title: Next Generation Sequencing RNA Seq data from UKE Phase I rVSV ZEBOV vaccine clinical trial, from full blood samples on Days 0,1,3,7

city: Bordeaux

first: Hadrien

last: Lorenzo

address: 32 rue de Nerac

department: Biostatistiques

institute: INSERM/INRIA

summary: 10 adult participants of dose group 3x10^6 pfu, and 10 participants of dose group 20x10^6 pfu. Reads were aligned to the human reference assembly (GRCh38.p7) using STAR software (v2.4.2a; option '--quantMode GeneCounts'). Gene annotation was obtained from Ensembl (release 79, ensemble.org). VOOM+Limma analysis (R software, version 3.2.2) was used to assess differential gene expression at each post-vaccination day (d1, d3 and d7) against baseline (d0). Next, we intergreted gene expression data and antibody response using an sPLS algorithm, in order to down-select genes correlating with multivariate antibody responses at days 28, 54, 84,180.

overall_design: 56 samples from D0, D1, D3 and D7 were analysed. Data from samples with low RIN (RIN <8, 17 samples), low RNA or library concentration (2 samples), missing samples (5 samples)  were set to missing.

first: Anne

last: Rechtien


title: Hop stunt viroid: Effect on host (Humulus lupulus) transcriptome and its interactions with hop powdery mildew (Podospheara macularis)

status: Public on Aug 29 2017

city: Pullman

first: Madhu

last: Kappagantu

state: WA

address: 345 Johnson Hall

department: Plant Pathology

country: USA

institute: Washington State University

type: Expression profiling by high throughput sequencing

summary: RNA sequence analysis of hop leaves infected with Hop stunt viriod revealed dynamic changes in hop gene expression.

overall_design: High Throughput Sequencing analysis was used to identify the effect of Hop stunt viroid and hop powdery mildew on hop transcriptome in single and mixed infections

first: Jeff

middle: M

last: Bullock

first: Mark

middle: E

last: Nelson

first: Kenneth

middle: C

last: Eastwell


title: OCT4 and SOX2 Work as Transcriptional Activators in Reprogramming Human Fibroblasts

status: Public on Aug 30 2017

city: New York

last: Ptashne

state: NY

address: 1275 York Ave

department: Molecular Biology Program

institute: Sloan Kettering Institute

type: Genome binding/occupancy profiling by high throughput sequencing

summary: SOX2 and OCT4, in conjunction with KLF4 and cMYC, are sufficient to reprogram human fibroblasts to induced pluripotent stem cells (iPSCs), but it is unclear if they function as transcriptional activators or as repressors. We now show that, like OCT4, SOX2 functions as a transcriptional activator. We substituted SOX2-VP16 (a strong activator) for wild-type (WT) SOX2, and we saw an increase in the efficiency and rate of reprogramming, whereas the SOX2-HP1 fusion (a strong repressor) eliminated reprogramming. We report that, at an early stage of reprogramming, virtually all DNA-bound OCT4, SOX2, and SOX2-VP16 were embedded in putative enhancers, about half of which were created de novo. Those associated with SOX2-VP16 were, on average, stronger than those bearing WT SOX2. Many newly created putative enhancers were transient, and many transcription factor locations on DNA changed as reprogramming progressed. These results are consistent with the idea that, during reprogramming, there is an intermediate state that is distinct from both parental cells and iPSCs

overall_design: We ectopically expressed, in human fibroblasts, proteins comprising either a strong activating  (VP16) or a repressing region (HP1) fused to each of the factors- OCT4, SOX2, KLF4 and cMYC (OSKM).   SOX2-VP16, in combination with the WT forms of the other three proteins, uniquely increased the efficiency of reprogramming, especially of cells taken from older (37-96 year old) donors. The mix evoked early (by day 5), and strong, expression of critical pluripotency genes (e.g. NANOG), and diminished the requirement for cMYC . Many pre-existing ‘active’ enhancers were attenuated, and a smaller number of new enhancers, especially at sites of OCT4, SOX2 and SOX2-VP16 binding, were created by day 5.  The activities of new enhancers created by SOX2-VP16 binding were generally greater than those created by WT SOX2. Thus SOX2 and OCT4 work as activators capable of creating new enhancers, and increasing the activating function of SOX2 increases the activities of the new enhancers and the efficiencies of reprogramming.

first: Santosh

last: Narayan

first: Shivangi

last: Shah

first: Gene

middle: O

last: Bryant


title: Notch reprograms mitochondrial metabolism for macrophage proinflammatory activation

city: Los Angeles

first: Vasu

last: Punj

state: CA

address: Biggy Street

institute: USC

summary: we demonstrate Notch1 pathway dictates M1 activation in mouse hepatic macrophages (HMacs) and Raw 264.7 cells by coupling its transcriptional upregulation of M1 genes with its metabolic upregulation of mitochondrial oxidative phosphorylation and ROS (mtROS) to augment the M1 gene induction. We used a genome wide Chip-seq approach to study in detail the transcriptional mechanism associated with Notch1

overall_design: Genome wide Identification of Notch1 binding partners in nuclear as well as mitochondrial DNA (mtDNA)

first: Jun

last: Xu

first: Feng

last: Chi

first: Tongsheng

last: Guo

first: W

middle: P

last: Lee

first: Samuel

middle: W

last: French

first: Hidekazu

last: Tsukamoto


title: An Nfic-Hedgehog Signaling Cascade Regulates Tooth Root Development

summary:
This study aimed to perform transcriptome profiling of Nfic-/- and corresponding control tooth germ at root initiation stage to identify differentially expressed for key regulators of root development.
Coordination between the Hertwig’s Epithelial Root Sheath (HERS) and apical papilla (AP) is crucial for proper root development process. The Hedgehog (Hh) signaling pathway and Nfic are both involved in tooth root development.

overall_design: mRNA profiling of apical half of tooth germ from 6 pairs of 4-day-old Nfic-/- and littermate Nfic+/- control mice were generated using Illumina Next-Seq 500

first: Yang

last: Liu

first: Jifan

last: Feng

first: Jingyuan

last: Li

first: Hu

last: Zhao

first: Thach-Vu

last: Ho

last: Chai


title: Neuronal activity promotes glioma growth

city: Stanford

first: Humsa

last: Venkatesh

address: 265 Campus Drive - Monje Lab

department: Neurology

institute: Stanford University

summary: Secreted molecules from active neurons promote glioma growth

overall_design: Cells were treated with either conditioned media from blue light exposed WT brain slices, or conditioned media from optogenetically stimulated Thy1::ChR2 slices

first: Michelle

last: Monje


title: Next Generation Sequencing Facilitates Quantitative Analysis of Pressure Type and control Transcriptomes

city: Shanghai

first: feng

last: qi

address: No, 800, Rd. Xiangyin

country: China

institute: The Second Military Medical University

type: Non-coding RNA profiling by high throughput sequencing

summary: With the aim to reveal the function of microRNAs in Hepatic stellate cells (HSCs) in response to portal hypertension, primary rat HSCs were exposed to pressure (10mmHg, 1 h) by using a pressure induced apparatus. Appling next-generation sequencing screened the pressurization induced miRNAs expression profile in HSCs. Among them miR-9a-5p was confirmed to be significantly increased after loading pressure in HSC by RT-PCR. It was found that inhibition of miR-9a-5p could significantly restrain HSCs proliferation and activation under pressure overload. Moreover, the results showed that the induction of miR-9a-5p upon pressure load might by increasing the phosphorylation of Akt but not FAK and Erk1/2. Luciferase reporter assay and western blot suggested that Sirt1 was a potential target gene of miR-9a-5p. Finally, we revealed that miR-9a-5p level was apparently higher in rat liver fibrotic model than in the normal control while Sirt1 level was decreased in fibrotic liver tissue. In conclusion, our results suggest that miR-9a-5p regulate HSCs proliferation through negative regulation of Sirt1 and suggest a potential biomarker for portal hypertension.

overall_design: Hepatic stellate cell microRNA profiles of 14-day activated pressure type and control were generated by deep sequencing

last: Qi

first: Liang

last: Zhu


title: Determination of S. enterica wild-type and ridA mutant Transcriptome Differential Expression

status: Public on Aug 28 2017

city: Athens

first: Diana

last: Downs

state: GA

address: 527 Biological Sciences Building

department: Microbiology

institute: University of Georgia

summary:
Purpose: Members of the broadly distributed Rid/YER057c/UK114 protein family have imine/enamine deaminase activity, notably on a 2-aminoacrylate (2AA). Strains of Salmonella enterica, and other organisms lacking RidA, have diverse growth phenotypes, attributed to the accumulation of 2AA. The goal of this study was to use  transcriptional differences between S. enterica wild-type and ridA strains to explore the breadth of the cellular consequences that resulted from accumulation of 2AA.
Methods: S. enterica LT2 mRNA profiles of wild-type (WT) and ridA mutant cells were generated by Next Generation Sequencing, in biological quadruplicate, using Illumina Nextseq (150 cycles) Mid Output Flowcell in the paired end mode with a read length of 75bp. The sequence reads that passed quality filters were analyzed by DEseq to call for statistically significant (FDR < 0.05) differential gene expression. qRT–PCR experiemnts were performed using SYBR Green assays to corroborate the differential expression for 9 of the genes identified as differentially expressed.
Results: Pair-wise comparison of gene expression identified 413 genes with statistically significant changes (186 higher expression, and 227 lower expression) in transcript abundance between ridA mutant and wild-type strains (FDR < 0.05).  Of these loci,when genes with no known function (STMxxxx and yxxX locus tags--120 genes) and genes showing less than a two-fold difference in expression were excluded,  84 genes remained which showed differential expression between strains. RNA-seq data had a linear relationship with qRT–PCR for four genes (napF, metH, dadX, and fliI) belonging to the 84 gene dataset, one gene (thiF) with an FDR < 0.05, but failing the two-fold cutoff threshold and one gene (sdaC) that did not meet the statistical cutoff (FDR > 005). Pearson's correlation coefficient (R2) for the relationship between RNAseq and qRT-PCR data was measured at 0.96. Analysis of the differentially expressed genes uncovered several areas of metabolism and physiology which may be affected by RidA elimination, and subsequent 2-aminoacrylate accumulation.
Conclusions: Our study represents the first detailed analysis on the transcriptional effect RidA elimination has in S. enterica LT2, using biologic replicates, and generated by RNA-seq technology. Our results uncovered a motility effect associated with the accumulation of 2-aminoacrylate in a ridA mutant as well as identified additional areas of metabolism impacted by the metabolic stress associated with 2AA accumulation. These data also emphasized the value of integrating global approaches with biochemical genetic approaches to understand the complex system of microbial metabolism.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

overall_design: S. enterica LT2 mRNA profiles from mid-log (OD650 = 0.6) WT and ridA cells grown in no-carbon E medium supplemented with 1 mM MgSO4, trace minerals, and 11mM D-glucose were generated by Next Generation Sequencing, in biological quadruplicate, using Illumina Nextseq (150 cycles) Mid Output Flowcell in the paired end mode with a read length of 75bp

first: Andrew

middle: J

last: Borchert


title: The ground-state and evolution of promoter directionality revealed by a functional evolutionary approach

city: Boston

first: L.

