1cre+/- mice at 8 weeks of age.  B220+CD43+ B cells were isolated from marrow by FACS and cells from two mice were pooled per sample.  Total RNA isolated by Trizol extraction.

middle: W

first: Kristy

middle: R

last: Stengel


title: Chromatin remodeling and dynamics of hematopoietic stem cells and progenitors

city: Shanghai

first: Xiang

last: Yu

state: Shanghai

address: 800 DongChuan

institute: Shanghai Jiao Tong University

summary: Hematopoietic stem cells (HSCs) have the capability to self-renew and differentiate into all blood cell lineages. How chromatin state regulates self-renewal and differentiation of HSC is not fully understood. Here, we provided the first global landscape of chromatin state in long term (LT)-HSCs, short term (ST)-HSCs and multipotent progenitor (MPP) by ATAC-seq analysis. We discovered that the promoter regions of genes that control cell cycle, and several important miRNAs were maintained as open chromatin state in HSCs. In addition, we found that promoter-TSS regions of many genes were occupied by nucleosomes in LT/ST-HSC and they become open chromatin regions in MPP. Furthermore, we uncovered 166 known transcription factors (TFs) including C/EBPs, GABPA, and FLI1can access to the promoter open chromatin in HSCs, and quarter of them displayed cell type-specific manner. Among them, we identified DNA cis-element of Krüppel-like factor family (KLF9, KLF10 and KLF14) were specifically enriched in LT-HSC. Meanwhile, we found that 8299 enhancers are established concomitantly with the formation of open chromatin sites, and they can be accessed by 153 TFs including GABPA, CTCF and RNUX1/RUNX2. Near hundred TF-binding motif are enriched in both promoter and enhancers, indicating they may direct the interaction between promoters and enhancers. Finally, we found 21.7% poised enhancers were preset in LT/ST-HSCs, and became active enhancers in MPP. Together, our finding provides new insightinto how chromatin state and transcriptionalregulatory networkare remodeledin promoter and enhancer regions during the differentiation of LT/ST-HSC to MPP.

overall_design: We examined chromatin structure using ATAC-seq in 3 cell types in C57BL/6 wild-type (CD45.2+)

first: Chao

first: Hong

first: Brian

last: Gregory

last: Huang


title: H3K36 Methylation Regulates Nutrient Stress Response in S. cerevisiae by Enforcing Transcriptional Fidelity

city: Chapel Hill

first: Austin

middle: J

last: Hepperla

state: NC

address: 7018B Mary Ellen Jones Building

department: Genetics

institute: University of North Carolina at Chapel Hill

summary: Set2-mediated methylation of H3K36 (H3K36me) regulates a diverse number of activities including DNA repair, mRNA splicing and the suppression of inappropriate or ‘cryptic’ transcription.  Here, we describe an unexpected connection between Set2-mediated H3K36me and the regulation of nutrient stress response.  We find cells deleted for SET2 (set2∆) are sensitive to inhibitors of Tor1, Tor2 and MAP kinase pathways that regulate the nutrient response pathway. Further genetic and biochemical analyses confirm a role for Set2-mediated H3K36me in nutrient stress response. At the molecular level, set2∆ cells demonstrate a dysregulated genome-wide transcriptional response to nutrient stress. Remarkably, newly initiated and bi-directional transcription events within the bodies of genes develop in set2∆ cells during nutrient stress.  Importantly, these antisense transcripts extend into the promoters of the genes they arise from, resulting in pervasive transcriptional interference.  Our results suggest that Set2-enforced transcriptional fidelity is critical to the proper regulation highly-tuned transcription programs.

overall_design: Examination of ribosome-depleted stranded RNA in WT or set2∆ in S. cerevisiae at 0, 30, 60, and 120 minutes after nutrient stress.

first: Stephen

last: McDaniel

first: Jie

first: Raghuvar

last: Dronamraju

first: Alexander

middle: T

last: Adams

first: Vidyadhar

middle: G

last: Kulkarni

first: Ian

last: Davis

middle: D

last: Strahl


title: Transcriptome analysis of MR1 reactive T cells

city: Singapore

first: Vipin

last: Narang

address: Immunos #04-01, 8A Biomedical Grove, Singapore-138648

country: Singapore

institute: Singapore Immunology Network (SIgN)

summary: MHC class I-related molecule MR1 presents riboflavin-derived microbial metabolites and folate-derivatives to mucosal-associated invariant T cells, but it is unknown whether MR1 can bind alternative antigens that stimulate other T cell lineages. Here we report that human T cells displaying diverse TCR-α and β chains recognize MR1-expressing cells in the absence of microbial ligands and respond to recombinant MR1 molecules loaded with antigens extracted from stimulatory targets. Transcriptome analysis revealed functional heterogeneity of MR1-reactive T cells (MR1T cells), which displayed differential expression of various transcription factors regulating T cell polarization, proliferation and apoptosis. Accordingly, MR1T cells displayed multiple profiles of chemokine receptor expression and secreted variable combinations of cytokines and growth factors, suggesting a diversity of immunological roles across numerous tissues. Functionally, MR1T cells were capable of inducing dendritic cell maturation and stimulating  anti-microbial responses in intestinal epithelial cells. These data demonstrate that MR1 presents endogenous antigens to a novel population of functionally diverse human T cells.

overall_design: mRNA profiles of two representative MR1T cell clones in resting (not exposed to antigen) and activated (stimulated with A375-MR1 antigen target cells and activated) states

first: Marco

last: Lepore

first: Gennaro

last: De-Libero

first: Lucia

last: Mori


title: Global transcriptional response of solvent-sensitive and solvent-tolerant Pseudomonas putida strains exposed to toluene

status: Public on Jun 04 2017

city: Malaga

first: Carlos

middle: Molina

last: Santiago

state: Malaga

address: Bulevar Louis Pasteur 49

department: MIcrobiology

country: Spain

institute: UMA

summary: We report the application of a high-throughput technique, RNA-seq, to study the transcriptomic response of P. putida KT2440 and DOT-T1E in the presence of toluene with the aim to study in more detail the mechanisms involved in toluene response in a toluene-sensitive and a toluene-tolerant strains.

sample_organism:
Pseudomonas putida KT2440
Pseudomonas putida DOT-T1E

overall_design: P. putida KT2440 and DOT-T1E mRNA profiles in the presence of control condition (M9), M9 plus toluene in vapor phase and M9 plus a shock of butanol at exponential phase

first: c

last: Molina-Santiago

first: J

last: Ramos


title: Selective stalling of human translation through small molecule engagement of the ribosome nascent chain

city: Berkeley

first: Jamie

last: Cate

state: CA

address: 748 Stanley Hall

institute: University of California

summary: We use ribosome profiling to demonstrate the selectivity of a small molecule, PF-06446846 that inhibits translation of its target by selectively inducing ribosome-stalling in a nascent chain sequence dependent manner.

overall_design:
Study 1: Huh7 cells were treated with 1.5 µM PF-06446846, 0.3 µM PF-06446846 or vehicle for 10 or 60 minutes, and subjected to ribosome profiling. This study included three biological replicates
Study 2: Huh7 cells were treated with 1.5 µM PF-06446846 or vehicle for 60 minutes and subjected to both ribosome profiling and mRNA-seq. This study included two biological replicates.

first: Nathanael

last: Lintner

first: Kim

last: McClure

first: Donna

last: Petersen

first: Allyn

last: Londregan

first: David

last: Piotrowski

first: Liuqing

last: Wei

first: Jun

last: Xiao

first: Michael

last: Bolt

first: Paula

last: Loria

first: Bruce

last: Maguire

first: Kieran

last: Geoghegan

first: Timothy

last: Rolph

first: Spiros

last: Liras

first: Jennifer

last: Doudna

first: Robert

last: Dullea


title: REST suppression mediates neural conversion of adult human fibroblasts via microRNA dependent  and independent pathways

status: Public on Jun 03 2017

city: Lund

first: Per

last: Brattas

address: Sölvegatan 17

country: Sweden

institute: Lund University

summary: Direct conversion of human fibroblasts into mature and functional neurons, termed induced neurons (iNs) was achieved for the first time five years ago. This technology offers a promising shortcut for obtaining patient and disease specific neurons for disease modeling, drug screening and other biomedical applications. However, fibroblasts from adult donors do not reprogram as easily as fetal donors and no current reprogramming approach is sufficiently efficient to allow the use of this technology using patient derived material for large scale applications. Here, we investigate the difference in reprogramming requirements between fetal and adult human fibroblasts and identify REST as a major reprogramming barrier in adult fibroblasts. Via functional experiments where we overexpress and knockdown the REST-controlled neuron specific microRNAs miR-9 and miR-124, we show that the effect of RESTi is only partially mediated via microRNA up-regulation. Transcriptional analysis confirmed that RESTi activates an overlapping subset of neuronal genes as microRNA overexpression and also a distinct set of neuronal genes not activated via microRNA overexpression. Based in this, we developed an optimized one-step method to efficiently reprogram dermal fibroblasts from elderly individuals using a single vector system and demonstrate that it is possible to obtain iNs of high yield and purity from aged individuals with a range of familial and sporadic neurodegenerative disorders including Parkinson’s, Huntington’s as well as Alzheimer’s disease.

