title: Demethylation of the protein phosphatase PP2A promotes the demethylation of histones to enable their function as a methyl group sink

city: Pittsburgh

first: Zheng

last: Kuang

address: 4400 Fifth Avenue

department: Biological Sciences

institute: Carnegie Mellon University

summary: Dysregulation of chromatin methylation is strongly linked to defects in cellular differentiation as well as a variety of cancers. How cells regulate the opposing activities of histone methyltransferase and demethylase enzymes to set the methylation status of the epigenome for proper control of gene expression and metabolism remains poorly understood. Here, we show that loss of methylation of the major phosphatase PP2A in response to methionine starvation activates the demethylation of histones through hyperphosphorylation of specific demethylase enzymes. In parallel, this regulatory mechanism enables cells to preserve SAM by increasing SAH to limit SAM consumption by methyltransferase enzymes. Mutants lacking the H3K36 demethylase Rph1 exhibit elevated SAM levels and are dependent on cysteine due to reduced capacity to sink the methyl groups of SAM. Therefore, PP2A directs the methylation status of histones by regulating the phosphorylation status of histone demethylase enzymes in response to SAM levels.

overall_design: Explore the binding of Rph1 to chromatin. Strains containing Rph1 that is tagged by the HA epitope tag grew under indicated conditions were collected  for ChIP-seq experiments. Please refer to the manuscript regarding experimental procedures about ChIP and library construction.

first: Cunqi

last: Ye

first: Benjamin

last: Sutter

last: Tu


title: p63 establishes epithelial enhancers de novo at critical craniofacial development genes

status: Public on Feb 15 2019

city: Philadelphia

first: Yemin

last: Lan

state: PA

address: 3400 Civic Center Blvd

country: USA

institute: University of Pennsylvania

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Longitudinal transcriptome profiling of post-treatment Lyme disease syndrome

city: San Francisco

first: Charles

last: Chiu

state: CA

address: 185 Berry Street, Box 0134

department: Laboratory Medicine

institute: University of California, San Francisco

summary: Most Lyme disease patients treated with appropriate antibiotics recover rapidly and completely, but a minority of patients develop persistent symptoms correlating with disseminated disease, a greater severity of illness at presentation, and delayed antibiotic therapy. When lingering or recurrent symptoms are associated with a functional decline and persist for greater than 6 months, patients are considered to meet clinical criteria for post-treatment Lyme disease syndrome (PTLDS), although the exact molecular mechanisms underlying this condition remain unknown. We performed longitudinal whole transcriptome sequencing of PTLDS patients' immune cells. No immune mechanism specific to PTLDS were uncovered to date.

overall_design: Gene expression profile from peripheral mononuclear blood cells (PBMC) of PTLDS patients was undertaken. Seven Lyme disease patients were sampled at 3 time points: acute Lyme pre-treatment (V1), 3 weeks later, immediately following completion of a standard course of antibiotics (V2), and 6 months following treatment completion (V5). Total RNA was extracted from 10e7 PBMC, followed by mRNA purification, paired-end barcode library preparation and sequencing on an Illumina HiSeq 2000.

first: Jerome

last: Bouquet

middle: Y


title: Ex vivo Dynamics of Human Glioblastoma Cells in a Microvasculature-on-a-Chip System Correlates with Tumor Heterogeneity and Subtypes

city: New York

first: Kam

last: Leong

state: NY

address: 3600 Broadway, RM450C

department: Biomedical Engineering

institute: Columbia University

summary: The perivascular niche (PVN) plays an essential role in brain tumor stem-like cell (BTSC) fate control, tumor invasion, and therapeutic resistance. We use a microvasculature-on-a-chip system as a PVN model to evaluate the ex vivo dynamics of BTSCs from ten glioblastoma patients. BTSCs were found to preferentially localize in the perivascular zone, where they exhibited either the lowest motility, as in quiescent cells, or the highest motility, as in the invasive phenotype, with migration over long distance. The degree of co-localization between tumor cells and microvessels varied significantly across patients. To validate these results from the microvasculature-on-a-chip system, single-cell transcriptome sequencing (10 patients and 21,750 single cells in total) was performed to identify tumor cell subtypes. The co-localization coefficient was found to positively correlate with proneural (stem-like) or mesenchymal (invasive) but not classical (proliferative) tumor cells. Furthermore, a gene signature profile including PDGFRA correlated strongly with the “homing” of tumor cells to the PVN. These findings demonstrate that our BTSC-on-a-chip model can recapitulate in vivo tumor cell dynamics and heterogeneity, representing a new route to study patient-specific tumor cell functions.

overall_design: Single cell RNA-seq of human glioblastoma cells from 10 patients.

first: Yang

last: Xiao

first: Rong

last: Fan


title: The Toxoplasma effector TEEGR promotes parasite persistence by modulating NF-κB signalling via EZH2

city: LA TRONCHE

first: Mohamed-ali

last: HAKIMI

state: Grenoble

address: Domaine de la Merci, Campus Santé

country: France

institute: CNRS

summary: The protozoan parasite Toxoplasma gondii has co-evolved with its homeothermic hosts (humans included) strategies that drive its quasi-asymptomatic persistence in hosts, hence optimizing the chance of transmission to new hosts. Persistence, which starts with a small subset of parasites that escape host immune killing and colonize the so-called immune privileged tissues where they differentiate into a low replicating stage, is driven by the interleukin 12 (IL-12)-interferon-γ (IFN-γ) axis. Recent characterization of a family of Toxoplasma effectors that are delivered into the host cell, in which they rewire the host cell gene expression, has allowed the identification of regulators of the IL-12-IFN-γ axis, including repressors. We now report on the dense granule-resident effector, called TEEGR (Toxoplasma E2F4-associated EZH2-inducing gene regulator) that counteracts the nuclear factor-κB (NF-κB) signalling pathway. Once exported into the host cell, TEEGR ends up in the nucleus where it not only complexes with the E2F3 and E2F4 host transcription factors to induce gene expression, but also promotes shaping of a non-permissive chromatin through its capacity to switch on EZH2. Remarkably, EZH2 fosters the epigenetic silencing of a subset of NF-κB-regulated cytokines, thereby strongly contributing to the host immune equilibrium that influences the host immune response and promotes parasite persistence in mice.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: TCF4 germline mutation and adult-onset SHH medulloblastoma

status: Public on Feb 14 2019

city: Paris

first: Julien

last: Masliah-Planchon

address: 26 rue d'Ulm

institute: Institut Curie

summary: Medulloblastoma (MB) is the most prevalent pediatric cerebral cancer, but is rare in adults. The vast majority of MB arises sporadically but some few cases occur in association with germline alterations in genes such as PTCH1, SUFU, APC, and TP53. Additional genes are responsible for MB predisposition including some that have probably not been described so far either due to the rarity of the cases and/or to the low penetrance. Here we report the case of a 27 years old woman affected by Pitt Hopkins syndrome due to a heterozygous germline pathogenic variant in TCF4 who has developed a Sonic Hedgehog (SHH)-driven MB. Somatic loss of function variants of TCF4 have been identified in SHH MB especially among adults and this case raises the question of a predisposition to late-onset SHH MB associated with TCF4 germline alteration.

overall_design: EPIC methylation array perform on the single patient's medulloblastoma

first: Franck

last: Bourdeaut


title: Small RNA sequencing of C. elegans mortal germline mutants

city: London

first: Peter

last: Sarkies

address: Du Cane Road

department: MRC Clinical Sciences Centre

country: United Kingdom

institute: Imperial College London

type: Non-coding RNA profiling by high throughput sequencing

summary: The meiotic phosphatase gsp-2 is identified as a novel factor promoting germline immortality

overall_design: Small RNAs (18-30 nucleotides) were sequenced from early and late generation animals


title: Absolute measurements of mRNA translation in C. crescentus reveal important fitness costs of Vitamin B12 scavenging

city: Bloomington

first: Jared

middle: Michael

last: Schrader

state: IN

address: 212 S Hawthorne Dr

department: Biology

institute: Indiana University

summary: Ribosome profiling samples of C. crescentus grown in M2G to measure absolute levels of mRNA translation in M2G media.

overall_design: Ribosome profiling samples were collected in log-phase of growth in M2G media.

middle: M


title: Small-molecule-based Human Genome G4 Profiling Reveals Potential Gene Regulation Activity

city: Wuhan

first: Weiwu

last: Zeng

state: Hubei

address: Bayi Road

department: College of Chemistry and Molecular Sciences

country: China

institute: Wuhan University

summary: G-quadruplexes (G4s) are a type of secondary structure of nucleic acids, the formation of which depends on the π-π stacking of guanine-rich sequences.  Herein, we present a readily accessible strategy, based on small molecule pulldown, for direct genomic G4 profiling of HEK 293T cells. A small molecule was rationally designed, containing PDP on one end and biotin on the other, joined by a 24-unit-long hydrophilic PEG linker. G4s isolation from genomic DNA annealed in potassium chloride buffer beforehand, has identified a total of 51446 PQS, which mainly distribute in introns and intergenic regions. Incubating cells with PDP for 3 h to 72 h resulted in the differential expression of a variety of genes, indicating a potential function of G4s in gene regulation.

overall_design: A small molecule was applied for pull-down of G-quadruplexes in the genome of HEK 293T cells. RNA-Seq was performed to measure gene expression difference upon addition of 1 µM PDP for 3 h, 24 h and 72 h.

first: W

first: F

last: Wu

first: C

last: Liu

first: Y

last: Yang

first: Z

first: X

last: Zhou


title: Impact of Tcf1/Lef1 deficiency on Treg cells

city: Washington

first: Weiqun

last: Peng

state: DC

address: 1918 F Street, NW , DC

institute: The George Washington University

summary: Comparison of transcriptome between control and Tcf1/Lef1-deficient Treg cells

overall_design: Splenocytes were harvested from Foxp3-Cre+, Tcf1/Lef1 wild-type or double floxed mice (male and at 16 weeks of age), and sorted for Foxp3-Cre-GFP+Thy1.2+CD4+ regulatory T cells

first: Hai-Hui

last: Xue


overall_design: Murine (BMDM) cells were left uninfected or infected for 24 hours with Pruku80, Pruku80ΔTEEGR or Pruku80ΔTEEGR+TEEGR (complemented) Toxoplasma type II strains before gene expression was measured. Three independent experiments were performed for each condition.

first: Laurence

last: Braun

first: Marie-Pierre

last: Brenier-Pinchart

first: Pierre-Mehdi

last: Hammoudi

first: Dominique

last: Cannella

first: Sylvie

last: Kieffer-Jaquinod

last: Vollaire

first: Véronique

last: Josserand

first: Bastien

last: Touquet

first: Yohann

last: Couté

first: Isabelle

last: Tardieux

first: Alexandre

last: Bougdour

first: Mohamed

middle: A

last: Hakimi


title: Transcriptome analysis of whole hippocampus from wild-type and TET1-deficient mice after electroconvulsive shock

city: Bronx

first: Deyou

last: Zheng

address: 1301 Morris Park Ave

institute: Albert Einstein College of Medicine

summary: We examined the effect of TET1 deletion on activity-dependent gene regulation by comparing RNA-seq expression profiles from the hippocampus of ECS-treated Tet1Δe4-/- and Tet1+/+ mice. We discovered that 34 genes were significantly upregulated and 184 genes were downregulated, suggesting a primary role for TET1 in activating gene expression. In order to test the hypothesis that TET1 is responsible for regulating activity-dependent genes, we cataloged a dataset of activity-dependent genes based on a literature review. While there was not significant enrichment for activity-dependent genes disrupted in Tet1-deficient mice, dysregulation of several activity-dependent genes were identified including the master memory gene regulator, Npas4. Gene Ontology analyses of the dysregulated genes detected a significant enrichment for genes involved in the extracellular region/matrix/space. Interestingly, RNA-seq revealed downregulation of Oxtr, the receptor which binds oxytocin.