middle: Stirling

last: Churchman

state: Massachusetts

address: 77 Avenue Lois Pasteur, NRB 356

department: Genetics

institute: Harvard Medical School

summary: Although the RNA polymerase (Pol) II machinery inherently initiates transcription in one direction, promoter regions are often “bidirectional” in vivo, giving rise to divergent RNA transcripts, many of which are non-coding and highly unstable. Here, we use a functional evolutionary approach to address whether bidirectional promoter regions are a mechanistic consequence of Pol II transcription or serve an evolved biological function.  This involves nascent transcript mapping in S. cerevisiae strains containing large segments of foreign, and hence evolutionarily irrelevant, yeast DNA.  Promoter regions in foreign species environments lose the directionality they have in their native species, indicating that DNA sequences and proteins co-evolve to promote directional transcription. Furthermore, fortuitous promoters emerge frequently in foreign DNA, and these produce equal transcription in both directions. Thus, without evolutionary pressure, the transcriptional ground state of promoter regions is intrinsically bidirectional. Interestingly, promoter regions of newly evolved genes tend to promote bidirectional transcription, and when fortuitous promoters arise in evolution, transcription factor binding sites are either purged through mutation or retained to enable new functionality. These results indicate that promoter regions are intrinsically bidirectional and are shaped by evolution to bias transcription of coding transcripts while suppressing non-coding transcriptional noise.

sample_organism:
Saccharomyces cerevisiae
Debaryomyces hansenii
Kluyveromyces lactis

overall_design: We transferred artificial chromosomes made of DNA extracted from K. lactis and  D. hansenii to S. cerevisiae and performed NET-Seq

first: Umut

last: Eser

first: Yi

last: Jin

first: Stirling

middle: L

first: Kevin

last: Struhl


title: The TNF receptor super family - NF-κB axis is critical to maintain effector regulatory T cells in lymphoid and non-lymphoid tissues [ChIP-seq]

city: Clayton

first: Wei

last: Shi

state: VIC

address: 15 Innovation Walk

department: Department of Biochemistry and Molecular Biology

country: Australia

institute: Monash University

summary: After exiting the thymus, Foxp3+ regulatory T (Treg) cells undergo further differentiation in the periphery resulting in the generation of effector (e)Treg cells, a process dependent on TCR signaling and the transcription factor IRF4. Here we show tumor necrosis factor receptor super family (TNFRSF) signaling plays a crucial role in the development and maintenance of eTreg cells. TNFRSF signaling activated the NF-κB transcription factor RelA and induced expansion and survival of eTreg cells in lymphoid and non-lymphoid tissues, including RORγt+ resident Treg cells in the small intestine. RelA regulated basic cellular processes in Treg cells, including cell survival and proliferation in response to TNFRSF signaling, but was not required for IRF4 expression or DNA binding, indicating that both pathways operate independently. Importantly, a similar pathway appeared to be active in humans, as patients with a point mutation in NF-κB1, a binding partner of RelA, had severely compromised Treg cells. Therefore, although TCR signaling is essential for eTreg cell differentiation, the TNFRSF-NF-κB axis was additionally required in a non-redundant manner to maintain the pool of eTreg cells.

overall_design: Identification of IRF4 and RelA/p65 target genes in murine regulatory T cells.

first: Ajith

last: Vasanthakumar

last: Liao

first: Axel

last: Kallies


title: Global transcriptome analysis of heterodimeric homeobox-driven zygote developmental program in Chlamydomonas reinhardtii

city: Berkeley

first: Sean

middle: D.

last: Gallaher

state: California

address: 176 Stanley Hall, room 408

department: California Institute for Quantitative Biosciences

institute: UC Berkeley

summary: Chlamydomonas reinhardtii provides an important model to study sexual reproduction in a unicellular context. Its sexual cycle culminates in the formation of diploid zygotes which differentiate into dormant spores that eventually undergo meiosis. Mating between haploid plus and minus gametes induces rapid cell wall shedding via the enzyme g-Lysin; cell fusion is followed by by heterodimerization of sex-specific homeobox transcription factors, Gsm1 and Gsp1, and initiation of zygote-specific gene expression. Developing zygotes secrete novel cell-wall materials that create multicellular aggregates called pellicle. To investigate the genetic underpinnings of zygote differentiation, we performed comparative transcriptome analysis of both pre- and post-mating samples. We identified 253 genes specifically enriched in early zygotes, 92% of which are not expressed in gsp1 null zygotes, indicating that the Gsm1/Gsp1 heterodimer is the main activator of the early zygote program. A cohort of genes induced by g-Lysin is shown to be negatively regulated in early zygotes at the post-transcriptional level in a Gsm1/Gsp1-dependent manner, enabling prompt transition to zygotic wall assembly.

overall_design: Natural zygotes are products of mt+ and mt- cells. To collect only the ones induced by the zygote developmental program, one mt- haploid and one mt+/mt- diploid strains were chosen for vegetative samples and for pseudozygotes that ectopically expressed GSM1 and/or GSP1 turn on the zygote program during N-starvation. Two zygote samples are made out of matings between one lab strain and one natural isolate, in order to collect the zygote-specific genes not specific to individual strain.

first: Jae-Hyeok

last: Lee

middle: D


title: Vegetally localised Vrtn functions as a novel repressor to modulate bmp2b transcription during dorsoventral patterning in zebrafish

status: Public on Aug 26 2017

city: Jinan

first: Ming

last: Shao

state: Shandong

address: 27# Shan Da Nan Lu Road

department: School of Lifesciences

institute: Shandong University

summary: The vegetal pole cytoplasm represents a crucial source of maternal dorsal determinants for patterning the dorsoventral axis of the early embryo. Removal of the vegetal yolk in the zebrafish fertilised egg before the completion of the first cleavage results in embryonic ventralisation, but removal of this part at the two-cell stage leads to embryonic dorsalisation. How this is achieved remains unknown. Here, we report a novel mode of maternal regulation of BMP signaling during dorsoventral patterning in zebrafish. We identify Vrtn as a novel vegetally localised maternal factor with dorsalising activity and rapid transport towards the animal pole region after fertilisation. Co-injection of vrtn mRNA with vegetal RNAs from different cleavage stages suggests the presence of putative vegetally localised Vrtn antagonists with slower animal pole transport. Thus, vegetal ablation at the two-cell stage could remove most of the Vrtn antagonists, and allows Vrtn to produce the dorsalising effect. Mechanistically, Vrtn binds a bmp2b regulatory sequence and acts as a repressor to inhibit its zygotic transcription. Analysis of maternal-zygotic vrtn mutants further shows that Vrtn is required to constrain excessive bmp2b expression in the margin. Our work unveils a novel maternal mechanism regulating zygotic BMP gradient in dorsoventral patterning.

overall_design: RNA seq of animal pole and vegetal pole, respectively.

first: De-li


title: Single-cell RNA-seq reveals intrinsic and extrinsic regulatory heterogeneity in yeast responding to stress

city: Madison

first: Audrey

last: Gasch

state: WI

address: 425G Henry mall

institute: University of Wisconsin

summary: Single-cell RNA sequencing before and after salt treatment in Saccharomyces cerevisiae.

overall_design: Dataset represents transcriptomes for 163 individual S. cerevisiae cells


title: Specific molecular signatures underlie response to Decitabine in CMML

city: Miami

first: Maria

last: Figueroa

state: FL

address: 1501 NW 10th Ave

department: Human Genetics

institute: University of Miami

type: Methylation profiling by high throughput sequencing

summary: Myelodysplastic syndromes and chronic myelomonocytic leukemia (CMML) are characterized by mutations in epigenetic modifiers and aberrant DNA methylation. DNA methyltransferase inhibitors (DMTis) are used to treat these disorders, but response is highly variable with few means to predict which patients will benefit. To develop a molecular means of predicting response at diagnosis, we examined baseline differences in mutations, DNA methylation, and gene expression in 40 CMML patients responsive and resistant to Decitabine (DAC). While somatic mutations did not differentiate responders and non-responders, we were able to identify for the first time 167 differentially methylated regions (DMRs) at baseline between responders and non-responders using next-generation sequencing. These DMRs were primarily localized to non-promoter regions and overlapped with distal regulatory enhancers. Using the methylation profiles, we developed an epigenetic classifier that accurately predicted DAC response at the time of diagnosis. Transcriptional analysis revealed that gene expression differences also exist at diagnosis between responders and non-responders. Genes up-regulated in responders were enriched in the cell cycle, potentially contributing to effective DAC incorporation. Two chemokines overexpressed in non-responders – CXCL4 and CXCL7 – were able to block the effect of DAC on normal CD34+ and primary CMML cells in vitro, suggesting their up-regulation contributes to primary DAC resistance.

overall_design: DNA methylation profiling in peripheral blood monocytes from 28 CMML patients (12 Dectiabine responders vs. 16 non-responders)

first: Kristen

last: Meldi

first: Tingting

last: Qin

first: Valeria

last: Santini


title: Genome-wide binding of SET, SETα and SETβ isoforms in ESCs

city: Jerusalem

first: Raghu

last: Edupuganti

address: 2-543, Silberman Building

department: Dept. of Genetics

country: Israel

institute: The Hebrew University

summary: We identified the genome wide binding sites of SET isoforms by ChIP-Seq

overall_design: Examination of SET binding sites in the mouse ESC genome and genome-wide localization of histone H1 in mouse ESCs by ChIP-Seq.

first: Edupuganti

middle: V

last: Ram

first: Eran

last: Meshorer


title: TAp73 is a marker of glutamine addiction in medulloblastoma

status: Public on Aug 25 2017

city: Homburg (Saar)

first: Marc

last: Remke

state: Saarland

address: Kirrberger Straße 100, Gebäude 9

department: Pediatric Translational Oncology Lab

country: Germany

institute: Universitätsklinikum des Saarlandes

summary: Metabolically-targeted therapies hold the promise of offering an effective and less toxic treatment for tumours including medulloblastoma, the most common malignant brain tumour of childhood. Current treatment relies on the sensitivity of these tumours to DNA damage that was discovered more than 50 years ago. Finding new tumour-specific susceptibilities to complement sensitivity to DNA damage is key to developing new more effective adjuvant therapies. The specific metabolic program of tumours is an attractive vulnerability, as restriction diet are low cost and easy to implement. Here, we present compelling pre-clinical evidence that glutamine restriction diet can be used as an adjuvant treatment for p73-expressing medulloblastoma.

overall_design: siRNA constructs targeting p73 (ID: 2671-AMBION) and a non-targeting control siRNA (scramble) were transfected with 10 pM siRNA with lipofectamine 3000 according to the supplier’s protocol for 48 hours

first: Daniel

last: Picard

last: Niklison-Chirou

first: Silvia

last: Marino


title: Genome wide binding of trr (ChIP-seq) and expression analysis (RNA-seq) of trr- and G9a mutant fly heads

city: Nijmegen

first: Tom

last: Koemans

address: Geert Grooteplein 10

department: Human genetics

country: Netherlands

institute: Radboudumc

summary: trr ChIP-seq, trr RNA-seq, G9a RNA-seq

overall_design: trr ChIP-seq profiles on 0-5 day old fly heads in two replicates and mRNA profiles of trr- and G9a mutant 0-5 days old fly heads in two and three replicates respectively.

