title: Transcriptomics analysis of bursal B-cells from the chick embryo

city: Mississippi State

first: Gregory

middle: Todd

last: Pharr

state: MS

address: 240 Wise Center Drive

department: College of Veterinary Medicine

institute: Mississippi State University

summary: The chicken bursa of Fabricius is a primary lymphoid tissue important for B-cell development. Our long-term goal is to understand the role of bursal microenvironment in an early B-cell differentiation event initiating repertoire development through immunoglobulin gene-conversion in the chick embryo. We hypothesize that early bursal B-cell differentiation is guided by signals through cytokine receptors. Our theory is based on previous evidence for expression of the receptor tyrosine kinase superfamily members and interleukin receptors in unseparated populations of bursal B-cells and bursal tissue. Knowledge of the expressed genes that are responsible for B-cell differentiation is a prerequisite for understanding the bursal microenvironment’s function. This project uses transcriptomic analysis to evaluate gene expression across early B-cell development. Approximately 90 million high quality clean reads were obtained from the cDNA libraries. The analysis revealed differentially expressed genes involved in the Jak-STAT pathway, Wnt signaling pathway, MAPK signaling pathway, metabolic pathways including tyrosine metabolism, Toll-like receptor signaling pathway, and cell-adhesion molecules. The genes predicted to encode surface receptors, signal transduction proteins and transcription factors identified in this study represent gene candidates for controlling B-cell development in response to differentiation factors in the bursal microenvironment.

overall_design: RNA-seq was performed with total RNA isolated from bursal B-cells at embryonic day (ED) 16 and ED 19 (n=3 biological replicates per embryonic time point).

first: Nikhil

last: Nuthalapati

first: Jeffrey

last: Evans

first: Robert

last: Taylor Jr

first: Scott

last: Branton

first: Bindu

last: Nanduri


title: mTORC1/AMPK responses define a core gene set for developmental cell fate switching

status: Public on May 22 2019

city: Bethesda

first: Cameron

last: Palmer

state: MD

address: 50 South Drive

department: National Institute of Diabetes and Digestive and Kidney Diseases

country: USA

institute: National Institutes of Health

type: Expression profiling by high throughput sequencing

summary: The kinases mTORC1 and AMPK are at the nexus of nutrient responses and control of cellular growth. However, responses to nutrient loss are complex and affect multiple transcriptional pathways. We are interested in the mTORC1-directed regulation of transcription networks that specifically regulate developmental decisions. Dictyostelium grow logarithmically as single cells in nutrient-rich media, but, upon nutrient withdrawal, growth ceases and cells enter a program for multi-cellular development. Within 30 minutes of starvation, >4,000 genes show significant (p<0.05) changes in gene expression patterns. However, we hypothesize that not all these gene changes are required for development and that many expression changes reflect stress response to a media shift supplementary to nutrient loss, apart from developmental effects. We, thus, sought ways to promote development in the absence of nutrient loss, to better focus on developmentally essential gene sets. Since kinases mTORC1 and AMPK function as nutrient and energy sensors, we first examined their relative activities in Dictyostelium during phases of rapid growth and starvation-induced development. We found that these kinases exhibited reciprocal patterns of activation under various conditions. With this knowledge, we identified rich media conditions that permitted rapid cell growth, but a growth/development switch upon the directed and reciprocal inactivation/activation of mTORC1/AMPK. Examination of gene expression under conditions of development in nutrient-rich media indicated that changes in expression of most starvation-regulated genes were not required for development. Our data suggest that the up-regulation of ~300 genes defines essential early signaling pathways for developmental induction, integrating cAMP/PKA circuitries and including many unclassified genes.

overall_design: We compared Dictyostelium discoideum gene expression by deep RNA-seq under conditions of stavation and rapamycin-induced development in nutrient-rich media and identify an extensive gene network involved in developmental signal transduction that is upregulated by both starvation and rapamycin and separate downregulated gene classes involved in protein synthesis and in DNA replication and cell division.

first: Pundrik

last: Jaiswal

first: Alan

last: Kimmel


title: Transcriptome changes caused by RBP-L knockdown in rice grains

city: Pullman

first: Li

last: Tian

state: WA

address: Clark hall, IBC, Washington State University

department: IBC

institute: Washington State University

summary: A T-DNA insertion within RBP-L 3’UTR resulted in 10-25% expression level of RBP-L gene compared to wild-type. The reduced expression of RBP-L caused partial mis-localization of glutelin and prolamine RNAs and conferred other general growth defects including dwarfism, late flowering and smaller seeds. Transcriptome analysis showed that RBP-L knockdown greatly affected the expression of prolamine family genes and many genes invovled in essential biological pathways during plant development.

overall_design: Total 6 samples were anlyzed, including 3 biological repeats from wild type (ZH11) and RBP-L knockdown (rbpl) line.

first: Thomas

middle: W

last: Okita


title: Expression profiles of microRNAs and transfer RNA-derived small RNAs in laser-induced choroidal neovascularization in mice.

status: Public on May 23 2019

city: Changsha

first: Yedi

last: Zhou

state: Hunan

address: No. 139, Middle Renmin Road

department: Department of Ophthalmology

country: China

institute: The Second Xiangya Hospital, Central South University

type: Non-coding RNA profiling by high throughput sequencing

summary: The purpose of the study was to investigate the roles and possible functions of the miRNAs and tsRNAs in choroidal neovascularization (CNV).The mouse model of laser-induced CNV was conducted by laser photocoagulation and the samples were collected 7 days after laser treatment. The expression profiles of miRNAs and tsRNAs were accessed by small RNA sequencing in RPE-choroid-sclera complexes of mice in CNV group and controls. Our study identified differential expressions of miRNAs and tsRNAs in CNV model, and these altered miRNAs and tsRNAs might be novel potential targets in treating CNVs in patients with neovascular age-related macular degeneration.

overall_design: The mouse model of laser-induced CNV was conducted by laser photocoagulation. The expression profiles of miRNAs and tsRNAs were accessed by small RNA sequencing (RNA-seq) in RPE-choroid-sclera complexes of mice in CNV group and control group.

first: Liwei

last: Zhang


title: The MYB5-driven MBW complex recruits a WRKY factor to enhance the expression of targets involved in vacuolar hyper-acidification and trafficking in grapevine

city: VR

first: Alessandra

last: Amato

address: strada le grazie 15

country: Italy

institute: University of Verona

summary: The accumulation of secondary metabolites and the regulation of tissue acidity contribute to important traits like color, astringency and acidity of grape berry which are essential to the value of the final product, the wine. Moreover, they influence the plant performance in response to the environment and to parasites and herbivores. In several plant species highly conserved WD-MYB-bHLH-WRKY (WMBW) transcriptional complexes determine color and acidity in epidermal cells. Here we investigated the function in grapevine (Vitis vinifera L.) of WMBW complexes involving two MYBs (VvMYB5a and VvMYB5b) and the WRKY-type transcription factor VvWRKY26. Using transgenic grapevine plants we show that these complexes affect different aspects of morphology, plant development, pH regulation, and pigment accumulation. Transcriptomic analysis identified a core set of putative target genes controlled by VvMYB5a, VvMYB5b and VvWRKY26 in different tissues. Our data indicate that VvWRKY26 enhances the expression of selected target genes induced by VvMYB5a/b. Among these target genes are enzymes of the biosynthesis of flavonoids, genes involved in cell-type identity and the P-type ATPases VvPH5 and VvPH1. In addition, VvWRKY26 is recruited specifically by VvMYB5a, reflecting the functional diversification of VvMYB5a and VvMYB5b. The expression of WBMW complexes in vegetative organs, such as leaves, indicates a possible function of vacuolar hyper-acidification in repulsion of parasites/herbivores and/or in developmental processes as shown by defects in transgenic grape plants where the WMBW complex is inactivated.

overall_design: Transcriptomic changes caused by the alteration of VvMYB5a, VvMYB5b and VvWRKY26 expression, were inspected by a microarray analysis performed on leaf RNA of selected transgenic lines and wild type plants. Three biological replicates of fully expanded leaves were collected before the onset of the altered phenotype in order to avoid secondary transcriptional effects.

first: Erika

last: Cavallini

first: Amanda

middle: R

last: Walker

first: Mario

last: Pezzotti

first: Mattijs

last: Bliek

first: Francesca

middle: M

last: Quattrocchio

first: Ronald

last: Koes

first: Benedetto

last: Ruperti

first: Edoardo

last: Bertini

first: Sara

last: Zenoni

first: Giovanni

middle: B

last: Tornielli


title: In vitro B cell activation by Th1 cells promotes the transcriptional programming of antibody-secreting cells, while B cell activation in presence of Th2 cells maintains the B cell identity transcriptional program

city: Birmingham

first: Frances

last: Lund

state: AL

address: 1720 2nd Avenue South

department: Microbiology

institute: University of Alabama at Birmingham

summary: To investigate the role of Th1 versus Th2 cell help on B cell activation and differentiation into B cell effectors and antibody secreting cells (ASCs), we utilized an in vitro culture system to activate B cells in the presence of Th1 or Th2 polarized CD4+ T cells. To obtain an unbiased mRNA profile of these cells, we performed a kinetic mRNA profiling analysis on Be1 cells (B cells cultured with Th1 cells) or Be2 cells (B cells cultured with Th2 cells) on days 1, 2, 3, and 4 of co-culture.

overall_design: We used Affymetrix chip analysis to perform mRNA profiling of C57BL/6J (B6) mouse splenic B cells co-cultured with Th1 or Th2 cells for 1-4 days.

first: Alex

last: Rosenberg

first: Wojciech

last: Wojciechowski

first: Adedayo

last: Hanidu

middle: E

first: Betty

last: Mousseau

first: Huiping

last: Jiang

first: Zhenhao

last: Qi

first: Scott

last: Brodeur


title: Decomposing cell identity for transfer learning across cellular measurements, platforms, tissues, and species.

city: St. Louis

first: Brian

middle: Stewart

last: Clark

state: Missouri

address: 660 S Euclid Ave; Campus Box #8096

department: Ophthalmology and Visual Sciences

institute: Washington University

summary: Bulk ATAC-seq and RNA-seq on sorted retinal cells from Chx10:GFP reporter mice

overall_design: Analysis of transfer learning across sequencing modalities

middle: S

first: Cristina

last: Zibetti

first: Seth

last: Blackshaw


title: RNA-seq of ATF7ip-deficient T cells

status: Public on May 21 2019

city: San Francisco

first: Michael

middle: Robert

last: Waterfield

state: CA

address: 513 Parnassus Ave MSB S-1076

department: Diabetes Center

institute: UCSF

summary:
RNA-seq performed in ATF7ip-deficient T cells reveals a defect in Th17 gene induction secondary to increased IL-2
T helper 17 cells (Th17) are critical for fighting infections at mucosal surfaces, however, they have also been found to contribute to the pathogenesis of multiple autoimmune diseases and Th17 cells have been targeted therapeutically.  Due to the role of Th17 cells in autoimmune pathogenesis, it is important to understand the factors that control Th17 development.  Here we identify the activating transcription factor 7 interacting protein (ATF7ip) as a critical regulator of Th17 differentiation. Mice with T-cell-specific deletion of Atf7ip have impaired Th17 differentiation secondary to the aberrant overproduction of IL-2 with T-cell receptor (TCR) stimulation and are resistant to colitis in vivo. ChIP-seq studies identified ATF7ip as an inhibitor of Il2 gene expression through the deposition of the repressive histone mark H3K9me3 in the Il2-Il21 intergenic region. These results demonstrate a new epigenetic pathway by which IL-2 production is constrained and this may open up new avenues for modulating its production.