overall_design: RNA-sequencing of whole hippocampus from 3 Tet1Δe4-/- and 3 Tet1+/+ mice 1.5-2 hours after electroconvulsive shock

first: Aaron

last: Towers

first: Ping

last: Wang

first: Yong-Hui

last: Jiang


title: The histone chaperone CAF-1 cooperates with the DNA methyltransferases to maintain Cd4 silencing in cytotoxic T cells

status: Public on Feb 13 2019

first: Craig

last: Thompson

address: 411 East 67th Street RRL 469

institute: Memorial Sloan Kettering Cancer Center

type: Methylation profiling by high throughput sequencing


title: Genome-wide mapping of Tcf1 occupancy in conventional and regulatory CD4+ T cells

first: Weiqun

last: Peng

summary: Determine genome-wide binding locations by Tcf1 in conventional and regulatory CD4+ T cells

overall_design: Foxp3-Cre-GFP mice at 8-10 weeks old were used to sort purify for conventional CD4+ (GFP–CD25–) cels, and regulatory CD4+ (GFP+CD25+) cells from the spleen, and the cells were used in ChIP-Seq analysis.

first: Hai-Hui

last: Xue


title: Development of gene expression signatures for progression and regression of atherosclerosis

city: Shanghai

first: Xiaolan

last: Yu

address: 800 Dongchuan RD, Minhang District

institute: Shanghai JiaoTong Univerisity

summary: To further study the important genes related with the diagnosis and prognosis of atherosclerosis, we have employed whole genome microarray expression profiling as a discovery platform to identify genes with the atherosclerosis. we established a rabbit model of progression and regression of atherosclerosis through balloon injury and high-cholesterol diet and normal diet. Rabbit abdominal aortas from atherosclerosis among control, model group (progression) and recovery groups (regression) were collected. We found that the differentially expressed genes mainly enriched in four clusters and genes associated with inflammation and extracellular matrix were returned to or close to normal levels much earlier than the genes associated with metabolism and sarcoplasmic proliferation, they kept down-regulation or up-regulation for a long time after normal diet. Expression of four genes (LPL，BMP7，MCP2 and SST) from this signature was quantified in the same RNA samples by real-time PCR and maybe used as novel biomarkers and targets for improving the diagnosis and prognosis of atheroscleross in the future.

overall_design: we established a rabbit model of progression and regression of atherosclerosis through balloon injury and high-cholesterol diet and normal diet. Rabbit abdominal aortas from atherosclerosis among control, model group (progression) and recovery groups (regression) were collected for gene chip.

first: Yan


title: Specific inhibition of splicing factor activity by decoy RNA oligonucleotides

city: Stockholm

first: Miri

last: Danan-Gotthold

address: Tomtebodavägen  16

country: Sweden

institute: Karolinska  institutet

summary: Alternative splicing, a fundamental step in gene expression, is deregulated in many diseases. Splicing factors (SFs), which regulate this process, are up- or down regulated or mutated in several diseases including cancer. To date, there are no inhibitors that directly inhibit the activity of SFs. We designed decoy oligonucleotides, composed of several repeats of a RNA motif, which is recognized by a single SF. Here we show that decoy oligonucleotides targeting splicing factors RBFOX1/2, SRSF1 and PTBP1, can specifically bind to their respective SFs and inhibit their splicing and biological activities both in vitro and in vivo. These decoy oligonucleotides present a novel approach to specifically downregulate SF activity and have the potential to treat diseases where SFs are up-regulated, such as cancer.

overall_design: The RNA-seq was performed on 2 independent biological replicates of cells transfected with SCRM or RBFOXi

first: Polina

last: Denichenko

first: Rotem

last: Karni

first: Erez

last: Levanon


title: Synaptic scaling regulates the transcriptome in hippocampal neurons

city: Coimbra

first: Joana

middle: Filipa

last: Fernandes

state: -- Please Select --

address: Rua Larga, Faculdade de Medicina 2º andar, lab 206A Coimbra

department: Life Sciences

country: Portugal

institute: Center for Neuroscience and Cell Biology

summary: To better comprehend how synaptic scaling affects the neuronal transcriptome, we used the whole genome microarray expression profiling in hippocampal cultures treated with AMPARs and synaptic NMDARs antagonists for 9h and 26h, or under control conditions. Gene ontology enrichment analysis showed altered transcripts associated with synaptic signalling and synaptic plasticity classes, including transcripts of several proteins already associated with synaptic scaling mechanisms.

overall_design: The effects of chronic synaptic activity blockade in gene expression were analyzed in primary cultures of rat hippocampal neurons treated for 9h or 26h with AMPARs antagonist GYKI-52466 and synaptic NMDARs antagonist MK-801. Three independent experiments were performed at each time (9 or 26 hours) as independent biological replicates.

first: Mariline

last: Silva

first: Beatriz

last: Rodrigues

first: Sandra

middle: D

last: Santos

first: Laura

last: Carreto

first: Manuel

first: Paulo

last: Pinheiro

first: Ana Luísa

last: Carvalho


title: Genome-wide map of proximity linkage to renin proximal promoter in rat

city: Milwaukee

first: Mingyu

last: Liang

state: Wisconsin

address: 8701 Watertown Plank Rd

department: Physiology

institute: Medical College of Wisconsin

summary: Physical proximity mapping through sequencing can provide an unbiased view of the chromatin close to the proximal promoter of the renin gene (Ren).  Our objective was to determine genomic regions that physically interact with the renin proximal promoter, using two different genetic backgrounds, the Dahl salt sensitive and normotensive SS-13BN, which have been shown to have different regulation of plasma renin in vivo.  The chromatin conformation capture method with sequencing focused at the Ren proximal promoter in rat-derived cardiac endothelial cells was used. Cells were fixed, chromatin close to the Ren promoter was captured, and fragments were sequenced.  The clustering of mapped reads produced a genome-wide map of chromatin in contact with the Ren promoter.  The largest number of contacts was found on chromosome 13, the chromosome with Ren, and contacts were found on all other chromosomes except chromosome X.  These contacts were significantly enriched with genes positively correlated with Ren expression and with mapped quantitative trait loci (QTLs) associated with blood pressure, cardiovascular and renal phenotypes. The results were reproducible in an independent biological replicate and in endothelial cells derived from a second rat stain.  The findings reported here represent the first map between a critical cardiovascular gene and physical interacting loci throughout the genome, and will provide the basis for several new directions of research.

overall_design: 4C-seq contact maps at Renin proximal promoter viewpoint in Rat cardiac endothelial cells from SS and SS13BN strains

first: Timothy

middle: J

last: Stodola

first: Pengyuan

last: Liu

first: Yong

first: Andrew

middle: K

last: Vallejos

first: Aron

last: Geurts

middle: S

last: Greene


title: The histone chaperone CAF-1 cooperates with the DNA methyltransferases to maintain Cd4 silencing in cytotoxic T cells (ATACseq II)

first: Craig

last: Thompson

summary: The transcriptional repression of alternative lineage genes is critical for cell fate commitment. Mechanisms by which locus-specific gene silencing is initiated and heritably maintained during cell division are not clearly understood. To study the maintenance of silent gene states, we investigated how the Cd4 gene is stably repressed in CD8+ T cells. Through CRISPR and shRNA screening, we identified the histone chaperone CAF-1 as a critical component for Cd4 repression. We found that the large subunit of CAF-1, Chaf1a, requires the N-terminal KER domain to associate with the histone deacetylases HDAC1/2 and the histone demethylase LSD1, enzymes that also participate in Cd4 silencing. When CAF-1 was lacking, Cd4 derepression was markedly enhanced in the absence of the de novo DNA methyltransferase Dnmt3a, but not the maintenance DNA methyltransferase Dnmt1. In contrast to Dnmt1, Dnmt3a deficiency did not significantly alter levels of DNA methylation at the Cd4 locus. Instead, Dnmt3a deficiency sensitized CD8+ T cells to Cd4 derepression mediated by compromised functions of histone modifying factors, including the enzymes associated with CAF-1. Thus, we propose that the heritable silencing of the Cd4 gene in CD8+ T cells exploits cooperative functions among the DNA methyltransferases, CAF-1, and histone modifying enzymes.

overall_design: There are 12 samples total. There are 10 samples consisting of sorted CD8+ T cells with or without expression of CD4 after knock-down with shRNAs targeting Dnmt1 or Chaf1a. There are 2 samples consisting of sorted CD8+ T cells after shRenilla knock-down and 2 samples consisting of sorted CD4+ T cells after shRenilla knock-down.

first: Charles

last: Ng

first: Martin

last: Aichinger

first: Tung

last: Nguyen

first: Christy

last: Au

first: Tariq

last: Najar

first: Lin

last: Wu

first: Kai

middle: R

last: Mesa

first: Will

last: Liao

first: Jean-Pierre

last: Quivy

first: Benjamin

last: Hubert

first: Genevieve

last: Almouzni

first: Johannes

last: Zuber

first: Dan

last: Littman


title: Identifying a Novel Connection Between the Fungal Plasma Membrane and pH Sensing

city: Durham

first: Hannah

middle: Elizabeth

last: Brown

state: NC

address: 303 Research Dr

department: Molecular Genetics and Microbiology

institute: Duke University

summary: To identify cellular processes similarly regulated by both Rim101 and Cdc50, we compared the transcriptomes of the rim101∆ and cdc50∆ strains against WT. We observed a partial overlap in the transcriptional perturbation shared by the mutant strains. Most notably, these data demonstrate a role for both Rim101 and Cdc50 in regulating the gene expression of membrane-associated proteins, including those involved in lipid bilayer composition and organization. Furthermore, this class of membrane-associated genes co-regulated by Rim101 and Cdc50 demonstrate similar expression changes in the two mutant strains in both direction and magnitude.

overall_design: Gene expression analysis of WT and rim101∆ and cdc50∆ mutant cells generated in triplicate by RNA-Sequencing.

first: Shannon

last: Esher

first: J

last: Alspaugh


title: GLP-1 signaling suppresses menin's transcriptional block by phosphorylation in beta cells

city: Shenzhen

first: Bowen

last: Xing

state: Guangdong

address: Nanhai Street 3688

institute: Shenzhen University

summary: We find that GLP-1 signaling-activated PKA directly phosphorylates menin at serine 487 residue, relieving menin mediated suppression of insulin expression in beta cells and islets of diabetic GK rat. Mechanistically, GLP-1-induced PKA activation leads to menin Ser487 phosphorylation, and phosphorylated menin gains increased binding affinity to cytoskeleton proteins such as beta actin and myosin. Sequestration of Ser487 phosphorylated menin from the Ins1 gene promoter leads to reduced binding of menin-associating repressive epigenetic regulators such as SUV39H1 and HDAC1 at the locus, resulting in increased Ins1 transcription. Our results have linked GLP-1 signaling to physiologically suppression of menin function in repressing insulin expression, and uncovered a potential step to modulate menin phosphorylation to improve T2D therapy.

overall_design: mRNA profiles of INS-1 cells overexpressing menin S487A or S487D mutant were generated by deep sequencing, in triplicate.