middle: S

first: Jamie

last: Kramer

first: A

last: Schenck

first: H

last: van Bokhoven


title: Mouse strain-specific chromatin and transcriptional states modulate the DNA-damage response to an inhalational carcinogen

city: Chapel Hill

first: Terry

last: Furey

state: North Carolina

address: 5022 Genetic Medicine Bldg, CB#7264

institute: University of North Carolina at Chapel Hill

summary: Genetically distinct individuals are differentially affected by the DNA damaging effects of exposure to environmental toxicants, but the mechanisms contributing to these differences are poorly understood. It is known that genetic variation affects the establishment of the gene regulatory landscape, and we hypothesized that this may significantly contribute to the observed heterogeneity in individual responses to exogenous cellular insults. In this study, we investigated how genetic variation and chromatin organization may dictate susceptibility to DNA damage. We measured DNA damage, mRNA and miRNA expression, and chromatin accessibility genome-wide in lung tissue from two genetically-divergent inbred mouse strains, C57BL/6J and CAST/EiJ, at baseline and in response to exposure to a model DNA-damaging chemical, 1,3-butadiene (BD). Our results show that unexposed CAST/EiJ and unexposed C57BL/6J mice have very different chromatin organization and transcription profiles in the lung. Importantly, in unexposed CAST/EiJ, which is more resistant to BD-induced DNA damage, we see increased transcription and a more accessible chromatin landscape around genes involved in detoxification pathways. Upon BD exposure, chromatin is significantly remodeled in C57BL/6J around these genes to more closely resemble that found in CAST/EiJ. This suggests that strain-specific differences in baseline chromatin organization and transcription contribute to the relative resistance of CAST/EiJ to the DNA damaging effects of BD. Based on these results, we propose more generally that differences in the baseline molecular state of key tissues, driven by unique genetic backgrounds, significantly contributes to inter-individual variability in response to DNA-damaging environmental agents.

overall_design: Investigation of strain-specific chromatin accessibility and gene expression differences in lung tissue from CAST/EiJ and C57BL/6J mice, and how the gene regulatory landscape changes in response to 1,3-Butadiene exposure

first: Jennifer

last: Israel

first: Jeremy

last: Simon

first: Terrence


title: O-GlcNAc expression levels epigenetically regulate colon cancer tumorigenesis by affecting the cancer stem cell compartment via modulating expression of transcriptional factor MYBL1

first: Huabei

last: Guo

address: 315 Riverbend Rd.

department: CCRC

summary: To study the regulation of colorectal adenocarcinoma progression by O-GlcNAc, we have focused on the O-GlcNAc-mediated epigenetic regulation of human colon cancer stem cells (CCSC). Xenograft tumors from colon tumor cells with OGT knockdown grew significantly slower than those formed from control cells, indicating a reduced proliferation of tumor cells due to inhibition of OGT expression. Significant reduction of CCSC population was observed in the tumor cells after OGT knockdown, while tumor cells treated with O-GlcNAcase inhibitor showed an increased CCSC population, indicating that O-GlcNAc levels regulated the CCSC compartment. When grown in suspension, tumor cells with OGT knockdown showed a reduced ability to form tumorspheres, indicating a reduced self-renewal of CCSC due to reduced levels of O-GlcNAc. ChIP-seq experiments using an anti-O-GlcNAc antibody revealed significant chromatin enrichment of O-GlcNAc modified proteins at the promoter of the transcription factor MYBL1, which was also characterized by the presence of H3K27me3. RNA-seq analysis showed an increased expression of MYBL1 in tumor cells with OGT knockdown. Forced overexpression of MYBL1 led to a reduced population of CCSC and tumor growth in vivo, similar to the effects of OGT silencing. Moreover, two CpG islands near the TSS site of MYBL1 were identified, and O-GlcNAc levels regulated their methylation status. These results strongly argue that O-GlcNAc epigenetically regulates MYBL1, functioning similarly to H3K27me3. The aberrant CCSC compartment observed after modulating O-GlcNAc levels, therefore, is likely to result, at least in part, from the epigenetic regulation of MYBL1 expression by O-GlcNAc, thereby significantly affecting tumor progression.

overall_design: Examination of Epigenetic regulation of colon tumor development by O-GlcNAc using in vitro tumor cell lines and in vivo SCID mice

first: Michael

last: Pierce


title: Murine mesenchymal stem/progenitor cells (MSPC): Ptpn11+/+ MSPC vs. Ptpn11E76K/+ MSPC

city: Atlanta

first: LEI

last: Dong

address: 1760 Haygood Drive NE, HSRB E3642

institute: Emory University

summary: Transcriptional profiling of mouse mesenchymal stem/progenitor cells (MSPC) comparing control Ptpn11+/+ MSPC with Ptpn11E76K/+ MSPC. By obtaining 20 million reads of sequence from two pair, we confirmed our cytokine/chemokine array data and quantitative ELISA data from both mouse and patient-derived specimens. CCL3, CCL12, CCL4, and CXCL12 (SDF-1) were aberrantly produced by Ptpn11 mutated MSPCs

overall_design: Examination of mouse  Ptpn11E76K/+ mesenchymal stem/progenitor cells (MSPC) transcriptional profiling compared to control Ptpn11+/+ MSPC, freshly isolated from Ptpn11E76K/+/Nestin and Ptpn11+/+/Nestin mice. Two replicate per array.

first: Lei

first: Cheng-kui

last: Qu


title: SBF2-AS1 promotes tumorigenesis as a miRNA sponge in lung cancer

status: Public on Aug 24 2017

city: Nanjing

first: Mantang

last: Qiu

state: Jiangsu

address: 42 Baiziting

department: Thoracic Surgery

institute: Cancer Institute of Jiangsu Province

summary: Long noncoding RNA (lncRNA) play important roles in the pathogenesis of cancer. LncRNA SBF2-AS1is unregulated in lung cancer tissues, while its biological function and molecular mechanism are largely unknown. RNA sequencing results suggest cell cycle-related genes are altered after SBF2-AS1 knockdown. In vivo and in vitro experiments confirm SBF2-AS1 could promote tumorigenesis of lung cancer. Further experiments prove SBF2-AS1 could bind with miR-338-3p and miR-362-3p to regulate various cell cycle-related genes, including E2F1. These results indicate the existence of ceRNA network driven by SBF2-AS1 through sponging miRNAs.

overall_design: A549 cells are plated into 6-well plate and then transfected small interfering RNA (siRNA) specifically targeting SBF2-AS1 or negative control (NC) siRNA. 24 hours after transfection, cells are harvested and extract total RNA with TRIZol reagent.

first: Rui

last: Chen

first: Rong

last: Yin

first: Lin

last: Xu


title: Comparative Total RNA-seq between WT and alba4-null Plasmodium yoelii parasites

city: University Park

first: Scott

middle: E.

last: Lindner

state: Pennsylvania

address: W224 Millennium Science Complex

department: Biochemistry and Molecular Biology

institute: Penn State University

summary: To determine the role of ALBA4 in mRNA homeostasis in Plasmodium parasites, we performed comparative total RNA-seq between a WT-GFP line and an alba4-null line. We performed these experiments at three points in the life cycle - asexual (schizont), sexual (gametocyte), and oocyst sporozoite stages. We found that ALBA4 has a multi-faceted role in mRNA homeostasis, and is involved in mRNA fate determination. ALBA4 appears to act in a stage-specific manner, affecting different sets of transcripts in each stage. Our data suggests that ALBA4 plays opposing roles - possibly promoting degradation in schizonts, while promoting mRNA protection in gametocytes. In oocyst sporozoites, it appears that ALBA4 has a mixed role, and may be involved in both degradation and protection of mRNAs.

overall_design: Schizonts or gametocytes were collected from mice infected with either a WT-GFP (control) or alba4-null parasite line, and purified by gentle centrifugation over a discontinuous gradient. Oocyst sporozoites were dissected from mosquitoes infected with either WT-GFP or alba4-null parasite lines, and purified twice by centrifugation over a discontinuous gradient. Following purification, RNA was extracted and purified and sequenced on a Illumina HiSeq 2500 in Rapid Run mode. For schizont and oocyst sporozoite samples, 100nt x 100nt paired-end sequencing was performed, and for gametocyte samples 100 nt single read sequencing was performed. Three biological replicates were performed for schizont and gametocyte stages, while two were performed for oocyst sporozoites.

first: Elyse

last: Munoz

last: Walker


title: Association of the zonula adherens with mRNAs

city: Charleston

first: Antonis

last: Kourtidis

state: SC

address: 173 Ashley Avenue

department: Regenerative Medicine and Cell Biology

institute: Medical University of South Carolina

summary: We report the association of the zonula adherens with a set of mRNAs, through the E-cadherin-p120 catenin binding partner called PLEKHA7.

overall_design: Isolation and identification of mRNAs associated to the zonula adherens in Caco2 colon cells, by formaldehyde intracellular cross-linking, RNA-immunoprecipiation (RNA-IP) by using a PLEKHA7 antibody (Sigma, HPA038610) and subsequent RNA isolation and RNA-sequencing. An IgG immunoglobulin was used in parallel and on the same lysates as negative RNA-IP control to exclude non-specific mRNA bindning, whereas total Caco2 mRNA was also isolated from the same cells and subjected to RNA sequencing, in order to caclulate fold-enrichment of mRNAs in the PLEKHA7 RNA-IP compared to total cellular mRNA content. Four indepedent experiements were performed.

first: E

middle: A

last: Thompson

first: Panos

middle: Z

last: Anastasiadis


title: A Fast Food Diet and Exercise Led to a Disrupted and Pathogenic Methylome in Mouse Liver

first: Dan

last: Zhou

address: 131 Dong 'an Road, Xuhui District

institute: Fudan University

summary: Fast food diet consumption and sedentary life style leads to energy excess, which elevates risks for obesity, metabolic syndrome, non-alcoholic fatty liver disease (NAFLD), and cancer. Exercise training conveys many health benefits in populations with or without these chronic conditions. Diet and exercise regulate gene expression by mediating epigenetic mechanisms globally and at select loci in an array of human tissues, however, such effects are less well documented in liver tissue. To dissect the epigenetic consequences of diet and exercise in liver, we measured DNA methylation using reduced representation bisulfite sequencing (RRBS) and transcriptome using RNA-seq in mice maintained on a fast food diet with sedentary lifestyle (FFC) or exercise (FFE) compared to control diet with (NCE) and without exercise (NCC). Our analyses demonstrate genome-wide differential DNA methylation at key regulatory regions, including different classes of promoters and enhancers, and differential regulation of gene clusters in each condition group. FFE gene expression is most differentially regulated, with enrichment of carbohydrate/lipid metabolic pathways and skeletal muscle development in altered gene sets. Through evaluation of putative protective effects of exercise on diet-induced DNA methylation and gene expression, we show that hypermethylation is effectively prevented, especially at promoters and enhancers, and hypomethylation is partially attenuated. We assessed diet-induced DNA methylation changes associated with cancer-related epigenetic modifications and identified significant increases at liver-specific enhancers in FFC and FFE, suggesting a repressive effect on the epigenomic signature specifying liver identity. Gaining methylation at a subset of gene promoters was associated with inhibition of tissue development and promotion of carcinogenic process. Taken together, our study demonstrates large-scale diet- and exercise-induced effects on the epigenetic landscape, emphasizing the functional relevance of epigenetic mechanisms as an interface between life-style modifications and phenotypic alterations.

overall_design: 2-3 replicates was conducted with RRBS, 3- 6 replicates were pooled for RNA-seq.