overall_design: Global gene expression analysis with RNA-seq was carried out in triplicate in ATF7ip-deficient naïve T cells and ATF7ip-deficient T cells in vitro differentiated under Th17 polarizing conditions for 24 hours and 72 hours in order to capture early and late changes in in gene expression

first: Jun

middle: H

last: Sin


title: H3K9me3 ChIP-seq in ATF7ip Knockout naïve T cells

type: Genome binding/occupancy profiling by high throughput sequencing

summary: T helper 17 cells (Th17) are critical for fighting infections at mucosal surfaces, however, they have also been found to contribute to the pathogenesis of multiple autoimmune diseases and Th17 cells have been targeted therapeutically.  Due to the role of Th17 cells in autoimmune pathogenesis, it is important to understand the factors that control Th17 development.  Here we identify the activating transcription factor 7 interacting protein (ATF7ip) as a critical regulator of Th17 differentiation. Mice with T-cell-specific deletion of Atf7ip have impaired Th17 differentiation secondary to the aberrant overproduction of IL-2 with T-cell receptor (TCR) stimulation and are resistant to colitis in vivo. ChIP-seq studies identified ATF7ip as an inhibitor of Il2 gene expression through the deposition of the repressive histone mark H3K9me3 in the Il2-Il21 intergenic region. These results demonstrate a new epigenetic pathway by which IL-2 production is constrained and this may open up new avenues for modulating its production.

overall_design: Naïve T cells were isolated by flow cytometry and H3K9me3 ChIP-seq was performed in duplicate CD4-Cre/ATF7ip+/fl vs CD4-Cre/ATF7ipfl/fl naïve T cells


title: Transcriptome changes caused by RBP-P mutations in rice seed

first: Li

last: Tian

summary: Two RBP-P mutants, P1MH and P3MH, carrying G401S and A252T point mutations, respectively, were obtained by TILLING studies (http://www.shigen.nig.ac.jp/rice/oryzabase). The A252T mutation site in P3MH lies within the linker sequence between the two RRM domains while the G401S substitutions in P1MH is located in the glycine-rich C-terminal region. Those mutations results in varying degrees of reduced RNA binding and/or protein-protein interactive properties of RBP-P. Transcriptome analysis on the dehulled 10-14 days old developing seeds from wild type, P1MH and P3MH mutants indicates that partial loss of RBP-P function caused the differential expression of storage protein genes and relevant genes involved in several essential biological processes during rice development.

overall_design: Total 9 samples were anlyzed, including 3 biological repeats from each genotype,wild type, P1MH (G401S) and P3MH (A252T)

first: Thomas

last: Okita


title: Modeling CMT1A with human induced pluripotent stem cell derived Schwann cells

city: Baltimore

first: Gabsang

last: Lee

address: 733 North Broadway

department: School of Medicine

institute: The Johns Hopkins University

summary:
We obtained skin fibroblasts from CMT1A and control patients, and generated hiPSCs which were subsequently differentiated into cd49d+ human Schwann cells.  We utilized microarray technology to explore the gene expression profiles of cd49d+ Schwann cells CMT1A hiPSCs, control hiPSCs, and control human embryonic stem cells in order to identify potentially disregulated pathways contributing to CMT1A pathogenesis.
Patient-specific human induced pluripotent stem cells (hiPSCs) hold great promise for disease modeling of genetic disorders. Often the findings from hiPSC-based studies are validated with genetically-corrected hiPSCs generated by precise genome editing technologies, however, alternatives that have not yet been employed are validation with embryonic stem cells harboring the same disease mutation or utilizing another reprogramming approach from somatic cells of same patients. Here we report that disease-relevant phenotypes found in Charcot-Marie-Tooth 1A (CMT1A)-hiPSC-derived Schwann cells were further confirmed by two additional congruent CMT1A models as an alternative to gene correction. We have devised a defined and relatively fast protocol for the direct derivation and prospective isolation of Schwann cells from hiPSCs, leading us to uncover a phenotype of dysregulated immune signaling in CMT1A-hiPSCs-Schwann cells. Our study illustrates the promise of applying hiPSC technology to one of the most common hereditary neuropathies for gaining new insights into human disease pathogenesis and treatment, and these results demonstrate the feasibility of verifying disease phenotypes by utilizing the malleability of cellular fates.

overall_design: hiPSC-Schwann cells from one CMT1A patient (3 samples), an unrelated patient (1 sample), a control hiPSC line (2 samples) and a control hESC line (2 samples) were analyzed using the Affy Primeview array

first: Bipasha

last: Mukherjee-Clavin


title: Effector TH17 cells give rise to long-lived TRM cells that are essential for an immediate response against bacterial infection

city: New Haven

last: Zhao

state: CT

address: 300 George Street

department: Pathology/Immunology

institute: Yale University

summary: Mucosal barrier surfaces serve as the critical first line of defense separating our bodies from the plethora of pathogenic microorganisms that inhabit our environment. Adaptive immunity provides life-long protection through the generation of a central and effector memory T-cell pool, memory B cells and the recently described population of tissue resident memory cells (TRM). The cellular origin of TRM CD4 cells is unknown and the contribution of this CD4 memory population to host defense still remains elusive. By using IL-17A tracking-fate-mouse models we found that a significant fraction of the CD4 TRM cells derive from IL-17A producing effector (TH17) cells following primary immunization. Maintenance of these resting exTH17 TRM cells is mediated by IL-7, produced by lymphatic endothelial cells. During a memory response, we show that neither antibodies, nor gd T cells, nor circulatory memory T cells are sufficient for the rapid host defense required to eliminate the pathogen. Using parabiosis and depletion studies, we demonstrated that CD4 exTH17 TRM cells play an important role in respiratory defense and bacterial clearance. Upon infection, exTH17 TRM cells rapidly produce IL-17A and IFN-γ to promote neutrophil infiltration and bacterial clearance. These studies delineate the origin, function and importance of airway CD4 TRM cells during bacterial infection, offering novel strategies for targeted vaccine design, which is especially imperative for those pathogens that are resistant to antibiotic treatment.

overall_design: We profiled the Single cell transcriptome of Lung cells (excluding CD4+ cells). Samples: Lung from naïve B6 mice and Lung from day 35 Klebsiella pneumoniae immunized mice.

first: Vesely

last: Amezcua

first: P

last: Pallis

last: Bielecki

first: J

middle: L

last: Siong

first: C

middle: C

last: Harman

first: L

last: Kroehling

first: R

last: Jackson

first: W

last: Bailis

last: Licona-Limon

first: H

last: Xu

first: N

last: Iijima

last: Pillai

first: D

last: Kaplan

last: Weaver

first: Y

last: Kluger

first: M

last: Kowalczyk

first: A

last: Iwasaki

last: Pereira

first: E

last: Esplugues

last: Gagliani

middle: A

last: Flavell


title: ZEB1 represses neural differentiation and cooperates with CTBP2 to dynamically regulate cell migration during neocortex development [ChIP-seq]

city: Shanghai

first: Qin

last: Shen

address: 1239 Siping Road

department: School of Life Sciences and Technology

institute: Tongji University

summary: Zinc finger E-box binding homeobox 1 (Zeb1) is a key regulator of epithelial-mesenchymal transition and cancer metastasis. Mutation of ZEB1 is associated with human diseases and defective brain development. Here we show that down-regulation of Zeb1 expression in the embryonic cortical neural progenitor cells (NPCs) is necessary for proper neuronal differentiation and migration. Overexpression of Zeb1 during neuronal differentiation when its expression normally declines blocks NPC lineage progression and disrupts multipolar-to-bipolar transition of differentiating neurons, leading to severe migration defects and subcortical heterotopia bands at the postnatal stage. We found that ZEB1 regulates a cohort of genes involved in cell differentiation and migration, including Neurod1 and Pard6b. Interestingly, interaction between ZEB1 and CTBP2 in the embryonic cerebral cortex is required for ZEB1 to elicit its effect on multipolar-to-bipolar transition but not its suppression of Neurod1. These findings provide insights into understanding the complexity of transcriptional regulation during neuronal differentiation.

overall_design: ChIP-seq of ZEB1 antibody enriched DNA and input DNA from dissociated cells of E14.5 mouse cortical tissues, in duplicates, using Illumina HiSeq Xten

first: Huanhuan

last: Wang

first: Zhengtao

last: Xiao

first: Jiangli

last: Zheng

first: Xiao-Ling

last: Hu

first: Xuerui

last: Yang


title: ZEB1 represses neural differentiation and cooperates with CTBP2 to dynamically regulate cell migration during neocortex development [RNA-seq]

overall_design: mRNA profiles of purified GFP+ cells from dissociated cortical cells at E16.5 that have been electroporated in utero with CAG-IRES-ZsGreen plasmid or CAG-Zeb1-IRES-ZsGreen plasmid at E14.5, in duplicate, using BGISEQ-500


title: ZEB1 represses neural differentiation and cooperates with CTBP2 to dynamically regulate cell migration during neocortex development

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

overall_design: Refer to individual Series


title: Single cell analysis of human fetal liver captures the transcriptional profile of hepatobiliary hybrid progenitors

city: London

first: Joe

last: Segal

address: 28 floor Tower wing, Great Maze pond

department: Centre of Stem Cell and Regenerative Medicine

country: United Kingdom

institute: Kings college London

summary: The liver parenchyma is composed of hepatocytes and bile duct epithelial cells (BECs). Controversy exists regarding the cellular origin of human liver parenchymal tissue generation during embryonic development, homeostasis or repair. Here we report the existence of a hepatobiliary hybrid progenitor (HHyP) population in human fetal liver using single-cell RNA sequencing. HHyPs are anatomically restricted to the ductal plate of fetal liver and maintain a unique transcriptional profile distinct from fetal hepatocytes, mature hepatocytes and mature BECs.  In addition, molecular heterogenicity within the EpCAM+ population of freshly isolated fetal and adult human liver reveals diverse gene expression signatures of hepatic and biliary lineage potential. Finally, we FACS isolated fetal HHyPs and confirmed their hybrid progenitor phenotype in vivo. Our study suggests that hepatobiliary progenitor cells previously identified in mice also exist in humans, and can be distinguished from other parenchymal populations, including mature BECs, by distinct gene expression profiles.

overall_design: Primary  samples from 5 2nd trimester human fetal livers and 3 uninjured adult human livers for single cell RNA sequencing by Smartseq2.