title: The histone chaperone CAF-1 cooperates with the DNA methyltransferases to maintain Cd4 silencing in cytotoxic T cells (ATACseq I)

first: Craig

last: Thompson

first: Charles

last: Ng


title: Endometrial epithelial cell transcriptome response to co-culture with adipose stromal cells

city: San Antonio

first: Yufan

last: Zhou

state: TX

address: 7703 Floyd Curl Dr

institute: UT health Science Center at San Antonio

summary: The role of obesity in endometrial cancer development is tested by co-culturing adipose stromal cells (ASCs) with endometrial epithelial cells and endometrial cancer cell Ishikawa for 21 days. Control cells (not exposed to ASCs) were incubated for the same duration.  RNA-seq identified differential expression due to ASC exposure

overall_design: Transcriptoms effects in enomdetrial epithelial cells is exmined by RNA-seq after adipose stromal cell co-culture

first: Nameer

middle: B

last: Kirma

first: Yugan


title: Transcriptional profiling of milk epithelial cells of Kashmiri and Jersey cattle

city: Gandarbal

first: Basharat

middle: Ahmad

last: Bhat

state: Kashmir

address: Shuhama

department: Animal Biotechnology

country: India

institute: Sher-e-Kashmir University of Agricultural Sciences and Technology

summary: The purpose of the present study was to provide a comprehensive transcriptome profiling of mammary gland and to find the key differences in the milk production and related traits between Jersey and Kashmiri cattle. Casein and whey protein genes were found to be highly expressed throughout the lactation cycle. Largest differences in DEGs was reported between D15 and D90 with 1805 genes in Kashmiri cattle and between D15 and D250 with 3392 genes in Jersey cattle.

sample_organism:
Bos taurus
Bos indicus

platform_organism:
Bos taurus
Bos indicus

overall_design: The milk samples were collected for epithelial cell isolation from three Kashmiri and three Jersey cattle, representing two study groups. The samples were collected at three time points, day 15 (D15), D90 and D250 of the lactation cycle. There were total three biological replicates per group.

first: Shakil

first: Syed

last: Mudasir Ahmad


title: A conserved genetic interaction between Spt6 and Set2 regulates H3K36 methylation

city: Boston

first: Rajaraman

last: Gopalakrishnan

state: MA

address: NRB 239, 77 Ave Louis Pasteur

department: Genetics

institute: Harvard Medical School

summary: The transcription elongation factor Spt6 and the H3K36 methyltransferase Set2 are both required for H3K36 methylation and transcriptional fidelity in Saccharomyces cerevisiae. By selecting for suppressors of a transcriptional defect in an spt6 mutant, we have isolated dominant SET2 mutations (SET2sup mutations) in a region encoding a proposed autoinhibitory domain. The SET2sup mutations suppress the H3K36 methylation defect in the spt6 mutant, as well as in other mutants that impair H3K36 methylation. ChIP-seq studies demonstrate that the H3K36 methylation defect in the spt6 mutant, as well as its suppression by a SET2sup mutation, occur at a step following the recruitment of Set2 to chromatin. Other experiments show that a similar genetic relationship between Spt6 and Set2 exists in Schizosaccharomyces pombe. Taken together, our results suggest a conserved mechanism by which the Set2 autoinhibitory domain requires multiple interactions to ensure that H3K36 methylation occurs specifically on actively transcribed chromatin.

overall_design: ChIP-Seq of Set2-HA, Rpb1, H3K36me3, H3K36me2, H3 in WT, spt6-1004, SET2-H366N and spt6-1004 SET2-H366N strains grown at 30oC and done in duplicate

first: Fred

last: Winston


title: Negative regulation of lymphoid specification by the transcription factor TAL1

status: Public on Feb 12 2019

city: Chicago

first: Barbara

middle: L

last: Kee

state: Illinois

address: 924 E57th st

department: Pathology

institute: The University of Chicago

summary: Lymphoid primed multipotent progenitors are a subset of MPPs that are undergoing specification to the lymphoid and myeloid cell fates. The transcription factors Lyl1 and E2A are both essential for the development LMPPs and can form a heterodimeric complex. We examined the consequences of E2A- or Lyl1-deficiency on development of LMPPs and on their gene expression program in comparison with wild-type LMPPs

overall_design: Examination of RNA present in Rag2-GFP+ and Rag2-GFP- HSC and LMPP isolated from control and VaviCre Tal1floxed/floxed mice.

first: Renee

last: dePooter

first: Sheila

last: Dias

first: Elizabeth

middle: T

last: Bartom

first: Michael

last: Okoreeh

first: Mikael

last: Sigvardsson


title: Impact of dietary antigen on gene expression of Peyer's patch T cells

city: Mainz

first: Matthias

last: Klein

address: Langenbeckstrasse 1

department: Inst. for Immunology

country: Germany

institute: University Medical Center Mainz

summary: Transcriptional profiling shows that Peyer´s patch CD4+ T cells from mice kept on dietary antigens are skewed towards a Tfh cell programme. Continous recognition of dietary antigens does not lead to classical signature of exhaustion.

overall_design: Examination of conventional and elemental diet on gene expression of PP T cells

first: Ulrich

last: Steinhoff


title: Seedling temperature responses in Arabidopsis RRS-7

city: Halle

first: Carolin

last: Delker

address: Betty-Heimann-Str. 5

department: Crop Physiology

institute: Martin Luther University Halle

summary:
Plants have the capacity to sense and respond to even small changes in ambient temperature. Numerous thermomorphogenic responses can be observed in Seedlings including elongation of the hypocotyl, petioles and the primary root while leaf blade areas are reduced. Main objective of the experiment was the assessment of tissue-specific transcriptome responses in Arabidopsis seedlings exposed to elevated ambient temperatures,
5 days old Arabidopsis seedlings grown at 20°C in LD were shifted for 3 or 24h to 28°C. Control plants were kept at 20°C. At time of harvest, cotyledons and roots were dissected and collected separately from the hypocotyl. To minimize circadian effects, plant material was grown in several successive batches and harvested only for a period of 30 min per timepoint on several consecutive days. Shifts and harvest was performed at midday to late afternoon (see ZT in overall design).

overall_design: Seeds of the Arabidopsis accession RRS-7 (CS22688) were surface sterilized, stratified for 4 days in sterile water and subsequently placed on square plates containing ATS medium (Lincoln et al. 1991, The Plant Cell) containing 1.5% Agargel. Seedlings were cultivated for 5d in LD (16h light, 8h dark) at 20°C in walk-in phytochambers with 120 µmol/m2/sec PAR generated from white lite LEDs in approx. 30 cm distance. On day 5, plates were either shifted to 28°C or kept at 20°C as controls. For 3h temperature treatments Seedlings were either shifted at ZT Dissection and harvest of plant material was carried out under the same conditions as cultivation for a total of 30 min for each timepoint. 3 biological replicates for each treatment, timepoint and plant organ were generated by pooling distinct sample sets collected over several successive harvesting sessions. Plant material was homogenized and RNA was extracted using RNeasy Plant Mini Kit (Qiagen) including an on-collumn DNase digestion. Extracted RNA was further processed at the NASC

first: Marcel

last: Quint


title: Quantitative analysis of transcriptome of wild-type and mcd1-1 mutant of Saccharomyces cerevisiae by PolyA RNAseq

city: Bengaluru

first: Shikha

last: Laloraya

state: Karnataka

address: New Biological Science Building

department: Biochemistry

institute: Indian Instritute of Science

summary: In this study, we performed RNAseq of PolyA enriched RNA from budding yeast cells that were either wild-type or having the mcd1-1 mutation.  By obtaining over 200 million reads of sequences from PolyA RNA, we mapped greater than 30 million reads per sample to the yeast genome (S288C R64-2-1_20150113)and generated transcriptomic profiles of wild-type and mcd1-1 mutant cells.  Comparison of the wild type and mutant transcriptomes revealed that 11.44% genes were upregulated, 4.99% were  downregulated and 83.57% were unaffected in the mutant with a fold change ≥2.0 and Padj value <0.05.  When the alterations in gene expression were analyzed with respect to chromosomal position, preferential derepression of subtelomeric (located within 20 kilo bases from the chromosome end) genes was observed in the mutant.

overall_design: PolyA mRNA profiles of wild type (WT) and mcd1-1 budding yeast cells were generated by deep sequencing, in quadruplicate, using Illumina HiSeq X.

first: Deepash

last: Kothiwal


title: Human Long Intergenic Noncoding RNA Linc-ADAL Knockdown in Mature Adipocytes using Lentiviral ShRNA

city: New York

first: Chenyi

last: Xue

institute: Columbia University

summary: Thousands of human long intergenic noncoding RNAs (lincRNAs) have been detected in human adipose tissue. Here we characterized the function of one human adipse lincRNA, linc-ADAL (chr5:115292235-115296985) in mature adipcoytes through loss-of-function studies. Our results indicate that knockdown of linc-ADAL in differentiated adipocytes modulated expression of lipid metabolism genes.

overall_design: Lentiviral based shRNAs were used to knockdown linc-ADAL in differentiated ASC-derived adipocytes. ASC-adipoctes were transduced on day 8 of adipogenic differentiation. Cells were harvested for RNA extraction on day 6 post-transduction.

first: Zhang

last: Xuan

first: Xue

last: Chenyi


title: Transcriptomic profiling following de novo hepatitis B vaccination reveals role of granulocytes in non-responders

city: Antwerpen

first: Nicolas

last: De Neuter

address: Middelheimlaan 1

country: Belgium

institute: University of Antwerp

summary: As hepatitis B virus is widely spread, WHO recommend vaccination from infancy to reduce acute infection and chronic carriers. However current subunit vaccines are not 100% efficacious and leaves 5-10% persistent non-responders unprotected. To handle large inter-individual variability in immune response after the first Engerix-B vaccination, we employed whole blood early gene expression signatures at day 3 and 7. Immune related pathways are differential expressed in the responders group mostly at day 3 and at day 7 in the non-responders. A notable difference between both groups are significant differential expressed genes at day 0, before vaccination, showing the inter-individual variation. The granulin precursor (GRN) was significant downregulated in responders while upregulated in non-responders. Further absolute granulocytes numbers were significant higher in non-responders. So there is a certain diversity in basic innate immune system.

overall_design: Whole blood mRNA gene expression profiles at day 0, 3 and 7 from individuals vaccinated with a de novo Engerix-B dose at day 0 (after blood draw).


title: Gene expression profiles in experimental uremic cardiomyopathy.

city: Atlanta

first: Gregory

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

summary:
Purpose: To define differentially regulated pathways in heart tissue from mice with chornic kidney disease (CKD) compared to age-matched controls.
Methods: CKD was induced in 5-week-old, male 129X1/SvJ mice (JAX) through five-sixths nephrectomy in a two-step surgery (n=5). Age-matched mice undergoing bilateral sham surgeries served as controls (n=5). Heart tissue was collected at 8 weeks of CKD for next generation sequencing.
Results: Hearts from mice with uremic cardiomyopathy yielded over 1,000 differentially-expressed mRNA transcripts compared to hearts from age-matched, sham-operated mice. Ingenuity biofunctions analysis identified significant enrichment for genes involved in Tissue Morphology, Immune Cell Trafficking, Cardiovascular Development and Function, and Humoral Immune Response. We focused on Ingenuity canonical pathways involving inflammation and immune system function including pathways needed for a T-cell mediated response: leukocyte extravasation, antigen presentation, dendritic cell maturation, T cell co-stimulatory signaling, and T-helper cell differentiation.
Conclusions: Left ventricles from mice with CKD display differential expression in a number of pathways suggesting inflammation and surprisingly involved genes involved in the adaptive immune system.

