title: Next Generation Sequencing Facilitates Quantitative Analysis of Transcriptomes in leaves of two subtropical trees grown under contrasting light

city: Guangzhou

first: Tai-Jie

last: Zhang

state: Guangdong

address: No. 55 West Zhongshan Avenue, Tianhe District

department: School of Life Science

institute: South China Normal University

summary:
Purpose: The goal of this study is to evaluate transcriptional regulation of the accumulation of phenols and anthocyanins in young leaves of subtropical forest tree species by using NGS-derived RNA-seq.

Methods: Leaf mRNA profiles of subtropical tree Schima superba and Cryptocarya concinna grown under contasting light were generated by deep sequencing, in triplicate, using Illumina. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks. FPKM produced by RSEM are provided.

Results: Assemblies of the sequence data yielded 61,618 and 64,413 unigenes for Schima superba and Cryptocarya concinna,respectively. Overall,75.14% and 66.46% of the unigenes were annotated in the protein database Nonredundant protein (Nr), Nonredundant nucleotide (Nt), Swiss-Prot、Kyoto Encyclopedia of Genes and Genomes (KEGG), Cluster of Orthologous Groups of proteins (COG) and Gene Ontology (GO) for S. superba and C concinna,respectively.A total of 3896, 3488 and 266 genes were differentially expressed in full light-exposed young leaf (FLY), low light-exposed young leaf (LYL) and low light-exposed mature leaf (LML) relative to low light-exposed mature leaf (FML) of S. superba, respectively, and 2097, 2047 and 211 genes were differentially expressed in the corresponding leaves of C. concinna.

Conclusions: Our study represents the first detailed analysis of transcriptomes in young and mature leaves of dorminant trees from a subtropical forest in China, with biologic replicates, generated by RNA-seq technology. Photosynthesis-related genes and phenol pathways-related genes were extensively down- and up-regulated in young versus mature leaves of the two species.

sample_organism:
Schima superba
Cryptocarya concinna

platform_organism:
Schima superba
Cryptocarya concinna

first: Chang-Lian

last: Peng


title: Gene expression analyses of GI eosinophils under homeostatic conditions

status: Public on Oct 01 2018

city: Tel Aviv

first: Hadar

last: Reichman

address: 30 Haim Levanon

department: Microbiology & Immunology

country: Israel

institute: Tel Aviv University

type: Expression profiling by high throughput sequencing

summary: RNA-seq was performed on eosinophils isolated from colons of naive C57/BL6 mice.

overall_design: 2 samples of naive colonic eosinophils

first: Ariel

last: Munitz


title: Identification of enhancer regulating Il9 gene

city: Pittsburgh

first: Rajneesh

last: Srivastava

state: Pennsylvania

address: 450 Technology Dr

department: Surgery, University of Pittsburgh

country: USA

institute: McGowan Institute for Regenerative Medicine

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
Enhancers regulating Th cell specific cytokine gene expression were studied and identified. However, Il9 regulating enhancer was not identified yet. Active enhancers are characterized with P300, STATs binding and active histone modifications such as H3K4me1 and H3K27ac.
Based on P300 ChIP seq analysis, we narrowed down enhancer candidates for Il9 gene expression.

overall_design: Identificaiton of enhancer regulating Il9 gene in Th9 cell using P300 binding, a active enhancer marker.

first: Mark

last: Kaplan

first: Byunghee

last: Koh


title: RNAseq to understand the host transcriptome during nontuberculous mycobacterial lung infection

status: Public on Sep 30 2018

city: Denver

first: Jennifer

last: Honda

state: CO

address: 1400 Jackson St. Neustadt D504

institute: National Jewish Health

summary: We sought to elucidate the differentially expressed host factors in bronchoalveolar lavage cells (BALc) from nontuberculous mycobacteria (NTM)-infected subjects by studying the host transcriptome in during infection. A heatmap was created from the normalized expression of selected genes that showed statistically significant differential expression between NTM-infected and uninfected subjects. Genes with similar expression patterns were grouped and the most highly expressed genes are shown. One of the most differentially expressed gene in the NTM-infected group was the CFD (complement factor D) gene. Of note, a statistically significant three-fold increase in expression of the CAMP gene, encoding the LL-37 peptide was observed in the NTM-infected subject group (padj=0.05).

overall_design: Bronchoalveolar lavage cell samples from 3 bronchiectatic patients with Mycobacterium intracellulare lung infection and 3 bronchiectatic patients without Mycobacterium intracellulare lung infection

middle: R

first: Thomas

last: Danhorn

first: Kendra

middle: N

last: Walton

first: Brian

middle: P

last: O'Connor

first: Sonia

middle: M

last: Leach


title: Parallel transcriptional programs driving early-starting inheritable lineage bias of myeloid, lymphoid and dendritic cells are initiated by distinct dosage of PU.1 and IRF8 in HSCs