first: Daniel

middle: J

last: Wesche

first: S

middle: T

last: Rashid


title: The subtype-specific transcriptional regulatory networks of intestinal innate lymphoid cells

city: Cincinnati

first: Emily

last: Miraldi

state: Ohio

address: 3333 Burnet Avenue, MLC 7038

department: Immunobiology and Biomedical Informatics

institute: Cincinnati Children's Hospital Medical Center


title: The subtype-specific transcriptional regulatory networks of intestinal innate lymphoid cells (ATAC-seq)

summary: Innate lymphoid cells (ILCs) comprise a population of immune cells that promote tissue homeostasis, defense against infections, and inflammatory disease. Yet, the transcriptional control of these functions is not well understood. Here, we leverage an experimental-computational approach for transcriptional regulatory network (TRN) inference, recently validated in an in vitro context, to construct genome-scale TRNs for ILCs isolated ex vivo from the intestine of mice. Chromatin accessibility and gene expression are the key data for our TRN inference method. Thus, we generated ATAC-seq and RNA-seq datasets for ILCs of the small and large intestine to integrate with publicly available ILC genomics data. From our ILC TRN, we predict target genes for hundreds of transcription factors (TFs), recovering both known and novel TF regulators of ILC subtype-specific gene expression patterns. The identified TFs include both activators and repressors of lineage-specific genes. Using KO mice, we validated predictions for two such TFs, MAF and BCL6, as previously unknown regulators affecting the balance of ILC3-ILC1. We additionally demonstrate the utility of our ILC TRN to describe gene expression responses to Bcl6 KO in ILC1, NK and ILC3 and predict TF regulators in each subtype. The ILC TRN and “core” ILC subtype networks are publicly available through an interactive Jupyter-notebook web interface. We anticipate that these maps of ILC subtype-specific transcriptional regulation will serve as an important community resource and lead to the development of new strategies for the control of subtype-specific behaviors, especially in the context of disease.

overall_design: Chromatin accessibility (ATAC-seq) of ILCs isolated from the small intestine and large intestine at steady state

first: Maria

last: Pokrovskii

first: Richard

last: Bonneau

first: Dan

last: Littman


title: The subtype-specific transcriptional regulatory networks of intestinal innate lymphoid cells (RNA-seq)

overall_design: Gene expression (RNA-seq) of innate lymphoid cells of the small intestine (SI) and large intestine (LI) lamina propria

first: Jason

last: Hall

first: David

last: Ochayon

first: Stephen

middle: N

last: Waggoner


title: Changes in skeletal muscle gene expression following nutrient consumption

city: Tallahassee

first: gang

last: wang

state: Florida

address: 319 Stadium Dr

department: The Center for Genomics and Personalized Medicine

institute: Florida State University

summary:
The objective of this study was to identify novel genes whose expression is sensitive to anabolic stimuli.
We used microarrays to detail the change in gene expression within the tibialis anterior muscle following an anabolic stimulus.  In this case, the anabolic stimulus was nutrient consumption.

overall_design: Male, C57Bl/6 mice aged 18 weeks were fasted beginning at 1800 hr.  The next morning (~0800 hr), mice were randomized to remain fasted or were allowed to refeed for 30 minutes.  Following the refeeding, all mice were fasted for an additional 4 hr until sacrifice.  Those mice not refed remained fasted until sacrifice at the same time of day as those mice that were refed.  At sacrifice, all mice were anesthetized with isoflurane, and the tibialis anterior muscle was extracted and flash frozen in liquid nitrogen

first: Bradley

last: Gordon


title: Targeting enhancer switching overcomes non-genetic drug resistance in acute myeloid leukaemia [ATAC-seq]

city: Melbourne

first: Mark

last: Dawson

state: VIC

address: 305 Grattan Street

country: Australia

institute: Peter MacCallum Cancer Centre

summary: The prevailing model of therapeutic resistance in cancer posits that malignant cells acquire genetic mutations in the context of therapeutic pressure that negate the efficacy of the drug. This mutation centric view of therapeutic resistance has recently been challenged by emerging evidence that shows a paucity of genetic diversity in malignant cells that evade therapeutic challenge emphasizing the role of epigenetic evolution in drug resistance. We have previously established that therapeutic resistance emerges in the absence of genetic adaptation from leukemia stem cells and whilst the clinical relevance of these findings has been established, what remains unanswered is whether transcriptional programs that confer resistance to therapies are pre-existing or acquired. It is also unclear how stable this adaptive transcriptional response is and whether it can be reversed. Here, we utilize a unique leukaemia model to highlight the key principles of epigenetic resistance. Using single cell RNA-seq with indexed flow sorting, we demonstrate that a form of Lamarckian evolution, namely transcriptional plasticity, drives epigenetic resistance. With a CRISPR-Cas9 screen we identify reciprocal regulators of the enhancer modification H3K4me1/2, LSD1 and MLL4, as important modulators of the resistant cell state. Knockdown or catalytic inhibition of LSD1 causes reversion to a drug sensitive state that is dependent on the lineage determining pioneer transcription factor Pu.1. Mechanistically, we establish that inhibition of LSD1 results in newly formed enhancers marked by H3K4me1/2, H3K27ac and Pu.1 binding, which facilitates the recruitment of transcriptional co-activators and activation of a differentiation gene expression program. We show that this enhancer-remodeling does not result in a simple linear reversion to the original chromatin state of drug naive cells, rather it reinstates the cells dependence on transcriptional co-activators including Med1 and Brd4 due to the formation of new enhancers with enhancer-promoter loops to canonical Brd4 target genes. Together these findings provide new insights into the molecular mechanisms that facilitate epigenetic resistance to cancer therapies and highlight new opportunities for therapeutic intervention to overcome transcriptional plasticity.

overall_design: ATAC-seq of BET inhibitor resistant and sensitive leukaemic cells, and resistant cells treated with LSD1 inhibitor and/or Pu.1 knock-down by shRNA and/or Irf8 overexpression vector

first: Charles

last: Bell

first: Enid

middle: Y

last: Lam


title: Targeting enhancer switching overcomes non-genetic drug resistance in acute myeloid leukaemia [Click-seq]

overall_design: Click-seq of BET inhibitor resistant and sensitive leukaemic cells and resistant cells treated with LSD1i with clickable BET inhibitor


title: Targeting enhancer switching overcomes non-genetic drug resistance in acute myeloid leukaemia [RNA-seq]

overall_design: RNA-seq of of BET inhibitor resistant and sensitive leukaemic cells treated with DMSO, BET inhibitor and/or LSD1 inhibitor


title: Targeting enhancer switching overcomes non-genetic drug resistance in acute myeloid leukaemia


title: Targeting enhancer switching overcomes non-genetic drug resistance in acute myeloid leukaemia [ChIP-seq]

overall_design:
ChIP-seq of epigenetic proteins and histone modifications in BET inhibitor resistant and sensitive cells and BET inhibitor resistant cells treated with LSD1i
ChIP-seq of epigenetic proteins in BET inhibitor resistant and sensitive cells and resistant cells treated with LSD1 inhibitor and/or Pu.1/Irf8 knock-down by shRNA


title: Enhancer remodeling overcomes therapeutic resistance driven by epigenetic evolution in cancer [HiChIP]

overall_design: HiChIP of I-BET resistant cells and resistant cells treated with LSD1 inhibitor


title: Whole transcriptomic analysis of zebrafish embryos of dyrk1aakrb1, dyrk1aa knock out mutant and Wild Type (WT) (+/+) in the background of Tg(kdrl:egfp) [32 hpf]

status: Public on May 20 2019

city: Daejeon

first: Jong Hwan

last: Kim

address: 125 Gwahak-ro, Yuseong-gu

department: Genome structure research center

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

summary: Purpose: The goals of this experiments are to analyze the transcriptomic change in dyrk1aakrb1 mutants compared with WT embryos by mRNA-seq technique.          Methods: Whole mRNA profiles of 32 hpf WT(+/+) and dyrk1aakrb1 mutants zebrafish embryos were generated by mRNA-seq techinque, in duplicate, using HiSeq 2500 (Illumina, Inc., USA).  Results: This analysis identified 354 transcripts as differentially regulated genes (DEG), of which 125 were up-regulated and 229 were down-regulated in dyrk1aakrb1 mutant (more than 2 fold and less than 0.5 fold respectively,; p value< 0.05).

overall_design: Whole transcriptomic analysis of zebrafish embryos of dyrk1aakrb1, dyrk1aa knock out mutant and WT (+/+) in the background of Tg(kdrl:egfp) at 32 hpf.

first: Hyun-Ju

last: Cho

first: Jeong-Soo

last: Lee

first: Jong

first: Seon


title: Targeting enhancer switching overcomes non-genetic drug resistance in acute myeloid leukaemia [CRISPR screen]

overall_design: Positive selection CRISPR-Cas9 screen with epigenetic library


title: Functional proteomics identified a PICS complex required for piRNA maturation and chromosome segregation

status: Public on May 19 2019

city: Hefei

first: chenming

last: zeng

state: Anhui

address: Huangshan Road 443

department: Life Science

institute: University of Science and Technology of China

summary: Piwi-interacting RNAs (piRNAs) play significant roles in suppressing transposons and nonself nucleic acids, maintaining genome integrity, and defending against viral infections, and are essential for fertility in a variety of organisms. In C. elegans, most piRNA precursors are transcribed by RNA polymerase II in the nucleus and are subjected to a number of processing and maturation steps. However, the biogenesis of piRNAs is still not fully understood. We used functional proteomics to study piRNA biogenesis in C. elegans and identified a piRNA processing and chromosome segregation (PICS) complex. The PICS complex contains two known piRNA biogenesis factors, TOFU-6 and PID-1, and three new proteins PICS-1, TOST-1, and ERH-2, which exhibit dynamic localization among different subcellular compartments. In the germlines of gravid animals, the PICS complex contains TOFU-6/PICS-1/ERH-2/PID-1, is largely concentrated at the perinuclear granule zone and engages in piRNA processing. During early embryogenesis, the TOFU-6/PICS-1/ERH-2/TOST-1 complex accumulates in the nucleus and plays essential roles in chromosome segregation and cell division. Interestingly, the functions of these factors in mediating chromosome segregation are independent of piRNA production. Therefore, we speculate that differential compositions of PICS factors may help cells coordinate distinct cellular processes.

overall_design: In this study, we compared total small RNAs from (1) control animals; (2) tofu-6 mutants; (3) pics-1 mutants;(4)erh-2 mutants; (5)tost-1 mutants; (6)prg-1 mutants

first: Shouhong

last: Guang


title: Organoids derived from directly reprogrammed human hepatocytes for modeling liver cancer initiation

first: Lulu

last: Sun

state: Shanghai

address: 320 Yueyang Road

institute: Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

summary: Hepatocellular carcinoma (HCC) and cholangiocarcinoma (ICC) are two main forms liver cancers with poor prognosis. Models for studying HCC and ICC development using human liver cells are urgently needed. Organoids serve as in vitro models for cancer studies as it recapitulates in vivo structures and microenvironment of solid tumors. Herein, we established liver cancer organoid models by introducing specific mutations into human induced hepatocyte (hiHep)-derived organoids. c-MYC and hRASG12V overexpression in hiHep organoids with repressed p53 activation by large T led to distinct HCC and ICC signatures. With these oncogenic mutations, the neoplastic hiHep organoids formed cancerous structures and possessed cancer-specific hallmarks. Comprehensive transcriptional analysis of liver cancer organoids revealed genes and pathways with disease-stage-specific alterations. Notably, with RAS mutations, hiHep organoids acquired biliary trans-differentiation, and showed a process of conversion from hepatocytes to ICC. To sum up, we have established a useful and convenient in vitro human organoid systems modeling liver cancer development.

overall_design:
During the in vitro neoplastic transformation process, transcriptional profiling of  hiHep organoids, c-MYC and RAS organoids were generated by RNA-seq analysis.