overall_design: Left ventricular mRNA profiles from 5 mice with CKD and 5 normal mice were generated using next generation RNA sequencing on the Illumina HiSeq 1000.

first: Pamela

last: Winterberg

first: Nirav

last: Patel


title: Identification of candidate genes and pathways in dexmedetomidine-induced cardioprotection in the rat heart by bioinformatics analysis [mRNA]

status: Public on Feb 11 2019

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

summary: Differentially expressed miRNAs and mRNAs after dexmedetomidine administration in rat hearts were successfully identified by conducting microarray analysis.

overall_design: mRNA and miRNA microarray analysis were conducted in a control group (administration of saline) and a dexmedetomidine group (administration of dexmedetomidine) using rat hearts

first: Yusuke

last: Yoshikawa

first: Michiaki

last: Yamakage


title: Identification of candidate genes and pathways in dexmedetomidine-induced cardioprotection in the rat heart by bioinformatics analysis [miRNA]


title: Identification of candidate genes and pathways in dexmedetomidine-induced cardioprotection in the rat heart by bioinformatics analysis

type:
Expression profiling by array
Non-coding RNA profiling by array

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

overall_design: Refer to individual Series


title: Sex-biased hippocampal pathology in the 5XFAD mouse model of Alzheimer's disease: A multi-omic analysis

city: Tallahassee

first: Joseph

middle: Ligon

last: Bundy

state: FL

address: 1115 W Call St

department: Department of Biomedical Sciences

institute: Florida State University

summary: Numerous neurological disorders, including Alzheimer's disease, display a sex-biased prevalence. To identify molecular correlates of this sex bias, we investigated sex-differences in molecular pathology in the hippocampus using the 5XFAD mouse model of Alzheimer's disease during early stages of disease progression (1, 2, and 4 months of age).

overall_design: Hippocampal mRNA from 1, 2, and 4 month old male and female 5XFAD mice were analyzed by RNA sequencing of 5 biological replicates using an Illumina HiSeq 2500

first: Cynthia

last: Vied

first: Crystal

last: Dawn-Badger

first: Richard

last: Nowakowski


title: Differential gene expression in NPHS2-Cre +/+ mouse glomeruli versus wild-type control

city: Birmingham

first: Caroline

last: Marshall

state: AL

address: 1720 2nd Ave S

department: Medicine/Nephrology

institute: University of Alabama at Birmingham

summary: To investigate differential gene expression that might account for the differing glomerular phenotype of NPHS2-Cre +/+ mice when compared with wild-type control, including altered GBM thickness, loss of normal foot process morphology, and decrease in podocyte number, RNA sequencing analysis was performed on glomeruli extracted from both NPHS2-Cre +/+ and wild-type control mice.

overall_design: Following isolation of glomeruli using Dynabeads from NPHS2-Cre +/+ and wild-type control mice (n=2 biological replicates per genotype, singly isolated), total RNA was extracted and RNA samples were submited for sample preparation and sequencing.

first: Rohan

last: Balkawade

first: Michael

last: Crowley

first: David

last: Crossman


title: Targeted elimination of senescent beta cells prevents Type 1 Diabetes

city: San Francisco

first: Anil

last: Bhushan

state: CA

address: 513 Parnassus ave

department: Diabetes Center

institute: UCSF

summary: scRNA-seq of Islets isolated from 8, 14 and 16 week NOD mice

overall_design: Examination of scRNA-seq in beta cells across three different age groups

first: Ajit

last: Shah

first: Peter

last: Thompson


title: TMK1-mediated transcriptional auxin signaling guides differential growth in plant

city: Shanghai

first: Renyi

last: Liu

state: Shanghai

address: 3888 Chenhua Road

department: Bioinformatics

institute: Shanghai Center for Plant Stress Biology

summary: Auxin plays diverse and profound roles in plants, regulating essentially all aspects of plant growth and development. Yet how auxin achieves such functional diversity and specificity is largely unknown. Here, we address how different concentrations of auxin determine developmental responses through auxin signaling pathways, which are essential for differential growth including apical hook development. We showed that a high auxin concentration at concave side of the apical hook stimulated the C-terminus cleavage and cytosolic translocation of Transmembrane Kinase 1 (TMK1), which then phosphorylates non-canonical IAA32 and IAA34.  Surprisingly, and in contrast to the previous report that auxin degrades IAA proteins through the TIR1/AFB auxin receptor to regulate gene expression, here we found that non-canonical IAA32 and IAA34 proteins were stabilized by the high auxin concentration through TMK1 cleavage to negatively regulate gene expression and inhibit growth. Thus, we demonstrated that TIR1/AFB-independent transcriptional auxin signaling regulated growth inhibition in response to the high auxin concentration.

overall_design: mRNA profiles of Col-0, tmk1-1 and iaa32iaa34 apical hook region

first: Min

last: Cao


title: Real-time quantitative PCR analysis of mouse colon samples

city: Ribeirao Preto

first: Vinicius

last: Kannen

state: SP

address: Av Café, s/ N°

department: DACTB

country: Brazil

institute: Universidade de São Paulo


title: Main constrains for RNAi induced by expressed long dsRNA in mouse cells

status: Public on Feb 10 2019

city: Prague

first: Filip

last: Horvat

address: Videnska 1083

country: Czech Republic

institute: Institute of Molecular Genetics of the ASCR

summary: Using a system expressing dsRNA molecules and luciferase reporters, we explored factors contributing to RNAi inefficiency in mouse embryonic stem cells (ESCs) and NIH3T3 fibroblasts that could explain previous contradictions concerning mammalian RNAi. Low and poorly processive Dicer activity combined with insufficiently abundant substrates appear to be the primary reason for RNAi inefficiency.

overall_design:
Bulk small RNA-seq of 8 NIH3T3 fibroblasts samples:
- 2 replicates transfected with pCag-EGFP Lin28IR
- 2 replicates transfected with pCag-EGFP MosIR
- 2 replicates transfected with pU6 Lin28IR
- 2 replicates transfected with pU6 MosIR

first: Petr

last: Svoboda

first: Radek

last: Malik


title: Global fine-tuning of translation by queuosinylation and Dnmt2-dependent tRNA methylation

city: Berlin

first: Ann

middle: E.

last: Ehrenhofer-Murray

address: Philippstr. 13

department: Institut für Biologie

institute: Humboldt-Universität zu Berlin

summary: In most eukaryotes, the wobble position of tRNA with a GUN anticodon is queuosine-modified (Q34). Q is synthesized exclusively by eubacteria and salvaged by eukaryotes as a nutrient to replace G34 in tRNAs. Q34 modification stimulates Dnmt2/Pmt1-dependent C38 methylation in the tRNAAsp anticodon loop in Schizosaccharomyces pombe. Due to the location of both modification in the anticodon loop, we anticipated an influence on translation. Our experimental setup allowed for the analysis of effects from each modification alone or a combination of both.

overall_design: Cytoplasmic RNA and Cytoplasmic RNA protected by ribosome from RNaseI  cleavage, were sequenced. Small RNA libraries were performed according to the protocol using NEB NEXT Small RNA library Prep Set for Illumina (Multiplex Compatible) E7330, and size-selected (120-170 base pairs) before sequencing.

first: Martin

last: Müller

first: Carine

last: Legrand


title: High-fat diet exposure, regardless of the induction of obesity, is associated with altered expression of genes critical for normal ovarian function

city: Aurora

first: Malgorzata

last: Skaznik-Wikiel

state: Colorado

address: 12700 East 19th Avenue

department: Obstetrics and Gynecology

institute: University of Colorado School of Medicine

summary: High-fat diet (HFD) induces diminished ovarian reserve and subfertility in female mice, irrespective of obesity. To further assess the impact of HFD on ovarian function, female mice were fed a 60% HFD or standard chow for 10 weeks and then HFD fed mice were separated into obese (HFOB) and lean (HFLN) groups.  RNA-sequencing of whole ovaries identified multiple differentially expressed genes involved in normal ovarian function (ovulation, luteinization, luteolysis) in both the HFLN and HFOB mice compared to the chow fed mice (q<0.05). Taken together, elevated dietary fat intake, regardless of obesity, is associated with impaired estrous cycles and altered expression of genes critical to normal ovulatory function.

overall_design: RNA-sequencing was performed on ovarian RNA after 10 weeks of HFD feeding. Three groups were assessed, those that became obese after HFD (HFOB), those that remained lean after HFD (HFLN) and controls fed chow for 10 weeks. Three animals in each group were used for RNA-sequencing.

middle: E

first: Natalie

last: Hohos


title: siRNA-mediated silencing of ORAI3 in MDA-MB-468 breast cancer cells exposed to hypoxia

city: Woolloongabba

first: Iman

last: Azimi

state: Queensland

address: 20 Cornwall St

country: Australia

institute: The University of Queensland

summary: Analysis of the effect of siRNA-mediated silencing of ORAI3 in MDA-MB-468 basal-like breast cancer cells exposed to 48 and 72 h hypoxia

overall_design: MDA-MB-468 cells were seeded in 96-well plates. Post plating (24 h), cells were transfected with siRNA for 48 h. Cells were then serum starved (0.5% FBS) for 24 h and exposed to hypoxic conditions (1% O2) for the indicated time-points. Total RNA was isolated and purified using an RNeasy Plus Mini Kit. Three independent biological replicates were collected for each treatment.

first: Gregory

last: Baillie

first: Sarah

last: Roberts-Thomson

last: Monteith


title: Phase Separation of Ligand-Activated Enhancers Licenses Cooperative Chromosomal Enhancer Assembly [GRO-seq_RAW]

city: San Diego

first: Qi

last: Ma

address: 9500 Gilman Dr,

institute: UCSD

summary: Acutely activated enhancer in response to cell signaling regulate transcrption by assembling phase separated ribonucleoprotein complex composed of transcription factors with disordered domains and RNA

overall_design: GROseq experiments was performed to examine the active transcription units and their response to signaling events and 1,6-hexanediol

first: Sreejith

last: Nair

first: Yuliang

last: Tang


title: Phase Separation of Ligand-Activated Enhancers Licenses Cooperative Chromosomal Enhancer Assembly [GRO-seq_MCF]


title: 3'-TARGET-seq: a novel method for high-sensitivity single-cell mutational analysis and parallel high throughput RNA-sequencing [Figures 5 and 6, Figure S7]

city: Oxford

first: Alba

last: Rodriguez-Meira

address: John Radcliffe Hospital/Headley Way

department: Weatherall Institute of Molecular Medicine

institute: University of Oxford

summary: We developed 3'-TARGET-seq, a single-cell genotyping and RNA-seq method, which allows accurate detection of multiple mutations within single-cells from genomic and coding DNA in parallel with high throughput 3'-biased whole transcriptome analysis, providing a powerful tool to link transcriptional and genetic tumor heterogeneity. Single cell whole transcriptome sequencing of 2798 Lineage-CD34+ HSPC (Hematopoietic Stem and Progenitor Cells) from patients with JAK2-V617F mutant myelofibrosis and normal controls using 3'-TARGET-seq reveals distinct molecular signatures associated with the presence of somatic mutations in single cells as well as distinct transcriptional profiles of WT cells from patient samples as compared with normal controls.