overall_design: mRNA profiles of fetal and adult fibroblasts 5 days after transduction of vectors expressing neural reprogramming factors were generated using deep sequencing in triplicates, using Illumina HiSeq 2000

first: Janelle

last: Drouin-Ouellet

first: Shong

last: Lau

last: Brattås

first: Daniella

last: Ottosson

first: Karolina

last: Pircs

first: Daniela

last: Grassi

first: Lucy

last: Collins

first: Romina

last: Vuono

first: Annika

last: Andersson Sjöland

first: Gunilla

last: Westergren-Torsson

first: Caroline

last: Graff

first: Lennart

last: Minthon

first: Håkan

last: Toresson

first: Roger

last: Barker

first: Johan

last: Jakobsson

first: Malin

last: Parmar


title: Genome-wide analyses for the cellular and chemical development regulator WetA in Aspergillus flavus

city: Madison

first: Ming-Yueh

last: Wu

state: WI

address: 1550 Linden Dr

department: Bacteriology

institute: University of Wisconsin-Madison

summary: Linking cell reproduction and survival is a key task of all life forms. All fungi in the genus Aspergillus reproduce by forming asexual spores called conidia, of which formation is governed by the central regulatory circuit, BrlA->AbaA->WetA. Here, we report that WetA is a key multi-functional regulator that bridged spore differentiation, long-term survival, and chemical development in Aspergillus flavus.

overall_design: 2-day old conidia mRNA profiles of  wild type (NRRL3357) and wetA deletion mutant were generated by deep sequencing, in triplicate, using Illumina HiSeq2500.

first: Matthew

last: Mead

first: Sun-Chang

last: Kim

first: Antonis

last: Rokas

first: Jae-Hyuk

last: Yu


title: Transcriptomics analysis reveals adaptive changes of hibernating retinas in 13-lined ground squirrel

city: Guangzhou

first: Yizhao

last: Luan

state: Guangdong

address: Xianlie South Rd. 54, Yuexiu Dist

department: Zhongshan Ophthalmic Center

institute: Sun Yat-sen university

summary: Hibernation is a seasonally adaptive strategy that allows hibernators to live through extreme cold condition and was viewed as a highly regulated physiological event. In spite of the profound reduction of blood flow to retina, hibernation causes no lasting retinal injury and hibernators show increased tolerance to ischemic insults during hibernation period. To understand the molecular changes of retina in response to hibernation we applied transcriptomic analysis to explore the changes of gene expression of 13-lined ground squirrel retinas during hibernation.

overall_design: Retinas of active and hibernating ground squirrels were collected in July and August, and January and February, respectively. 6 hibernating animals, 4 awake animals were included.

first: Wei

last: Li

first: Jingxing

last: Ou

first: Zhi

last: Xie


title: Fine mapping and candidate gene analysis of two loci conferring resistance to Phytophthora sojae in soybean

city: West Lafayette

first: Meixia

last: Zhao

state: IN

address: 915 W State Steet

department: Agronomy

institute: Purdue University

summary: Phytophthora root and stem rot caused by the oomycete pathogen Phytophthora sojae, is one of the most destructive diseases of soybean. Deploying soybean cultivars carrying race-specific resistance conferred by Rps genes is the most practicalapproach to managing this disease. Previously, two Rps genes, RpsUN1 and RpsUN2 conferring broad spectra of resistance to P. sojae isolates, were identified in a landrace PI 567139B and mapped to a 6.5-cM region on chromosome 3 and a 3.0-cM region on chromosome 16, corresponding to 840 kb and 600 kb of sequences, respectively,of the soybean reference genome. By analyzing ten and nine recombinants defined by genotypic and phenotypic screening of the 826 F2:3 families derived from two reciprocal crosses between the two parental lines of the mapping populations, RpsUN1 and RpsUN2 were further narrowed to a 151-kb region that harbors five genes including three NBS-LRR genes, and a 36-kb region that contains four genes including five NBS-LRR genes, respectively, according to the reference genome. Analysis of expressional changes of these nine genes before and after inoculation with the pathogen suggest that the counterparts of Glyma.03g034600 in the RpsUN1 region and the counterparts of Glyma.16g215200 and Glyma.16g214900 in the RpsUN2 region of PI 567139B may be associated with the resistance to P. sojae. It is also suggested that unequal recombination between different NBS-LRR genes in the mapped regions may have occurred, resulting in the formation of two recombinants with inconsistent genotypes and phenotypes detected by molecular markers within the fine-mapped regions. The haplotypes of genomic regions surrounding RpsUN1 and RpsUN2 in the entire soybean germplasm deposited in the US soybean germplasm collection were analyzed towards a better understanding of the origins of these two novel sources of resistance and screening of effective markers for marker-assisted selectionof these two resistance genes for soybean breeding.

overall_design: 2 samples were sequenced, 1 inoculated with P. sojae, the other 1 were mock-inoculated

first: Linghong

first: Feng

last: Lin

first: Weidong

last: Wang

first: Jieqing

last: Ping

first: Joshua

middle: C

last: Fitzgerald

first: Shuai

first: Lianjun

last: Sun

first: Chunmei

last: Cai

first: Jianxin

last: Ma


title: Gene Expression Analysis of Melanoma Cells Treated with 6-Thio-dG In Vitro

status: Public on Jun 02 2017

city: Philadelphia

first: Tian

last: Tian

state: PA

address: 3615 Civic Center Blvd

department: Center of Applied Genomics

institute: Children's Hospital of Philadelphia

summary: Telomerase promoter mutations are highly prevalent in human tumors including melanoma. Telomere transcriptional signatures are enriched in a subset of therapy-naïve melanomas associated with worse overall survival, in BRAF-mutant intrinsically resistant melanoma cells that evade MAPK inhibitors (MAPKi), as well as in a subset of post-treatment tumor biopsies derived from patients who have disease progression on MAPKi or the immune checkpoint inhibitors, anti-CTLA-4 or anti-PD1. We demonstrate the efficacy of a telomerase-directed nucleoside, 6-thio-2'-deoxyguanosine (6-thio-dG) that results in telomere dysfunction and cell death in various models of therapy-resistant cells. Furthermore, 6-thio-dG significantly inhibits tumor growth of primary tumor biopsy cultures derived from patients who had disease progression on multiple therapies including anti-CTLA-4 or anti-PD1.

overall_design: A375 and LOX-IMVI BR melanoma cells were treated with the control, 6-Thio-dG and BIBR 1532. RNA was purified from two biological replicates for RNA sequencing.

first: Zhang

last: Gao


title: Temporal Dynamics of Neurogenomic Plasticity in Response to Social Interactions in Male Threespined Sticklebacks [ChIP-Seq]

city: Urbana

first: Alison

last: Bell

state: Illinois

address: Justin Smith Morrill Hall, 505 S Goodwin Ave #393

department: Animal Biology

institute: University of Illinois at Urbana Champaign

summary: Animals exhibit dramatic immediate behavioral plasticity in response to social interactions, and brief social interactions can shape the future social landscape. However, the molecular mechanisms contributing to behavioral plasticity are unclear. Here, we show that the genome dynamically responds to social interactions with multiple waves of transcription associated with distinct molecular functions in the brain of male threespined sticklebacks, a species famous for its behavioral repertoire and evolution. Some biological functions (e.g., hormone activity) peaked soon after a brief territorial challenge and then declined, while others (e.g., immune response) peaked hours afterwards. We identify transcription factors that are predicted to coordinate waves of transcription associated with different components of behavioral plasticity. Next, using H3K27Ac as a marker of chromatin accessibility, we show that a brief territorial intrusion was sufficient to cause rapid and dramatic changes in the epigenome. Finally, we integrate the time course brain gene expression data with a transcriptional regulatory network, and link gene expression to changes in chromatin accessibility.  This study reveals rapid and dramatic epigenomic plasticity in response to a brief, highly consequential social interaction.

overall_design: Adult males were collected from Putah Creek, a freshwater population, in spring 2013 and maintained in the lab on a 16:8 (L:D) photoperiod and at 18° C in separate 9-liter tanks. Males were provided with nesting material including algae, sand and gravel and were visually isolated from neighbors. All males were in the ‘territorial’ phase of the nesting cycle, i.e. defending a territory. Males were randomly assigned to either the experimental or control group. Males in the experimental group were presented with a smaller, unrelated male intruder confined to a flask. Males in the control groups were presented with an empty flask. At the same time as a confined intruder was introduced to an experimental male’s tank, an empty flask was introduced into a paired control male’s tank. After 5 min the flask was removed, and after a predetermined period (see below) males were quickly netted and sacrificed by decapitation within seconds following an IACUC approved protocol (#15077) of the University of Illinois at Urbana-Champaign. For ChIP Sequencing diencephalon tissue samples were collected 30 and 120 minutes after the flask was introduced.

first: Syed

last: Bukhari


title: Temporal Dynamics of Neurogenomic Plasticity in Response to Social Interactions in Male Threespined Sticklebacks