During the in vitro neoplastic transformation process, transcriptional profiling of ProliHH organoids, c-MYC- and RAS- transfected ProliHH organoids were generated by RNA-seq analysis.

first: Lijian

last: Hui


title: Targeting enhancer switching overcomes non-genetic drug resistance in acute myeloid leukaemia [single cell RNA-seq adaptation]

overall_design: Single-cell RNA-seq of BET inhibitor resistant and sensitive leukaemic cells, and resistant cells treated with BET inhibitor


title: Targeting enhancer switching overcomes non-genetic drug resistance in acute myeloid leukaemia [single cell RNA-seq]

overall_design: Single-cell RNA-seq of BET inhibitor resistant and sensitive leukaemic cells, and resistant cells treated with BET inhibitor. The file SingleCellInfo.xlsx contains cell barcode and BET inhibitor resistance status.


title: Loss of p53 dictates Wnt-dependent systemic inflammation in breast cancer

city: Amsterdam

first: Max

middle: D

last: Wellenstein

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

summary: Cancer-associated inflammatory processes in the tumour microenvironment, as well as systemically, are strongly linked with poor disease outcome in cancer patients. For most human solid tumour types, high systemic neutrophil-to-lymphocyte ratios (NLR) are associated with increased metastasis and poor overall survival and recent experimental studies have demonstrated a causal relationship between neutrophils and metastasis formation. However, to date, the cancer cell-intrinsic mechanisms dictating the substantial heterogeneity in systemic neutrophilic inflammation between tumour-bearing hosts are largely unresolved. Using a panel of 16 distinct genetically engineered mouse models (GEMMs) for breast cancer, we demonstrate that tumour cell-intrinsic loss of p53 changes the phenotype and function of macrophages in the microenvironment, leading to activation of a systemic inflammatory cascade that drives neutrophil expansion. Mechanistically, p53 loss in cancer cells induces secretion of Wnt ligands that act in a paracrine fashion to stimulate IL-1b production from tumour-associated macrophages. Intratumoural IL-1β production stimulates an inflammatory cascade leading to the systemic accumulation of neutrophils. Pharmacological and genetic blockade of cancer cell-derived Wnt secretion reverses IL-1β expression by macrophages and subsequent systemic neutrophilic inflammation. Collectively, using pre-clinical mouse models for breast cancer, we demonstrate a novel mechanistic link between loss of p53 in cancer cells, Wnt ligand secretion and systemic immune activation. This illustrates the importance of cancer cell-intrinsic genetic aberrations in dictating cancer-associated inflammation. These insights set the stage for personalized immune intervention strategies for cancer patients.

overall_design: In this study, gene expression profiles of tumours from genetically engineered mouse models (GEMMs) were analysed using RNA sequencing. Analysis was performed on bulk tumours of 10 GEMMs with different tissue-specific mutations driving tumorigenesis, totalling to 125 different tumours (n=5 or more per group). Subsequently, samples were grouped according to p53 status of the tumour (models containing Trp53 floxed alleles, or not) and comparisons were made between p53-KO and p53-WT tumours.

first: Seth

last: Coffelt

first: Danique

last: Duits

first: Martine

last: van Miltenburg

first: Maarten

last: Slagter

first: Iris

last: de Rink

first: Linda

last: Henneman

first: Sjors

last: Kas

first: Cheei-Sing

last: Hau

first: Kim

last: Vrijland

first: Anne

middle: P

last: Drenth

first: Eva

last: Schut

first: Renske

last: de Korte-Grimmerink

first: Ingrid

last: van der Heijden

first: Lodewyk

middle: F

last: Wessels

first: Ton

last: Schumacher

first: Jos

last: Jonkers

first: Karin

last: de Visser


title: Whole Transcriptome RNA-seq in Peromyscus maniculatus fibroblasts

status: Public on May 18 2019

city: Columbia

first: Youwen

last: Zhang

state: South Carolina

address: 715 Sumter Street CLS109

department: Drug Discovery and Biomedical Sciences

institute: University of South Carolina (Columbia)

summary: Analysis of gene expression can be challenging, especially if it involves genetically diverse populations that exhibit high variation in their individual expression profile. Despite this variation though, it is conceivable that in the same individuals a high degree of coordination is maintained between transcripts that belong to the same signaling modules and are associated with related biological functions. To explore this further, we calculated the correlation in the expression levels between each of ATF4, CHOP (DDIT3), GRP94, DNAJB9 (ERdj4), DNAJ3C (p58IPK) and HSPA5 (BiP/GRP78) with the whole transcriptome in primary fibroblasts from deer mice following induction of endoplasmic reticulum (ER) stress. Since these genes are associated with different transducers of the unfolded protein response (UPR) we postulated that their profile, in terms of correlation of transcripts, reflects distinct UPR branches engaged and therefore different biological processes. Standard gene ontology analysis was able to predict major functions associated with the corresponding transcript, and of the UPR arm related to that, namely regulation of the apoptotic response by ATF4 (PERK arm) and the ER stress associated degradation for GRP94 (IRE1). BiP, being a global regulator of the UPR, was associated with activation of ER stress in a rather global manner. Pairwise comparison in the correlation coefficients for these genes’ associated transcriptome showed the relevance of selected genes in terms of expression profiles.

overall_design: Whole Transcriptome expression examination of Peromyscus transcriptome after induction of unfolded protein response

first: Y

first: A

last: Havighorst

first: D

last: Altomare

first: M

last: Lucius

first: E

last: Farmaki

first: I

last: Chatzistamou

last: Shtutman

first: H

last: Kiaris


title: Editing the Sickle Cell Disease Mutation in Primary Human Hematopoietic Stem Cells: Comparison of Endonucleases and Homologous Donor Templates

city: Los Angeles

first: Yerbol

middle: Z.

last: Kurmangaliyev

address: 675 Charles E. Young Drive South

institute: University of California, Los Angeles

summary: Site-specific correction of a point mutation causing a monogenic disease in autologous hematopoietic stem and progenitor cells (HSPCs) can be used as a treatment of inherited disorders of the blood cells. Sickle Cell Disease (SCD) is an ideal model to investigate the potential use of gene editing to transvert a single point mutation at the β-globin locus (HBB). We compared the activity of ZFNs and CRISPR/Cas9 for editing and homologous donor templates delivered as single-stranded oligodeoxynucleotides (ssODN), adeno-associated virus serotype 6 (AAV6), integrase-deficient lentiviral vectors (IDLV) and adenovirus 5/35 serotype (Ad5/35) to transvert the base-pair responsible for SCD in HBB in primary human CD34+ HSPCs. We found that the ZFNs and Cas9 directed similar frequencies of nuclease activity. In vitro, AAV6 led to the highest frequencies of homology-directed repair (HDR), but levels of base-pair transversions were significantly reduced when analyzing cells in vivo in immune-deficient mouse xenografts, with similar frequencies achieved with either AAV6 or ssODN. AAV6 also caused significant impairment of colony-forming progenitors and human cell engraftment. Gene correction in engrafting hematopoietic stem cells may be limited by the capacity of the cells to mediate HDR, suggesting additional manipulations may be needed for high efficiency gene correction in HSPCs

overall_design:
To assess effects of the reagents involved in editing on gene expression profiles of CD34+ PBSCs, we performed RNA-sequencing (RNA-Seq) of total RNA isolated from cells 24 hours post-editing.

Mock - Control
RNP - ribonucleoprotein, Cas9 + sgRNA
ssODN - DNA donor template, single-stranded oligodeoxynucleotides
AAV6_BG - DNA donor template, AAV6 based vector, version 1
AAV6_BG_HRPT - DNA donor template, AAV6 based vector, version 2

first: Zulema

last: Romero

first: Donald

last: Kohn


title: Genome-wide map of Flagx3-DnaA bound to DNA in exponentially growing Sinorhizobium meliloti cultures

city: Giessen

first: Matthew

last: McIntosh

address: Heinrich-Buff-Ring 26-32

department: Microbiology and Molecular Biology

country: Germany

institute: University of Giessen

summary: The genome of Sinorhizobium meliloti, a model for studying plant-bacteria symbiosis, contains the genes coding for eight LuxR-like proteins. Two of these, SinR and ExpR, are essential for quorum sensing (QS). Roles and regulation surrounding the others are mostly unknown. Here, we reveal the DNA recognition sequence and regulon of the LuxR-like protein SMc00877. Unlike ExpR, which uses the long chain acyl homoserine lactones (AHLs) as inducers, SMc00877 functioned independently of AHLs and was even functional in Escherichia coli. A target of SMc00877 is sinR, the major regulator of AHL production in S. meliloti. Disruption of SMc00877 decreased AHL production. A weaker production of AHLs resulted in smaller microcolonies, starting from single cells, and delayed AHL dependent regulation. SMc00877 was expressed only in growing cells in the presence of replete nutrients. Therefore, we renamed it NurR (nutrient sensitive LuxR-like regulator). We traced this nutrient-sensitive expression to transcription control by the DNA replication initiation factor, DnaA, which is essential for growth. These results indicate that NurR has a role in modulating the threshold of QS activation according to growth. We propose growth behavior as an additional prerequisite to population density for the activation of QS in S. meliloti.

overall_design: This data includes a control and a sample, both with replicates. The control contains genomic DNA from the wild type strain, the sample contains genomic DNA enriched via Flag-tagged DnaA crosslinked to the DNA. The only difference between the wild type strain and the sample was the presence of an N-terminal Flag tag on the protein DnaA. The Flag-tagged DnaA/DNA complex was captured using anti-Flag beads.

first: Daniel-Timon

last: Spanka


title: Growth disrupting mutations in epigenetic regulatory molecules are associated with abnormalities of epigenetic aging

city: Exeter

first: Aaron

middle: Richard

last: Jeffries

state: Devon

address: RILD, Royal Devon & Exeter Hospital, Barrack Road

department: Medical School

institute: University of Exeter

type: Methylation profiling by genome tiling array

summary:
Germline mutations in fundamental epigenetic regulatory molecules including DNA methyltransferase 3A (DNMT3A) are commonly associated with growth disorders, whereas somatic mutations are often associated with malignancy. We profiled genome-wide DNA methylation patterns in DNMT3A c.2312G>A; p.(Arg771Gln) carriers in a large Amish sibship with Tatton-Brown-Rahman syndrome (TBRS) and their mosaic father.
This defined widespread DNA hypomethylation at specific genomic sites enriched at locations annotated to genes involved in morphogenesis, development, differentiation, and malignancy predisposition pathways. TBRS patients also displayed highly accelerated DNA methylation aging.

overall_design: 12 samples

first: J

last: Mill

last: Baple

last: Crosby

first: R

last: Maroofian


title: Transcriptome analysis of small molecule-mediated astrocyte-to-neuron reprogramming

city: University Park

first: Gong

last: Chen

state: PA

address: Old Main

institute: Penn State University

summary: Human astrocytes can be efficiently reprogrammed into functional neurons in culture by the addition of four small molecules. RNA-seq was performed to assess transcriptome alterations at different time points to characterize the molecular mechanisms.

overall_design: RNA profiles of small molecule-treated human astrocyte culture at 6 time points throughout reprogramming, 3 replicates each.