overall_design: We isolated single HSPCs from patients with JAK2V617F mutant myelofibrosis patient samples and aged-matched normal controls and processed them using 3'-TARGET-seq, a novel method for parallel mutational analysis and high throughput whole transcriptome sequencing from the same single cell. We analyzed a cohort of patients with  JAK2-V617F mutation and several cooperating mutations in spliceosome components (SF3B1, U2AF1, SRSF2), epigenetic modifiers (TET2, ASXL1) and signalling genes (CBL). We performed differential expression analysis between different genetic subclones from multiple patients as well as cells obtained from normal donors. We also analyzed molecular signatures corresponding to every combination of mutations found in single cells as well as molecular signatures of WT cells from patient samples as compared to WT cells from normal controls.

first: A

first: Adam

last: Mead


title: Phase Separation of Ligand-Activated Enhancers Licenses Cooperative Chromosomal Enhancer Assembly [ChIP-seq]

summary: Signal stimulation activate enhancers by acutey assembling phase separated ribonucleoprotein complexes on transcriptional enhancers

overall_design: ChIP-Seq experiments were designed to understand the genomic distribution of the factors in response to signal stimulation

first: Sreejtih


title: Full-length TARGET-seq resolves molecular signatures of distinct genetic subclones in MPN patients [full length TARGET-seq patient samples; Figures 3,4]

summary: We developed TARGET-seq, a single-cell genotyping and RNA-seq method, which allows accurate detection of multiple mutations within single-cells from genomic and coding DNA in parallel with whole transcriptome analysis, providing a powerful tool to link transcriptional and genetic tumor heterogeneity. Single cell whole transcriptome sequencing of Lineage-CD34+ HSPC (Hematopoietic Stem and Progenitor Cells) from patients with myeloproliferative neoplasms and normal controls using full-length TARGET-seq reveals distinct molecular signatures associated with the presence of somatic mutations in single cells as well as distinct transcriptional profiles of WT cells from patient samples as compared with normal controls.

overall_design: We isolated single HSPCs from patients with myeloproliferative neoplasms and normal controls using full-length TARGET-seq, a novel method for parallel mutational analysis and whole transcriptome sequencing from the same single cell. We analyzed a cohort of patients with different combinations of JAK2 V617F, TET2 and EZH2 mutations, and performed differential expression analysis between mutant and WT cells from the same patient as well as cells obtained from normal donors.  We also analyzed molecular signatures corresponding to every combination of mutations found in single cell as well as molecular signatures of WT cells from patient samples as compared to WT cells from normal controls.


title: Phase Separation of Ligand-Activated Enhancers Licenses Cooperative Chromosomal Enhancer Assembly [Gro-Seq]

summary: Detailed analysis of estrogen mediated enhancer landscape and chromosomal architectural changes specifically in human chromosome 21.

overall_design: GRO-Seq experiments were designed to study the active transcription in response to estrogen treatement and how it is affected by deletion of first-tier enhancers


title: Transcriptomic changes associated with the depletion of RNA degradosome components PNPase, RNase E and RNase J in Mycobacterium tuberculosis.

status: Public on Feb 09 2019

city: Lodz

first: Przemysław

middle: Adam

last: Płociński

state: lodzkie

address: Lodowa 106

department: Mycobacterium Physiology and Genetics

country: Poland

institute: Institute of Medical Biology of the Polish Academy of Sciences

summary: RNA-Seq results accompanying submission of a manuscript describing roles of RNA degradosome components PNPase, RNase E and RNase J in shaping the transcriptome of the H37Rv Mycobacterium tuberculosis. Next generation sequenicing results are provided for three independent biological replicates for the wild type control, genetic knockout of RNase J and CRISPR/Cas9 (DNA cleavage defiecient) regulated knockdowns of PNPase and RNase E along with a control strain expressing solely the Cas9 enzyme, not the target sgRNA. We have found that removal of RNase J had little effect on the transcriptional profile of investigated strain, while depletion of PNPase or RNase E altered about a quarter of the entire transcriptome, including changes to non-coding RNA.

overall_design: Total RNA transcriptomic profiles, following ribodepletion with Ribo-Zero kit(Illumina) of M.tuberculosis strains depleted of RNA degradosome components PNPase, RNase E and RNase J, in triplicate, RNA/cDNA libraries prepared with KAPA stranded RNA preparation kit, True Seq v2 single indexing used for multiplexing.

first: Maria

last: Macios

first: Joanna

last: Houghton

first: Emilia

last: Niemiec

first: Renata

last: Płocińska

first: Anna

last: Brzostek

first: Marcin

last: Słomka

first: Jarosław

last: Dziadek

first: Douglas

last: Young

first: Andrzej

last: Dziembowski


title: Phase Separation of Ligand-Activated Enhancers Licenses Cooperative Chromosomal Enhancer Assembly [HiC-seq]

first: Qi

overall_design: in situ Hi-C experiments are designed to elucidate 3D chromatin landscape in human breast cancer cells (MCF7) under basal and estrogen treated conditions.


title: TARGET-seq: novel method for single-cell mutational analysis and parallel RNA-sequencing [validation in cell lines; Figure 2 and Figure S3]

summary: We developed TARGET-seq, a single-cell genotyping and RNA-seq method, which allows accurate detection of multiple mutations within single-cells from genomic and coding DNA in parallel with whole transcriptome analysis, providing a powerful tool to link transcriptional and genetic tumor heterogeneity. Single cell whole transcriptome analysis of JURKAT, SET2 and HSPCs using SMART-seq+, mRNA targeting (tSMARTseq) or TARGET-seq reveals very good correlations between methods.

overall_design: Whole transcriptome analysis of single cells processed using SMART-seq+, mRNA targeting and TARGET-seq methods. We analyzed sequencing metrics, library quality and potential biases using TARGET-seq as compared to SMART-seq+ or mRNA targeting methods (tSMARTseq), in two different human cell lines (JURKAT and SET2) and primary HSPCs (Hematopoietic Stem and Progenitor Cells).


title: Genome-wide identification and comparison of mRNAs, lncRNAs, and circRNAs in porcine intramuscular, subcutaneous, retroperitoneal, and mesenteric adipose tissues

city: Nanjing

first: Xin

last: Liu

state: Jiangsu

department: College of Animal Science and Technology

institute: Nanjing Agricultural University

summary: Long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs), which were proved to play a crucial role in regulating cell differentiation and tissue development. However, the expression profiles of different RNAs, such as mRNA, lncRNAs, and circRNAs in different adipose tissues, are still largely unclear. To shed light on this issue, we performed the systematic analysis of mRNAs, lncRNAs, and circRNAs obtained from intramuscular adipose tissues (IAT), subcutaneous adipose tissues (SAT), visceral adipose tissues (RPAT), and mesenteric adipose tissues (MAT) tissues of Chinese Erhualian pigs using high-throughput sequencing. A total of 1,695, 1,878, 494, 1,300, 902, and 355 differentially expressed (DE) mRNAs, 318, 399, 192, 251, 249, and 347 DE lncRNAs, 1,367, 1,007, 999, 1,153, 1,256, and 837 DE circRNAs were identified in IAT versus SAT, IAT versus RPAT, SAT versus RPAT, MAT versus IAT, MAT versus SAT, and MAT versus RPAT, respectively. Gene ontology (GO) enrichment analyses showed these DE genes were mainly involved in lipid metabolic and immune response. Next the co-expression network construction of mRNAs-lncRNAs revealed several key lncRNAs such as MSTRG.604204 and MSTRG.604206 might associated with lipid metabolic. Tissue specific analysis indicated that circRNA exhibited the highest tissue specificity than lncRNA and mRNA, and the IAT had the most tissue specific lncRNA, mRNA, and circRNA compared with other tissues. Taken together, this study gives us a novel clue to the role of mRNAs, lncRNAs and circRNAs in fat metabolism, thus improving our understanding of the regulation mechanism of different gene expression profiles in adipose deposition

overall_design: mRNA, lncRNA, and circRNA profiles of intramuscular adipose (IAT), subcutaneous adipose (SAT),retroperitoneal adipose (RPAT), and mesenteric adipose (MAT) of Erhualian pigs were generated by RNA-Seq using Illumina HiSeq X Ten

first: Lifan

last: Zhang


title: Single-cell combinatorial indexing ATAC-seq of HCC1143 with MEK, PI3K, and BET inhibition

status: Public on Feb 08 2019

city: Portland

first: Andrew

last: Adey

state: OR

address: 3181 S.W. Sam Jackson Park Rd, RHH, L103

department: MMG

institute: Oregon Health & Science University

summary: We performed single-cell combinatorial indexing ATAC-seq on the basal-like TNBC cell line HCC1143 under MEK, PI3K, BET and combination treatments as well as DMSO controls

overall_design: Cells were cultured and exposed to inhibitors or vehicle for 72 hours and processed in a single batch of sci-ATAC-seq using transposition barcodes for sample tracking to eliminate batch effects downstream

middle: C

first: Rosalie

last: Sears


title: Exploring the effects of different sample preparation factors on RNA sequencing

city: Baltimore

first: Yuji

state: MD

address: 660 W. Redwood Street

institute: University of Maryland

summary: We investigated the effects of different sample preparation factors on RNA-seq experiments, including RNA concentration, library storage time, and cryopreserved condition, by comparing their sequencing biases, gene expression profiles, and biological function using primary B cell and CD4+ cell blood samples in healthy subjects.

overall_design: The effects of RNA concentration, library storage time, and cryopreserved condition for RNA-seq experiments

first: Larry

last: Pease


title: A pathogenic CtBP1 missense mutation causes altered cofactor binding and transcriptional activity

city: St. Louis

first: Govindaswamy

last: Chinnadurai

state: MO

address: 1100 South Grand Blvd

department: Molecular Microbiology and Immunology

institute: Saint Louis University

summary: We previously reported a pathogenic de novo W342 mutation in the transcriptional corepressor CtBP1 in four independent patients with neurodevelopmental disabilities.  Here, we report the clinical phenotypes of seven additional individuals with the same recurrent de novo CtBP1 mutation.  Within this cohort we identified consistent CtBP1-related phenotypes of intellectual disability, ataxia, hypotonia and tooth enamel defects present in all patients. The W342 mutation in CtBP1 is located within a region implicated in a high affinity-binding cleft for CtBP-interacting proteins.  Unbiased proteomic analysis demonstrated reduced interaction of several chromatin modifying factors with the CtBP1 W342 mutant.  Genome-wide transcriptome analysis in human glioblastoma cells lines expressing -CtBP1 R342 (wt) or W342 mutation revealed changes in the expression profiles of genes controlling multiple cellular processes.  Patient-derived dermal fibroblasts were found to be more sensitive to apoptosis during acute glucose deprivation compared to controls.  Glucose deprivation strongly activated the BH3-only pro-apoptotic gene NOXA, suggesting a link between enhanced cell death and NOXA expression in patient fibroblasts.  Our results suggest that context-dependent relief of transcriptional repression of the CtBP1 mutant W342 allele may contribute to deregulation of apoptosis in target tissues of patients leading to neurodevelopmental phenotypes.

overall_design: Total RNA samples were isolated from 3 different cultures of HTB17 cells that overexpressed CtBP1 wt or the pathogenic mutant, W342 and analyzed by high- throughput RNA sequencing.

first: Thirugnana

last: Subramanian


title: methyl-ATAC-seq measures DNA methylation at accessible chromatin

city: Ithaca

first: Roman

last: Spektor

state: New York

address: 618 Tower Rd, Vet Research Tower, Room T2 007

institute: Cornell University

summary: Here we describe methyl-ATAC-seq (mATAC-seq), which implements modifications to ATAC-seq, subjecting the output to BS-seq. Merging these assays into a single protocol identifies the locations of open chromatin, and reveals the DNA methylation state of the underlying DNA.

overall_design:
Examination of 2 different methods (Omni-ATAC-seq and mATAC-seq) on HCT116 and DKO (DNMT1 and DNMT3B double knockout) cells.