first: Keith

last: Robertson


title: Industrial antifoam agents impair ethanol fermentation and induce stress responses in yeast cells

city: Hørsholm

first: Jens Christian

last: Nielsen

address: Hørsholm Kongevej

country: Denmark

institute: Gubra

summary: In this study, we investigated the impact of industrial antifoam agents on the physiology and transcriptome of the industrial ethanol Saccharomyces cerevisiae strain CAT-1. We showed that under industrial molasses fermentations similar to the ones used for ethanol production in Brazil, antifoam agents had detrimental effects on productivity, viability and lead to increased stress responses in yeast.

overall_design: Exposure of yeast cells to antifoam agents during sugar cane molasses fermentations employed in Brazil.

first: Jens

first: Christopher

middle: T

last: Workman

first: Thiago

last: Basso


title: Cannabinoid Modulation of Eukaryotic Initiation Factors (eIF2α and eIF2B1) and Behavioral Cross-Sensitization to Cocaine in Adolescent Rats

city: New York

first: Philippe

last: Melas

address: 1051 Riverside Drive

institute: Columbia University

summary: Reduced eukaryotic Initiation Factor 2 (eIF2)α phosphorylation (p-eIF2α) enhances protein synthesis, memory formation, and addiction-like behaviors. However, p-eIF2α has not been examined with regard to psychoactive cannabinoids and cross-sensitization. Here, we find that a cannabinoid receptor agonist (WIN 55,212-2 mesylate [WIN]) reduced p-eIF2α in vitro by upregulating GADD34 (PPP1R15A), the recruiter of protein phosphatase 1 (PP1). The induction of GADD34 was linked to ERK/CREB signaling and to CREB-binding protein (CBP)-mediated histone hyperacetylation at the Gadd34 locus. In vitro, WIN also upregulated eIF2B1, an eIF2 activator subunit. We next found that WIN administration in vivo reduced p-eIF2α in the nucleus accumbens of adolescent, but not adult, rats. By contrast, WIN increased dorsal striatal levels of eIF2B1 and ΔFosB among both adolescents and adults. In addition, we found cross-sensitization between WIN and cocaine only among adolescents. These findings show that cannabinoids can modulate eukaryotic initiation factors, and they suggest a possible link between p-eIF2α and the gateway drug properties of psychoactive cannabinoids.

overall_design: RNAseq from PC12 cell line with a 6 hour DMSO or WIN treatment.

first: Eric

last: Kandel


title: Effect of Hypoxia in Severe Preeclampsia through Epigenetic Regulation

status: Public on Aug 27 2017

city: Shanghai

first: Fei

last: Lan

address: No131 Dongan Road, Xuhui District.

institute: Institute of Biochemical Science

summary: Though the pathophysiology of preeclampsia (PE) is unclear worldwide, placental hypoxia has been implicated in the pathologic processes of PE.In this study, we profiled the transcriptome in BeWo and JEG-3 cells cultured in hypoxic condition or normal ones based on the RNA sequencing dataset. After filtered the low-quality ones, the RNA readers was aligned to human genome hg19 by TopHat and then assembled by Cufflinks. The expression value of each transcript was calculated and consequently differentially expressed genes were screened out. CD39 and ZDHHC14 were found to have both different mRNA in hypoxic cells and abnormal methylation level in severely preeclamptic placentas. The mRNA expression of CD39 and ZDHHC14 in placental tissues were analyzed using qRT-PCR. The differential methylated regions (DMRs) of CD39 and ZDHHC14 were confirmed by MassARRY EppiTYPER. The effect of hypoxia on trophoblast cells was detected with western blotting and enzyme linked immunosorbent assay. The results showed CD39 and ZDHHC14were significantly lower in severe PE placenta, hypoxia significantly reduced the expression of CD39 and ZDHHC14 and the secretion of CD39 in trophoblast cells. Therefore, we believed hypoxia plays an important role in the processes of severe PE via decreasing the expression of CD39 and ZDHHC14 by changing their methylation level in placenta.

overall_design: mRNA profiles of three cell lines at five stages and two different conditions were generated by deep sequencing, using HiSeq 2500.

first: Lisa

last: Zhu

first: Ruitu

last: Lv


title: Learned Helplessness Regulates Synapse Related LncRNAs in Mouse Hippocampus

first: NASHAT

last: ABUMARIA

address: 130 Dong An Road

department: Institute of Brain Science and Department of Laboratory Animal Science

summary:
Purpose: RNA sequencing (RNA-Seq) has revolutionized systems-based analysis of cellular pathways. The goal of this study is to find learned helplessness/depression regulates synapse related long noncoding RNAs (lncRNAs) in mouse hippocampus
Methods: compared the differential expression of mRNA and lncRNAs in learned helplessness (LH) group, nonlearned helplessness (NLH) group and Ctrl group, using GO analysis, pathway enrichment and co-expression
Results: We found that 2163 or 1396 mRNA are different expressed in LH compared with Control or NLH group, 199 or 142 lncRNAs are different expressed in LH compared with Control or NLH group, respectivly. Then we applied complex bioinfomatics analysis to do lncRNAs functional analysis, finding dendritic spine morphogenesis, chemical synaptic transmission and synaptic potential signaling pathway are common between LH group compared with Ctrl group and LH group compared with NLH group. Further more we found that the identified lncRNAs are mediating several cellular functions such as: protein transport, ion transport, mRNA processing, regulation of dendritic spine development, regulation of neuron projection development and regulation of GTPase activity. Interestingly, there was strong regulation of lncRNAs related to synapse.
Conclusions: Our study is the first attempt to explore the possibility that lncRNAs might be involved in helplessness using RNA sequencing. And we found some lncRNAs have strong functions in synapse regulation.

overall_design: Hippocampus mRNA and lncRNAs profiles of LH/Ctrl and LH/NLH group mice were generated by RNA-Seq.

first: Chaoqun

last: Li

first: Feifei

last: Cao


title: SET is essential for pluripotency, proliferation and differentiation of mouse embryonic stem cells

first: Raghu

last: Edupuganti

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

overall_design: Refer to individual Series


first: Mary

last: Galinski

address: 954 Gatewood Road

department: Vaccine Center at Yerkes

summary:
[Original Title] Malaria Host Pathogen Interaction Center Experiment 03: Host and parasite gene transcript abundance measures from bone marrow for Macaca mulatta infected with Plasmodium coatneyi Hackeri strain from 7 time points over a 101 day study of acute, recrudescent, and chronic infections.
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 coatneyi

platform_organism:
Macaca mulatta
Plasmodium coatneyi

overall_design: Malaria-naive male rhesus macaques (Macaca mulatta), approximately four years of age, were inoculated intravenously with salivary gland sporozoites produced and isolated at the Centers for Disease Control and Prevention from multiple Anopheles species (An. dirus, An. gambiae, and An. stephensi) and then profiled for clinical, hematological, parasitological, immunological, functional genomic, lipidomic, proteomic, and metabolomic measurements. The experiment was designed for 101 days, and pre- and post-101 day periods to prepare subjects and administer curative treatments respectively. The anti-malarial drug artemether was subcuratively administered to all subjects at the initial peak of infection, one out of the five macaques received four additional subcurative treatments for subsequent recrudescence peaks.  The experimental infection in one subject was ineffective but the macaque was followed-up for the same period of 101 days. The different clinical phases of the infection were clinically determined for each subject.  Blood-stage curative doses of artemether were administered to all subjects at the end of the study.  Capillary blood samples were collected daily for the measurement of CBCs, reticulocytes, and parasitemias. Capillary blood samples were collected every other day to obtain plasma for metabolomic analysis. Venous blood and bone marrow samples were collected at seven time points for functional genomic, proteomic, lipidomic, and immunological analyses. The seven-time point collections were used to generate these results.  This dataset was generated from bone marrow samples from 5 individuals collected 7 times over the 101-day experiment. A total of 35 samples were collected. Within the MaHPIC, this project is known as ‘Experiment 03’.  This dataset was produced by Drs. Mark P. Styczynski and Yan Tang at Georgia Institute of Technology and Dr. Steven E. Bosinger, Nirav Patel, and Greg Tharp at the Emory University Yerkes Genomics Core. To access other publicly available results from E03 and other MaHPIC Experiments, including clinical results (specifics on drugs administered, diet, and veterinary interventions), and other omics, visit http://plasmodb.org/plasmo/mahpic.jsp. This page will be updated as datasets are released to the public.  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/.

first: Steven

last: Bosinger

first: Monica

last: Cabrera-Mora

first: Jung-Ting

last: Chien

first: Jeremy

last: DeBarry

middle: R

first: Trenton

last: Hoffman

first: Jay

last: Humphrey

first: Jianlin

last: Jiang

first: Regina

last: Cordy

first: Chester

last: Joyner

first: Jessica

last: Kissinger

first: Stacey

last: Lapp

first: Nicolas

last: Lackman

first: Esmeralda

last: Meyer

first: Alberto

last: Moreno

first: Mustafa

last: Nural

first: Suman

middle: B

last: Pakala

first: Nirav

last: Patel

first: Mark

last: Styczynski

first: Yan

last: Tang

first: Greg

last: Tharp


title: TonEBP/NFAT5 controls inflammatory transcriptional response to TNF-a in nucleus pulposus cells

city: Philadelphia

first: Makarand

last: Risbud

state: PA

address: 1015 Walnut St.

department: Orthopaedic Surgery

institute: Thomas Jefferson University

summary: RNA sequencing of nucleus pulposus cells transduced with shRNA (control or TonEBP-targeted) and either untreated or treated with TNF-a (24h)

overall_design: Total mRNA was collected from primary nucleus pulposus cells and subjected to RNA sequencing, n=3 for all experimental groups

first: Zariel

last: Johnson


title: Human RNase L Employs a Signaling Mechanism to Arrest Translation

city: Princeton

first: Alexei

last: Korennykh

address: Schultz Laboratory, Washington Road

institute: Princeton University

summary: To identify small RNA cleaved by RNaseL, we captured intracellular RNA with 2'-3' cyclic phosphates by ligation an Illumina-compatible adaptor and the RNA ligase RtcB.

overall_design: Small RNAs with 2'-3' cyclic phosphate were ligated to an adaptor with RtcB and converted to Illumina small RNA sequencing libraries.  Three independent methods were used to activate RNase L: transfection of poly-IC, a synthetic dsRNA, semi-permeabilization of cells in the presence of 2-5A, and overexpression of RNase L.  We also examined basal activity of RNase L by 2'-3' cyclic phosphate small RNA in WT and RNase L knockout Hap1 cells.  Additionally, we showed that the Ire1, an RNase L homologue, does not cleave small RNAs. Last, we show that A549 do not show mRNA decay after prolonged treatment with 2-5A.