first: Ningxin

last: Ma

first: Jiuchao

last: Yin


title: Exome-wide rare loss-of-function variant enrichment study in 21,347 Han Chinese individuals identifies four new susceptibility genes for psoriasis [psoriasis patients]

status: Public on May 24 2019

first: Chao

last: Yang

address: #69 Meishan Road, Hefei230032, Anhui, China

institute: First Affiliated Hospital of Anhui Medical University

type:
Genome variation profiling by array
SNP genotyping by SNP array

summary: Most psoriasis-related genes or loci identified through genome-wide association studies (GWASs) represent common clusters and are located in non-coding regions of the human genome, providing only limited evidence for the role of coding variants in psoriasis. Two exome-wide case-control genotyping data sets  were obtained from our previous study. Quality control was established for each data set, and the remaining markers in each were annotated using ANNOVAR. Gene-based analysis was performed on the annotation results. A total of 250 and 35 genes in the Exome_Fine and Exome_Asian Array cohorts, respectively, exceeded the threshold (P < 4.43 × 10-6). Merged gene-based analysis was then conducted on the same set of SNPs from seven genes common to both arrays, and the chi-square test was used to confirm all gene-based results. Ultimately, four new susceptibility genes were identified: BBS7 (Pcombine = 1.38 × 10−29), GSTCD (Pcombine = 8.35 × 10−47), LIPK (Pcombine = 1.02 × 10−19) and PPP4R3B (Pcombine = 1.79 × 10−33). This study identified four new susceptibility genes for psoriasis through a gene-based method using rare variants, contributing to our understanding of the pathogenesis of psoriasis.

overall_design: To contributing to our understanding of the pathogenesis of psoriasis, we performed gene-based analysis in cohorts genotyped using Exome_Fine Array and Exome_Asian Array in the data sets from our previous psoriasis studies. The following data included 8,949 samples (4,179 cases and 4,770 controls) in Exome_Asian Array.


title: Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria

city: Newyork

first: Xiangwu

last: Ju

address: 1230 York Avenue

institute: The Rockefeller University

summary: The complexity and intricacy of prokaryotic transcriptomes—once deemed well understood and simple—are increasingly being discovered and appreciated. The ability to determine full-length sequences of all transcripts in the cell is essential for understanding the gene regulatory repertoire of a species. Standard RNA-seq requires fragmentation of RNA for short-read sequencing, which automatically decouples the 5' sequence of a RNA molecule from its 3' sequence. Intramolecular ligation of 5' and 3' ends represents a potential strategy for simultaneously capturing the sequences of both termini. However, counterintuitively, it is more challenging to circularize prokaryotic transcripts than eukaryotic ones due to a lack of poly(A) tails. Consequently, a method capable of comprehensively profiling full-length transcripts in prokaryotes is still urgently needed. In this work, we developed a workflow, termed SEnd-seq, that simultaneously reads both ends of all bacterial RNAs—including small non-coding RNAs—with single-nucleotide resolution. This method enabled us for the first time to determine the correlated occurrence of transcription start sites (TSS) and termination sites (TTS) across the whole transcriptome, and achieve an unprecedented map of its operon architecture. Using E. coli as a model system, we identified thousands of new TSS and TTS, many of which were found to be condition dependent. These results significantly expand our knowledge of the regulatory elements existing in the E. coli genome and improve our understanding of many aspects of bacterial RNA metabolism.

overall_design: We developed a high-throughput and unbiased method (SEnd-seq) to prepare the RNA-seq library, which could be used to analyze the E.coli transcriptome. We also used RNA-seq and ChIP-seq to verify some results.

first: Shixin

last: Liu


title: Transcriptome profiling of interaction effects of soybean cyst nematodes and soybean aphids on soybean.

city: Brookings

first: Madhav

middle: P.

last: Nepal

state: South Dakota

address: Northern Plains Biostress 249D

department: Biology and Microbiology

institute: South Dakota State University

summary:
Purpose: Soybean aphid, Aphis glycines Matsumura (Hemiptera: Aphididae) and soybean cyst nematode, Heterodera glycines Ichinohe, (SCN) are the two most economically important pests of soybean, Glycine max (L.) Merr., in the Midwest. Although the soybean aphid is an aboveground pest and SCN is a belowground pest there is evidence that concomitant infestations result in improved SCN reproduction. This study is aimed to characterize the three-way interactions among soybean, soybean aphid and SCN using demographic and genetic datasets.
Results: More than 1.1 billion reads (61.4 GB) of transcriptomic data were yielded from 47 samples derived from the experiment using whole roots of G. max. The phred quality scores per base for all the samples were higher than 30. The GC content ranged from 43 to 45% and followed the normal distribution. After trimming, more than 99% of the reads were retained as the clean and good quality reads. Upon mapping these reads, we obtained high mapping rate ranging from 73.8% to 94.3%. Among the mapped reads, 67.1% to 87.6% reads were uniquely mapped.
Conclusions: The comprehensive understanding of these transcriptome data would help in understanding the molecular interactions among soybean, A. glycines, and H. glycines. The use of multifaceted bioinformatics approaches could facilitate finding candidate genes and their function that might play a crucial role in various pathways for host resistance against both soybean aphids and SCN. For differential gene expression analysis, EdgeR, limma, and DEseq2 could be used. Apart from standalone tools like iDEP, Galaxy (https://usegalaxy.org), CyVerse (http://www.cyverse.org), and MeV (http://mev.tm4.org) could also be used for both analysis and visualization of RNA- seq data.

overall_design:
Methods: Two genotypes of Glycine max [H. glycines susceptible (Williams 82 PI 518671), and H. glycines resistant (MN1806CN)] cultivars with three treatments/cultivar: soybean aphids (Biotype 1), SCN (HG type 0), or SCN: soybean aphids in a randomized complete block design (RCBD) with six blocks were used to evaluate the three-way interactions. The entire experiment was repeated eight times. The experiment was conducted in a greenhouse water bath using cone-tainers. Treatments receiving SCN were infested at planting with 2000 nematode eggs. Treatments with soybean aphids were infested at second trifoliate growth stage (V2) with 15 soybean aphids. Soybean aphid populations were counted 5, 15, and 30 days post-infestation (dpi). SCN eggs were sampled at 30 dpi. The whole roots were sampled from 5d and 30d time points post soybean aphid infestation for library construction and sequencing using Illumina Hiseq 3000.The whole roots were sampled from 5d and 30d time points post soybean aphid infestation for library construction and sequencing using Illumina Hiseq 3000.
SRP178193, PRJNA514200

first: Surendra

last: Neupane

first: Adam

last: Varenhorst


title: Seasonal adaptations of the hypothalamo-neurohypophyseal system of the dromedary camel

status: Public on May 17 2019

city: Bristol

first: DAVID

last: MURPHY

state: AVON

address: Whitson Street

department: Medicine and Dentistry

institute: University of Bristol

summary: The “ship of the desert”, the one-humped Arabian camel (Camelus dromedarius), has a remarkable capacity to survive in conditions of extreme heat without needing to drink water. One of the ways that this is achieved is through the actions of the antidiuretic hormone vasopressin (AVP) and the natriuretic hormone oxytocin (OXT), both of which are made in a specialised part of the brain called the hypothalamo-neurohypophyseal system (HNS), but exert their effects at the level of the kidney to, respectively, provoke water conservation and salt excretion. Interestingly, our electron microscopy studies have shown that the ultrastructure of the camel HNS changes according to season, suggesting that in the arid conditions of summer the dromedary’s HNS is in a state of permanent activation, in preparation for the likely prospect of water deprivation. Based on our camel genome sequence, we have carried out an RNAseq analysis of the camel HNS in summer and winter.

overall_design: Camels We used RNAseq to describe the transcriptomes of the camel Supraoptic nucleus in both winter and summer

first: Fatma

middle: Z

last: Alim

first: Elena

middle: V

last: Romanova

first: Yea-Ling

last: Tay

first: Ahmad

last: Rahman

first: Kok-Gan

last: Chan

first: Mark

last: Rogers

first: Bruce

middle: R

last: Southey

first: Michael

last: Greenwood

first: Andre

last: de Souza Mecawi

first: Mohammad

last: Mustafa

first: Nicole

last: Mahy

first: Colin

last: Campbell

first: José

last: Antunes-Rodrigues

first: Jonathan

last: Sweedler

first: David

last: Murphy

first: Charles

last: Hindmarch


title: The X-linked DDX3X RNA helicase dictates translation re-programming and metastasis in melanoma

city: Lund

first: Göran

last: Jönsson

address: Medicon Village

country: Sweden

institute: Lund University

summary: The X-linked DDX3X gene encodes an ATP-dependent DEAD-box RNA helicase frequently altered in various human cancers including melanomas. Despite its important roles in translation and splicing, how DDX3X dysfunction specifically rewires gene expression in melanoma remains completely unknown. Here we uncover a DDX3X-driven post-transcriptional program that dictates melanoma phenotype and poor disease prognosis. Through an unbiased analysis of translating ribosomes we identified the microphtalmia-associated transcription factor, MITF, as a key DDX3X translational target that directs a proliferative-to-metastatic phenotypic switch in melanoma cells. Mechanistically, DDX3X controls MITF mRNA translation via an internal ribosome entry site (IRES) embedded within the 5’ untranslated region. Through this exquisite translation-based regulatory mechanism, DDX3X steers MITF protein levels dictating melanoma metastatic potential in vivo and response to targeted therapy. Together these findings unravel a post-transcriptional layer of gene regulation that may provide a unique therapeutic vulnerability in aggressive male melanomas.

overall_design: We sequenced transcripts associated with translationally active ribosomes (polysomes) isolated by sucrose gradient fractionation from DDX3X and control siRNA-transduced HT144 cells. Experiments were performed in duplicates.

first: Katja

last: Harbst

first: Martin

last: Lauss


title: Reactivation of PTEN tumor suppressor for cancer treatment through inhibition of a MYC-WWP1 inhibitory pathway

city: Boston

middle: David

last: Lee

state: MA

address: 3 Blackfan Circle, Rm. 424

institute: BIDMC

summary: Activation of tumor suppressors for the treatment of human cancer has been a long sought, yet elusive strategy. PTEN is a critical tumor suppressive phosphatase that is active in its dimer configuration at plasma membrane. Poly-ubiquitination by the ubiquitin E3 ligase WWP1 (WW domain containing ubiquitin E3 ligase 1) suppressed the dimerization, membrane recruitment, and function of PTEN. Either genetic ablation or pharmacological inhibition of WWP1 triggered PTEN reactivation, and unleashed tumor suppressive activity. WWP1 appears to be a direct MYC (MYC proto-oncogene) target gene and was critical for MYC-driven tumorigenesis. We identified indole-3-carbinol, a compound found in cruciferous vegetables, as a natural and potent WWP1 inhibitor. Thus, our findings unravel a potential therapeutic strategy for cancer prevention and treatment through PTEN reactivation.

overall_design: Profiling of murine dorsolateral prostate cancer tumors in a Hi-Myc genetic background with genetic or pharmacological perturbation of WWP1.