Genome_build: hg19
Supplementary_files_format_and_content: bw for all samples, bedGraph and cov files also for mATAC-seq samples
bw files for visualization of coverage generated using Deeptools
bedGraph files for visualization of DNA methylation generated using Bismark
cov files for analysis of DNA methylation generated using Bismark

first: Paul

last: Soloway


title: Transcriptional profile of thymic and splenic regulatory T cells, sufficient and deficient in miR-181a

city: Munich

first: Natalia

last: Zietara

address: Großhadernerstr. 9

department: Immunology

institute: LMU Munich

summary: MicroRNAs (miRNAs) are expressed from a class of small non-protein coding RNA molecules. Growing evidence shows that miRNAs are potent mediators of post-transcriptional gene silencing and emerged to be critical in the regulation of innate and adaptive immune responses (Ansel KM, Immunol Rev 2013, p5; Baumjohann D, Nature Rev Immunol 2013, p666). MicroRNA-181a (miR-181a) constitutes the most prominently expressed miRNA species in DP thymocytes (Neilson JR, Genes Dev 2007, p578; Kirigin FF, JI 2012, p3257) and has been associated with modulating TCR signal strength via targeting serine/threonine as well as tyrosine phosphatases (Li Q-J, Cell 2007, p147). Consequently, elevated expression of miR-181a results in reduced phosphatase activity and increased TCR signal strength. The effect of aberrant expression of miR-181a on TCR signaling has been already analyzed employing short-term assays and in vitro organ cultures. Our group started to investigate the consequences of miR-181a/b-1 deletion on T cell development in vivo in the steady state. To this end, we developed a new mouse model - miR-181a/b-1 knockout mice (Zietara N et al, PNAS 2013b). During investigations of the immune system of miR-181a/b-1 deficient mice we discovered that these miRNAs are critical for the development of invariant natural killer (NK) T cells. Such cells are known to be selected by a high affinity agonist ligands, thus they are particularly sensitive to the modulation of TCR signaling thresholds, which is achieved by miR-181a/b-1 (Zietara N et al, PNAS 2013b). Furthermore we hypothesized that similar regulation might apply for the other T cell populations selected under high TCR signal strength, like Treg cells. Thus our current research focuses on the role of miR-181a/b-1 during Treg cell development in the thymus as well as on their function in the periphery.

overall_design: Foxp3+CD4+CD25+ cells were sorted from thymi and spleens of miR181+/- (control) and miR181-/- (test) mice. 2 control groups and 2 test groups were subjected to analysis. Control group one consisted of 3 female mice and one male mouse; control group two consisted of 4 female mice and 1 male mouse; test group one consisted of 2 females and 1 male mouse; test group two consisted of 2 females and 1 male mouse;

first: Andreas

last: Krueger


title: Transcriptome analysis of heterotopic ossification mesenchymal stromal cells

city: VILLEJUIF

first: christophe

last: desterke

address: 14-16 avenue Paul Vaillant Couturier

department: UFR medecine institute Andre Lwoff

institute: university Paris Sud11

summary: Heterotopic Ossification (HO) is the abnormal formation of ectopic bone in soft tissues generally in muscles surrounding joints such hip, knee, elbow or shoulder. The etiology of this pathology is not known but it is well established that the risk of HO is increased after traumatic brain or spinal cord injuries and also after fractures or burns. Patients with HOs suffer from pain and the range of motion from limbs with ectopic bone is highly reduced. Currently, the only effective treatment for HOs is surgical resection but they can reoccur after resection underpinning that a better understanding of its pathophysiology is required to cure patients. To date, the nature of osteogenic precursor cells (of mesenchymal origin) forming HOs is not fully elucidated and remains to be defined. A transcriptional analysis of mesenchymal stromal cells (MSCs) from HOs would help identifying molecules that could be therapeutically targeted.

overall_design: Transcriptome analysis was performed on mesenchymal stromal cells (MSCs) from HOs and amplified in vitro after 2 passages. Agilent Whole Human Genome Oligo Microarrays were used to compare expression profiling of MSCs from NHO patients and from bone marrow of healthy donors.

first: Fédéric

last: Torossian

first: Christophe

last: Desterke

first: Bernadette

last: Guerton

first: Jean-Jacques

last: Lataillade

first: Marie-Caroline

last: Le Bousse-Kerdilès


title: Gene expression changes associated with loss of KDM5 in drosophila intestine tissue

city: Nanjing City

first: Xingyin

last: Liu

state: Jiangsu Province

address: Long Mian Street No.1

institute: Nanjing Medical University

summary: To determine the gene expression changes associated with loss of KDM5 in drosophila intestine tissue, we performed RNA-seq analyses for these dissected intestine tissue from wildtype and kdm5 mutant. These analyses revealed different expressed genes between kdm5 mutant compared to wildtype in intestine tissue. These differentially expressed genes were enriched in the innate immune pathway through Gene ontology(GO) enrichment analysis.

overall_design: Find the differentially expressed genes between wt and kdm5 mutants in the intestine tissue.

first: Qisha


title: The histone demethylase KDM5 protein shapes the gut microbiome and regulates innate immunity pathway

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

overall_design: Refer to individual Series


title: Gut microbiota analysis of kdm5 mutant and the flies with KDM5 knockdown in intestine tissue

summary:
To determine microbiota composition associated with loss of KDM5 in intestine, we carried out 16S rRNA seq analyses of dissected intestine from wildtype and kdm5 mutant. [GSM2628181-GSM2628190]. A total of 78 operational taxonomic units (OTUs) were identified in the sequence data. There were about 15 genera much less abundant in kdm5 mutant compared to wildtype. The kdm5 mutant were sensitive to pathogen.

To confirm the microbiota associated with loss of KDM5 in intestine, 16S rRNA of new flies were sequenced and analyzed by Majorbio Bio-Pharm Technology Co. Ltd. (Shanghai, China) [GSM3243472-GSM3243481]. A total of 107 operational taxonomic units (OTUs) were identified in the sequence data. There were about 20 genera much less abundant in kdm5 mutant compared to wildtype.

To confirm the microbiota associated with loss of KDM5 drosophila feeding with Lactobacillus plantarum, 16S rRNA of kdm5 mutant flies were sequenced and analyzed by Novogene Bioinformatics Technology Co., Ltd. (Tianjin, China) [GSM3263522-GSM3263527]. A total of 92 operational taxonomic units (OTUs) were identified in the sequence data.

To confirm the microbiota associated with KDM5 knockdown in intestine, 16S rRNA of Myo1A-Gal4TS/+ and Myo1A-Gal4TS/+;+/kdm5RNAi flies were sequenced and analyzed by Biomarker Co. Ltd. (Beijing, China). [GSM3507915-GSM3507924]. A total of 50 operational taxonomic units (OTUs) were identified in the sequence data. There was a significant different based on the genus level between two groups.

overall_design:
Examination of microbiota composition by loss of KDM5 in drosophila intestine.
Total genome DNA from 30 adult fly midguts was extracted using the kit (Tiangen, Beijing, China). DNA concentration and purity was assessed on the Qubit@ 2.0 Fluorometer (Thermo Scientific). 16S rRNA genes were amplified used the specific V3-V4 primers 338F-806R. All PCR products and operate electrophoresis on 2% agarose gel for detection. Samples with bright main strip between 400-450bp were chosen for further experiments.

first: Kun

last: Chen


title: Nuclear import of the DSCAM-cytoplasmic domain drives signaling capable of inhibiting synapse formation

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

institute: VIB

summary: DSCAM and DSCAML1 are immunoglobulin and cell adhesion-type receptors serving important neurodevelopmental functions including control of axon growth, branching, neurite self-avoidance and neuronal cell death. The signal transduction mechanisms or effectors of DSCAM receptors however, remain poorly characterized. We used a human ORFeome library to perform a high-throughput screen in mammalian cells and identified novel cytoplasmic signaling effector candidates including the Down syndrome kinase Dyrk1a, STAT3, USP21, and SH2D2A. Unexpectedly, we further found that the intracellular domains (ICDs) of DSCAM and DSCAML1 specifically and directly interact with IPO5, a nuclear import protein of the beta-importin family, via a conserved nuclear localization signal. The DSCAM ICD is released by gamma-secretase dependent cleavage and both the DSCAM and DSCAML1 ICDs efficiently translocate to the nucleus. Furthermore, RNA-sequencing confirms that expression of the DSCAM as well as the DSCAML1 ICDs alone can profoundly alter the expression of genes associated with neuronal differentiation and apoptosis, as well as synapse formation and function. Gain-of-function experiments using primary cortical neurons show that increasing the levels of either the DSCAM or the DSCAML1 ICD leads to an impairment of neurite growth. Strikingly, increased expression of either full-length DSCAM or the DSCAM ICD, but not the DSCAML1 ICD, significantly decreases synapse numbers in primary hippocampal neurons. Taken together, we identified a novel membrane-to-nucleus signaling mechanism by which DSCAM receptors can alter the expression of regulators of neuronal differentiation, synapse formation and function. Considering that chromosomal duplications lead to increased DSCAM expression in trisomy 21 our findings may help to uncover novel mechanisms contributing to intellectual disability in Down syndrome.

overall_design: We generated four isogenic HEK293 t-Rex-Flp-In cell lines. The HEK293 t-Rex-Flp-In expression system offers stable, Tetracycline inducible and homogeneous expression of transgenes from a defined genomic locus. The four cell lines either (1) stably express the YFP-HA-tagged DSCAM ICD, (2) stably express the YFP-HA-tagged DSCAML1 ICD, (3) serve as a cytoplasmic YFP-HA control or (4) serve as a nuclear YFP-HA control. For each cell line, three independent replicates of transgene expression were analyzed by RNA deep sequencing (RNA-Seq). The global transcriptome changes of cells expressing the YFP-tagged DSCAM/L1 ICDs versus cells expressing nuclear YFP-HA (YFP-nls) as control were determined. Genes that were already differentially expressed in cytoplasmic versus nuclear YFP expressing cells (p- value ≤ 0.1) were excluded from the analysis, as these genes are unlikely affected by DSCAM/L1 ICD expression.

first: Sonja

middle: M

last: Sachse

first: Dietmar

last: Schmucker


title: Real-time quantitative PCR analysis of U87ΔEGFR intracranial mouse models treated with bevacizumab

status: Public on Feb 07 2019

city: Okayama

first: Kazuhiko

last: Kurozumi

state: Okayama

address: 2-5-1, Shikata-cho, Kita-ku

department: Neurological Surgery

institute: Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences

summary:
The combination of bevacizumab with temozolomide and radiotherapy was shown to prolong progression-free survival in newly diagnosed glioblastoma patients, and this emphasizes the potential of bevacizumab as a glioma treatment. However, while bevacizumab effectively inhibits angiogenesis, it has also been reported to induce invasive proliferation. This study examined gene expression in glioma cells to investigate the mechanisms of bevacizumab-induced invasion.
We made a human glioma U87ΔEGFR cell xenograft model by stereotactically injecting glioma cells into the brain of animals. We administered bevacizumab intraperitoneally three times per week. At 18 days after tumor implantation, the brains were removed for histopathology and mRNA was extracted. In vivo, bevacizumab treatment increased glioma cell invasion. qRT-PCR array analysis were perfomed.