city: New York City

first: Kang

last: Liu

state: New York

department: Dept of Microbiology & Immunology

institute: Columbia University

summary: In the traditional model of hematopoiesis, blood lineages diversify from HSCs through a sequential process of hierarchical bifurcation. Each of these bifurcation nodes comprises multipotent progenitors that are assumed to be homogeneous and equipotent in terms of their potency. The isolation of dendritic cell (DC) progenitors with either myeloid or lymphoid potency has led to the notion of “convergent development”, and an ongoing debate on the origin of DCs and their relationship with myeloid and lymphoid lineages. We have used a clonal assay combining with statistical modeling to quantify the yield of granulocytes (G), monocytes (M), lymphocytes (L) and three subsets of DCs from single human CD34+ progenitor cells of nine different phenotypes, and traced the potency of their individual progeny. We show that multipotent progenitors are not in fact equipotent, but instead exhibit a bias toward one specific lineage; this lineage bias is established at the HSC stage and transmitted to most progeny, with bifurcation to other lineages only occurring infrequently. Critically, these lineage biases can be correlated to lineage-specific transcriptional programs that are reinforced during division.  We performed computational analysis to correlate transcriptomes and lineage composition of individual phenotype-defined progenitor cells. This enabled us to identify 32 common transcription factor (TF) candidates that interact physically and form genetic regulatory networks, with lineage-specific developmental programs initiated and reinforced based on the distinct dosage combination of these common TFs. Our analysis reveals that early expression of high levels of IRF8 and intermediate levels of PU.1 protein correlates with a bias towards CD141+ DC and plasmacytoid DC lineages in vivo, and that this pattern is inheritable from progenitors to mature cells. We have therefore arrived at a coherent model of DC development driven by parallel and inheritable programs defined by distinct dosages of TFs including PU.1 and IRF8, a developmental model that may apply to other lineages as well.

overall_design: mRNA profiles of human cord blood CD34+ hematopoietic progenitors from healthy donors

first: Yu

middle: J

last: Zhou

first: Wenji

last: Ma

first: Yufeng

last: Shen


title: Next generation sequencing of leaf transcriptome from taro (Colocasia esculenta) cultivars Niue, Palau 10, and Sam-07

city: Pago Pago

first: Ndeme

last: Atibalentja

state: AS

address: 5319 College Road

department: Division of Agriculture, Community, and Natural Resources

institute: American Samoa Community College

summary: Despite the fact that taro, colocasia esculenta, is an important staple food for millions of people around the world, its genome and transcriptome sequence has not yet been investigated. The objective of this study was to generate transcriptome sequence information from taro cultivars Niue, Palau 10, and Sam-07. Niue and Sam-07 are highly susceptible to the taro leaf blight (TLB) disease caused by Phytophthora colocasiae, to which Palau 10 is resistant. The analysis of the taro transcriptome will facilitate gene discovery, including genes that are responsible for TLB-resistance. Moreover, microsatellites (SSRs) developped from these data will be useful for marker-assisted breeding of improved taro cultivars, QTL mapping, and characterization of the genetic diversity in taro.

overall_design: Three RNA-seq samples were obtained from the leaves of each of three taro cultivars, including Niue (CePaCT Accession # CE/SM/05); Ngerruuch (CePaCT Accession # CE/PAL/10), aka Palau 10 or P-10; and Samasama  (CePaCT Accession Number: CE/SM/10), aka Sam7.

first: Kathleen

last: Keating

first: Gloria

last: Rendon

first: Chris

last: Fields

first: Alvaro

middle: G

last: Hernandez

middle: L

last: Wright

first: Emily

last: Ilaoa

first: Shalley

middle: T

last: Fiafia

first: Ian

middle: B

last: Gurr

first: Seth

last: Galea'i

first: Daniel

last: Aga

first: Aufa'i-Apulu

last: Areta

first: Emey

last: Silafau

first: Jessie

last: Suesue

first: Eleasaro

last: Sialoi


title: MicroRNA spectrum of porcine serum, plasma, semen, urine and bile exsome

status: Public on Sep 27 2018

city: Rongchang

first: Jie

last: Zhang

state: Chongqing

address: Xueyuan road #160

department: College of Animal Science

country: China

institute: Southwest University

type: Non-coding RNA profiling by high throughput sequencing

summary: Exsome microRNA stably present in various body fluids (such as amniotic fluid, breast milk, blood, bronchial lavage, malignant ascites fluid, tears, saliva, and urine) shown to be associated with various pathological conditions. We report the microRNA expression profiles in porcine serum, plasma, semen, urine and bile exsome at postnatal 180-days-old by a deep sequencing technology.

overall_design: Exsome microRNA profiles of 180-days-old porcine 5 body fluids were generated by deep sequencing using Illumina HiseqTM 2500.


title: Transcriptomic responses of Serratia liquefaciens cells grown under simulated Martian conditions of low temperature, low pressure, and CO2-enriched anoxic atmosphere.