first: Yu-Ru

first: Pier

last: Pandolfi


title: Intrinsic Resistance to MEK Inhibition Through BET Protein Mediated Kinome

city: Philadelphia

first: yinfei

last: tan

address: 333 cottman ave

department: Genomic Core

institute: Fox Chase Cancer Center

summary: Mutation or deletion of Neurofibromin (NF1), an inhibitor of RAS signaling, frequently occurs in epithelial ovarian cancer (EOC), supporting therapies that target downstream RAS effectors, such as the RAF-MEK-ERK pathway. However, no comprehensive studies have been carried out testing the efficacy of MEK inhibition in NF1-deficient EOC.  Here, we performed a detailed characterization of MEK inhibition in NF1-deficient EOC cell lines using kinome profiling and RNA sequencing. Our studies showed MEK inhibitors were ineffective at providing durable growth inhibition in NF1-deficient cells due to kinome reprogramming. MEKi-mediated destabilization of FOSL1 resulted in induced expression of RTKs and their downstream RAF and PI3K signaling overcoming MEKi therapy. MEKi synthetic enhancement screens identified BRD2 and BRD4 as integral mediators of the MEKi-induced RTK signatures. Inhibition of BET proteins using BET bromodomain inhibitors (BETi) blocked MEKi-induced RTK reprogramming, indicating BRD2 and BRD4 represent promising therapeutic targets in combination with MEKi to block resistance due to kinome reprogramming in NF1-deficient EOC.

overall_design: Examination of the global effects on transcription in response to trametinib (GSK212) in A1847 cells.

first: Alison

middle: M

last: Kurimchak

first: James

middle: S

last: Duncan


title: Transcriptome analysis of the effect of maternal lactation diet (dried distilers grains and solubles-DDGS versus control) on longissimus muscle composition of mature steer progeny.

city: West Lafayette

first: Theresa

last: Casey

state: Indiana

address: 175 S. University Street

department: Animal Sciences

institute: Purdue University

summary:
Background. Steer progeny suckled by cows fed a dried distillers grains and solubles (DDGS) diet the first three months of lactation were heavier during feedlot finishing and had significantly lower marbling and larger longissumus muscles than steer suckled by cows fed a control diet (CON).  These differences were profound in that progeny were managed and fed identically from weaning until finishing, and suggested that the developmental program of muscle composition was established during the suckling period.
Purpose. Transcriptomes of longissimus muscle were measured using next generation sequencing to investigate whether there were any developmental clues to the differences in marbling scores and muscle content between steers suckled by DDGS (n=5) versus control (CON; n=5) diet fed cows during lactation.
Methods. Multiparous Angus × Simmental cows with male progeny were fed one of two diets supplemented with either DDGS or soybean meal (CON), from calving until day 129 postpartum (PP).  After conclusion of the treatments at 129 days postpartum, cow–calf pairs were comingled and managed as one group until weaning at 219 days postpartum. Steers were then transitioned to a common diet. Longissimus muscle (LM) biopsies were obtained from steers suckled by cows fed DDGS (n=5) and CON (n=5) 10 d prior to slaughter. RNA was extracted from LM. Total RNA isolated and Library Prep Kit was used to generate library for measuring messenger RNA molecules.  Library was sequenced on an Illumina HiSeq2500 platform.  FastQC (v 0.10.1) was used to assess sequence quality, and quality trimming was done using FASTX toolkit (v 0.0.13). Bases with less than Phred33 score of 30 were removed and resulted in reads of at least 50 bases. Reads were mapped against the bowtie2-indexed Bos taurus genome using Tophat (v 2.0.9) with default parameters, and the genome annotation file (.gtf) from Ensembl was used to associate the genome with annotated features. Raw read counts of each sample for each gene feature were generated with HTSeq (v 0.5.3p7) using Tophat output and Bos taurus annotations. Counts were merged using custom perl scripts and used for downstream differential gene expression (DE) analysis. DE pairwise analysis between samples CON and DDGS was done with ‘R’ (Version 2.15.2).  Counts matrix, library sizes, and experimental design were combined to create an object using edgeR (v 3.0.3) package.
Results. Number of reads per sample ranged from 79,530,352 to 58,600,824. After trimming there were 77,569,706 to 57,307,614 per sample.  The percent of reads that mapped to bovine genome per sample ranged from 77.3 to 92.3%, and averaged 86.3% across all samples.  Number of reads per gene ranged from one to over two-hundred ninety thousand counts per million (CPM) reads.  There were 809 genes differentially expressed (P-adj<0.1) between CON and DDGS muscle.  Of these 637 were upregulated and 172 downregulated in DDGS relative to CON.  Overall the DDGS versus CON muscle transcriptomic signature was pro-myogenic and anti-adipogenic. In particular, myokines/satellite cell maintenance factors were found among upregulated (LIF, CNTF, FGFB1, EPHB1) genes.  The anti-adipogenic signature was typified by the upregulation of anti-inflammatory cytokines and receptors (IL1RAP, IL1RL2, IL13RA2, IL1F10,), and downregulation of expression of inflammation/inflammatory cytokines and receptor (TNF, IL6R CXCL9), which suggests a selection of differentiation pathways away from adipogenic line. While the upregulation of TGFB, SPP1 and INHBA supports selection of fibroblast lineage of cells.
Conclusion. The lactation phase of production can effect meat quality by affecting transcriptional signatures that favor myogenesis and depress inflammation.

overall_design: Longissimus muscle total RNA was isolated from steer progreny of cows fed dried distillers gains and solubles (DDGS, n=5) or control diet (SBM, n=5) during lactation and sequenced on an Illumina HiSeq2500 platform

first: Jyothi

last: Thimmapuram

first: Jon

last: Schoonmaker


title: Ribo-seq of Toxoplasma-infected host cells

city: Indianapolis

first: Michael

middle: James

last: Holmes

state: IN

address: 635 Barnhill Drive

department: Pharmacology & Toxicology

institute: Indiana University School of Medicine

summary: Toxoplasma gondii is a ubiquitous obligate intracellular parasite that infects the nucleated cells of warm-blooded animals. From within the parasitophorous vacuole in which they reside, Toxoplasma tachyzoites secrete an arsenal of effector proteins that can reprogram host gene expression to facilitate parasite survival and replication. Gaining a better understanding of how host gene expression is altered upon infection is central for understanding parasite strategies for host invasion and for developing new parasite therapies. Here, we applied ribosome profiling coupled with mRNA measurements to concurrently study gene expression in the parasite and in host human foreskin fibroblasts. By examining the parasite transcriptome and translatome, we identified potential upstream open reading frames that may permit the stress-induced preferential translation of parasite mRNAs. We also determined that tachyzoites reduce host death-associated pathways and increase survival, proliferation, and motility in both quiescent and proliferative host cell models of infection. Additionally, proliferative cells alter their gene expression in ways consistent with massive transcriptional rewiring while quiescent cells were best characterized by re-entry into the cell cycle. We also identified a translational control regimen consistent with mTOR activation in quiescent cells, and to a lesser degree in proliferative cells. This study illustrates the utility of the method for dissection of gene expression programs simultaneously in parasite and host.

sample_organism:
Homo sapiens
Toxoplasma gondii RH

platform_organism:
Homo sapiens
Toxoplasma gondii RH

overall_design: Ribosome profiling and RNA-seq of Toxoplasma-infected confluent and subconfluent human foreskin fibroblasts in triplicate

first: Premal

last: Shah

first: Ronald

middle: C

last: Wek

first: William

last: Sullivan Jr


title: Transcritptome analysis of anterior dorsal pericardial wall (aDPW) and cardiac outflow tract (OFT) from control and Hand2flox/flox; Mef2c-AHF-Cre embryos at E9.5

city: Nanjing

first: Meng

last: Xia

state: JiangSu

address: XueFu Road 12

department: Model Animal Research Center

institute: Nanjing unversity

summary: We aim to explore the gene expression difference in control and Hand2 mutant embryos and  potential mechnisam downstream of Hand2 involved in OFT epithelium regulation.

overall_design: Examination of transcriptome expression between control and Hand2 mutant embyos in aDPW and OFT tissues

first: Wen

last: Luo

first: Hengwei

last: Jin

first: Zhongzhou

last: Yang


title: DNA Methylation of primary human fibroblasts across replicative lifespan in normal and hyperglycemic conditions

status: Public on May 16 2019

city: New York

first: Gabriel

last: Sturm

state: NY

address: 40 Haven Avenue

department: Psychiatry

institute: Columbia University

summary: Genome wide DNA methylation profiling of normal (5.5mM) and high (25mM) glucose samples from primary human fibroblasts across the cellular lifespan. The Illumina Infinium EPIC Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 866,836 CpGs. Samples included 12 normal glucose time points and 14 high glucose time points, as well as, 6 technical replicates of normal glucose timepoint at 34.8 days. Methylation data was used to estimate the rate of aging occuring across replicative lifespan using several DNA methylation based Aging Clocks. Other analysis include comparing the overlap of age-related CpGs in vitro to in vivo, and describing the diverse kinetics of methylation sites across cellular lifespan.

overall_design: Bisulphite converted DNA from the 31 samples were hybridised to the Illumina Infinium EPIC Human Methylation Beadchip v1.0

first: Andres

last: Cardenas

first: Marie-Abèle

last: Bind

first: Steve

last: Horvath

first: Shuang

last: Wang

first: Yunzhang

first: Sara

last: Hägg

first: Michio

last: Hirano

first: Martin

last: Picard


title: RNA-seq analysis of YAP-overexpressing mouse embryonic fibroblasts

city: New Haven

first: Amaleah

middle: Ann

last: Hartman

address: 10 Amistad St.

department: Cell Biology

institute: Yale University

summary: Here, we report that YAP-overexpression in MEFs causes changes in gene expression of many microenvironmental proteins.

overall_design: Examination of the transcriptomes of mouse embryonic fibroblasts overexpressing a control vector versus one encoding Yes-associated protein, FACS-sorted based on vector-encoded fluorescent reporter.

first: Xiao

last: Hu

first: Xinyue

last: Chen

first: Anna

middle: E

last: Eastman

first: Cindy

first: Shangqin

last: Guo


title: RNA-seq analysis of YAP-overexpressing mouse embryonic fibroblasts in the context of reprogramming

summary: Here, we report that YAP-overexpression inhibits the establishment of the pluripotency network.

overall_design: Examination of the transcriptomes of emergent colony types after reprogramming and culture for 75 days of mouse embryonic fibroblasts overexpressing a control vector versus one encoding Yes-associated protein.


title: JAK/STAT inhibition in macrophages promotes therapeutic resistance by inducing expression of protumorigenic factors

city: Minneapolis

first: Todd

last: Knutson

state: MN

address: 117 Pleasant St SE

department: Minnesota Supercomputing Institute

institute: University of Minnesota

summary: Tumor-associated macrophages contribute to tumor progression and therapeutic resistance in breast cancer. Within the tumor microenvironment, tumor-derived factors activate pathways that modulate macrophage function. Using in vitro and in vivo models, we find that tumor-derived factors induce activation of the Janus kinase (JAK)/signal transducer and activator of transcription 3 (STAT3) pathway in macrophages. We also demonstrate that loss of STAT3 in myeloid cells leads to enhanced mammary tumorigenesis. Further studies show that macrophages contribute to resistance of mammary tumors to the JAK/STAT inhibitor ruxolitinib in vivo and that ruxolitinib-treated macrophages produce soluble factors that promote resistance of tumor cells to JAK inhibition in vitro. Finally, we demonstrate that STAT3 deletion and JAK/STAT inhibition in macrophages increases expression of the pro-tumorigenic factor cyclooxygenase-2 (COX-2) and that COX-2 inhibition enhances responsiveness of tumors to ruxolitinib. These findings define a novel mechanism through which macrophages promote therapeutic resistance and highlight the importance of understanding the impact of targeted therapies on the tumor microenvironment.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Primary human macrophages were treated with breast tumor cell (MCF7, MDA-MB-231, or control) conditioned medium, in combination with ruxolitinib (or control), and processed for gene expression analysis in triplicate. Bone marrow derived macrophages from STAT3 wild type or STAT3 conditional knockout mice were extracted and were processed for gene expression analysis in triplicate.