overall_design: Eighteen days after tumor implantation, U87ΔEGFR mouse models treated with bevacizumab or PBS were sacrificed (n=3 to 4 per group). RNA analysis was conducted with an Extracellular Matrix & Adhesion Molecules RT Profiler PCR Array (PAHS-013Z) (QIAGEN; Hilden, Germany), according to the manufacturer’s instructions. Expression of genes encoding 84 human cell adhesion molecules and ECM components was evaluated in brain tumor tissue after bevacizumab treatment relative to control (PBS).

first: Toshihiko

last: Shimizu

first: Ishida

last: Joji


title: Single-cell RNA sequencing of inflammatory tissue T cells in eosinophilic esophagitis

city: Cincinnati

first: Yael

last: Haberman

state: OH

address: 3333 Burnet Ave

department: Gastroenterology

institute: Cincinnati Children's Hospital

summary: T cell heterogeneity is highly relevant to allergic disorders. We resolve the heterogeneity of human tissue CD3+ T cells during allergic inflammation, focusing on a tissue-specific allergic disease, eosinophilic esophagitis (EoE). We investigated 1,088 single T cell derived from patients with a spectrum of disease activity. Eight disparate tissue T cell subtypes (designated T1-T8) were identified, with T7 and T8 enriched in the diseased tissue. The phenotypes of T7 and T8 resemble putative TREG (FOXP3+) and effector Th2 (GATA3+)-like cells, respectively. Prodigious levels of IL-5 and IL-13 were confined to HPGDS+ CRTH2+ IL-17RB+ FFAR3+CD4+ T8 effector Th2 cells. EoE severity closely paralleled a lipid/fatty acid–induced activation node highlighted by the expression of the short-chain fatty acid receptor FFAR3. Ligands for FFAR3 induced Th2 cytokine production from human and murine T cells including in an in vivo allergy model. Therefore, we have elucidated the defining characteristics of tissue-residing CD3+ T cells in EoE, a specific enrichment of CD4+ TREG and effector Th2 cells, confinement of type 2 cytokine production to the CD4+ effector population, a highly likely role for FFAR3 in amplifying local Th2 responses in EoE, and a resource to further dissect tissue lymphocytes and allergic responses.

overall_design: Single-cell transcriptome profililng of esophagus biopsies from patients with active eosinophilic esophagitis (EoE, n=11), in remission (n=6), and without disease (n=5)

first: Ting

last: Wen

first: Bruce

last: Aronow

first: Yrina

last: Rochman

first: Mark

first: Kiran

last: KC

first: Phillip

last: Dexheimer

first: Philip

last: Putnam

first: Vincent

last: Mukkada

first: Heather

last: Foote

first: Kira

last: Rehn

first: Sam

last: Darko

first: Daniel

last: Douek

first: Marc

last: Rothenberg


title: UBR7 is a novel E3 ubiquitin ligase for H2BK120 and acts as a tumor-suppressor in breast cancer [RNA-Seq]

city: Houston

first: Kunal

last: Rai

state: TX

address: 1801 East Rd

department: Genomic Medicine

institute: MD Anderson Cancer Center

summary: Plant Homeo Domain (PHD) is a versatile chromatin reader/effector module which recognizes methylated, acetylated or unmodified histone substrates and regulates cellular gene expression programs. Although PHD domains shows selective epigenetic recognition of methylated, acetylated and unmodified histone substrates, there has been no previous report on its catalytic function regulating malignant transformation of cells. Here we report that PHD finger of UBR7 (Ubiquitin Protein Ligase E3 Component N-Recognin 7 (Putative)), in isolation or in context of full length protein, harbors E3 ubiquitin ligase activity towards monoubiquitination of histone H2B at lysine 120 . Knockdown of UBR7 in MCF10a and breast cancer cells decreased H2BK120ub both at the global levels and on specific genes. Conversely, overexpression of wild type, but not catalytic mutant, rescued H2BK120ub levels. Low UBR7 expression was associated with basal-like and triple negative breast cancers as well as showed poor expression in metastatic tumors. Consistently, UBR7 loss resulted in invasion properties, induced epithelial-to-mesenchymal transition and promoted metastasis. Conversely, ectopic expression of UBR7 reduced cell growth, invasion and tumor growth in mouse fat pad. Mechanistically, UBR7 reduced H2BK120ub gene body of cell-adhesion related genes as well as gene expression including on CDH4 gene. Importantly, rebuilding CDH4  levels rescued invasion phenotypes seen in UBR7-low cells. Collectively, our results establish that UBR7 PHD has novel H2B ubiquitin ligase activity and it suppresses tumor growth in basal-like breast cancers.

overall_design: Triplicate total RNA profiles in Wild Type and UBR7-shRNA MCF10A Cell Line

first: Christopher

last: Terranova


title: Functional Cardiac Fibroblasts Derived from Human Pluripotent Stem Cells via Second Heart Field Progenitors

city: Madison

first: Timothy

last: Kamp

state: WI

address: 1111 Highland Ave

institute: University of Wisconsin - Madison

summary: Cardiac fibroblasts (CFs) play critical roles in heart development, homeostasis, and disease. The limited availability of human CFs from native heart impedes investigations of CF biology and their role in disease. Human pluripotent stem cells (hPSCs) provide a highly renewable and genetically defined cell source, but efficient methods to generate CFs from hPSCs have not been described. Here, we show differentiation of hPSCs using sequential modulation of Wnt and FGF signaling to generate second heart field progenitors that efficiently give rise to hPSC-CFs. The hPSC-CFs resemble native heart CFs in cell morphology, proliferation, gene expression, fibroblast marker expression, production of extracellular matrix and myofibroblast transformation induced by TGFβ1 and angiotensin II. Furthermore, hPSC-CFs exhibit a more embryonic phenotype when compared to fetal and adult primary human CFs.  Co-culture of hPSC-CFs with hPSC-derived cardiomyocytes distinctly alters the electrophysiological properties (EP) of the cardiomyocytes compared to co-culture with dermal fibroblasts (DFs). The hPSC-CFs provide a powerful cell source for research, drug discovery, precision medicine, and therapeutic applications in cardiac regeneration.

overall_design: We performed RNA-seq for hPSC-CFs, primary CFs and DFs to compare the gene expression for each type of fibroblasts. We also added the hPSC-CMs and hPSCs as the positive and negativ controls in the RNA-seq to compare the gene expression for cardaic factors. Five cell types (hPSC-CFs, human adult CFs and DFs, hPSC-CMs and hPSCs) with 2 biological replicates for each cell type of a total 10 samples were sequenced.

first: Jianhua

last: Zhang

first: Ran

last: Tao

first: Scott

last: Swanson

first: Jennifer

last: Bolin

first: Ron

last: Stewart

first: James

middle: A

last: Thomson


title: A focused deep mutational scan on the Env transmembrane and proximal cytosolic regions reveals an absence of sequence features for MA association

city: Urbana

first: Erik

last: Procko

state: IL

address: 601 S Goodwin Ave

department: Biochemistry

institute: University of Illinois

summary: The HIV-1 surface glycoprotein Env binds target receptors to mediate fusion of the viral and host cell membranes during infection.  Env is incorporated with very low density into virions, and in some cell types, regions within the long cytosolic C-terminal tail may mediate direct or indirect associations with Gag during virus assembly and budding.  Here, the mutational landscape is determined across the transmembrane and proximal cytosolic domains of Env (001428 isolate from clade C) interacting with the MA domain of Gag at cellular membranes.  No evidence is found in a derivative line of HEK293 cells for specific motifs that mediate Env/MA associations.

overall_design: A single site-saturation mutagenesis (SSM) library was constructed in the Env protein from strain 001428, focused on residues N677-L753 (HXB2 reference numbering).  Env was truncated at residue L753 for enhanced surface expression, and fused via a GGSG linker to the C-terminal half (VC) of split Venus.  The 001428(753)-VC Env library was transfected into Expi293F cells stably expressing MA fused to the N-terminal half (VN) of split Venus.  When 001428(753)-VC and MA-VN are in close physical proximity, the respective halves of Venus can fold into a functional fluorophore.  This method for investigating protein interactions within living cells is known as bimolecular fluorescence complementation (BiFC).  The transfected cells were screened by fluorescence-activated cell sorting (FACS) for Env expression based on staining with the broadly neutralizing antibody PG16, and for either high or low BiFC signal.  Transcripts in the sorted cell populations were deep sequenced, and the frequencies of all single amino acid substitutions were compared to the naive plasmid library.  Sorting experiments were independently replicated.


title: Overexpression and knockdown experiment for circCSNK1G3

city: Toronto

first: Housheng

middle: Hansen

last: He

state: Ontario

address: 101 College Street

country: Canada

institute: University of Toronto

summary: Standard RNA analyses using microarrays and low-coverage polyadenylation enriched RNA-Sequencing (RNA-Seq) cannot fully characterize the complexity of the cancer transcriptome. To fully elucidate the transcriptome of prostate tumours, we performed ultra-deep total RNA-Seq on 144 localized prostate tumours with long-term clinical follow up. Analysis of linear RNAs identified a transcriptomic subtype associated with the aggressive intraductal carcinoma subhistology, and a fusion gene profile that differentiates localized from metastatic prostate cancers. Analysis of back-splicing events identified widespread RNA circularization, with the average tumour expressing 7,140 distinct circular RNAs. The degree of aberrant circRNA production is correlated to disease progression in multiple clinical cohorts. Loss of function screens identified 11.3% of the screened circRNAs as essential to prostate cancer proliferation, and for 93.6% of these, their parental linear genes are not required for proliferation. Follow-up studies on circCSNK1G3 revealed its role in regulating cell cycle progression. Ultra-deep transcriptome sequencing thus provides a more comprehensive view of the linear and circular transcriptional and functional landscapes of localized prostate cancer.

overall_design: RNA-seq after the knockdown and overexpression of circCSNK1G3

first: Sujun

last: Chen

first: Xin

last: Xu

first: Fraser

last: Sores

last: Hansen He


title: Transcriptional changes associated with overexpression of TBX3 isoforms (TBX3iso1 and TBX3iso2) in the DCIS-like 21NT cell line (ChIP)

city: London

first: Alan

last: Tuck

address: 339 Windermere Rd

department: Pathology and Laboratory Medicine

institute: Western University

type: Genome binding/occupancy profiling by array

summary:
Purpose: The acquisition of cellular invasiveness of breast epithelial cells and subsequent transition from ductal carcinoma in situ (DCIS) to invasive breast cancer is a critical step in breast cancer progression. Very little is known about the molecular dynamics governing this transition. We have previously shown that overexpression of the transcriptional regulator TBX3 in DCIS-like 21NT cells results in increased survival, growth, and invasiveness. In this study we explore the role of TBX3 in breast cancer progression pathways, focusing specifically on its involvement in the induction of EMT and the transition from DCIS to invasive mammary carcinoma.
Methods: Total mRNA was isolated from 21NT transfected cell lines. Sequencing was conducted using an Illumina HiSeq 2500 sequencer, comparing the resultant transcriptional profiles with overexpression of either TBX3 isoform (TBX3iso1 or TBX3iso2) as fold changes relative to the empty vector control. RNA-Seq data was integrated with ChIP-array data downstream to assess direct targets of TBX3 isoforms and relate it to the process of EMT. TBX3, SLUG and TWIST1 expression were assessed by immunohistochemistry in two independent early-stage (Stage 0 and Stage 1) breast cancer cohorts.
Results: An EMT-related transcriptional profile was observed with overexpression of TBX3iso1 and TBX3iso2. Using genome-wide bioinformatic approaches in conjunction with more conventional in vitro studies, we have identified SLUG and TWIST1 as downstream targets of TBX3 and have assessed their expression by immunohistochemistry in two different patient cohorts. Our findings suggest that TBX3 facilitates the process of early invasion in DCIS lesions by promoting the induction of EMT and tumor progression through the low-grade pathway. Finally, we propose a progression model in which SLUG is an important and necessary effector downstream of TBX3, leading to increased motility, invasiveness, and induction of key invasiveness-associated genes.
Conclusions: This is the only existing study which has conducted assessment of transcriptional changes associated with TBX3 isoforms (TBX3iso1 and TBX3iso2). Our published study has identified the transcriptional regulator TBX3 as an enabler of EMT in non-high grade, pre-invasive lesions of the breast, inducing SLUG and promoting the transition from in situ (DCIS) to invasive breast cancer.