status: Public on Sep 26 2018

city: Merritt Island

first: Wayne

last: Nicholson

state: FL

address: Space Life Sciences Laboratory 505 Odyssey Way Room 201B

department: Microbiology and Cell Science

institute: University of Florida

summary: Results from previous experiments indicated that the Gram-negative a-proteobacterium Serratia liquefaciens strain ATCC 27592 was capable of growth under low temperature (0°C), low pressure (0.7 kPa), and anoxic, CO2-dominated atmosphere--conditions intended to simulate the near-subsurface environment of Mars (Schuerger A.C. et al., Astrobiology 13: 115-131, 2013). To probe the response of its transcriptome to this extreme environment, S. liquefaciens ATCC 27592 was cultivated under 4 different environmental simulations: 0°C, 0.7 kPa, CO2 atmosphere (Condition A); 0°C, ~101.3 kPa, CO2 atmosphere (Condition B); 0°C, ~101.3 kPa, ambient N2/O2 atmosphere (Condition C); and 30°C, ~101.3 kPa, N2/O2 atmosphere (Condition D; ambient laboratory conditions). RNA-seq was performed on ribosomal RNA-depleted total RNA isolated from triplicate cultures grown under Conditions A-D and the datasets generated were subjected to transcriptome analyses. The data from Conditions A, B, or C were compared to laboratory Condition D. Significantly differentially expressed transcripts were identified belonging to a number of KEGG pathway categories. Up-regulated genes under all Conditions A, B, and C included those encoding transporters (ABC and PTS transporters); genes involved in translation (ribosomes and their biogenesis, biosynthesis of both tRNAs and aminoacyl-tRNAs); DNA repair and recombination; and non-coding RNAs. Genes down-regulated under all Conditions A, B, and C included: transporters (mostly ABC transporters); flagellar and motility proteins; genes involved in phenylalanine metabolism; transcription factors; and two-component systems. The results are discussed in the context of Mars astrobiology and planetary protection.

overall_design: mRNA profiles of Serratia liquefaciens cells grown under 4 differential environmental conditions.

first: Patricia

last: Fajardo-Cavazos

first: Michael

middle: D

last: Morrison

last: Miller

first: Andrew

middle: C

last: Schuerger


title: Human HAP1 cells before and after nutrient deprivation

status: Public on Sep 28 2018

city: Utrecht

first: Janneke

last: Peeters

address: Heidelberglaan 100

country: Netherlands

institute: UMC Utrecht

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

overall_design: Refer to individual Series


title: Transcriptomic profiling of human HAP1 cells before and after nutrient deprivation

summary: Autophagy is a lysosomal degradation pathway critical for maintaining cellular homeostasis and viability, and is predominantly regarded as a rapid and dynamic cytoplasmic process. To improve our understanding of the transcriptional and epigenetic events associated with autophagy, we performed genome-wide transcriptomic and epigenomic profiling after nutrient deprivation in human wildtype and autophagy-deficient cells. We observed that nutrient deprivation leads to the transcriptional induction of numerous autophagy-associated genes. These transcriptional changes are reflected at the epigenetic level (H3K4me3, H3K27ac, and H3K56ac) and are independent of autophagic flux.

overall_design: Transcriptome analysis of HAP1 WT, ATG7KO and RB1CC1KO cells with and without amino acid + serum starvation (6h EBSS). For each sample 3 replicates were included.

first: Jorg

last: van Loosdregt

first: Michal

last: Mokry


title: miRNA sequencing of serum exosomes from hepatocellular carcinoma and liver cirrhosis patients

city: Beijing

first: Yurong

last: Wang

address: 28 Fu-Xing Road

institute: Chinese PLA General Hospital

summary: Exosomal microRNAs have recently been studied as potential diagnostic marker for various malignancies, including hepatocellular carcinoma (HCC). The aim of this study was to investigate serum exosomal microRNA profiles as HCC diagnostic marker. Transmission electron microscopy and western blot were used to identify serum exosomes. Deep sequencing was performed to screen differentially expressed microRNAs between HCC (n=5) and liver cirrhosis (LC, n=5) group. Three upregulated and two downregulated microRNAs were selected for qPCR analysis. The levels of selected microRNAs were normalized to Caenorhabditis elegans miR-39 microRNA mimics. Serum exosomal level of miR-122, miR-148a, and miR-1246 were further analyzed and significantly higher in HCC than LC and normal control (NC) group (P<0.001), but not different from chronic hepatitis group(p>0.05). The receiver operating characteristic curve was used to evaluate diagnostic perfromance of candidate microRNAs. Area under the curve (AUC) of miR-148a was 0.891 [95 % confidence interval (CI), 0.809-0.947] in discriminating HCC from LC, remarkably higher than alpha fetoprotein (AFP) (AUC: 0.712, 95 % CI: 0.607-0.803). Binary logistic regression was adpoted to establish the diagnostic model for discriminating HCC from LC. And the combination of miR-122, miR-148a and AFP increased the AUC to 0.931 (95% CI, 0.857-0.973), which can also be applied for distinguishing early HCC from LC. miR-122 was the best for differentiating HCC from NC (AUC: 0.990, 95% CI, 0.945-1.000). These data suggests that serum exosomal microRNAs signature or their combination with traditional biomarker may be used as a suitable peripheral screening tool for HCC.

overall_design: Deep sequencing was performed to screen differentially expressed serum exosomal microRNAs between HCC (n=5) and liver cirrhosis (LC, n=5) group.

first: Yaping

last: Tian


title: NFAT5 ChIP-seq in mouse bone marrow-derived macrophages (BMDM)

city: Barcelona

first: Cristina

last: Lopez-Rodriguez

address: Carrer Dr. Aiguader, 88

department: Medicine and Life Sciences

country: Spain

institute: Universitat Pompeu Fabra

summary: Chromatin from wild-type and NFAT5-deficient BMDM was immunoprecipitated with anti-NFAT5 antibodies and ultrasequenced to identify NFAT5 binding sites in steady state macrophages (BMDM)

overall_design: BMDM were generated by culturing bone marrow cell suspensions from wild-type and NFAT5-deficient mice in 25% (vol/vol) conditioned medium from M-CSF-producing L929 cells for 7 days.