first: Jesse

last: Donovan

first: Sneha

last: Rath


title: Jasmonate Regulates Plant Responses to Reoxygenation through Activation of Antioxidant Synthesis

city: Guangzhou

first: Lujun

last: Yu

state: Guandong

address: xingangxilu 135

institute: Sun Yat-sen University

summary: Submergence induces hypoxia in plants; exposure to oxygen following submergence, termed reoxygenation, produces a burst of reactive oxygen species. The mechanisms of hypoxia sensing and signaling in plants have been well studied, but how plants respond to reoxygenation remains unclear. Here, we show that reoxygenation in Arabidopsis thaliana involves rapid accumulation of jasmonates (JAs) and increased transcript levels of JA biosynthesis genes. Application of exogenous methyl jasmonate improved tolerance to reoxygenation in wild-type Arabidopsis; also, mutants deficient in JA biosynthesis and signaling were very sensitive to reoxygenation. Moreover, overexpression of the transcription factor gene MYC2 enhanced tolerance to post-hypoxic stress and myc2 knockout mutants showed increased sensitivity to reoxygenation, indicating that MYC2 functions as a key regulator in the JA-mediated reoxygenation response. MYC2 transcriptionally activates members of the VITAMIN C DEFECTIVE (VTC) and GLUTATHIONE SYNTHETASE (GSH) gene families, which encode rate-limiting enzymes in the ascorbate and glutathione synthesis pathways. Overexpression of VTC1 and GSH1 in the myc2-2 mutant suppressed the post-hypoxic hypersensitive phenotype. The JA-inducible accumulation of antioxidants may alleviate oxidative damage caused by reoxygenation, improving plant survival after submergence. Taken together, our findings demonstrate that JA signaling interacts with the antioxidant pathway to regulate reoxygenation responses in Arabidopsis.

overall_design: 4 mRNA samples

first: Li-Bing

last: Yuan

first: Yang-Shuo

last: Dai

first: Li-Juan

last: Xie

first: Lu-Jun

first: Ying

last: Zhou

first: Yong-Xia

last: Lai

first: Yi-Cong

last: Yang

first: Le

last: Xu

first: Qin-Fang

last: Chen

first: Shi

last: Xiao


title: Cancer-specific retargeting of BAF complexes by a prion-like domain [RNA-Seq]

city: Boston

first: Sowmya

last: Iyer

state: MA

department: Pathology

institute: Massachusetts General Hospital

summary: Alterations in the function of transcriptional regulators can orchestrate oncogenic programs that are critical for the transformation and survival of cancer cells. Here we show that the BAF chromatin remodeling complex, which is mutated in over 20% of human tumors, interacts with EWSR1, a member of the FET family of proteins containing prion-like domains that are frequent partners in oncogenic fusions with transcription factors. In Ewing sarcoma, characterized by the EWS-FLI1 fusion, we find that the BAF complex is recruited by EWS-FLI1 to tumor specific enhancers at GGAA microsatellite repeats and contributes to the activation of target genes. This process depends on tyrosine residues that are necessary for the aggregation properties of the EWSR1 prion-like domain and is a neomorphic feature of EWS-FLI1 compared to the wild type ETS transcription factor FLI1. Furthermore, fusion of short fragments of the EWSR1 prion-like domain to FLI1 is sufficient to recapitulate EWS-FLI1-mediated gene expression. Our studies demonstrate that the aggregation properties of prion-like domains can retarget chromatin regulatory complexes to establish and maintain oncogenic gene expression and proliferation.

overall_design:
Ewing sarcoma cell lines (A673 and SK-N-MC) were analyzed by RNA-seq. EWS-FLI1 was depleted by infection with lentiviral shRNAs (shFLI1 and shGFP control).   Mesenchymal stem cells (MSCs) were analyzed by RNA-seq. EWS-FLI1, wild-type FLI1 and the mutant proteins EWS(YS37)-FLI1, SYGQ2-FLI1 and BAF47-FLI1 were expressed in MSCs with lentiviral expression vectors. In a separate experiment, MSCs were also co-infected with lentiviral shRNA targeting the BAF complex subunit BRG1/SMARCA4 and with a lentiviral vector expressing EWS-FLI1.

Raw data not provided for primary cells due to patient privacy concerns. Submitter states that the raw data for these samples will be submitted to dbGaP.

first: Gaylor

last: Boulay

first: Miguel

last: Rivera


title: Identification of Lef1-dependent genes in zebrafish and mouse hypothalamus

city: Salt Lake City

first: Yuanyuan

state: Utah

address: 20 South 2030 East, Bldg. 570 BPRB, Rm. 456

institute: University of Utah

summary: We performed RNA-seq with dissected control and Lef1 mutant hypothalami from 3 days post-fertilization (3dpf) zebrafish, embryonic day 14.5 (E14.5) and postnatal day 22 (P22) mouse. We identified Lef1-dependent genes involved in an anxiolytic function in both species, but those genes are different between zebrafish and mouse.

sample_organism:
Danio rerio
Mus musculus

platform_organism:
Danio rerio
Mus musculus

overall_design: Hypothalamic transcriptome of control and Lef1 mutant zebrafish and mouse at different stages were generated by deep sequencing, in triplicate.

first: Richard

middle: I

last: Dorsky


title: Cancer-specific retargeting of BAF complexes by a prion-like domain [ChIP-Seq]

overall_design:
ChIP-seq for the BAF complex subunits BAF155 and SMARCA2 in Ewing sarcoma cells (SK-N-MC). EWS-FLI1 was knocked-down with lentiviral shRNA.  HA-tagged EWSR1 was expressed in Ewing sarcoma cells (A673) using a lentiviral expression vector and ChIP-seq was performed using an anti-HA antibody.
ChIP-seq for the histone modification H3K27ac, the transcription factor FLI1 and the BAF subunit BAF155 in mesenchymal stem cells (MSC). EWS-FLI1, wild-type FLI1 and the mutant proteins EWS(YS37)-FLI1, SYGQ2-FLI1 and BAF47-FLI1 were expressed in MSCs with lentiviral expression vectors. The FLI1 antibody used recognizes FLI1, EWS-FLI1 and the mutant proteins.

Raw data not provided for primary cells due to patient privacy concerns. Submitter states that the raw data for these samples will be submitted to dbGaP.


title: Exogenous Transposable Elements Circumvent Homology Permitting the Dissection of Expression Dependent Silencing

city: Columbus

first: R. Keith

last: Slotkin

state: OH

address: 500 Aronoff Laboratory, 318 W. 12th Ave.

department: Molecular Genetics

institute: The Ohio State University

summary: The propagation of epigenetic marks has received a great deal of attention, yet the initiation of epigenetic silencing on a new transgene, virus, or transposable element remains incompletely characterized. The overlapping function of multiple silencing mechanisms has obscured this area of investigation. Here, we have revealed two broad mechanisms that are both able to initiate silencing independently: homology-based silencing and expression-dependent silencing. By transforming exogenous transposable elements into Arabidopsis, we circumvented homology-based silencing allowing us to isolate and investigate the molecular mechanism of expression-dependent silencing. We found that several small RNA-generating mechanisms all trigger de novo expression-dependent RNA-directed DNA methylation (RdDM) through RNA Polymerase V. In addition, the silencing of transposable elements fragments stalls at the RdDM phase, while full-length elements quickly progress through RdDM to maintenance methylation and heterochromatin formation. We found that there is a narrow window of time for the transition to a fully silenced state. Transformation into a mutant genotype followed by introgression into wild-type does not result in the same level of silencing as direct transformation into wild-type. This demonstrates that the genotype of transposable element insertion or transgene transformation is key for establishing the transgenerational extent of epigenetic silencing.

overall_design: Examination of flower bud small RNAs from wild type and various mutants transformed with the exogenous TE transgene, iTto. Small RNA sequences from untransformed wt Col juvenile leaf control are also included.  Untransformed flower bud control is available at GSM2102963.

first: D

last: Fultz

first: R

middle: K


title: Cancer-specific retargeting of BAF complexes by a prion-like domain


title: Cellular responses to human cytomegalovirus infection.

city: Chicago

first: Adam

last: Oberstein

state: IL

address: 835 South Wolcott Ave.

department: Microbiology and Immunology

institute: University of Illinois

summary: Here we perform a systems analysis of the HCMV host-cell transcriptome across two cell-types.

overall_design: Total RNA profiles of mock- and HCMV-infected MRC-5 and ARPE-19 cells in biological duplicate, at three time-points.

first: Thomas

last: Shenk


title: RNA-seq transcriptonal profiling in human K562 cells with or without dCas9 and sgRNAs

city: Memphis

first: Jian

state: Tennessee

address: 262 Danny Thomas Place, MS 345

institute: St. Jude Children's Research Hospital

summary: Cis-regulatory elements (CREs) are commonly recognized by correlative chromatin features, yet the molecular composition of the vast majority of CREs in chromatin remains unknown. Here we describe a CRISPR affinity purification in situ of regulatory elements (CAPTURE) approach to unbiasedly identify locus-specific chromatin-regulating protein complexes and long-range DNA interactions. Using an in vivo biotinylated endonuclease-deficient Cas9 protein and sequence-specific guide RNAs, we show high-resolution and selective isolation of chromatin interactions at a single copy genomic locus. Purification of human telomeres using CAPTURE identifies known and new telomeric factors. In situ capture of individual constituents of the enhancer cluster controlling human β-globin genes establishes evidence for composition-based hierarchical organization of enhancer structure. Furthermore, unbiased analysis of chromatin interactions at disease-associated cis-elements and developmentally controlled super-enhancers reveals spatial features causally regulate gene transcription. Thus, comprehensive analysis of locus-specific regulatory composition provides mechanistic insight into genome structure and function in development and disease.

overall_design: RNA-seq was performed to determine the effects on global gene expression in K562 cells stably expressing Flag-bio-tagged dCas9 and sgRNAs targeting several regulatory elements within the β-globin cluster (sgHS2, sgHBG and sgHS1-5) or the non-targeting sgRNA (sgGal4).

first: Xin

last: Liu

first: Yuannyu

last: Zhang


title: Expression analysis of wt and maternal Trim28 mutant E3.5 embryos

city: Singapore

first: Diana

middle: HP

last: Low

address: #03-06, 61 Biopolis Drive, Proteos

country: Singapore

institute: Institute of Molecular and Cell Biology

summary: We performed RNAseq on 4 individual E3.5 control and maternal Trim28 blastocysts respectively in order to detect transcriptional differences amog the 2 cohorts which are to be linked to epigentic reprogramming defcts at early stages.

overall_design: mRNA isloated from E3.5 embryos was reverse transcribed into cDNA using the SMART-Seq® Ultra® Low Input RNA Kit (Clontech), followed by sequencing library preparation using the Nextera DNA Library Preparation Kit (Illumina) according to manufacturers instructions.

first: Daniel

middle: M

last: Messerschmidt

middle: H


title: The  Glycogen Synthase Kinase-3 Phosphoproteome: GSK-3 Phosphorylates Multiple Splicing Factors and Regulates Alternative Splicing

first: Kristen

last: Lynch

address: 906 Stellar Chance Labs 422 Curie Blvd

department: Biochemistry and Molecular Biophysics

institute: University of Pennsylvania

summary: Glycogen Synthase Kinase-3 (GSK-3) is a constitutively active, ubiquitously expressed protein kinase that regulates multiple signaling pathways. Over 100 putative GSK-3 substrates have been reported in diverse cell types based on in vitro kinase assays or genetic and pharmacological manipulation of GSK-3. Many more have been predicted based on a recurrent GSK-3 consensus motif, but this prediction has not been tested by analyzing the GSK-3 phosphoproteome. We used stable isotope labeling of amino acids in culture (SILAC) and mass spectrometry to analyze the repertoire of GSK-3 dependent substrates in mouse embryonic stem cells (ESCs). A comparison of wild-type and Gsk3a;Gsk3b knockout (DKO) ESCs revealed prominent GSK-3-dependent phosphorylation of multiple splicing factors and regulators of RNA biosynthesis, as well as proteins that regulate transcription, translation, and cell division. We demonstrate direct, GSK-3-dependent phosphorylation of the splicing factors RBM8A and PSF as well as the nucleolar protein NPM1. RNA sequencing to compare the transcriptomes of wild-type and Gsk3 DKO ESCs identified more than 210 genes that are alternatively spliced in a GSK-3-dependent manner, supporting a broad role for GSK-3 in regulating alternative splicing. Overall, this study provides the first unbiased analysis of the GSK-3 phosphoproteome and strong evidence for GSK-3 as a regulator of alternative splicing.