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

overall_design: Refer to individual Series


title: Temporal Dynamics of Neurogenomic Plasticity in Response to Social Interactions in Male Threespined Sticklebacks [RNA-Seq]

overall_design: Adult males were collected from Putah Creek, a freshwater population, in spring 2013 and maintained in the lab on a 16:8 (L:D) photoperiod and at 18° C in separate 9-liter tanks. Males were provided with nesting material including algae, sand and gravel and were visually isolated from neighbors. All males were in the ‘territorial’ phase of the nesting cycle, i.e. defending a territory. Males were randomly assigned to either the experimental or control group. Males in the experimental group were presented with a smaller, unrelated male intruder confined to a flask. Males in the control groups were presented with an empty flask. At the same time as a confined intruder was introduced to an experimental male’s tank, an empty flask was introduced into a paired control male’s tank. After 5 min the flask was removed, and after a predetermined period (see below) males were quickly netted and sacrificed by decapitation within seconds following an IACUC approved protocol (#15077) of the University of Illinois at Urbana-Champaign. For RNA Sequencing diencephalon and telencephalon tissue samples were collected 30, 60 or 120 minutes after the flask was introduced, with n=10 males per time point (5 experimental and 5 control).


title: JUN-Mediated downregulation of EGFR signaling is associated with resistance to gefitinib in EGFR-mutant NSCLC cell lines

city: Los Angeles

first: Vasu

last: Punj

address: Biggy Street

institute: USC


title: Phosphorylated SIRT1 associates with replication origins to prevent excess replication initiation and preserve genomic stability

city: Bethesda

first: Christophe

last: Redon

state: MD

address: 37 Convent Drive

institute: NIH

summary: Chromatin structure affects DNA replication patterns, but the role of specific chromatin modifiers in regulating the replication process is yet unclear. We report that phosphorylation of the human SIRT1 deacetylase on Threonine 530 (T530-pSIRT1) modulates DNA synthesis. T530-pSIRT1 associates with replication origins and inhibits replication from a group of ÒdormantÓ potential replication origins, which initiate replication only when cells are subject to replication stress. Although both active and dormant origins bind T530-pSIRT1, active origins are distinguished from dormant origins by their unique association with an open chromatin mark, histone H3 methylated on lysine 4.  SIRT1 phosphorylation also facilitates leading and lagging strand coordination. SIRT1 T530 phosphorylation is essential to prevent DNA breakage upon replication stress and cells harboring SIRT1 that cannot be phosphorylated exhibit a high prevalence of extrachromosomal elements, hallmarks of perturbed replication. These observations suggest that SIRT1 phosphorylation modulates the distribution of replication initiation events to insure genomic stability.

overall_design: Nascent strands were purified with the lambda exonuclease methods from HCT116 cells, which untreated or was treated 200nM aphidicolin for 24hrs and released into freshmedium, then cultured another 24hrs and cell cycle fractionated K562. Chromatin from unsyncrhonized untreated cultures of HCT116 cells was subjected to ChIP-Seq with antibody directed against T530-pSIRT1, S139-pMCM2 and H4K16Ac. Chromatin from cell cycle fractionalted K562 cells are subject to ChIP-Seq with antibody directed against T530-pSIRT1 and S139-pMCM2

first: M

middle: I

last: Aladjem


title: MyoD and FoxO3 mediated hotspot interaction orchestrates super-enhancer activity during myogenic differentiation

first: Jiajian

last: Zhou

address: No. 2 Lujing Road, Yuexiu District,

department: Dermatology Hospital

institute: Southern Medical University

summary: Super-enhancers (SEs) are cis-regulatory elements enriching lineage specific key transcription factors (TFs) to form hotspots. A paucity of identification and functional dissection promoted us to investigate SEs during myoblast differentiation. ChIP-seq analysis of histone marks leads to the uncovering of SEs which remodel progressively during the course of differentiation. Further analyses of TF ChIP-seq enable the definition of SE hotspots co-bound by the master TF, MyoD and other TFs, among which we perform in-depth dissection for MyoD/FoxO3 interaction in driving the hotspots formation and SE activation.

overall_design: The CRISPR/Cas9 system was used to delete hotspots (H1_KO, H23_KO, H34_KO, H3_KO) and knockout MyoD expression (Myod1_KO) in C2C12 cell line following published protocols (Ran, F. A. et al., 2013; Huang, J. et al., 2016). Double deletion of H2 and H3 was generated by deleting H3 in H2 KO cell line. Similarly, double deletion of H3 and H4 was generated by deleting H3 in H4 KO cell line. Both WT and KO C2C12 cells were induced to differentiate by culturing in differentiation medium (DMEM, 2% horse serum and 1% pen/strep) and processed for H3K27ac ChIP-seq.

first: Huating

first: Hao

first: Xianlu

middle: L

last: Peng

first: Karl

last: So

first: Liangqiang

last: He

first: Yu


title: RNA-seq analysis of ESR1 mutations in T47D and MCF7 cell lines

city: Pittsburgh

first: Amir

last: Bahreini

address: 204 Craft Ave A430

department: Human Genetics

institute: University of Pittsburgh

summary: Purpose: Transcriptome analysis of ESR1 mutant cells was performed via sequencing total RNA in T47D and MCF7 cell lines containing Y537S and D538G mutations.

overall_design: Methods: Individual ESR1 WT and mutant T47D and MCF7 clones were hormone deprived in CSS for three days, pooled, and plated in quadruplicates in 6-well plates. The cells were treated with veh or 1nM E2 for 24 hrs, RNA was isolated and subjected to sequencing. Differential expression analysis was performed by DEseq2 and R was used to conduct statistical analysis tests

first: Steffi

last: Oesterreich


title: Optimized Method for Robust Transcriptome Profiling of Minute Tissues Using Laser Capture Microdissection and Low-Input RNA-Seq

city: Roanoke

first: Shannon

last: Farris

state: VA

address: 2 Riverside Circle

department: Fralin Biomedical Research Institute

institute: Virginia Tech

summary:
Purpose: To determine the optimal RNA extraction and library generation protocols for mouse hippocampal tissue acquired by laser capture microdissection (LCM).
Methods: Hippocampal subregion CA2 was captured from eight micron fresh frozen brain sections from AMIGO2 EGFP mice. Total RNA was extracted using the PicoPure (LCM standard) and QIAGEN micro RNeasy RNA extraction kits. RNA quantity and quality was assessed using a Bioanalzyer. Resulting RNA was used to generate cDNA libraries using NuGEN or SMARTer low input RNA-Seq library kits. We compared the effects of RNA quality and library generation approach to determine the methods that detected the greatest number of genes/exons with even coverage using minimal rounds of PCR.
Results: We determined that the QIAGEN RNA extraction kit resulted in far superior RNA compared to the Picopure RNA extraction kit. We also found the NuGEN library generation kit that depletes ribosomal RNA towards the end of the protocol, led to higher cDNA library yields that required fewer rounds of PCR while providing even gene coverage and detection.

overall_design: RNA from laser-captured tissue from mouse hippocampus was extracted using two low input methods generating a lower quality RNA sample (RIN 7, PicoPure) and higher quality sample (RIN 9, QIAGEN). Each sample was used to prepare cDNA using two commerically available low-input library generation methods (Clontech or NuGEN). The effect of RNA quality and library generation method were compared. The effect of shearing cDNA and PCR amplification were also tested for libraries made with the QIAGEN extracted RNA and NuGEN library kits (3 libraries, 16, 18 or 20 cycles of PCR). The libraries were multiplexed and run on the Illumina NextSeq500 instrument.

first: James

last: Ward


title: PAPTRAP

city: St Louis

first: Joseph

last: Dougherty

state: Missouri

address: 4566 Scott Ave, box 8232

department: Genetics and Psychiatry

institute: Washington University

summary: We report the mRNAs bound to ribosomes in peripheral astrocyte processes, thus suggesting local translation in astrocytes.

overall_design: Isolation of a synaptoneurosome fraction from mouse cortex in which Astrocyte ribosomes were labeled with eGFP. Immunoprecipitation of GFP from this fraction to obtain astrocyte ribosomes away from the cell body. Performed RNA seq on these purified ribosomes and their bound mRNAs.

first: Kristina

last: Sakers

first: A

last: Lake

first: R

last: Khazanchi

last: Ouwenga

last: Vasek

last: Dani


title: JUN-Mediated downregulation of EGFR signaling is associated with resistance to gefitinib in EGFR-mutant NSCLC cell lines [ChIP-seq]

first: Vasu

last: Punj

summary: The Epidermal Growth Factor Receptor (EGFR) regulates a diverse set of biological processes including cell growth, proliferation, and differentiation.  Deregulation of the EGFR pathway has been implicated in a variety of human diseases including cancer.  Gefitinib and erlotinib are tyrosine kinase inhibitors (TKIs) that have demonstrated clinical benefit for patients with Non-small cell lung cancer (NSCLC) and EGFR activating mutations.  However, patients invariably acquire resistance to TKI treatment through a number of mechanisms.  We utilized in vitro models of NSCLC with EGFR activating mutations and derived three isogenic cell lines with acquired resistance to gefitinib. We next studied genomewide mRNA expression in resistance  and wild type cells  and their effect in the  reprogramming of  pathways in lung cancer cell line models..