first: Luca

last: Cozzuto


title: Single cell sequencing of hippocampus tissues in traumatic brain injury

city: Los Angeles

first: Douglas

last: Arneson

state: CA

address: 2000 Terasaki Life Sciences Bldg 610 Charles E Young Drive East

department: Integrative Biology and Physiology

institute: UCLA

summary: A single cell suspension was generated from 24hr TBI and Sham mouse hippocampi, and single-cell mRNAseq libraries were generated with Drop-Seq.

overall_design: Drop-Seq was performed on four separate days using the same age (10 week) and strain (C57BL/6) mice. On day 1, Sham1 and TBI1 were obtained. On day 2, TBI2 was obtained. On day 3, Sham2 was obtained. On day 4, Sham3 and TBI3 were obtained.

first: X

last: Yang

first: D


title: Long-term in vitro expansion of epithelial stem cells enabled by pharmacological inhibition of PAK1-ROCK-Myosin II and TGF-β signaling (RNA-seq)

city: St. Louis

first: Hyung Joo

last: Lee

state: MO

address: 4515 McKinley Avenue

department: Department of Genetics

institute: Washington University School of Medicine

summary: Despite substantial self-renewal capability in vivo, epithelial stem and progenitor cells located in various tissues expand for a few passages in vitro in feeder-free condition before they succumb to growth arrest. Here we describe the EpiX™ method that utilizes small molecules that inhibit PAK1-ROCK-Myosin II and TGF-β signaling to achieve over one trillion-fold expansion of human epithelial stem and progenitor cells from skin, airway, mammary and prostate glands in the absence of feeder cells. Transcriptomic and epigenomic studies show that this condition helps epithelial cells to overcome stresses for continuous proliferation. EpiX-expanded basal epithelial cells differentiate into mature epithelial cells consistent with their tissue origins. Whole genome sequencing reveals that the cells retain remarkable genome integrity after extensive in vitro expansion without acquiring tumorigenicity. EpiX technology provides a solution to exploit the potential of tissue-resident epithelial stem and progenitor cells for regenerative medicine.

overall_design: mRNA profiles of human foreskin keratinocytes in different culture conditions were generated by deep sequencing, in duplicate, using Illumina NextSeq.

first: Chengkang

first: Ting


title: Therapeutic effects of Tie2 activation in treatment of neovascular age-related macular degeneration over conventional VEGF blockade.

city: Irvine

first: Hosung

last: Bae

address: 839 Health Sciences Road Sprague Hall, Room 150

institute: UC Irvine

summary: To investigate a potential therapeutic effect of ABTAA on NV-AMD, we employed a mouse model of laser-induced CNV, that mimics human NV-AMD. A laser photocoagulation on mouse retinas was performed to rupture RPE and Bruch’s membrane, and then the effects of ABTAA were compared with those of VEGF-Trap.

overall_design: RPE-choroidal complex was obtained from enucleated eyes and flat-mounted on polyethylene naphthalate membrane (Carl Zeiss). CNV and surrounding tissues (a two-fold larger diameter than CNV itself), including RPE and choroid, were collected using laser capture microdissection (PALM MicroBeam, Carl Zeiss) and subjected to RNA isolation.

first: Gou

middle: Y

last: Koh


title: Structural Remodeling of the Human Colonic Mesenchyme in Inflammatory Bowel Disease [2]

city: Oxford

first: James

last: Kinchen

address: Weatherall Institute of Molecular Medicine, John Radcliffe Hospital

department: Nuffield Department of Medicine

country: United Kingdom

institute: University of Oxford

summary: Intestinal health is sustained by cooperation between diverse cell types, including epithelial cells, immune cells and stromal cells. Colonic stromal cells provide critical structural support but also regulate mucosal immunity, tolerance and inflammatory responses. Although mucosal stromal cells display substantial variability and plasticity, a paucity of unique genetic markers has precluded the identification of distinct stromal populations and functions. We used single-cell RNA-sequencing to uncover heterogeneity and subtype-specific markers of individual colonic stromal cells in health and ulcerative colitis (UC). Marker-free transcriptional clustering revealed four distinct stromal populations in healthy colon, corresponding to myofibroblasts and three previously unknown distinct subsets of fibroblasts. These fibroblast subsets were substantially remodeled in UC compared to healthy colon: inflamed UC colon was depleted for a healthy fibroblast subpopulation associated with epithelial cell homeostasis, and enriched for a novel disease-associated subtype expressing pro-inflammatory genes. Thus, we have discovered new, molecularly distinct colonic stromal cell subtypes that are altered in human disease.

overall_design: Colonic lamina propria mesenchymal cells from 3 healthy donors. 183 single cell libraries, 6 bulk controls, 3 empty well controls. Individual donors processed as separate batches with Fluidigm C1 IFCs and pooled for sequencing (2 x Illumina HiSeq 2500 lanes).