overall_design: 2 biological replicates of Gsk3a+/+;Gsk3b+/+ (Wild Type) and Gsk3a-/-;Gsk3b-/- (DKO) E15 mouse embryonic stem cells were analyzed by RNA-Seq

first: Shinde

last: Mansi

first: Sidoli

last: Simone

first: Kulej

last: Katarzyna

first: Mallory

middle: J

last: Michael

first: Radens

last: Caleb

first: Reicherter

last: Amanda

first: Barash

last: Yoseph

first: Lynch

middle: W

last: Kristen

first: Garcia

last: Benjamin

first: Klein

last: Peter


title: Development of an In Vitro Human Liver System for Interrogating Non-Alcoholic Steatohepatitis

city: Charlottesville

first: Mark

middle: Jon

last: Lawson

state: Virginia

address: 501 Locust Avenue, Suite 301

department: Computational Biology

institute: HemoShear Therapeutics

summary: A barrier to drug development for non-alcoholic steatohepatitis (NASH) is the absence of translational pre-clinical human-relevant systems. An in vitro liver model was engineered to incorporate hepatic sinusoidal flow, transport, and lipotoxic stress risk factors (glucose, insulin, free fatty acids) with co-cultured primary human hepatocytes, hepatic stellate cells (HSC), and macrophages. Transcriptomic, lipidomic, and functional endpoints were evaluated and compared to clinical data from NASH patient biopsies. The lipotoxic milieu promoted hepatocyte lipid accumulation (4-fold increase, p<0.01) and a lipidomics signature similar to NASH biopsies. Hepatocyte glucose output increased with decreased insulin sensitivity. These changes were accompanied by increased inflammatory analyte secretion (e.g. IL6, IL8, ALT). Fibrogenic activation markers increased with lipotoxic conditions, including secreted TGFβ (>5-fold increase, p<0.05), extracellular matrix gene expression, and HSC activation. Significant pathway correlation existed between this in vitro model and human biopsies. Consistent with clinical trial data, 0.5μM obeticholic acid in this model promoted a healthy lipidomic signature, reduced inflammatory and fibrotic secreted factors, but also increased ApoB secretion, suggesting a potential adverse effect on lipoprotein metabolism. Lipotoxic stress activates similar biological signatures observed in NASH patients in this system, which may be relevant for interrogating novel therapeutic approaches to treat NASH.

overall_design: 17 Samples. 8 NASH, 9 Control (Low Glucose, Low Insulin)

first: Ryan

middle: E

last: Feaver

first: Banumathi

last: Cole

first: Stephen

last: Hoang

first: Svetlana

last: Marukian

first: Robert

last: Figler

first: Arun

last: Sanyal

first: Brian

last: Wamhoff

first: Ajit

last: Dash


title: High throughput characterization of the m6A demethylase FTO by CLIP and RNAseq

city: Stockholm

first: Marek

last: Bartosovic

address: Solnavagen 9

country: Sweden

institute: Karolinska Institute

summary: We performed the CLIP-seq analysis of RNAs bound by 3xFLAG-tagged FTO protein stably expressed in human HEK293 cells. In parallel, we profiled the transcriptome of the same cells by RNA-seq, which was used for CLIPseq bioinformatics analysis as an input. The CRISPR-Cas9 was used to knock-out FTO expression in HEK293 to compare the mRNA expression changes and exon usage between FTO KO and WT cell lines. All experiments were performed in three replicates.

overall_design: CLIP-seq analysis of RNAs bound by 3xFLAG-tagged FTO protein and RNA-seq of wildtype and FTO KO HEK293 cells.

first: Helena

last: Covelo-Morales

first: Pavlina

last: Gregorova

first: Dominika

last: Hrossova

first: Grzegorz

last: Kudla

first: Stepanka

last: Vanacova


title: CAPTURE-3C-seq analysis of cis-element-mediated long-range DNA interactions

first: Jian

last: Xu

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: We combined the chromatin interaction assays (Chromatin Conformation Capture or 3C) with the high affinity dCas9 purification approach to unbiasedly identify single genomic locus-associated long-range interactions (CAPTURE-3C-seq).

first: Xin

last: Liu

first: Yuannyu

last: Zhang

first: Yong

last: Chen


title: RNA sequencing of skeletal muscle of myotonic dystrophic (DM1) patients

city: ILLKIRCH

first: nicolas

last: charlet

address: 1 Rue laurent Fries

country: France

institute: IGBMC

summary:
Introduction: Myotonic dystrophy of type 1 (DM1), the most common dystrophy in adults, is an autosomal dominant inherited disease, affecting around 1 in 8000 person. Patients suffering from DM1 develop essentially muscle disorders such as myotonia, muscle weakness, muscle loss and atrophy. The disease is caused by the mutation of the DMPK "Dystrophia Myotonica Protein Kinase" gene. The mutation correspond to an abnormally large expansion of CTG tri-nucleotides repeats located in the 3'-untranslated region of this gene. Expanded CTG repeats are normally transcribed, but accumulates in RNA aggregates that sequester RNA-binding proteins such as the splicing regulator MBNL1. Consequently, due to MBNL1 sequestration, DM1 is characterized by aberrant splicing of a wide number of mRNA, which are themselves responsible for the symptoms observed in the disease.
Purpose: To determine as much as possible novel splicing misregulations taking place in DM1 skeletal muscle, we performed a paired-end RNA sequencing (RNA-seq) using muscles samples of normal individuals (CTRL, n=3) versus muscles of DM1 patients (DM1, n=3). The data was analyzed by a bioinformatical software, called MISO, in order to map the alternative splicing changes between normal and DM1 muscle. The aim of this study was to get a broad and precise view of the splicing changes occurring in DM1 muscle.

overall_design: PolyA RNA extracted from skeletal muscle biopsies originating from normal individuals (CTRL, n=3) or patients suffering of myotonic dystrophy type I (DM1, n=3), were analyzed by massive paired-end RNA sequencing.

first: Michel

last: Ney

first: Emilie

last: Chautard

first: Didier

last: Auboeuf

first: Bernard

last: Jost

first: Eric

last: Wang

first: Masanori

middle: P

last: Takahashi

first: Nicolas

last: Charlet-Berguerand


title: RNAseq analysis of Rpl13a-snoless and wild type islets

city: St. Louis

first: Jean

last: Schaffer

state: MO

address: 660 S Euclid Ave # 8125

institute: Washington University School of Medicine

summary:
Purpose: To gain further mechanistic insight into phenotypic differences between wild type pancreatic islets and islets with loss of function of 4 Box C/D snoRNAs from the Rpl13a locus (U32a, U33, U34 and U35a).
Methods:High quality total RNA (RIN ≥ 8.5) was prepared from hand-picked islets (n = 4 mice/genotype) using TRIZOL reagent, treated with Turbo DNAse (Thermo Fisher), and used to prepare SeqPlex RNAseq libraries (Sigma).  Sequencing was performed by the Washington University Genome Technology Access Center using two lanes of Illumina HiSeq 2500, 1x50. Reads were demultiplexed and trimmed, and STAR alignment and quantification analysis was carried out using the Partek Flow platform. Uniquely aligned reads were quantified to identify genes with at least a two-fold change between genotypes with p < 0.05 and FDR step-up of 0.05.
Results:We observed 2-fold or greater differences in the expression of only six genes.
Conclusions: Our data indicate that loss-of-function of snoRNAs from the Rpl13a locus is associated with modest changes in mRNA abundance.

overall_design: Examination of murine pancreatic islet mRNA differential expression between wild type mice and mice with loss-of-function of U32a, U33, U34, and U35a snoRNAs.

first: Kelly

middle: D

last: Pyles


title: RNA-seq Analysis of the effect of Tfcp2l1 knockdown on Human ESC maintenace

status: Public on Aug 23 2017

city: Hefei

first: shoudong

last: ye

address: No 111, Jiu Long Road

department: Cell Biology

institute: Anhui University

summary: Purpose:The goal of this study is to analyze the candidate genes motified byTfcp2l1 knockdown to regulated the human embryonic stem cell (ESC) fate through RNA-seq approach.

overall_design: HES2 human ESCs infected with scramble or Tfcp2l1 knockdown lentivirus were cultured in 10%KSR basal media supplemented with 10 ng/ml FGF2 and 10 ng/ml Activin A  for three passages and then were collected by using Trizol. These samples were sent to BGI (China) company to do deep sequencing by using BGISEQ-500.

first: Shoudong

last: Ye


title: Med1 is Necessary for Cardiac Function

city: Iowa City

first: Long-Sheng

last: Song

state: IA

address: 285 Newton Rd

department: Internal Medicine

institute: University of Iowa

summary: Analysis of ventricular derived mRNA from Med1fl/fl and Med1fl/fl cardiac knockout mice.  Results provide insight into the molecual rmechanisms underlying dilated cardiomyopathy.

overall_design: Methods: Ventricular samples (4 per group) from 21-day-old Med1fl/fl and Med1 cardiac knockout mice were used to generate polyA enriched stranded RNA libraries followed by RNAseq using the Illumina HiSeq platform.  Raw sequence reads were analyzed with BaseSpace (www.illumina.com) by aligning reads to the mus musculus mm10 genome using the TopHat Alignment app.  Transcripts were assembled and significant differentially expressed genes were determined with the Cufflinks Assembly and DE app using a false discovery rate <0.05. qRT–PCR validation was performed using SYBR Green assays

first: Chad

last: Grueter


title: Zika Virus Has Oncolytic Activity against Glioblastoma Stem Cells

city: Cleveland

first: Briana

last: Prager

address: 9500 Euclid Ave.

institute: Cleveland Clinic

summary: We explored the utility of oncolytic virus therapy against glioblastoma with Zika virus (ZIKV), a flavivirus that induces cell death and differentiation of neural precursor cells in the developing fetus. ZIKV preferentially infected and killed glioblastoma stem cells (GSCs) relative to differentiated tumor progeny or normal neuronal cells. The effects against GSCs were not a general property of neurotropic flaviviruses, as West Nile Virus (WNV) indiscriminately killed both tumor and normal neural cells. ZIKV potently depleted patient-derived GSCs grown in culture and in organoids. Moreover, mice with glioblastoma survived substantially longer and at greater rates when the tumor was inoculated with a murine adapted strain of ZIKV. Our results suggest that ZIKV is an oncolytic virus that can preferentially target GSCs, and thus, genetically modified strains that further optimize safety could have therapeutic efficacy for adult glioblastoma patients.

overall_design: RNA-seq of glioblastoma stem cells and non-stem tumor cells. These samples have not been infected with Zika virus.