first: Emily

middle: A

last: Irey

first: Chelsea

last: Lassiter

first: Nicholas

middle: J

last: Brady

first: Pavlina

last: Chuntova

first: Ying

first: Christine

last: Henzler

first: Thomas

last: Chaffee

first: Rachel

middle: I

last: Vogel

first: Andrew

last: Nelson

first: Michael

last: Farrar

first: Kathryn

middle: L

last: Schwertfeger


title: Deep sequencing of somatosensory neurons reveals molecular determinants of intrinsic physiological properties

first: David

last: Ginty

address: 210 Longwood Avenue

department: Neurobiology

institute: Harvard Medical School

summary: To explore the molecular basis of the distinct intrinsic membrane properties and other dstinguishing features of functionally defined DRG neuron subtypes, we bulk-sequenced RNA at high depth of genetically-labeled DRG neurons to generate transcriptome profiles of eight major DRG neuron subtypes. The trancriptome profiles revealed differentially expressed and functionally relevant genes, including voltage-gated ion channels. Guided by the transcriptome pofiles, electrophysiological analyses using pharmacological and genetic manipulations as well as computational modeling of DRG neuron subtypes were undertaken to assess the functions of select voltage-gated potassium channels (Kv1, Kv2, Kv3, and Kv4) in shaping action potential (AP) waveforms and firing patterns of the DRG neuron subtypes. Our findings show that the transcriptome profiles have predictive value for defining ion channel contributions to sensory neuron subtype-specific intrinsic physiological properties.

overall_design: We made use of genetic tools developed that selectively label each of eight DRG neuron subtypes with fluorescent reporters, first purifying labeled neurons to homogeneity using flow cytometry (FACS) and then extracting RNA from these purified neuronal populations. DRGs from all axial levels were used for FACS, except for proprioceptors which were purified from thoracic ganglia, because the PVIRES-Cre; Ai14 proprioceptor labeling strategy was found to label a subset of limb level cutaneous LTMRs as well. DRGs from multiple mice were combined for FACS, and neurons from multiple rounds of sorting were combined to obtain sufficient amounts of RNA for each sequencing reaction. At least three biological replicates with a total of 26 samples were sequenced for each neuronal subtype. RNA libraries were prepared and subsequently sequenced using an Illumina HiSeq2000 platform at an average depth of ~70 million mapped reads per sample. This depth translates to an average detection level of 12,226 genes per sample. By using well characterized mouse lines for specific labeling of neuronal subtypes, this analysis links gene expression patterns to sensory neuron subtypes defined by their distinct in vivo properties as well as their corresponding intrinsic properties.

first: Yang

last: Zheng

first: Ling

last: Bai

middle: D


title: SCAF4 and SCAF8, Transcriptional Anti-Terminator Proteins

city: London

first: Richard

last: Mitter

state: LONDON

address: 1 Midland Road

department: Bioinformatics & Biostatistics

institute: The Francis Crick Institute

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

overall_design: Refer to individual Series


title: Exome-wide rare loss-of-function variant enrichment study in 21,347 Han Chinese individuals identifies four new susceptibility genes for psoriasis [healthy controls]

status: Public on May 25 2019

city: Hefei

first: Chao

last: Yang

overall_design: To contributing to our understanding of the pathogenesis of psoriasis, we performed gene-based analysis in cohorts genotyped using Exome_Fine Array and Exome_Asian Array in the data sets from our previous psoriasis studies. The following data included 12,398 samples (6,489 cases and 5,909 controls) in Exome_Fine Array.


title: TGF-β signaling plays an essential role in the lineage specification of mesenchymal stem/progenitor cells in fetal bone marrow

status: Public on May 15 2019

city: Saint Louis

first: Grazia

last: Abou-Ezzi

address: 660 South Euclid Avenue

institute: Washington Univeristy in Saint Louis

summary:
TGF-β regulates fetale bone marrow niche emergence.  Abrogating TGF-β signaling in mesenchymal cells during development results in a marked expansion of adipocytes and CAR cells in the bone marrow, while osteoblasts are reduced.
RNA expression data from Osx-Cre targeted mesenchymal stromal cells obtained from E16.5 mouse hindlimbs of transgenic mice lacking Tgfbr2 in mesenchymal stromal cells or littermate controls.

overall_design: TdTomato+ hematopoietic lineage- (CD45, B220, CDllb, and Gr1) cells were sorted from the hindlimbs of E16.5 Osx-Cre, Ai9 or Osx-Cre, Tgfbr2flfl Ai9 mice.   RNA was isolated and expression profiling performed.

first: Daniel

last: Link


title: SCAF4 and SCAF8, Transcriptional Anti-Terminator Proteins (TT-Seq)

summary: Accurate regulation of RNA Polymerase II (RNAPII) transcriptional termination is a prerequisite for correct gene expression. Here we describe a role for SCAF4 and SCAF8 as anti-terminators, suppressing the use of early, alternative polyadenylation sites (PASs). The SCAF4/8 proteins bind the hyper-phosphorylated RNAPII C-terminal repeat domain (CTD) modified on both Ser2 and Ser5, and are detected at early, alternative PASs. Concomitant knockout of human SCAF4 and SCAF8 results in altered PAS selection, leading to expression of truncated mRNAs and proteins lacking functional domains, and is cell-lethal. While SCAF4 and SCAF8 thus work redundantly to suppress early termination, they also have independent, non-essential functions. SCAF8 is a positive RNAPII elongation factor, whereas SCAF4 is required for correct termination at canonical transcription termination sites in the presence of SCAF8. Together, SCAF4 and SCAF8 coordinate the transition between elongation and termination, directing PAS selection to ensure correct RNAPII transcriptional termination in human cells.

overall_design: To study the function of SCAF4 and SCAF8 in human cells, we used CRISPR-Cas9 nickase technology to generate single and double knockouts (KOs) in HEK293 Flp-In TREX cells, which also contained a single copy of a doxycycline (Dox)-inducible SCAF4 or SCAF8 rescue construct, with the encoded GFP-tagged protein expressed at near-normal levels. All cell lines were maintained in the presence of Dox to ensure expression of the CRISPR-resistant rescue gene during and after KO cell line generation. Expression of the rescue protein reaches undetectable levels after 5 days growth in Dox-free media, resulting in effective single of double KOs. Due to the manner in which these cell lines were generated, a total of 12 cell types (6 different cell lines grown with or without Dox) were often analysed together. For example, SCAF4 SCAF8 double KOs were generated either by first knocking out SCAF4 and then SCAF8, or vice versa, and these different cell lines were in turn also derived from cell lines containing either a Dox-inducible SCAF4- or a SCAF8 rescue gene, giving rise to a total of 4 genotypically identical SCAF4 SCAF8 dKO cell lines. Moreover, a SCAF4 SCAF8 double KO that expresses a rescue gene (i.e. grown in the presence of doxycycline) is effectively a single KO; for example, a SCAF4 SCAF8 double KO expressing the SCAF4 rescue gene is genotypically and phenotypically a single SCAF8 KO cell line. For PAR-CLIP experiments, HEK293 Flp-In TREX cells stably expressing FLAG-tagged SCAF4 or SCAF8 were used for FLAG immunoprecipitations from RNA-protein crosslinked extracts.

first: Lea

middle: H

last: Gregersen

first: Alejandro

middle: P

last: Ugalde

first: Takayuki

last: Nojima

first: Jesper

middle: Q

last: Svejstrup


title: SCAF4 and SCAF8, Transcriptional Anti-Terminator Proteins (PAR-CLIP)


title: Decreased SATB1 expression promotes AML cell proliferation through NF-κB activation

city: Guangzhou

first: Xiaodan

last: Luo

address: NO.151 Yanjiang West Street, Yuexiu District

institute: The First Affiliated Hospital of Guangzhou Medical University

summary: Global gene expression profiles were analyzed in HL-60 cells with SATB1 knockdown to investigate the mechanisms underlying the regulation of AML cell growth by SATB1.Genes that displayed two-fold up-regulation or  0.5-fold down-regulation in expression in comparisons were selected for further analyses. Arrays with poor quality according to the manufacturer's recommendations were excluded from further analysis.We found the differentially expressed genes were involved in NF-κB, MAPK and PI3K/Akt signaling pathways. Nuclear NF-κB p65 levels were significantly increased in SATB1 depleted HL-60 cells.

overall_design: Gene expression was compared between HL-60 SATB1-shRNA1 cells and HL-60 CTR cells. Genes that displayed two-fold up-regulation or  0.5-fold down-regulation in expression in comparisons were selected for further analyses. Arrays with poor quality according to the manufacturer's recommendations were excluded from further analysis.

first: Lihua

last: Xu

first: Xiaohong

last: Wu

first: Huo

last: Tan

first: Lian

last: Liu


title: Global DNA methylation reflects spatial heterogeneity and molecular evolution of lung adenocarcinomas

city: Heidelberg

first: Martin

last: Sill

address: Im Neuenheimer Feld 280

department: Division of Pediatric Neurooncology

institute: DKFZ

summary: Lung adenocarcinoma (ADC) is the most prevalent subtype of lung cancer and characterized by considerable morphological and mutational heterogeneity. However, little is known about the epigenomic intratumor variability between spatially separated histological growth patterns of ADC. In order to reconstruct the clonal evolution of histomorphological growth patterns, we performed global DNA methylation profiling of 27 primary tumor regions, seven matched normal tissues, and six lymph node metastases from seven ADC cases. Additionally, we investigated the methylation data from 369 samples of the TCGA ADC cohort. All regions showed varying degrees of methylation changes between segments of different, but also of the same growth patterns. Similarly, copy number variations were seen between spatially distinct segments of each patient. Hierarchical clustering of promoter methylation revealed extensive heterogeneity within and between the cases. Intra-tumor DNA methylation heterogeneity demonstrated a branched clonal evolution of ADC regions driven by genomic instability with subclonal copy number changes. Notably, methylation profiles within tumors were not more similar to each other than to those from other individuals. In two cases, different tumor regions of the same individuals were represented in distant clusters of the TCGA cohort, illustrating the extensive epigenomic intratumor heterogeneity of ADCs. Importantly, we found no evidence for the lymph node metastases to be derived from a common growth pattern. Instead, they had evolved early and separately from a particular pattern in each individual primary tumor. In summary, our results suggest that extensive variation of epigenomic features contributes to the molecular and phenotypic heterogeneity of primary ADCs and lymph node metastases.