first: Alison

last: Simmons


title: Structural Remodeling of the Human Colonic Mesenchyme in Inflammatory Bowel Disease


title: Structural Remodeling of the Human Colonic Mesenchyme in Inflammatory Bowel Disease [3]

overall_design: Ulcerative colitis colonic lamina propria mesenchymal cells from 3 donors. 178 single cell libraries, 7 bulk controls, 7 empty well controls. Individual donors processed as separate batches on Fluidigm C1 IFCs and pooled for sequencing (1 x Illumina HiSeq 4000 lane).


title: The NFkB subunit RELA is a master transcriptional regulator of the committed epithelial-mesenchymal transition in airway epithelial cells

city: Galveston

first: Allan

last: Brasier

state: TX

address: 301 Univ. Blvd

department: Medicine

institute: University Texas Medical Branch

summary: The epithelial-mesenchymal transition (EMT) is a multistep dedifferentiation program important in tissue repair. Here, we examined the role of the transcriptional regulator NFkB in EMT of human primary small airway epithelial cells (hSAECs). Surprisingly, transforming growth factor β (TGFβ) activated NFkB/RELA proto-oncogene, NFkB subunit (RELA) translocation within 1 day of stimulation, yet induction of its downstream gene regulatory network occurred only after 3 days. A time course of TGFβ-induced EMT transition was analyzed by RNA-Seq in the absence or presence of inducible shRNA-mediated silencing of RELA. In WT cells, TGFβ stimulation significantly affected the expression of 2,441 genes. Gene set enrichment analysis identified Wnt, cadherin, and NFkB signaling as the most prominent TGFβ-inducible pathways. By comparison, RELA controlled expression of 3,138 overlapping genes mapping to Wnt, cadherin, and chemokine signaling pathways. Conducting upstream regulator analysis, we found that RELA controls six clusters of upstream transcription factors, many of which overlapped with a transcription factor topology map of EMT developed earlier. RELA triggered expression of three key EMT pathways: (1) the Wnt/β-catenin morphogen pathway, (2) the JUN transcription factor, and (3) the Snail family transcriptional repressor 1 (SNAI1). RELA binding to target genes was confirmed by ChIP. Experiments independently validating Wnt dependence on RELA were performed by silencing RELA via genome editing and indicated that TGFβ-induced WNT5B expression and downstream activation of the Wnt target AXIN2 are RELA-dependent. We conclude that RELA is a master transcriptional regulator of EMT upstream of Wnt morphogen, JUN, SNAI1-ZEB1, and interleukin-6 autocrine loops.

overall_design: RNA-seq transcriptome profiling of TGF-Beta stimulated RelA wildtype and knock-down cells

first: Steven

last: Widen


title: Aligning single-cell developmental and reprogramming trajectories identifies molecular determinants of reprogramming outcome

city: Seattle

first: Cole

middle: Bruce

last: Trapnell

state: WA

address: William H. Foege Hall, 3720 15th Ave NE

department: Genome Sciences

institute: University of Washington

summary: Cellular reprogramming through manipulation of defined factors holds great promise for large-scale production of cell types needed for use in therapy, as well as for expanding our understanding of the general principles of gene regulation. MYOD-mediated myogenic reprogramming, which converts many cell types into contractile myotubes, remains one of the best characterized model system for direct conversion by defined factors. However, why MYOD can efficiently convert some cell types into myotubes but not others remains poorly understood. Here, we analyze MYOD-mediated reprogramming of human fibroblasts at pseudotemporal resolution using single-cell RNA-Seq. Successfully reprogrammed cells navigate a trajectory with two branches that correspond to two barriers to reprogramming, with cells that select incorrect branches terminating at aberrant or incomplete reprogramming outcomes. Differential analysis of the major branch points alongside alignment of the successful reprogramming path to a primary myoblast trajectory revealed Insulin and BMP signaling as crucial molecular determinants of an individual cell’s reprogramming outcome, that when appropriately modulated, increased efficiency more than five-fold. Our single-cell analysis reveals that MYOD is sufficient to reprogram cells only when the extracellular milieu is favorable, supporting MYOD with upstream signaling pathways that drive normal myogenesis in development.

overall_design: scRNA-seq experiment for MYOD-mediated human fibroblasts reprogramming. HSMM derivation, expansion and differentiation was as previously described (Trapnell et al., 2014). Foreskin Human Fibroblasts obtained from commercial vendor (Stemgent) were expanded in alpha-mem supplemented with glutamax, 10% FBS and 16ng/ul of FGF-b (ThermoFisher Scientific). The fibroblasts were then infected with a mixture of lentiviruses encoding hTERT (and Puromycin resistance gene), Tetracycline Repressor (and Geneticin resistance gene) and TR-controlled hMYOD (and Blasticidin resistance gene) (ThermoFisher Scientific). All the resistance genes are constitutively expressed and therefore triple selection was performed and maintained using 1ug/ml of Puromycin, 500ug/ml of Geneticin and 2ug/ml of Blasticidin to generate the hFib-MYOD line.   To perform reprogramming and differentiation experiments HSMM and hFib-MYOD cells were plated in 24-well formats at a density of 50.000 cells per well. Gelatin was sometime used as a coating agent with no significant difference with respect to uncoated dishes. Differentiation and reprogramming was induced using a differentiation media containing alpha-mem supplemented with glutamax and 2% HS (ThermoFisher Scientific), supplemented with 2ug/ml of doxycycline to enact MYOD expression. When indicated, Insulin was used at 8ug/ml (ThermoFisher Scientific), BMP inhibitor LDN-193189 was used at 0.1uM (Stemgent), LSD1 inhibitor RN-1 was used at 1uM (EMD Millipore). At the indicated time points, cells were harvested by gentle dissociation using TrypLE (ThermoFisher Scientific) and processed for full-length transcriptome sequencing using the Fluidigm C1 Single Cell or bulk mRNA sequencing as previously described (Trapnell et al., 2014). Cells were loaded onto the microfluidic chip at a concentration of ~250 cells/μl to maximize the number of single cells captured and minimize the occurrence of doublets. In some instances, cells were reloaded if the majority of capture sites were not occupied on the first attempt. As in Trapnell et al, 2014, captured cells were scored by manual on-chip microscopic inspection to determine if they were singletons and free of other debris.