first: Zhe

last: Zhu

first: Jeremy

middle: N

last: Rich

first: Milan

last: Chheda


title: Murine myeloid response to experimental fibrosis

city: PARIS

first: Stephane

last: Le Crom

address: 46 rue Ulm

department: Genomic Core Facility

institute: IBENS

summary: We report the response of murine hepatic macrophages to chronic CCl4 administration in wild-type mice and mice with a myeloid-specific deletion of interferon regulatory factor 5

overall_design: Examination of myeloid-transcriptome response to chronic carbon tetrachloride administration

first: F

last: Alzaid

first: N

last: Venteclef

first: S

last: Lemoine

first: C

last: Blugeon


title: Modulation of gene transcription and epigenetics of colon carcinoma cells by bacterial membrane vesicles

city: Göteborg

first: Sergiu

last: Netotea

address: Chalmersplatsen 4

institute: Chalmers tekniska högskola AB

summary: We have investigated the genomic and epigenetic consequences of co-culturing colorectal carcinoma cells with membrane vesicles from pathogenic bacteria Vibrio cholerae and non-pathogenic commensal bacteria Escherichia coli. Our study has revealed that membrane vesicles from pathogenic and commensal bacteria have a global impact on the gene expression of coloncarcinoma cells. The changes in gene expression correlated positively with both epigenetic changes and chromatin accessibility of promoters at transcription start sites of genes induced by both types of membrane vesicles. Moreover, we have demonstrated that membrane vesicles obtained only from V. cholerae induced the expression of genes associated with tumour differentiation. Altogether, our study suggests that the observed genomic changes in host cells might be due to specific components of membrane vesicles and does not require communication by direct contact with the bacteria.

overall_design: Examination of mRNA profiles of three samples: untreated HCT8 cells (control), treated with membrane vesicles from V. cholerae, treated with membrane vesicle from E. coli (in triplicates), generated by RNAsequencing

first: Svitlana

last: Vdovikova

first: Siv

last: Gilfillan

first: Sun

last: Wai

first: Antoni

last: Rodriguez


title: Comparative Analysis of Alternative Polyadenylation in S. cerevisiae and S. pombe

city: Newark

first: Bin

last: Tian

state: NEW JERSEY

address: 205 South Orange Ave., CC-F1230

department: Department of Microbiology, Biochemistry and Molecular Genetics

institute: Rutgers University

summary: APA mechanisms in S. pombe and S. cerevisiae are largely different, distinctly impacting gene expression, antisense transcripts and 3’UTR evolution, and core processing factors regulate APA in a PAS-dependent manner.

sample_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

first: Xiaochuan

last: Liu

first: Mainul

last: Hoque

first: Marc

last: Larochelle

first: Jean-François

last: Lemay

first: Nathan

last: Yurko

first: James

middle: L

last: Manley

first: François

last: Bachand


title: Time course profiling of scRNA-seq of non-directed differentiation of human Neural precursor cells (NPCs) generated from hESC

city: Little Rock

first: PIROON

last: JENJAROENPUN

state: AR

address: 4301 W Markham Slot 782

institute: University of Arkansas for Medical Sciences

summary: Human pluripotent stem cells (hPSC) offer a unique cellular model to study the molecular details underpinning embryonic development. We profiled single-cell RNA-seq (scRNA-seq) on 957 single cells collected at 6 time points over a 30-day period of non-directed differentiation of human neural progenitor cells (NPC) generated from hESC. Computational and experimental analyses of this comprehensive data set enabled us to: 1) define distinct subpopulations of developing neurons and their specific gene expression patters; 2) elucidate alternative cell developmental trajectories within discrete time points of the differentiating populations; and 3) decipher gene regulatory networks and validated key regulators (transcription factors and lincRNAs) that dictate alternative cell fate specifications. In this submission, 957 bam files are provided: 1) 573 single cells from time course profiling (day 0, 1, 5, 7, 10, 30) as first batch and 2) 384 single cells from time course profiling (day 0, 3, 7, 14) as second batch.

overall_design: Reference the SRA Study accession (SRP097299) and BioProject accession (PRJNA360884)

first: Jiaxu

last: Wang

first: Piroon

last: Jenjaroenpun


title: Systematic Identification of Regulatory Variants Associated with Cancer Risk

city: Beijing

first: Xiaoyue

address: 5 Dongdansantiao, Dongcheng District

institute: Chinese Academy of Medical Sciences

summary: We adapted the self-transcribing active regulatory region sequencing (Starr-seq) strategy to systematically identify the SNPs that affect gene expression by modulating activities of regulatory elements.  Among 10,673 SNPs linked with 996 GWAS-identified cancer-risk SNPs, we found 70 regulatory variants for which the two alleles conferred different regulatory activities.  We analyzed one of them in-depth and confirmed its target by CRIPSR-Cas9 technology. Our results will help the interpretation of GWAS results and better cancer risk assessment.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: Starr-seq analysis in 293T cell lines (2 replicates), Input plasmid library before transfection (2 replicates)

first: Song

first: Yuwen

first: Qin

last: Zhang

first: Jiayu

last: Wu

first: Junbo

last: Liang

first: Shan

last: Yu

first: Gong-Hong

last: Wei

first: Kevin

last: White


title: Gene expression profiling of multiple tissue types from three species of cobweb weaving spiders

city: LEXINGTON

first: Nadia

middle: Antoine

last: Ayoub

state: VA

address: 204 West Washington Street

department: Biology

institute: Washington and Lee University

summary: Spider silk synthesis is an emerging model for the evolution of tissue-specific gene expression and the role of gene duplication in functional novelty, but its potential has not been fully realized. Accordingly, we quantified transcript (mRNA) abundance in seven silk gland types and three non-silk gland tissues for three cobweb-weaving spider species. Evolutionary analyses based on expression levels of thousands of homologous transcripts and phylogenetic reconstruction of 605 gene families demonstrated conservation of expression for each gland type among species. Despite serial homology of all silk glands, the expression profiles of the glue-forming aggregate glands were divergent from fiber-forming glands. Also surprising was our finding that shifts in gene expression among silk gland types were not necessarily coupled with gene duplication, even though silk-specific genes belong to multi-paralog gene families. Our results challenge widely accepted models of tissue specialization and significantly advance efforts to replicate silk-based high-performance biomaterials.

sample_organism:
Latrodectus geometricus
Latrodectus hesperus
Steatoda grossa

overall_design: We isolated mRNA from seven types of silk glands and three non-silk gland tissues for three species of cobweb weaving spiders. We aimed for two replicate isolations of each tissue, but failed to obtain sufficient material for all tissue types for each species. Each replicate RNA isolate included tissue from 8-29 individuals.

middle: A

first: Thomas

last: Clarke

first: Jessica

last: Garb

first: Cheryl

middle: Y

last: Hayashi


title: The landscape of A-to-I RNA editome from 462 individuals human genomes

status: Public on Aug 31 2017

first: Wenjie

last: Shu

address: Taiping Road 27

institute: Beijing Institute of Radiation Medicine

type:
Third-party reanalysis
Other

summary: A-to-I editing, as a post-transcriptional modification process mediated by ADAR, plays a crucial role in many biological process in metazoans. However, how and to what extent that A-to-I editing diversifies and shapes the population diversity at the RNA level is largely unknown. We employed 462 mRNA-sequencing data from five populations of the Geuvadis Project and identified 16,518 A-to-I editing sites, forming a landscape of RNA editome of the human genome. By exploration of RNA editing within and between populations, we discovered non-adaption of nonsynonymous editing in the evolution, and revealed geographic restriction of rare editing sites. Moreover, we showed that RNA editing can characterize the subtle but substantial divergence between different populations, especially those from different continents. Altogether, we demonstrated RNA editing can well depict the nature and structure of populations at RNA level, which provides insights into the process of how A-to-I editing shapes population diversity at transcriptomic level. Our work will facilitate the understanding of the landscape of RNA editome at population-scale, and be helpful to interpret difference in the distribution and prevalence of disease among individuals and across populations.

overall_design:
We employed 462 mRNA sequencing samples from the CEU, FIN, GBR, TSI and YRI populations from Geuvadis project (ENA study accession number:ERP001942; BioProject accession number: PRJEB3366; home page: http://www.geuvadis.org/web/geuvadis/rnaseq-project) and identified a total of 16,518 A-to-I editing sites. By analyzing the sharing of identified RNA editing sites in each population and among populations, we revealed that the landscape of human RNA editome could reflect unique nature of human populations. We present a broad representation of A-to-I RNA editome from human genomes, which will be of immense use to future studies in investigating RNA editing at population level.

data processing:
mRNA-seq reads were aligned to the hg19 genome assembly using STAR (version 2.5.2b) with default parameter.

Duplicated reads that mapped to the same location were removed using Picard (version 1.141)(https://broadinstitute.github.io/picard/) with default parameter.

Reads with a mapping quality <20 were removed using samtools(version 1.3.1) with parameter '-q 20'.

Variants were called using the GATK(version 3.5.0) HaplotypeCaller tool with options stand_call_conf of 20 and stand_emit_conf of 0.

Candidate RNA editing site were called using the following filtering steps: (1) all variants present in dbSNP (except SNPs of molecular type 'cDNA', database version 137, http://www.ncbi.nlm.nih.gov/SNP/) and the 1000 Genomes Project were removed; (2) variants located in the first 6 bp from either end of a sequence read were discarded; (3) in non-Alu regions, we removed sites in simple repeats according to RepeatMasker annotation, discarded intronic candidates if they were located within 4 bp of all known splicing junctions according to Ensembl gene annotations, and removed sites in homopolymer runs of ?5 bp; (4) variant sites in regions of high similarity to other parts of the genome were discarded using the BLAST-like alignment tool (BLAT); (5) each RNA editing site is required to exhibit coverage of at least ten reads and at least three edited reads and to be present in more than three individuals of a population; (6) the editing type of each site was inferred based on the strand of overlapping annotated genes and only A-to-I base changing editing sites were retainned.

Genome build: hg19

processed data file content: Tab-delimited text files include basic information of identified A-to-I editing sites for each sample;  basic information includes chromosome, position, strand, reference base, altered base, edting level, the number of reference reads, the number of altered reads of each A-to-I editing site.

The SRA Run accessions used in this reanalysis study are listed in the supplementary file names.