overall_design: Genome wide study on the transcriptional binding profile with C-JUN in parental (HCC827) and EGFR-TKI (HCC827 ZDR3) resistance cells using a ChIP_seq.

first: Kian

last: Kani

first: Paymaneh

last: Malihi

first: Carolina

last: Garri

first: Anthony

last: Nguyen

first: Janet

last: Lee

first: Lindsey

last: Hughes

first: Damien

last: Wood

first: AY

last: Joo

first: Jonathan

last: Katz

first: David

middle: B

last: Agus

first: Parag

last: Mallick


title: Thyroid hormone receptor beta in the ventromedial hypothalamus is essential for the physiological regulation of food intake and body weight

status: Public on Jun 01 2017

city: Cambridge

first: Brian

middle: Yee Hong

last: Lam

address: Box 289 Addenbookes Hospital, Hills Road

department: Metabolic Research Laboratories

institute: University of Cambridge

summary: The obesity epidemic is a significant global health issue. Improved understanding of the mechanisms which regulate appetite and body weight will provide the rationale for the design of novel anti-obesity therapies. Thyroid hormones play a key role in metabolic homeostasis through their interaction with thyroid hormone receptors (TR) which function as ligand inducible transcription factors. The TR beta isoform (TRβ) is expressed in the ventromedial hypothalamus (VMH), a brain area important for control of energy homeostasis. Here we report that selective knock down of TRβ in the VMH of adult mice results in severe obesity due to hyperphagia and reduced energy expenditure. The observed increase in body weight is of a similar magnitude to murine models of the most extreme forms of monogenic obesity. These data identify TRβ in the VMH as a major physiological regulator of food intake and energy homeostasis.

overall_design: RNAseq analysis was performed using hypothalamic RNA from thyroid hormone receptor beta flox/flox mice stereotaxically injected with either a recombinant adeno-associated virus (rAAV) expressing a Cre-GFP fusion protein to generate mice with reduced thyroid hormone receptor beta (TRβ) expression in the ventromedial hypthalamus (VMH-TRβ-) mice, or controls injected with rAAV encoding GFP into the VMH (VMH-GFP).

first: Saira

last: Hameed

first: Michael

last: Patterson

first: Waljit

last: Dhillo

first: Sofia

last: Rahman

first: Yue

last: Ma

first: Christopher

last: Holton

first: Apostolos

last: Gogakos

first: Giles

last: Yeo

last: Polex-Wolf

first: Wiebke

last: Fenske

first: Jimmy

last: Bell

first: Jelena

last: Anastasovska

first: Jacques

last: Samarut

first: Stephen

last: Bloom

first: J

last: Bassett

first: Graham

last: Williams

first: James

last: Gardiner


title: JUN-Mediated downregulation of EGFR signaling is associated with resistance to gefitinib in EGFR-mutant NSCLC cell lines [RNA-seq]

first: Vasu

last: Punj

overall_design: Differntial expresssion profile of transcripts of  parental (HCC827) and EGFR-TKI (HCC827 ZDR3) resistance cells

first: Kian

last: Kani

first: Paymaneh

last: Malihi

first: Carolina

last: Garri

first: Anthony

last: Nguyen

first: Janet

last: Lee

first: Lindsey

last: Hughes

first: Damien

last: Wood

first: AY

last: Joo

first: Jonathan

middle: E

last: Katz

first: David

last: Agus

first: Parag

last: Mallick


title: AKHR F1 heterozygous progeny of obese parents and controls, 10-11 days old adults

city: SALT LAKE CITY

first: Carl

last: Thummel

state: UT

institute: University of Utah School of Medicine

summary: Transgenerational effects of parental metabolic state have been shown, but the mechanism is still unclear. Here we present transcriptome sequencing data from AKHR heterozygous F1 progeny, either from obese maternal or paternal parents, compared to genetically matched heterozygous controls or to wild-type controls

overall_design: 3 AKHR heterozygous samples descended from obese maternal parents, 3 AKHR heterozygous samples descended from obese paternal parents, 3 AKHR heterozygous samples descended from non-obese parents, and 3 wild-type controls, independent biological replicates and independent experimental replicates (1 set of samples from each experimental replicate)

first: Rebecca

middle: A

last: Palu

first: Sophia

last: Praggastis


title: Selective inhibition of EZH2 by a small molecule inhibitor regulates microglia gene expression essential for inflammation

city: Ansan

first: Young Gyu

last: Chai

state: Gyeonggi-do

address: 55 Hanyangdaehak-ro

department: Molecualr & Life Science

country: South Korea

institute: Hanyang Univ.

summary: Impressive studies have been well documented that Enhancer of zeste homolog 2 (EZH2) could have a role in inflammation as well as a wide range of malignancies; however, the underlying mechanisms remain largely unaddressed. Microglial activation is a key process in the production and release of numerous pro-inflammatory mediators that plays an important role in central nervous system (CNS) inflammation and neurodegeneration. Therefore, our aim was to investigate whether inhibition of EZH2 with selective small molecule inhibitors EPZ-6438 protects against neonatal microglia activation. First, we find that BV-2 microglia, LPS can rapidly increase EZH2 mRNA level and subsequently we performed gene expression profiles and networks in resting, EPZ-6438, LPS and LPS+EPZ-6438 challenged BV-2 microglia by transcriptome RNA sequencing and bioinformatic analyses. By examining RNA sequencing we identified EPZ-6438 target genes and co-regulated modules that were critical in inflammation. We also identified unexpected relationships between the inducible transcription factors (TFs), motif strength, and the transcription of key inflammatory mediators. Furthermore, we showed that EPZ-6438 controls important inflammatory genes targets by modulating interferon regulatory factor (IRF) 1, IRF8, Signal transducer and activator of transcription (STAT) 1 levels at their promoter site. Our unprecedented findings demonstrate that pharmacological interventions built upon EZH2 inhibition by EPZ-6438 could be a useful therapeutic application in neuroinflammatory diseases associated with microglia activation.

first: Young

first: Jin


title: Small RNA Sequencing analysis in Macrophages

city: New Haven

first: Yajaira

last: Suarez

state: Connecticut

address: 10 Amistad Street

department: Comparative Medicine

institute: Yale University School of Medicine

type: Non-coding RNA profiling by high throughput sequencing

summary: Analysis of miRNA  content of Bone Marrow derived macrophages in resting non-activated conditions

overall_design: Total RNA isolated from Bone Marrow derived macrophages in resting non-activated conditions


title: Malaria Host Pathogen Interaction Center Experiment 04: Host and parasite gene transcript abundances, from whole blood, of Macaca mulatta infected Plasmodium cynomolgi treated with artemether over 7 time points in a 100 day study

city: Atlanta

first: Mary

last: Galinski

state: GA

address: 954 Gatewood Road

department: Vaccine Center at Yerkes

institute: Emory University

summary: This project is part of the Malaria Host-Pathogen Interaction Center (MaHPIC) - a transdisciplinary malaria systems biology research program initially supported by an NIH/NIAID contract (# HHSN272201200031C, 2012-2017; see http://www.systemsbiology.emory.edu). The MaHPIC continues with ongoing support from the Defense Advanced Research Project Agency (DARPA) and others. The MaHPIC generates many data types (e.g., clinical, hematological, parasitological, metabolomics, functional genomics, lipidomics, proteomics, immune response, telemetry) and mathematical models, to iteratively test and develop hypotheses related to the complex host-parasite dynamics in the course of malaria in non-human primates (NHPs), and metabolomics data via collaborations with investigators conducting clinical studies in malaria endemic countries, with the overarching goal of better understanding human disease, pathogenesis, and immunity. Curation and maintenance of all data and metadata are the responsibility of the MaHPIC:  Mary Galinski mary.galinski@emory.edu (MaHPIC Program Director), Jessica Kissinger jkissinger@uga.edu (MaHPIC Co-Program Director), and Alberto Moreno alberto.moreno@emory.edu (MaHPIC Co-Program Director).

sample_organism:
Macaca mulatta
Plasmodium cynomolgi strain B

overall_design: Malaria-naive male rhesus macaques (Macaca mulatta), approximately three years of age, were inoculated intravenously with salivary gland sporozoites isolated at the Centers for Disease Control and Prevention from multiple Anopheles species (An. dirus, An. gambiae, and An. stephensi) and then profiled for parasitological, clinical, immunological, functional genomic, lipidomic, proteomic, and metabolomic measurements. The experiment was designed for 100 days, and pre- and post-100 day periods to prepare subjects and administer curative treatments respectively. The anti-malarial drug artemether was subcuratively administered to three subjects during the primary parasitemia to suppress clinical complications and to all animals for curative treatment of blood-stage infections to allow detection of relapses. One subject was euthanized during the 100-day experimental period due to clinical complications of malaria. The anti-malarial drugs chloroquine and primaquine were administered to all remaining subjects at the end of the study for curative treatment of the liver- and blood-stage infections, respectively. Plasma samples were acquired every other day from capillary blood and at seven-time points from venous blood.  The seven-time point collections were used to generate these results.  This dataset was generated from whole blood samples from 5 individuals collected 7 times over the 100-day experiment. Since one animal was euthanized after time point 3 (meaning 4 potential samples were not collected from this animal, 2 samples failed library preparation, and one sample was collected from a blood transfusion donor animal, a total of 30 samples were collected.  The experimental design and protocols for this study were approved by the Emory University Institutional Animal Care and Use Committee (IACUC).  These results are a product of a consortium of researchers known as the Malaria Host Pathogen Interaction Center (MaHPIC).  For more information on the MaHPIC, please visit http://www.systemsbiology.emory.edu/ .  Within the MaHPIC, these data were collected as part of 'Experiment 04' (E04).  To access other publicly available results from E04 and other MaHPIC Experiments, including clinical results (specifics on drugs administered, diet, and veterinary interventions), and other omics data sets, please visit http://plasmodb.org/plasmo/mahpic.jsp .