first: Davide

last: Cacchiarelli


title: Structural Remodeling of the Human Colonic Mesenchyme in Inflammatory Bowel Disease [1]

overall_design: Colonic epithelial cells from 3 healthy donors. 92 single cell libraries, 3 bulk controls, 1 empty well control. Individual donors processed as separate batches on Fluidigm C1 IFCs and pooled for sequencing (1 x Illumina HiSeq 2500 lane).


title: RNA expression in anterior nasal septum cartilage of wildtype and Fgfr2+/S252W Apert syndrome model mice at embryonic day (E)14.5.

status: Public on Sep 25 2018

city: New York

first: Harm

middle: van

last: Bakel

address: One Gustave L. Levy Place, Box 1498

department: Genetics and Genomic Sciences

institute: Mount Sinai School of Medicine

summary: The nasal capsule cartilage of Apert  Fgfr2+/S252W mice increases in size compared to wildtype cartilage during embryonic craniofacial development. Increased levels of markers of cell proliferation can be detected in the Apert  Fgfr2+/S252W anterior nasal septum cartilage compared to wildtype at E14.5. We have performed laser capture microdissection of this cartilage in these genotypes at this age to generate RNA-Seq libraries and compare gene expression. Expression analysis shows increased expression of genes related to chromosome condensation, nuclear division, and the cell cycle in Apert  Fgfr2+/S252W anterior nasal septum cartilage compared to wildtype.

overall_design: Laser capture microdissection was performed on fresh frozen sections of three wildtype and three mutant mice. RNA was isolated from the six individual samples, converted to RNA-Seq libraries, and sequenced on the Illumina HiSeq 2500 platform.

first: Greg

last: Holmes

first: Courtney

last: O’Rourke

first: Susan

last: Motch Perrine

last: Lu

last: van Bakel

first: Joan

last: Richtsmeier

first: Ethylin

last: Wang Jabs


title: A new N6-methyladenosine methyltransferase ZCCHC4 mediates rRNA methylation and mRNA interaction

city: Chicago

first: zhike

last: lu

state: IL

address: 5801 South Ellis Avenue

department: department of chemistry

institute: University of Chicago

summary: N6-methyladenosine (m6A) plays critical roles in a wide range of physiological and pathological processes, and m6A methyltransferases are still being discovered for different RNA species in mammals. Here report a new m6A methyltransferase ZCCHC4 that methylates ribosomal RNA (rRNA) and interacts with messenger RNA (mRNA), ZCCHC4 has methylation activity on rRNA with a preference for AAC consensus sequence. ZCCHC4 can affect global translation through m6A methylation, mostly on 28S rRNA.

overall_design: We used PAR-CLIP to identify the binding targets of ZCCHC4 in HeLa cells. We used polysome sequencing to identify targets of ZCCHC4 wild type and knock out HepG2 cell for translation. We used m6A-seq to identify changes in m6A and RNA expression ZCCHC4 KO HepG2 cells.

first: Honghui

last: Ma

first: Xiaoyun

last: Wang

first: Jiabin

last: Cai

first: Zhike

first: Ruitu

last: Lv

first: Tao

last: Pan

first: Yang

last: Shi

first: Chuan

last: He


title: Epigenetic profiling of human HAP1 cells before and after nutrient deprivation

first: Janneke

last: Peeters

overall_design: Examination of H3K27ac, H3K56ac, H3K4me3 and RNA Polymerase II in HAP1 cells with and without amino acid + serum starvation (3h EBSS). Two replicates were included for each ChIP.

first: Jorg

last: van Loosdregt

first: Michal

last: Mokry


title: Targeting a phospho-STAT3-miRNAs pathway improves vesicular hepatic steatosis in an in vitro model

city: Rome

first: Matteo

last: Pallocca

address: Via Fermo Ognibene

country: Italy

institute: Italian National Cancer Institute "Regina Elena"

summary:
Non-alcoholic fatty liver disease (NAFLD) is a leading cause of chronic liver disease. Although genetic predisposition and epigenetic factors contribute to the development of NAFLD, our understanding of the molecular mechanism involved in the pathogenesis of the disease is still emerging. Here we investigated a possible role of a microRNAs-STAT3 pathway in the induction of hepatic steatosis.
Differentiated HepaRG cells (dHepaRG) treated with the fatty acid sodium oleate recapitulated features of liver vesicular steatosis and activated a cell-autonomous inflammatory response, inducing STAT3-Tyrosine-phosphorylation. With a genome-wide approach (Chromatin Immunoprecipitation Sequencing), many phospho-STAT3 binding sites were identified in fatty dHepaRG and several STAT3 and/or NAFLD-regulated microRNAs showed increased expression levels, including miR-21. Innovative CARS (Coherent Anti-Stokes Raman Scattering) microscopy revealed that chemical inhibition of STAT3 activity decreased lipid accumulation and deregulated STAT3-responsive microRNAs, including miR-21, in lipid overloaded dHepaRG cells. We were able to show in vivo that reducing phospho-STAT3-miR-21 levels in C57/BL6 mice liver, by long-term treatment with metformin, protected mice from aging dependent hepatic vesicular steatosis. Our results identified a microRNAs-phosphoSTAT3 pathway involved in the development of hepatic steatosis, which may represent a molecular marker for both diagnosis and therapeutic targeting.