overall_design:
Assessed direct transcriptional targets of TBX3 isoforms; chromatin immunoprecipitation (ChIP) was conducted in duplicate using either a rabbit anti-TBX3 antibody or rabbit IgG antibody in 3 cell lines (empty vector, TBX3iso1 overexpression, or TBX3iso2 overexpression)
Peaks from the non-specific IgG ChIPs were subtracted from specific TBX3 ChIPs for each cell line.
Differential probe intensities between TBX3iso1 or TBX3iso2 vs empty vector were determined by ANOVA and enriched regions of significance were determined using the MAT algorithm.

first: Milica

last: Krstic

first: Bart

last: Kolendowski

first: Matthew

middle: J

last: Cecchini

first: Carl

middle: O

last: Postenka

first: Haider

last: Hassan

first: Joseph

last: Andrews

first: Connor

middle: D

last: MacMillan

first: Karla

last: Williams

first: Hon

last: Leong

first: Muriel

last: Brackstone

last: Torchia

first: Ann

middle: F

last: Chambers


title: TARGET-seq: novel method for single-cell mutational analysis and parallel RNA-sequencing

city: Oxford

first: Alba

last: Rodriguez-Meira

address: John Radcliffe Hospital/Headley Way

institute: University of Oxford


title: Gene expression analyses in native eosinophils sorted from C57BL6J bone marrow

first: Artem

last: Barski

address: 3333 Burnet Av

department: Allergy

summary: We took a global approach to identify the genome-wide transcriptome in native murine eosinophils sorted from the bone marrow of C57BL6J mice at homeostasis.

overall_design: RNA Seq eosinophils sorted from C57BL6J bone marrow. RNA Seq libraries were prepared from 2 independent sorts.

first: Patricia

last: Fulkerson


title: Loss of function shRNA screen on circRNA and linear genes in PCa cell lines

first: Housheng

last: He

overall_design: Functional genomic screen with shRNA on circRNA and linear genes was carried out in 4 PCa cell lines (LNCaP, 22Rv1, PC-3 and V16A).

first: Sujun

last: Chen

first: Xin

last: Xu

last: Sores

last: Hansen He


title: RNA-sequencing of adult C57/Bl6 lymph nodes

city: Riverside

first: R

last: Dill

state: CA

address: 900 University Ave.

institute: University of California, Riverside

summary: Given the increased T cell mediated DTH response to Candida albicans in female compared to male mice, we asked whether female and male lymphnodes differed in their expression of genes relevant to cell recruitment.

overall_design: Pooled Lymph Nodes of C57Bl/6  Wild-type Female N=6, Wild-type Male N=6, or C57Bl/6 Four Core Genotype XY Male N=3 mice were analyzed by RNAseq for differences in gene expression.

first: Riva

first: Ameae

last: Walker


title: α1ACT is essential for survival and early cerebellar programming in a critical neonatal window [ChIP-Seq]

status: Public on Feb 06 2019

city: Chicago

first: Yan

last: Li

address: 900 East 57th St.

department: Center for Research Informatics

institute: The University of Chicago

summary: Previous study has shown that alpha1ACT is a transcription factor involved with regulating neuronal gene expression. We further performed ChIP-seq using pc12 cell lines stably expressing pcDNA3-alpha1ACT or control pcDNA3 vectors to identify genomic locus directly occupied by alpha1ACT

overall_design: A total of 6 sequencing files collected from chromatin immunoprecipitation at day 3 were used for the ChIP-Seq study. Among them, 3 sequencing files were obtained from EV expressed tissues treated with M2 and 1804 antibody beads respectively, and corresponding ChIP-Seq input. The other 3 sequencing files corresponding to α1ACT expressed tissues treated with M2 and 1804 antibody and corresponding ChIP-Seq input.

first: Xiaofei

last: Du

first: Christopher

last: Gomez

first: Cenfu

last: We

first: Daniel

last: Parviz Hejazi Pastor

first: Eshaan

middle: R

last: Rao

first: Giorgio

last: Grasselli

first: Jack

last: Godfrey

last: Palmenberg

first: Jorge

last: Andrade

first: Christian

last: Hansel


title: α1ACT is essential for survival and early cerebellar programming in a critical neonatal window [RNA-Seq]

summary: Previous study has shown that alpha1ACT is a transcription factor involved with regulating neuronal gene expression. We performed a time-series RNA-seq study using pc12 cell lines stably expressing pcDNA3-alpha1ACT at 4 time points (6hr, 24hr, 3day, and 10day) to explore the transcriptional profiles that capture transient and prolonged dynamic changes regulated by alpha1ACT during cell cycle and differentiation

overall_design: PC12 cell lines expressing pcDNA3 (EV) and expressing pcDNA3-α1ACT at 4 different time points (6h, 24h, 3d, 10d) were analyzed by Agilent Bio-analyzer and submitted to university of Chicago Functional genomic facility for library preparation (TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold, RS-122-2301) and sequencing on Illumina HiSeq2500 platform, with 3 biological replicates for each condition.

first: Ann


title: RNA-seq after KD or OE of circRNAs or linear gene

first: Housheng

last: He

summary: The cancer transcriptome is remarkably complex, including low-abundance transcripts, many not polyadenylated. To fully characterize the transcriptome of localized prostate cancer, we performed ultra-deep total RNA-Seq on 144 tumours with rich clinical annotation. This revealed a linear transcriptomic subtype associated with the aggressive intraductal carcinoma sub-histology and a fusion profile that differentiates localized from metastatic disease. Analysis of back-splicing events showed widespread RNA circularization, with the average tumour expressing 7,232 circular RNAs (circRNAs). The degree of circRNA production was correlated to disease progression in multiple patient cohorts. Loss of function screening identified 11.3% of highly-abundant circRNAs as essential for cell proliferation; for ~90% of these, their parental linear transcripts were not essential for cell proliferation. Individual circRNAs can have distinct functions, with circCSNK1G3 promoting cell growth by interacting with miR-181. These data advocate for adoption of ultra-deep RNA-Seq without poly-A selection to interrogate both the linear and circular transcriptome.

overall_design: RNA-seq was performed aftercircGOLPH3 and circSTAU2 KD and OE and siCSNK1G3

last: Chen

first: Fraser

middle: H


title: Heme and GATA1 coordinately regulate erythroid differentiation

city: Osaka

first: Shinya

last: Tanaka

state: Osaka

address: 2nd Fl. IFReC Research Building, Osaka University 3-1 Yamadaoka, Suita

department: Immunology Frontier Research Center

institute: Osaka University


title: mini-INTACT reveals social isolation-induced epigenetic changes in Drosophila dopaminergic neurons

city: Ashburn

first: Pavan

middle: K

last: Agrawal

state: VA

address: 19700 Helix Dr

institute: HHMI Janelia Research Campus

summary: We introduce a more sensitive method for purifying specific cell-types from small numbers of fly heads for epigenomic analysis: a method we call ‘mini-INTACT’.  We modified the INTACT method in Drosophila [Henry G. L. et al., Nucleic Acids Research, 2012, 1–14] to enable purification of genetically tagged rare cell types from Drosophila brain requiring ~50-100 fold less material. We used male fruit flies as a model to examine the effects of social-isolation vs. social-enrichment on the epigenome and transcriptome of dopaminergic neurons defined by expression of the TH-GAL4 driver. Using ChIP-seq on mini-INTACT purified nuclei, RNA-seq and bioinformatic analysis, we identify regulation of the transcriptome and behavior by Activity Related Genes who’s expression is induced by social enrichment.

overall_design:
Genome wide occupancy profiling for histone modification marks by high throughput sequencing. Two or three biological replicates were used for each condition. Corresponding input DNA was used as control (ChIP-seq).
Expression profiling by high throughput sequencing on FACS purified dopaminergic neurons isolated from group-housed and single-housed fruit fly adult male brains. Three biological replicates were used for each condition (RNA-seq).


title: Heme and GATA1 coordinately regulate erythroid differentiation [RNA-seq]

summary: In mice lacking the heme exporter, FLVCR, differentiation fails at the CFU-E/proerythroblast stage from excessive heme and reactive oxygen species. We show that Flvcr1-deleted CFU-E/proerythroblasts have low GATA1 mRNA and GATA1-target gene mRNAs along with increased ribosomal protein mRNAs as a direct result of increased heme. Thus heme increases ribosomal protein transcription when globin production needs to be increased, and when heme is excessive, GATA1 is reduced allowing for normal termination of erythroid differentiation. This demonstrates that heme and GATA1 are co-master regulators of erythroid differentiation.

overall_design: Total RNA obtained from erythroid cells of mice with Flvcr deleted compared to those of wild-type mice and wild-type mice treated with EPO.

first: Raymond

last: Doty


title: Evolution of TAM gene expression in ID8  tumors

city: Heidelberg

first: Juan

last: Rodriguez-Vita

address: Im Neuenheimer Feld 280

institute: DKFZ

summary:
Gene expression was analyzed in peritoneal macrophages and TAM from mice injected with ID8 ovarian cancer cells intraperitoneally 5 and 21 days after tumor cell injection.
Tumor-associated macrophages (TAM) have been shown to have important roles in the malignant progression of various cancers. However, macrophages also posses intrinsic tumoricidal activity and can promote the activity of cytotoxic lymphocytes, but they rapidly adopt an alternative phenotype within tumors, associated with immune-suppression and trophic functions that support tumor growth. The mechanisms that promote TAM polarization in the tumor-microenvironment remain poorly understood, these mechanisms may represent important therapeutic targets to block the tumor-promoting functions of TAM and restore their anti-tumor potential. Here we have characterized TAM in a mouse model of metastatic ovarian cancer. We show that ovarian cancer cells promote membrane-cholesterol efflux and the depletion of lipid rafts from macrophages. Increased cholesterol efflux promoted IL-4 mediated reprogramming while inhibiting IFNg-induced gene expression. These studies reveal an unexpected role for tumor-induced membrane-cholesterol efflux in driving the IL-4 signaling and the tumor-promoting functions of TAM, while rendering them refractory to pro-inflammatory stimuli. Thus, preventing cholesterol efflux in TAM could represent a novel therapeutic strategy to block pro-tumor functions and restore anti-tumor immunity.

overall_design: In total 6 samples; 2 PM, 2 Day5, 2 Day21

first: Pieter

last: Goossens

first: Anders

last: Etzerodt

first: Marion

last: Masse

first: Olivia

last: Rastoin

first: Victoire

last: Gouirand

first: Miranda

last: Van Eck

first: Thomas

last: Ulas

first: Olympia

last: Papantonopoulou

first: Magali

last: Bebien

first: Martin

last: Turner

first: Thien

middle: P

last: Manh

first: Marc

last: Dalod

first: Nathalie

last: Auphan-Anezin

first: Joachim

middle: L

last: Schultze

first: Toby

last: Lawrence