first: Dalia

last: Arafat

first: Steve

last: Bosinger

first: Monica

last: Cabrera

first: Jeremy

last: DeBarry

first: Swetha

last: Garimalla

first: Jay

last: Humphrey

first: Ebru

last: Karpuzoglu

first: Jessica

last: Kissinger

first: Stacey

last: Lapp

first: Kevin

first: Regina

last: Joice

first: Chet

last: Joyner

first: Esmeralda

last: Meyer

first: Alberto

last: Moreno

first: Vishal

last: Nayak

first: Mustafa

last: Nural

first: Suman

last: Pakala

first: Nirav

last: Patel

first: Yan

last: Tang

first: Greg

last: Tharp


title: F2 progeny of AKHR mutant and obese parents and controls, 10-11 days old adults

first: Carl

last: Thummel

summary: Transgenerational effects of parental metabolic state have been shown, but the mechanism is still unclear. Here we present transcriptome sequencing data from the F2 progeny of obese maternal or paternal grandfathers compared to genetically matched wild-type controls

overall_design: 3 samples descended from obese grandfathers through the maternal F1, 3 samples descended from obese grandfathers through the paternal F1, and 3 wild-type controls, independent biological replicates and independent experimental replicates (1 set of samples from each experimental replicate)

first: Rebecca

last: Palu

first: Sophia

last: Praggastis

middle: S


title: Genome-wide binding of condesin upon SET1 knockdown

city: Kansas City

first: Jennifer

last: Gerton

address: 1000 E. 50th Street

institute: Stowers Institute for Medical Research

summary: We reported the effect of condensin binding to the genome upon SET1 knockdown. ChIP-seq experiments of condensin (NCAPH2) were performed in control and SET1 knockdown cells.  We found that condensin binding was significantly reduced upon SET1 knockdown.

overall_design: To study the role of SET1 on condensin binding

first: Kobe

last: Yuen


title: RNA-Sequencing of Regenerating Lacrimal Glands

city: Boston

first: Driss

last: Zoukhri

state: MA

address: 1 Kneeland st. DHS635

department: Comprehensive Care

institute: Tufts University

summary: The purpose of the present studies was to use CyTOF and RNA-Seq technologies to identify cells and genes involved in lacrimal gland repair that could be targeted to treat diseases of lacrimal gland dysfunction. Lacrimal glands of female BALB/c mice were experimentally injured by intra-glandular injection of interleukin 1 alpha (IL-1α). The lacrimal glands were harvested at various time points following injury (1 to 14 days) and used to either prepare single cell suspensions for CyTOF immuno-phenotyping analyses or to extract RNA for gene expression studies using RNA-Seq.  CyTOF immuno-phenotyping identified monocytes and neutrophils as the major infiltrating populations 1 and 2 days post injury.  Clustering of significantly differentially expressed genes identified 13 distinct molecular signatures: 3 associated with immune/inflammatory processes included genes up-regulated at days 1-2 and 3 associated with reparative processes with genes up-regulated primarily between days 4 and 5.  Finally, clustering identified 65 genes which were specifically up-regulated 2 days post injury which was enriched for muscle specific genes. The expression of select muscle-related proteins was confirmed by immunohistochemistry which identified a subset of cells expressing these proteins. Double staining experiments showed that these cells are distinct from the myoepithelial cells. We conclude that experimentally induced injury to the lacrimal gland leads to massive infiltration by neutrophils and monocytes which resolved after 3 days. RNAseq and immunohistochemistry identified a group of cells, other than myoepithelial cells, that express muscle-related proteins that could play an important role in lacrimal gland repair.

overall_design: RNA-Seq profiles were generated from 1, 2, 3, 4, 5, 7, and 14 days post IL-1α injury, 14 days post saline injection, and untreated lacrimal glands.  Each experimental group was performed in triplicate.

first: Dillon

last: Hawley

first: Jian

last: Ding

first: Suharika

last: Thotakura

first: Scott

last: Haskett

first: Hema

last: Aluri

first: Claire

last: Kublin

first: Audrey

last: Michel

first: Lisa

last: Clapisson

first: Michael

last: Mingueneau


title: A damaged genome's transcriptional landscape through multilayered expression profiling around in situ-mapped DNA double-strand breaks

city: Milan

first: Fabrizio

last: d'Adda di Fagagna

state: Mi

address: Via Adamello 16

country: Italy

institute: IFOM - The FIRC Institute of Molecular Oncology

summary:
Background: Of the many types of DNA damage, DNA double-strand breaks (DSB) are probably the most deleterious. Mounting evidence points to an intricate relationship between DSBs and transcription. A cell system in which the impact on transcription can be investigated at precisely mapped genomic DSBs is essential to study this relationship.
Methods: Here in a human cell line, we map genome-wide and at high-resolution the DSBs induced by a restriction enzyme and we characterize their impact on gene expression by four independent approaches by monitoring steady-state RNA levels, rates of RNA synthesis, transcription initiation and RNA polymerase II elongation.
Results: We consistently observe transcriptional repression in proximity to DSBs. Downregulation of transcription depends on ATM kinase activity and it is sensitive to the distance from the DSB.
Conclusions: Our study couples for the first time high-resolution mapping of DSBs with multilayered transcriptomics to dissect the events shaping gene expression after DSB induction at multiple endogenous sites.

overall_design:
BLISS (Breaks Labeling In Situ and Sequencing), 1 replicate per condition, 2 conditions (Induced and Uninduced)
gamma-H2AX ChIP-seq, 1 replicate per condition, 2 conditions (Induced and Uninduced)
RNA-seq, 1 replicate per condition, 2 conditions (Induced and Uninduced)
RNA-seq of DMSO-treated or ATMi-treated samples, 1 replicate per condition and per treatment, 2 conditions (Induced and Uninduced), 2 treatments (DMSO and ATMi)
Bru-seq (metabolic pulse-labeling of RNA with bromouridine followed by sequencing), 4 different time points after AsiSI induction, 1 replicate per condition, 2 conditions (Induced and Uninduced)
CAGE (cap-analysis of gene expression) , 1 replicate per condition, 2 conditions (Induced and Uninduced)
Total RNAPII ChIP-seq (CTD4H8), 1 replicate per condition, 2 conditions (Induced and Uninduced)
Elongating RNAPII ChIP-seq (Ser 2), 1 replicate per condition, 2 conditions (Induced and Uninduced)

first: Fabio

last: Iannelli

first: Alessandro

last: Galbiati

first: Ilaria

last: Capozzo

first: Quan

last: Nguyen

first: Brian

last: Magnuson

first: Flavia

last: Michelini

first: Giuseppina

last: D'Alessandro

first: Matteo

last: Cabrini

first: Marco

last: Roncador

first: Sofia

last: Francia

first: Nicola

last: Crosetto

first: Mats

last: Ljungman

first: Piero

last: Carninci


title: Auxin regulates functional gene groups in a fold-specific manner in Arabidopsis root

city: Novosibirsk

first: Daniil

last: Wiebe

address: Lavrentyeva 10

country: Russia

institute: ICG SBRAS

summary:
Auxin plays a pivotal role in virtually every aspect of plant morphogenesis. It simultaneously orchestrates a wide variety of processes, including cell wall biogenesis, transition through the cell cycle, and metabolism of a wide range of chemical substances, among others. The coordination principles for such complex regulation in a cell at a system level are poorly understood.
Here, we apply a whole-genome approach to estimate the coherence of the auxin-regulated transcriptional response in gene groups, united by a certain biological process, molecular function or cell component, based on the fold change of the expression level.
The corresponding analysis of RNA-Seq data for Arabidopsis roots treated with auxin for 6 h revealed that the intervals for the fold change of gene expression levels are quite narrow for many functional gene groups. The fold-specific manner of auxin response in most of these groups was confirmed using independent microarray data. To predict the mechanisms underlying such a coordinated expression, we performed motif enrichment analysis, which revealed TBX1-3, SBX, REG and TCP/site 2 as the candidates associated with fold-specific responses to auxin.