overall_design: ChIP-Seq for phospho-STAT3 with differentiated HepaRG cells treated for 4 days with 250 µM of sodium oleate or vehicle as control.

first: Silvia

last: Di Cocco

first: Natalia

last: Pediconi

first: Francesca

last: Guerrieri

first: Laura

last: Belloni

last: Piconese

first: Abigail

last: Nunn

first: Sabrina

last: Strano

first: Giovanni

last: Blandino

first: Fabio

last: Marra

first: Massimo

last: Levrero


title: Heart Chamber Evolution Reveals Roles of Gene/Genome Duplications on Continuous Character Evolution in Vertebrates

city: Shanghai

first: Gang

middle: Biao

last: Liu

state: Shanghai

address: 2005 Songhu Rd

department: School of life science

institute: Fudan univeristy

summary: We sequenced at mRNA level in adult hearts of zebrafish, pamprey and sea squirt. Combined with other 11 vertebrate heart RNA-Seq data online, we conducted comprehensive evolutionary genomic analyses to address the contribution of gene/genome duplications on heart structure evolution. We observed that number of duplicate genes expressed in heart increased gradually with the increase of heart chamber number along the vertebrate phylogeny, despite that most of them were duplicated at the time near to the origin of vertebrates or more ancient. Our research provides a clear-cut example to show the relationship among gene duplication, continuous character evolution like heart structure evolution and nature selection.

sample_organism:
Ciona intestinalis
Petromyzon marinus
Danio rerio

overall_design: Examination of mRNA levels in thirteen vertebrate samples with different cardiac chamber number, and one invertebrate (sea squirt).

first: Yangyun

last: Zou

first: Gangbiao

first: Libing

last: Shen

first: Zhan

last: Zhou

first: Ling

last: Sun

last: Zhong

first: Hongyan

last: Wang

first: Zhixi

last: Su

first: Xun

last: Gu


title: Expression profiling by high throughput sequencing and transcriptome-wide association study study the metabolic mechanism of the formation of atorvastatin lactone and the risk to statin-induced myotoxicity

city: Guangzhou

first: Shilong

state: Guangdong Province

address: 106 Zhongshan Road, Weilun Bldg

institute: Guangdong Provincial Key Laboratory of Coronary Heart Disease Prevention

summary: Statin-induced myotoxicity (SIM) is one of the principal reasons for atorvastatin (AT) non-adherence and/or discontinuation, contributing to adverse cardiovascular outcomes. To date, the genetic mechanism of SIM is far from well-illustrated. Published data in vitro and in vivo indicated that atorvastatin lactone (ATL) is the key metabolite to induce myotoxicity. We therefore hypothesis that genetic variants increasing the formation of ATL can increase the risk to statin-induced myotoxicity. And a transcriptome-wide association study (TWAS) integrating genome wide variants and gene expression data will applied to identify expression quantitative trait loci (eQTL) associated with the formation of ATL and different bioinformatic tools will then be applied to reveal the potential causal impact of eQTLs on the formation of ATL.

overall_design: Liver mRNA profiles of 26 non-liver-cancer and 27 liver-cancer patients were generated by deep sequencing, in triplicate, using Illumina HiSeqTM 2000


title: Meis genes regulate RA/FGF signaling to control multiple steps of limb development

city: Madrid

first: Carlos

last: Torroja

state: Madrid

address: Melchor Fernandez Almagro, 3

department: Bioinformatics Unit

institute: Centro Nacional de Investigaciones Cardiovasculares (CNIC)

summary: Vertebrate limbs develop by integrating signals that control patterning along three main orthogonal axes. Flank-produced retinoic acid (RA) is initially required for limb induction and establishment of the apical ectodermal ridge (AER), a distal signaling center that produces fibroblast growth factors (FGFs), which are essential for limb growth and distalization. Once the AER is established, RA:FGF antagonism determines the restricted expression of a set of genes that control limb proximodistal patterning. Essential for this antagonism is the activation by FGF of the RA-degrading enzyme CYP26B1 in the distal limb bud. In addition, sonic hedgehog produced from the zone of polarizing activity (ZPA) is essential for distal limb anteroposterior patterning and contributes to RA reduction by cooperating in CYP26B1 activation. Meis transcription factors are expressed in the proximal limb bud, are activated by RA and can regulate proximodistal limb development; however, the mechanisms underlying their activity remain unknown. Here we studied Meis function in the mouse limb bud through Meis2 conditional overexpression and elimination of Meis1 and Meis2. We found that Meis activity is first required for limb bud initiation and the proper establishment of the AER and ZPA signaling centers, and subsequently for the development of proximal limb structures. Functional genomic analyses reveal that Meis is an important conveyor of the RA:FGF antagonism through the regulation of components of the RA and FGF signaling pathways, including CYP26B1. In addition, Meis regulates a set of proximal limb genes controlling proximodistal patterning and differentiation. Our work reveals a regulatory module essential for limb patterning and potentially co-opted in other patterning processes involving RA:FGF antagonism.