overall_design: The IlluminaHumanMethylationEPIC (Illumina, San Diego, USA) array data from n=40 different lung adenocarcinomas tissues were used to obtain genome-wide assessment of DNA methylation, according to the manufacturer’s instructions at the Genomics and Proteomics Core Facility of the German Cancer Research Center (DKFZ) as described previously (Pajtler et al. Cancer Cell. 2015; 27 (5), 728-743)

first: Steffen

last: Dietz


title: SCAF4 and SCAF8, Transcriptional Anti-Terminator Proteins (3'-Seq)


title: Caspase-8 promotes c-Rel-dependent inflammatory cytokine expression and resistance against Toxoplasma gondii

city: Phiadelphia

first: Corbett

middle: T

last: Berry

address: 3800 Spruce St

institute: University of Pennsylvania

summary: Caspase-8 is a critical regulator of apoptosis, programmed necrosis, and inflammatory gene expression. Caspase-8 is necessary for optimal transcription of inflammatory and antimicrobial host defense genes, including Il12 and Il1b. While the mechanisms of caspase-8-mediated control of apoptosis and programmed necrosis are well-described, how caspase-8 controls inflammatory gene expression is less clear. We show that caspase-8 is necessary for optimal nuclear translocation of the NF-κB family member c-Rel, and consequently, for recruitment of c-Rel to caspase-8-dependent gene promoters. Furthermore, caspase-8 deficiency led to an inability to control acute Toxoplasma gondii infection. These findings provide new insight into how caspase-8 contributes to inflammatory gene expression and host defense.

overall_design: Total RNA-sequencing

first: Alex

last: Delaney

first: Igor

last: Brodsky


title: SCAF4 and SCAF8, Transcriptional Anti-Terminator Proteins (DRB-Seq)

first: Richard

last: Mitter


title: SCAF4 and SCAF8, Transcriptional Anti-Terminator Proteins (mNET-Seq)


title: Convergent Genetic Aberrations in Murine and Human T Lineage Acute Lymphoblastic Leukemias

status: Public on May 14 2019

city: San Francisco

first: Benjamin

last: Huang

state: CA

address: 1450 3rd Street

institute: University of California San Francisco

summary: The lack of predictive preclinical models is a fundamental barrier to translating knowledge about the molecular pathogenesis of cancer into improved therapies. Insertional mutagenesis (IM) in mice is a robust strategy for generating malignancies that recapitulate the extensive inter- and intra-tumoral genetic heterogeneity found in advanced human cancers. While the central role of "driver" viral insertions in IM models that aberrantly increase the expression of proto-oncogenes or disrupt tumor suppressors has been appreciated for many years, the contributions of cooperating somatic mutations and large chromosomal alterations to tumorigenesis are largely unknown. Integrated genomic studies of T lineage acute lymphoblastic leukemias (T-ALLs) generated by IM in wild-type (WT) and Kras mutant mice reveal frequent point mutations and other recurrent non-insertional genetic alterations that also occur in human T-ALL. These somatic mutations are sensitive and specific markers for defining clonal dynamics and identifying candidate resistance mechanisms in leukemias that relapse after an initial therapeutic response. Primary cancers initiated by IM and resistant clones that emerge during in vivo treatment close key gaps in existing preclinical models, and are robust platforms for investigating the efficacy of new therapies and for elucidating how drug exposure shapes tumor evolution and patterns of resistance.

overall_design: mRNA profiles of IM-induced murine leukemias were generated by extracting bone marrow cells from diseased mice and Illumina-based deep sequencing approaches.

first: Kevin

last: Shannon


title: Gene expression in Arabidopsis thaliana leaves after chilling and/or herbivory by Pieris brassicae or Mamestra brassice larvae or after mechanical wounding

city: Berlin

first: Reinhard

last: Kunze

state: Berlin

address: Albrecht-Thaer-Weg 6

department: Institute of Biology

institute: Freie Universität Berlin

summary: To investigate the impact of a plant´s response to abiotic stress on plant defense against subsequent biotic stress, we determined the transcriptional response of Arabidopsis thaliana to low temperature stress (4°C) and subsequent mechanical wounding or larval feeding damage by the herbivores Mamestra brassicae (generalist) and Pieris brassicae (specialist). In total, 21%, 4% and 14% of all genes responsive to M. brassicae, P. brassicae or mechanical wounding were differentially regulated in previously cold-treated compared to untreated plants.

overall_design: Arabidopsis thaliana Col-0 wild type plants were grown under short day conditions (8 h/16 h light/dark) at 20°C for 7 weeks. Subsequently (i) the plants were transferred to 4°C for 5 days or (ii) as controls plants grew untreated for five days. Next, the chilling treated plants were transferred back to 20°C and all plants rested for 1 day at 20°C. Next, P. brassicae or M. brassicae larvae were allowed to feed for 2 days, or mechanical wounding was applied two times per day on leaf 17 at a respective leaf region of chilling-treated or untreated plants. Control plants were not exposed to larvae. From all treated and untreated plants material from leaf 17, next to feeding/ wounding sites was harvested for transcriptome analysis.

first: Jana

last: Oberländer

first: Vivien

last: Firtzlaff

first: Monika

last: Hilker


title: Pathway-Level Information ExtractoR (PLIER) for gene expression data

first: Stuart

last: Sealfon

address: One Gustave L. Levy Place

department: Department of Neurology

institute: Icahn School of Medicine at Mount Sinai

summary: A major challenge in gene expression analysis is to accurately infer relevant biological insight, such as  variation in cell type proportion or pathway activity, from global gene expression studies.  We present a general solution for this problem that  outperforms available cell proportion inference algorithms, and is more widely useful to automatically identify specific pathways that regulate gene expression.  Our method improves replicability and biological insight when applied to trans-eQTL identification.

overall_design: Make cell type predictions based on expression data and validate by flow cytometery

first: E

last: Zaslavsky

first: M

last: Chikina


title: The ovulatory signal precipitates LRH-1 transcriptional switching mediated by differential chromatin accessibility.

city: Sherbrooke

first: Nicolas

last: Gévry

state: Québec

address: 2500 boulevard de l'université

country: Canada

institute: Université de Sherbrooke

summary: In the ovary, follicular growth and maturation are complicated processes that involve a series of morphological and physiological changes in oocytes and somatic cells leading to ovulation and luteinization, essential processes for fertility in females. Given the complexity of ovulation, characterization of genome-wide regulatory elements is essential to understand the mechanisms governing the expression of specific genes in the rapidly differentiating follicle. We therefore employed a systems biology approach to determine global transcriptional mechanisms during the early stages of the ovulatory process. We demonstrate that, following the hormonal signal that initiates ovulation, granulosa cells undergo major modification of distal regulatory elements which coincides with cistrome reprogramming of the indispensable orphan nuclear receptor, liver receptor homolog-1 (LRH-1). This cistromic reorganization correlates with the extensive changes in gene expression in ovarian granulosa cells, leading to ovulation. Together, our study yields a transcriptional map of unprecedented detail, delineating ovarian cell differentiation during the initiation of ovulation. It further demonstrates the power of complementary global approaches to accurately characterize molecular events that direct the multiple and rapid changes that characterize reproductive processes.

overall_design: Genomic profile of regulatory elements by FAIRE-seq and genomic binding of LRH-1 in mouse granulosa cells before (-OvS) and following the ovulatory signal (+OvS). Transcriptional program of LRH-1 cKO vs control (CTL) granulosa cells before and following the ovulatory signal.

first: Stephanie

last: Bianco

last: Gevry

first: Bruce

last: Murphy


title: The Spatiotemporal Control of Zygotic Genome Activation

first: George

middle: E.

last: Gentsch

state: Greater London

department: Developmental Biology Laboratory

summary: One of the earliest and most significant events in embryonic development is zygotic genome activation (ZGA). In several species, bulk transcription begins at the midblastula transition (MBT) when, after a certain number of cleavages, the embryo attains a particular nuclear-to-cytoplasmic (N/C) ratio, maternal repressors become sufficiently diluted, and the cell cycle slows down. Here we resolve the frog ZGA in time and space by profiling RNA polymerase II (RNAPII) engagement and its transcriptional readout. We detect a gradual increase in both the quantity and the length of RNAPII elongation before the MBT, revealing that >1,000 zygotic genes disregard the N/C timer for their activation and that the sizes of newly transcribed genes are not necessarily constrained by cell cycle duration. We also find that Wnt, Nodal, and BMP signaling together generate most of the spatiotemporal dynamics of regional ZGA, directing the formation of orthogonal body axes and proportionate germ layers.

overall_design: This study generated four 4sU-Seq samples and 48 RNA-Seq samples.

first: James

last: Smith


title: Simple Nutrients Bypass the Requirement for HLH-30 in Coupling Lysosomal Nutrient Sensing to Survival.

city: St. Louis, USA

first: Abhinav

last: Diwan

address: 660 S. Euclid Ave, CSRB-NTA 827a

institute: Washington University School of Medicine

summary: In this study, we subjected worms deficient in HLH-30, a master regulator of lysosome biogenesis, to starvation followed by refeding various food sources and analyzed their transcriptional profiles.

overall_design: Starvation and refeeding in two different groups of worms

first: Scot

last: Matkovich


title: Valdivieso A, Ribas L, Piferrer F. Ovarian transcriptomic signatures of zebrafish females resistant to different environmental perturbations.

city: BARCELONA

first: Alejandro

last: Valdivieso

state: BARCELONA

address: PASSEIG MARÍTIM DE LA BARCELONETA, 37-49

country: Spain

institute: Insituto de Ciencias del Mar

summary: Two-condition experiment, Control vs. High density level. Biological replicates: ovaries of 6 control replicates and ovaries of 6 high density level replicates.

overall_design: At 6 days post fertilization, fish were placed in 2.8-liter tanks. The high density effects were studied during gonadal development (6–90 dpf) at 74 fish/liter condition. At 90 dpf, fish were sacrificed and gonads were dissected and flash frozen. RNA was extracted by Trizol (Sigma) and were hybridized individually in 4x44K Agilent platform (G2519F).

first: Laia

last: Ribas

first: Francesc

last: Piferrer


title: Gene transcription and chromatin accessibility of conventional NK cells and ILC1s in spleens of uninfected and Toxoplasma gondii-infected Mice

first: Eugene

last: Park

state: MO

address: 4616 Lindell Blvd, Apt 201

institute: Washington University

summary: RNA sequencing and ATAC-seq of conventional NK cells and ILC1s in uninfected mice and mice that were infected 5 wk previously with the Type II Prugniaud strain of T. gondii

overall_design: RNA-seq and ATAC-seq analysis of conventional NK cells and ILC1s in T. gondii-infected mice


title: Nucleosome position mapping by micrococcal nuclease analysis of S. cerevisiae cells in raffinose and galactose containing media

city: Amsterdam

first: Tineke

last: Lenstra

address: Plesmanlaan 121

department: Gene Regulation

institute: Netherlands Cancer Institute

summary: We analyed the nucleosome positions by using 2 concentrations of micrococcal nuclease of yeast strains that were grown in raffinose and galactose containing media (synthetic complete).

overall_design: Mnase-seq of 2 strains grown in raffinose and 2 strains grown in galactose, each at two different concentrations of MNase

first: Daniel

middle: R

last: Larson


title: Genomic Analysis of Wild Type and FOXA2-/- ES-derived Pancreatic Progentiors

first: Hyein

middle: Sophia

last: Cho

address: 430 E 67th St

department: Developmental Biology

institute: Memorial Sloan Kettering Cancer Center

overall_design: Histone and transcription factor ChIP-seq for the genotypes of WT and FOXA2-KO per each differentiation stage

first: Danwei

last: Huangfu

first: Christina

last: Leslie


title: Chromatin Landscape Analysis of Wild Type and FOXA2-/- ES-derived Pancreatic Progenitors

overall_design: Examination of duplicates per genotypes for each differentiation stage

middle: S


title: Transcriptomic and Chromatin Landscape Analysis of Wild Type and FOXA2-/- ES-derived Pancreatic Progenitors

overall_design: Refer to individual Series