overall_design: mRNA profiles of 3 dag wild type (WT) and 6h IAA treated Arabidopsis roots were generated by RNA sequencing, in triplicate, using AB SOLiD technology

first: Nadya

last: Omelyanchuk

first: Victoria

middle: V

last: Mironova

first: Gennadii

last: Vasiliev


title: C/EBPepsilon ChIP-sequencing of C57BL/6 mice bone marrow cells

city: St. John's

first: Touati

last: Benoukraf

state: NL

address: Craig L. Dobbin Genetics Research Centre,

department: Faculty of Medicine, Division of BioMedical Sciences

country: Canada

institute: Memorial University of Newfoundland

summary: To characterize the genome wide C/EBPepsilon binding sites, ChIP-sequencing with C57BL/6 mice bone marrow cells were performed. To prevent artifact from PCR amplifiation, sequencing or antibody specificity, two controls of input DNA and ChIP-sequencing of C/EBPepsilon knock-out bone marrow cells were used. Two data sets derived from two anti-C/EBPepsilon antibodies, N-terminal (GTX109155) and C-terminal (SC-158) antibody against wild type and C/EBPepsilon knock-out bone marrow cells were generated.

overall_design: Two C terminal and N terminal antibodies against C/EBPepsilon on C57BL/6 wild type and C/EBPepsilon knock-out mice bone marrow cells

first: Hyung

last: Suh

first: Tong

last: Yin

first: Qi

last: Cao

first: Jonathan

last: Said

first: Stephen

last: Lee

first: Ricky

last: Lim

first: Henry

last: Yang

first: Pavithra

last: Shyamsunder

first: Vikas

last: Madan

first: H

middle: P

last: Koeffler


title: Whole brain gene expression in Lake Malawi cichlid F1 hybrids

city: Stanford

first: Ryan

last: York

address: 371 Serra Mall

institute: Stanford University

summary: Most behaviors are associated with heritable genetic variation. Genetic mapping has revealed genomic regions or, in a few cases, specific genes explaining part of this variation. However, understanding how genetic divergence shapes behavioral evolution remains unclear. Here we analyze the evolution of an innate extended phenotype: bower building among male cichlid fish of Lake Malawi, which build bowers of two types, pits and castles.  F1 hybrids of pit-digging and castle-building species perform sequential construction of first pit and then castle bowers. Analysis of brain gene expression in these hybrids showed that genes near behavior-associated variants display behavior-dependent allele-specific expression with preferential expression of the pit-species allele during pit digging, and of the castle-species allele during castle building. These genes are highly enriched for functions and pathways involved in neurodevelopment and neural plasticity. Our results suggest that natural behaviors can be associated with complex genetic architectures that alter behavior via cis-regulatory differences whose effects on gene expression are specific to the behavior itself.

sample_organism: Copadichromis virginalis x Mchenga conophoros

overall_design: F1 hybrids of the species Mchenga conophoros (castle builder) and Copadichromis virginalis (pit digger) were produced and run through three independent behavioral paradigms targetting: pit-digging behavior, castle-building behavior, and social isolation. Whole brains were extracted and processed for analyses of allele-specific expression using RNA-seq.

first: R


title: A Comprehensive Roadmap of the Mammalian Ribo-interactome Connects Metabolism Enzymes with Specialized ER-Ribosomes

first: Gerald

last: Tiu

state: California

address: 279 Campus Dr., Beckman Center B309

summary: The ribosome has considerably increased in size during metazoan evolution in the form of an RNA shell that could serve as a platform for yet unknown protein interactions. Here, we have comprehensively identified the mammalian ‘ribo-interactome’ by establishing a ribosome affinity purification method. Our findings reveal a multitude of novel ribosome interacting factors, encompassing unanticipated functional categories including energy metabolism, cell redox homeostasis, as well as key protein and RNA modifying enzymes. These findings led us to characterize ufmylation, a novel posttranslational modification on ribosomes, and define its substrates. We further show that pyruvate kinase, a key enzyme for stem cell and cancer metabolism, is an RNA binding protein that unexpectedly interacts with specialized sub-pools of ribosomes at the endoplasmic reticulum (ER) and coordinates the localization and translation of ER destined mRNAs. Collectively, these studies uncover that the ribo-interactome imbues a new layer of regulatory potential in translating the genome.

overall_design: Examination of ribosome footprints and RNA expression in mESCs upon PKM knockdown and of PKM RNA binding in mESCs

first: Deniz

last: Simsek

last: Flynn

first: Gun

middle: W

last: Byeon

first: Kathrin

last: Leppek

first: Adele

middle: F

last: Xu

first: Howard

middle: Y

last: Chang

first: Maria

last: Barna


title: Alternative cleavage and polyadenylation analysis in an isoform-resolved way by Second- and Third-Generation Sequencing technologies

city: Ann Arbor

first: Kin Fai

last: Au

state: MI

address: 100 Washtenaw Avenue

department: Department of Computational Medicine and Bioinformatics

institute: University of Michigan

summary: Alternative cleavage and polyadenylation (APA) is emerging as an important mechanism of gene regulation in eukaryotes and plays important regulatory roles in human development and diseases. Despite the widespread application of Second Generation Sequencing (SGS) technology for polyadenylation site identification, matching each identified polyadenylation site within a gene to its derived isoform remains a major challenge. To achieve the isoform-resolved APA analysis, we developed a tool termed “IDP-APA” that constructs truly expressed isoforms and identifies polyadenylation sites by integrating the respective strengths of Third Generation Sequencing (TGS) long reads and SGS short reads. Compared to existing tools, IDP-APA demonstrated superior performance in both isoform reconstruction and polyadenylation site identification. Applications to human embryonic stem cells, breast cancer cells and brain tissue from a patient with Alzheimer’s disease revealed prevalent APA events and cell-/tissue-specific APA patterns, especially in an isoform-resolved way.

overall_design: Construct expressed isoform and analyze APA events in two human samples with TGS (PacBio) long read and SGS (Illumina) short read data: human embryonic stem cells (H1 cell line, H1-hESC) and brain tissue from a patient with Alzheimer’s disease (Brain-AD).

first: Yunhao

last: Wang

first: Xiu-Jie

first: Kin-Fai


title: Salicylic acid-dependent and -independent transcriptome changes in response to methyl-erythritol cyclodiphosphate accumulation

city: Botanical Garden

first: Marta

last: Bjornson

state: Zurich

address: Zollikerstrasse 107

country: Switzerland

institute: University of Zurich (UZH, Switzerland)

summary: MEcPP overaccumulation in the ceh1 mutant results in significant transcriptome changes as reported by microarrays, of which some are dependent on the SA accumulation in this mutant. In order to gain better resolution of transcriptomic changes in ceh1 as well as the SA dependence of these changes, we performed RNAseq analysis of RNA extracted from wt, ceh1, eds16 deficient in SA production, and ceh1/eds16

overall_design: Three biological replicates each of Col-0 (=p, =wt), ceh1, eds16, ceh1/eds16

first: Bjornson

last: Marta

first: Dehesh

last: Katayoon


title: Landscape of CEBPe target genes in mouse bone marrow

first: Touati

last: Benoukraf

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

overall_design: Refer to individual Series


title: Transcriptomic analysis of depleted uranium effects on adult zebrafish and progeny

city: Saint Paul lez Durance

first: olivier

last: ARMANT

address: Cadarache BP3

department: SERIS

institute: IRSN

summary: This dataset describe the transcriptomic profiling of adult brain, gonades (testis and ovaries) of adult zebrafish exposed to 20µg/L of depleted uranium for 10 days. The progeny of the exposed fishes were also analysed at two-cells stage and 96 hours post fertilization

overall_design: Biological samples (adult dissected tissues and whole embryos and larvae) were tested by RNASeq in duplicates

first: Olivier

last: Armant


title: Wt anti neutrophils with L34

city: Madrid

first: Fatima

last: Sanchez-Cabo

address: Melchor Fernandez Almagro

institute: CNIC

summary: We postulate here that the changes induced by the deletion in neutrophils are similar to the changes that appear in mice lacking p38g/d in the myeloid cell

overall_design: Transcriptome analysis of Lyzs cre mice fed with MCD, Lyzs p38g/d KO fed with MCD, and  Lyzs cre mice treated with ab against Ly6G fed with MCD

first: Guadalupe

last: Sabio


title: Innate versus adaptive lymphoid cell fate choice is controlled by the E-Id protein axis [ATAC-Seq]

city: Kyoto

first: Kazuko

last: Miyazaki

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

country: Japan

institute: Institute for Life and Medical Sciences, Kyoto University

summary: The lymphoid branch of the immune defense is composed of innate and adaptive immune cells. Using multiple genetic strategies we demonstrate that in the thymus E2A and HEB act in synergy to establish T cell identity and to suppress the aberrant development of innate lymphoid cells that include ILC2 and LTi-like cells.  We found that E2A and HEB induce T cell fate by activating the expression of an ensemble of genes encoding for proteins associated with Notch- and pre-TCR signaling and to promote TCRβ antigen receptor assembly. We show that E2A and HEB act in early T progenitors (ETPs) to establish and maintain a T-lineage specific enhancer repertoire, including regulatory elements associated with the Notch1/3 and Rag1/2 gene loci. Based on these and previous observations we propose that the E-Id protein axis specifies innate versus adaptive lymphoid cell fate.