**NOTE: All processed data files have been replaced on July 3rd, 2018 by the submitter ***

first: Zhangyi

last: Ouyang

first: Hao

last: Li

first: Xiaochen

last: Bo


title: The transcription factor Tcf1 ensures the development and cytotoxic function of NK cells by limiting the expression of Granzymes

city: Lausanne

first: Paolo

last: Angelino

address: Quartier Sorge, Bâtiment Génopode

department: BCF

country: Switzerland

institute: SIB Swiss Institute of Bioinformatics

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

overall_design: Refer to individual Series


title: JAG1 Mediated Notch Signaling Regulates Secretory Cell Differentiation of the Human Airway Epithelium

city: New York

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

summary:
Background: Basal cells (BC) are the stem/progenitor cells of the human airway epithelium capable of differentiating into secretory and ciliated cells. Notch signaling activation increases BC differentiation into secretory cells, but the role of individual Notch ligands in regulating this process is unknown
Results: The objective of this study was to define the role of the Notch ligand JAG1 in regulating BC differentiation. JAG1 over-expression in BC increased secretory cell differentiation, with no effect on ciliated cell differentiation. Conversely, knockdown of JAG1 decreased expression of secretory cell genes.
Conclusions: These data demonstrate JAG1 mediated Notch signaling regulates differentiation of BC into secretory cells.
This study demonstrates that expression of the Notch ligand JAG1 is highly enriched in basal stem/progenitor cells (BC) of the human airway epithelium and that modulation of its expression levels during differentiation of BC play an important role in regulating secretory cell differentiation with no effect on ciliated cell differentiation.  These observations have implications for developing novel targets to specifically modulate levels of secretory cells in human airway disorders.

overall_design:
RNA sequencing of primary (Passage 0) and immortalized BC was performed on cells once they had reached 70-80% confluence.
The 8 RNA-Seq samples in this submission were all normal, nonsmoker samples without any over-expression or knock-down.
The 8 RNA-Seq samples show the BCiNS1.1 cell line samples to be similar to the primary basal cell (BC) samples.

first: Kazunori

last: Gomi

first: Michelle

middle: R

last: Staudt

first: Jacqueline

last: Salit

first: Robert

last: Kaner

first: Jonna

last: Heldrich

first: Allison

last: Rogalski

first: Vanessa

last: Arbelaez

first: Ronald

middle: G

last: Crystal

first: Matthew

middle: S

last: Walters


title: Imprinted genes in Capsella rubella

city: Sentul

first: Marcelinus

middle: Rocky

last: Hatorangan

state: Jawa Barat

address: Cijayanti, Babakan Madang

department: Biotechnology

country: Indonesia

institute: PT SMART, Tbk.

summary: Genome-wide identification of imprinted genes in C. rubella.

overall_design: Two replicates of Capsella rubella reciprocal hybrid seeds

first: Claudia

last: Köhler


title: E2F3a mediates cocaine action in nucleus accumbens via alternative splicing and transcription

first: Immanuel

last: Purushothaman

state: New York

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

summary: Long-lasting changes in neuronal gene expression in brain reward regions, including the nucleus accumbens (NAc), contribute to the persistent functional changes in the addicted brain. Our group and others have demonstrated that altered expression or activity of several candidate transcription factors in NAc regulates drug responses. In a recent study from our group (Feng et al., 2014), involving large-scale genome-wide datasets, E2F3 was predicted as a prominent upstream regulator of cocaine-induced changes in gene expression and alternative splicing. Here, we show that E2F3a, but not E2F3b, expression in NAc regulates cocaine-induced locomotor and reward behavior. Furthermore, we demonstrate that E2F3a overexpression recapitulates a considerable portion of genome-wide transcriptional profiles and alternative splicing induced by cocaine administration. We further validate functional binding of E2F3a at several target genes following cocaine exposure. These novel findings support a crucial role for E2F3a in the regulation of cocaine-elicited behavioral states and molecular mechanisms.

overall_design: mRNA profiles were generated in response to viral-mediated overexpression of E2F3a or GFP followed by either saline or cocaine treatment, with a sample size of 3-4 per group.

first: Hannah

middle: M

last: Cates

first: Eric

last: Nestler


title: DNA methylation dynamics during early plant life

city: Lyon

first: Daniel

last: Bouyer

address: 46 Allée d'Italie

department: ENS-Lyon/RDP

institute: CNRS

summary: We uncover distinct DNA methylation dynamics over genes and repeat sequences during early plant life in Arabidopsis. While gene body methylation, which is restricted to CG sites and concerns 20-30% of all genes is detected at all stages examined, it typically fluctuates over a few CGs, with no coherent pattern. In contrast, transposable elements and their relics as well as other repeat sequences, have consistently high methylation levels at CGs and show increasing CHG and especially CHH methylation during embryogenesis. Remarkably, methylation reaches 100% at many individual CHH sites in the mature embryo, compared to the 10-20% methylation usually observed at CHH sites in seedlings or adult plants. Moreover, the progressive increase in CHG and CHH methylation in embryos mirrors the loss of DNA methylation at CG and CHG sites in the endosperm, suggesting transfer of information from the endosperm to the embryo, presumably in the form of small RNAs. Finally, impairing the embryo to seedling transition through loss of PRC2 activity results in the persistence of high CHH methylation levels after germination and specifically over sequences that are targeted by the RNA-directed DNA methylation (RdDM) machinery. Collectively, our findings indicate a lack of extensive resetting of DNA methylation patterns during early plant life and point instead to an important role of RdDM in targeting DNA methylation to transposable element and other repeat sequences in all cells of the mature embryo.

overall_design: Bisulfite sequencing of mature embryos and early seedlings in wild type and fie mutants and small RNA-seq from 10 day wildtype seedling.

first: François

last: Roudier

first: Vincent

last: Colot


title: The transcription factor Tcf1 ensures the development and cytotoxic function of NK cells by limiting the expression of Granzymes [ChIP-Seq]

first: Paolo

last: Angelino

summary: The transcription factor Tcf1 plays an essential role for the development of NK cells, however, its precise role for NK cell development, maturation and function is poorly understood. Here we show that distinct domains of Tcf1 direct bone marrow progenitors towards the NK cell lineage and mediate lineage commitment and NK cell expansion, and that Tcf1 downregulation is required for terminal NK cell maturation. Impaired NK cell development in the absence of Tcf1 is explained by increased cell death due to excessive expression of Granzyme family proteins, which results in NK cell self-destruction. In addition, excessive Granzyme B expression leads to target cell induced NK cell death and consequently reduced target cell killing by NK cells lacking Tcf1. Mechanistically, Tcf1 prevents excessive Granzyme B expression by binding to a newly identified enhancer element upstream of the Granzyme B locus. These data identify an unexpected requirement to limit the expression of cytotoxic effector molecules for lymphocyte development.

overall_design: Splenic NK cells from Tcf7+/+ and Tcf7-/- mice were cultured with IL-2 for five days, and chromatin-immunoprecipitation (ChIP) was performed using antibodies against Tcf1 and the active epigenetic mark H3K4me3. DNA from these ChIPs was purified, amplified, and sequenced as single-end 100 base reads.

first: Beena

last: Jeevan-Raj

first: Mauro

last: Delorenzi

first: Werner

last: Held


title: MicroRNA profiles by deep sequencing (miRNA-seq) of human clear cell renal cell carcinoma (ccRCC) samples from patients treated with tyrosine kinase inhibitors (TKIs)

city: Madrid

first: Inglada

last: Lucía

state: Madrid

address: C/ Melchor Fernández Almagro, 3

department: Human Cancer Genetics

country: Spain

institute: CNIO

summary: The majority of metastatic clear cell renal cell carcinoma (ccRCC) patients are treated with tyrosine kinase inhibitors (TKIs) in first line, however, a fraction are refractory to these drugs. MicroRNAs (miRNA) are regulatory molecules that have proven to be accurate biomarkers in cancer. Here we identified miRNA predictive of progressive disease under TKI treatment. Whole miRNA expression was quantified by deep-sequencing in a discovery set of 74 metastatic ccRCC cases uniformly treated with TKIs. Twenty nine miRNAs were found to be differentially expressed in the tumors of patients who progressed under TKI therapy. Among six miRNAs selected for validation, an over-expression of miR-1307-3p, miR-155-5p, miR-221-3p, miR-425-5p and miR-222-3p was confirmed in patients with progressive disease as best response. A 2 miRNA-based classifier could discriminate individuals with progressive disease upon TKI treatment with a better predictive value than clinicopathological risk factors commonly used. miRNAs significantly associated with progression-free survival and overall survival  were identified, and 7 miRNAs were found to overlap as predictive for early progressive disease, PFS and OS.

overall_design: Deep-sequencing in a discovery set of metastatic ccRCC cases uniformly treated with TKIs. In the tumor bank of the University Hospitals Leuven (Belgium), we searched for metastatic ccRCC patients treated with sunitinib, sorafenib or pazopanib as first-line anti-VEGFR-TKIs with available archived formalin-fixed paraffin embedded (FFPE) primary tumors and nephrectomy as first therapeutic intervention. Previous immunotherapy or chemotherapy was allowed, but previous exposure to other targeted therapies was an exclusion criterion. miRNA NGS was performed in 81 cases identified, but subsequently 5 cases were excluded because no CT scan evaluating anti-VEGFR-TKI response was available (they all had less than 1 month TKI treatment), 1 case was a misclassified papillary RCC and 1 patient developed a secondary tumor potentially affecting TKI response. Therefore, 74 ccRCCs were included in the analysis.

first: Benoit

last: Beuselinck

first: Lucia

last: Inglada-Perez

first: Osvaldo

last: Graña

first: Cristina

last: Rodríguez-Antona


title: Epigenetic landscapes in wild-type and dimer-mutant Notch regulated T-LL cells

city: Charlottesville

first: Chongzhi

last: Zang

institute: University of Virginia

summary: NOTCH/RBPJ/MAML ternary transcriptional complex binds to regulatory element and drives gene expression. The complex can function as monomer and dimer. How dimeric complexes regulate gene expression in human cancer is not well studied. Here, we integrate genomic data sets and analyze Notch dimeric complexes-regulated transcriptome and cis-regulatory elements. A subset of coding and non-coding RNA is Notch dimeric complexes-associated. Dimeric complexes recognition sequence enriched in functional dynamic Notch sites and majority of dimer recognition sequence located in (super-)enhancers. Using CRISPR-Cas9-mediated genome editing, we evaluated the function of one dimer-responsive element located in the promoter region of a noncoding RNA NDANR1 and 5' end 16kb away from HES5. Mutation of SPS in this element reduced expression of HES5 and NDANR1. This finding indicates that dimer-responsive elements can function as enhancer for HES5 and at the same time can function as promoter for noncoding RNA NDANR1. Our study reveals the pervasive role of Notch dimeric complexes in transcriptional regulation in human cancer genome.

overall_design: Identifying genomic profiles of histone modifications H3K27ac in wild-type Notch (ICN1) and dimer-mutant (R1984A) induced human T-cell acute lymphocytic leukemia cell lines.

first: Hongfang

last: Wang

first: Sujun

last: Chen

first: X

last: Liu

first: Jon

middle: C

last: Aster


title: Ubiquitination-dependent control of sexual differentiation in fission yeast

city: Montpellier

first: Domenico

last: Libri

address: 1919 route de Mende

institute: IGMM - CNRS

summary: In fission yeast, meiosis-specific transcripts are selectively eliminated during vegetative growth by the combined action of the YTH-family RNA-binding protein Mmi1 and the nuclear exosome. Upon nutritional starvation, the master regulator of meiosis Mei2 inactivates Mmi1, thereby allowing expression of the meiotic program. Here, we show that the E3 ubiquitin ligase subunit Not4/Mot2 of the evolutionarily conserved Ccr4-Not complex, which associates with Mmi1, promotes suppression of meiotic transcripts expression in mitotic cells. Our analyses suggest that Mot2 directs ubiquitination of Mei2 to preserve the activity of Mmi1 during vegetative growth. Importantly, Mot2 is not involved in the constitutive pathway of Mei2 turnover, but rather plays a regulatory role to limit its accumulation or inhibit its function. We propose that Mmi1 recruits the Ccr4-Not complex to counteract its own inhibitor Mei2, thereby locking the system in a stable state that ensures the repression of the meiotic program by Mmi1.

overall_design: Total RNAs from wild type (triplicate), mot2∆ (duplicate) and rrp6∆ (duplicate) strains were analyzed by high-throughput sequencing

first: Fabrizio

last: Simonetti

first: Tito

last: Candelli

first: Sebastien

last: Leon

first: Mathieu

last: Rougemaille