overall_design: Examination of transcriptome and open chromatin regions in wild-type and E2Afl/flHEBfl/flIL7RCre ETPs by RNA-seq and ATAC-seq.

first: Masaki

first: Yin

last: Lin

first: Cornelis

last: Murre


title: Innate versus adaptive lymphoid cell fate choice is controlled by the E-Id protein axis


title: Innate versus adaptive lymphoid cell fate choice is controlled by the E-Id protein axis [RNA-Seq]


title: mRNA Profiling of miR-17 family inhibition using TuD lentiviral vector in HepG2 and SK-Hep1 hepatocellular carcinoma cell lines [RNA-Seq]

city: San Diego

first: Vivek

last: Kaimal

state: CA

address: 10614 Science Center Dr.

department: Bioinformatics

institute: Regulus Therapeutics

summary: To functionally characterize the role of miR-17 family in HCC, lentiviral vector-based miR inhibitor TuD was used to inhibit miR-17 family of microRNAs in HepG2 and SK-Hep1 HCC cell lines

overall_design: Methods: HepG2 and SK-Hep1 HCC cell lines were acquired from American Type Culture Collection (ATCC) and miR-17 TuD or NC TuD expressing lines were generated. mRNA profiling of miR-17 TuD or NC TuD expressing samples was performed using Illumina NGS. Total RNA was extracted as per manufacturer’s instructions (RNeasy kit, Qiagen). RNA quality was assessed using BioAnalyzer (Agilent). mRNA expression profiles were determined using next-generation sequencing (NGS) on the Illumina HiSeq 2000 platform producing 50bp paired-end reads. Bowtie/TopHat suites were used to align the reads to mouse genome or transcriptome and RSEM were used to quantify gene abundances. Gene level counts were then normalized with the R/Bioconductor package limma using the voom/variance stabilization method.

first: Xinqiang

last: Huang

first: Adam

last: Pavlicek


title: RNA-seq analysis of genes regulated by S5 at different development stages

city: shenzhen

first: yiming

last: yu

state: --- Select a state ---

address: 1088 Xueyuan Avenue

institute: Southern University of Science and Technology

summary: Hybrid sterility is a major form of postzygotic reproductive isolation, which is a widespread phenomenon in plants. Hybrids between two subspecies of the Asian cultivated rice (Oryza sativa L.), indica and japonica, are usually highly sterile. A killer-protector system composed of three closely linked genes, ORF3, ORF4 and ORF5 at the S5 locus, has been unveiled to regulate hybrid female fertility. We performed transcriptomic analysis of wild type Balilla, sterile BalillaORF5+ (Balilla with a transformed ORF5+) and  fertility-restored BalillaORF3+ORF5+ (Balilla with a transformed ORF3+ and a transformed ORF5+) at S1 (before meiosis), S2 (during meiosis) and S3 (after meiosis) respectively. By comparing the differentially expressed genes in different comparisons, we proposed a model for the mechanisms of the S5 mediated hybrid sterility.

overall_design: Transcriptome of two replicates of Balilla, BalillaORF5+  and BalillaORF3+ORF5+ at S1, S2, and S3 stages were collected, respectively. Differentially expressed genes in BalillaORF5+ vs. Balilla and BalillaORF3+ORF5+ vs. Balilla were analyzed further.

first: Yanfen

last: Zhu

first: Qifa

last: Zhang


title: Genome-wide microRNA transcriptome profiles in Control and Schizophrenia hiPSC-dervied NPC [miRNA-seq]

city: Buffalo

first: Michal

last: Stachowiak

state: NY

address: 3435 Main Street

department: Pathology and Anathomical Sciences

institute: State University of New York at Buffalo

summary: We Report the genome-wide RNA expression levels in control and schizophrenia hiPSC dervied NPC treated with neuronal media for 2 days.  In total, 440 microRNA expression were detected in all samples, of which 16 were dysregualted.

overall_design: Examination, identification and comparision of microRNA expression profliles in control and schizophrenia npc

middle: K


title: Lipid Nanoparticle-Mediated Delivery of Anti-miR-17 Family Oligonucleotide Suppresses Hepatocellular Carcinoma Growth


title: Transcriptome profiling of Dmrta2 KO neural progenitor cells derived from mouse embryonic stem cells (mESCs)

city: Cardiff

first: Fraser

last: Young

address: Maindy Road

department: Neuroscience and Mental Health Research Institute

institute: Cardiff University

summary: The goal of this study was to use RNAseq to identify genes that are differentially expressed by cortical neural progenitor cells upon loss of Dmrta2. Datasets were gathered from two separate mESC lines, Dmrta2-/- and a control Dmrta2-flox/flox

overall_design: Three biological replicates samples were sequenced for each mESC line. The Dmrta2-flox/flox dataset was used as a control.

first: Xinsheng

first: Nicole

last: Gennet

first: Meng

last: Li


title: Ly6C high monocytes and their macrophage descendants regulate neutrophil function and clearance in acetaminophen-induced liver injury

city: REHOVOT

first: Steffen

last: Jung

address: Herzl

department: Immunology and Regenerative Biology

country: Israel

institute: The Weizmann Institute of Science

summary: Monocyte-derived macrophages play a pivotal role in the resolution of Acetaminophen-Induced Liver Injury (AILI). Timely termination of neutrophil activity and their clearance are essential for liver regeneration following injury. Here, we show that infiltrating Ly6Chi monocytes, their macrophage descendants, and neutrophils spatially and temporally overlap in the centrilobular necrotic areas during the necro-inflammatory and resolution phases of AILI. We utilized MC-21 anti mouse CCR2 to induce the ablation of circulating Ly6Chi monocytes.  RNA sequencing-based profiling of neutrophils from Ly6Chi monocyte-deficient(MC-21 treated mice) versus normal livers (PBS-treated mice) revealed 449 genes that were differentially expressed with at least two-fold change (p ≤ 0.05). Nutrophils from monocyte-ablated livers exhibited decreased expression of NADPH Oxidase 2.  Moreover, in the absence of Ly6Chi monocytes, neutrophils exhibited an altered transcriptomic profile associated with reduced innate activity concomitantly with increased cell survival.Collectively, our findings reveal that liver-infiltrating Ly6Chi monocytes regulating neutrophil activity and survival following AILI.

overall_design: Neutrophils (defined as Ly6G+CD11b+Ly6Clo cells) were sorted at 24h following AILI from normal livers (n=4) or livers that are deficient for Ly6Chi infiltrating monocytes (n=3). RNA-seq based transcriptomicn profiling was performed to deliniate the effect of monocyte deficiency on nuetrophil activity and survival.

first: Chen

last: Varol


title: Transcriptome analysis of Cdc73 deletion in AML cells

city: Indianapolis

first: James

last: Ropa

state: IN

address: 950 W Walnut St

institute: Indiana University

summary: The Polymerase Associated Factor (PAFc) complex is an epigenetic regulating complex that has been shown to to be important for Acute Myeloid Leukemias harboring an MLL chromosomal translocations, such as MLL-AF9 leukemias. This study describes the transcriptomic profiling of AML cells following genetic deletion of the PAFc subunit Cdc73.

overall_design: Cdc73floxed cells were transformed to an AML using MLL-AF9 oncogene transduction. The cells were also transduced with a 4OHT inducible CreER. The cells were then treated for 24 or 48 hours with 4OHT to induce genetic excision of Cdc73 and polyA mRNA was isolated for sequencing of the transcriptome. Biological duplicates are labelled _1 and _2.

first: Andrew

middle: G

last: Muntean


title: RNA sequencing of LSK cells from mice with JAK2 mutation and HMGA2 expression

city: Fukushima

first: Kazuhiko

last: Ikeda

state: Fukushima

address: 1 Hikariga-oka

department: Blood Transfusion and Transplantation Immunology

institute: Fukushima Medical University

summary: Either loss of EZH2 or redcuction of let-7 induces  expression of HMGA2 and provokes severe myelofibrosis in mice carrying JAK2V617F. Therefore we compared gene expression profiles of LSK cells among WT mice,  Hmga2-Tg mice, JAK2V617F-Tg mice, JAK2V617F/Hmga2 double-Tg mice, and JAK2V617F-Tg/EZH2 conditional KO mice.

overall_design: LSK cells sorted from 4-5 mice in each type.

first: Ueda

last: Koki

first: Ikeda

last: Kazuhiko

first: Oshima

last: Motohiko

first: Iwama

last: Atsushi


title: Non-coding RNAs and DNA methylation synergistically regulate neural fate determination from rhesus monkey embryonic stem cell

first: Guanyu

last: Ji

state: GuangDong

address: 14th of middle jinxiu road

department: R&D

institute: GENEDOHEALTH

type: Methylation profiling by high throughput sequencing

summary: Rosette neural stem cells (R-NSCs) represent early stage of neural development and possess full neural differentiation and regionalization capacities. R-NSCs are considered as stem cells of neural lineage and have important implications in study of neurogenesis and cell replacement therapy. However, the molecules regulating their functional properties remain largely unknown. Rhesus monkey is ideal model to study human neural degenerative diseases and plays intermediate translational roles as therapeutic strategies evolve from rodent systems to human clinical applications.   In this study, we describe the interactions of DNA methylation, mRNA and ncRNAs (miRNA and lncRNAs) during neural differention from ESCs. We show that DNA methylation, mRNAs and ncRNAs may together act as genetic switches or fine-tuners to ensure nerural fate determination upon proper stimuli.

overall_design: Whole genome MeDIP-seq and lncRNA-seq of rhesus monkey

first: Tao

last: Tan


title: RNA-seq experiments from Saccharomyces cerevisiae overexpressing ubiquitin-related protein Hub1

city: Martinsried

first: Sittinan

last: Chanarat

address: Am Klopferspitz 18

country: Germany

institute: MPI biochemistry

summary: We report introns more efficiently spliced in cells overexpressing ubiquitin-related protein Hub1

overall_design: Yeast RNA profiles of wild-type HUB1 and HUB1-overexpressing haploid cells deficient in RNA surveillance pathway were generated by deep sequencing, in triplicate, using Illumina HiSeq 2500 system.

first: Ramazan

last: Karaduman

first: Boris

last: Pfander

first: Stefan

last: Jentsch


title: Dynamics of the transcriptome and methylome during the regeneration of rice

city: Taipei

first: Moloya

last: Gohain

state: Taipei

address: 128, SEC.2 ACADEMIA ROAD, NANGANG DISTRICT

department: INSTITUTE OF PLANT AND MICROBIAL BIOLOGY

country: Taiwan

institute: ACADEMIA SINICA

summary: Tissue culture is used to establish desired phenotypes in plants. Callus culture and regeneration are critical steps in this process. Calli of Oryza sativa japonica (cv. TNG67) and Oryza sativa indica (cv. IR64) have varying regeneration efficiencies. Genetic diversity could partly account for such differences but the epigenetic response to different cell culture environment could also play a role. We aimed to study the role of DNA methylation during the tissue culture process in determining its outcome.

sample_organism:
Oryza sativa Indica Group
Oryza sativa Japonica Group

overall_design: We studied the transcriptomes (RNA-seq) and methylomes (BS-seq) of TNG67 and IR64 rice in comparisons between the embryonic stage (T0) versus 1. callus induced (T1) 2. callus sub-cultured (T2) 3. failed (TF) and 4. successfully (TS) regenerated calli. The transcription data of IR64 during these stages are represented as I0, I1, I2 IS and IF ad of TNG67 are represented as J0, J1,J2,JS and JF.The methylome data of IR64 during the different stages are represented as i0. i1, i2, iS and iF while TNG67 methylome data at different stages of tissue culture is termed as j0, j1, j2, jS and jF. I0, i0, J0 and j0 correspond to T0; I1, i1, J1 and j1 correspond to T1; I2,i2,J2 and j2 correspond to T2; IS,iS, jS and jS correspond to TS and IF, iF, JF, jF correspond to TF.

first: Fei-Man

last: Hsu

first: Kshitij

last: Tandon

first: Archana

last: Allishe

first: Lin-Yun

last: Kuang

first: Yue-Le

last: Hsing

first: Pao-Yang

last: Chen


title: Whole transcriptome analysis of diaphragms from FKRPP448L-NSG and NSG mice induced by swimming exercise

city: Minneapolis

first: Alessandro

last: Magli

state: MN

address: 2231 6th St SE

department: Medicine

country: USA

institute: University of Minnesota

summary: Muscle pre-injury is commonly used prior to cell transplantation to enhance engraftment and to further promote homing of injected cells to diseased muscles. To better understand the changes that occurred in the diaphragm upon swimming (1hour/day for 2 weeks), we analyzed global changes using RNA-Seq in dystrophic FKRPP448L-NSG mice as well as in NSG control mice.

overall_design: Diaphragm mRNA profiles of 8-10 week old  FKRPP448L-NSG and NSG mice were generated by deep sequencing, in triplicate.

first: Rita

last: Perlingeiro


title: Genome wide impact of loss of mechanoluminal stimulation on neonatal intestine

city: Los Angeles

first: Tracy

last: Grikscheit

address: 4650 Sunset Boulevard Mailstop#100

institute: Children's Hospital Los Angeles

summary:
Purpose: Surgical treatment of congenital and neonatal intestinal diseases often requires resection of intestine and/or diverstion of luminal flow. Subsequent growth on enteral nutrition alone depends on adaptation of the remaining bowel. The role of mechanoluminal stimulation in driving intestinal adaptation and the effects of depriving the intestine of mechanoluminal stimulation are unknown.
Methods: 5 pairs of intestine from neonatal surgical patients were obtained at ileostomy reversal. The proximal segment contiguous with enteral feeding was denoted “fed” and the distal segment without luminal flow was denoted “unfed". Following RNA extraction, these samples underwent deep sequencing.
Results: Fed intestine had increased expression of genes involved in inflammation and immune regulation and steroid secretion. Unfed intestine had increased expression of genes involved in digestion and transport.
Conclusion: Independent of external influences, the presence or absence of enteral mechanoluminal stimulation causes significant alterations in gene expression in intestine.

overall_design: Profiles of paired fed and unfed neonatal intestine were generated by deep sequencing in triplicate.

first: Minna

last: Wieck

first: Brendan

last: Grubbs

first: Matt

last: Thornton


title: Drosophila retrotransposon and inverted repeat-derived endogenous siRNAs are differentially processed in distinct cellular locations

city: St. Louis

first: Mindy

last: Steiniger

address: 1 University Blvd.

institute: University of Missouri-St. Louis

summary: Endogenous small interfering (esi)RNAs repress mRNA levels and retrotransposon (retroTn) mobility in Drosophila somatic cells. EsiRNAs are primarily generated from transposon and inverted repeat (hairpin) loci in Drosophila culture cells. After discovering a nucleus specific physical interaction between the essential esiRNA cleavage enzyme Dcr2 and Symplekin, a component of the core cleavage complex (CCC) required for 3’ end processing of mRNAs, we investigated cellular localization of esiRNA biogenesis and overlap between these pathways. We found that knockdown of CCC components perturbs esiRNA levels and that retroTn precursor transcripts are highly enriched in the nucleus while hairpin RNAs are predominantly cytoplasmic. Additionally, retroTn and hairpin-derived esiRNAs have distinct physical characteristics. Combined, these observations support a novel mechanism in which differences in localization of esiRNA precursors impacts esiRNA biogenesis; hairpin-derived esiRNAs are generated in the cytoplasm independent of Dcr2-Symplekin interactions, while retroTns are processed in the nucleus.

overall_design: This submission includes 18 raw data files. Two samples (Blank control, Symplekin and CPSF73 RNAi-depleted) are represented by three technical triplicate raw data files. RNA-seq and small RNA-seq data are provided for each sample.

first: Andrew

last: Harrington

first: Michael

middle: R

last: McKain

first: Daniel

last: Michalski

first: Kaylyn

middle: M

last: Bauer


title: A comparison of nucleosome organization in Drosophila cell lines

city: La Jolla

first: Graham

last: McVicker

address: 10010 N Torrey Pines Rd

institute: Salk Institute

summary: We report the profiling of nucleosomes across 4 drosophila cell lines.

overall_design: Examination of nucleosome positioning in 4 drosophila cell lines

first: Rebecca

last: Martin

first: John

last: Maiorano

last: Marko

first: Greg

last: Beitel

first: Yvonne

last: Fondufe-Mittendorf


title: RNA-Seq data for AKT, BAD, ERBB2, IGF1R, RAF1 and KRAS(G12V) overexpressed samples with twelve green fluorescent protein control samples using human mammary epithelial cells

city: Salt Lake City

first: Mumtahena

last: Rahman

state: UT

address: 20 South 2030 East, Rm 420

department: Biomedical Informatics

institute: University of Utah

summary: The goal was to capture the transcriptional activity due to over-expression of AKT, BAD, ERBB2, IGF1R, RAF1 and KRAS(G12V) genes .Overexpressions were validated using Western Blots. Illumina RNA-Seq technology was used to capture the downstream transcriptional activity. Reads were 101 base pairs long and single ended. An R open source package “Rsubread” was used to align and quantify the read using UCSC hg19 annotation. The integer-based gene counts were later normalized in TPM .

overall_design: Profiles of gene expression, downstream of  AKT, BAD, ERBB2, IGF1R, RAF1 and KRAS(G12V) over-expression, were generated in cells derived from breast and used to generate a gene-expression signatures.

first: L

last: Jackson

first: M

first: S

last: MacNeil

last: Piccolo

first: A

middle: H

last: Bild


title: miRNA sequencing of MIBC

city: Houston

first: Andrea

last: Ochoa

state: TX

address: 1515 Holcombe

institute: UT MD Anderson Cancer Center

summary: small RNA sequencing of 62 muscle-invasive bladder cancers

overall_design: 62 invasive tumors were used to perform small RNA sequencing. The data was used to identify differentially expressed miRNAs in the intrinsic subtypes of muscle-invasive bladder cancer

first: Woonyoung

last: Choi

first: David

middle: J

last: McConkey