overall_design: Examination of gene profile on distal limb bud tips of mice overexpressing Meis2

first: Alberto

last: Roselló-Diez

first: Miguel

last: Torres


title: Transcriptomic profile of FACS-isolated reactive or SOCS3-deactivated astrocytes from the hippocampus of wildtype and 9-month old APP/PS1dE9 mice

city: Paris

first: Noémie

last: Robil

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

summary:
We analyzed the transcriptional profile of  astrocytes from 1) WT mice infected with AAV-GFP,  2) reactive astrocytes from 9-month old APP/PSdE9 mice infected with AAV-GFP and 3) de-activated astrocytes from 9-month old APP/PSdE9 mice infected with AAV-SOCS3
We show SOCS3 normalizes the inflammatory profile of APP astrocytes

overall_design: Total RNA was extracted from GFP+ astrocytes isolated by FACS from WT and APP/PS1dE9 mice injected with an AAV targeting astrocytes and encoding GFP alone (controls, N=7 WT-GFP, N=4 APP-GFP) or SOCS3 and GFP (N=5 APP-SOCS3, same total viral load). Non GFP+ cells (including microglia, neurons, non infected astrocytes, called OTHER) were analyzed as  well, in 3 samples of the control WT-GFP group.

first: Kelly

last: Ceyzériat

first: Marie-Ange

last: Palomares

first: Jean-François

last: Deleuze

first: Robert

last: Olaso

first: Carole

last: Escartin


title: Cranial pericytes derived from neural crest cells reveal an inherent cell type-specific defect in Alzheimer's Disease

status: Public on Sep 22 2018

first: Ruchi

last: Bajpai

address: 2250 Alcazar St

department: Center for Craniofacial Molecular Biology

institute: University of Southern California

summary: Forebrain microvasculature is defective in Alzheimer's disease. To model the role of cranial pericytes in influencing endothelial cell functions, we developed a method for cranial-pericyte derivation from iPSCs. Our studies reveal inherent defects in cranial pericytes from familial AD iPSC. We also demonstrate a similar pathophysiology in perimary pericytes isolated from sporadic AD patients that can be rescued.

overall_design: Comparison of primary and in vitro derived pericytes, as well as fAD and sAD versus control pericytes

first: Casey

last: Griffin


title: Stella prevents excessive de novo DNA methylation during mouse oogenesis

status: Public on Sep 24 2018

first: Zhuqiang

last: Zhang

address: 15 Datun Road, Chaoyang District.

institute: Institute of Biophysics, CAS

type: Methylation profiling by high throughput sequencing

summary: Oocyte acquires developmental competence during its maturation. This stage is accompanied with large-scale alteration in transcription, and series of genome-wide epigenetic reprogramming, including de novo establishment of DNA methylation. However, our understanding of mechanisms regulating this process is limited. To investigate the role of Stella (Dppa3) in de novo methylation during mouse oogenesis, here we measured DNA methylation by RRBS and expression profiles by RNA-seq in PGCs and oocytes at serveral development stages, including genotypes of both Stella (Dppa3) +/- and Stella -/-.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: We measured DNA methylation by RRBS and expression profiles by RNA-seq in PGCs and oocytes at serveral development stages (E13.5, D5, D10, D20, MII), including genotypes of both Stella (Dppa3) +/- and Stella -/-. DNA methylation of sperm with both genotypes were also measured by RRBS for comparision.

first: Yingfeng

last: Li

first: Jiayu

last: Chen

first: Hua

last: Huang

first: Xiang

first: Shaohua

last: Xu

first: Qiang

last: Dong

first: Jiajun

last: Tan

first: Yong

last: Zheng

first: Guo-Liang

first: Zhigao

first: Hailin

first: Bing

last: Zhu


title: SEUSS: A scalable screening platform to assess transcriptomic and fitness effects of transcription factor overexpression

city: La Jolla

first: Yan

last: Wu

state: California

address: 9500 Gilman Drive

department: Bioengineering

institute: UCSD

summary: Understanding the complex effects of genetic perturbations on cellular state and fitness in human pluripotent stem cells (hPSCs) has been challenging using traditional pooled screening techniques which typically rely on unidimensional phenotypic readouts. Here, we use barcoded open reading frame (ORF) overexpression libraries with a coupled single-cell RNA sequencing (scRNA-seq) and fitness screening approach, a technique we call SEUSS (ScalablE fUnctional Screening by Sequencing), to establish a comprehensive assaying platform. Using this system, we perturbed hPSCs with a library of developmentally critical transcription factors (TFs), and assayed the impact of TF overexpression on fitness and transcriptomic cell state across multiple media conditions. We further leveraged the versatility of the ORF library approach to systematically assay mutant gene libraries and also whole gene families. From the transcriptomic responses, we built genetic co-perturbation networks to identify key altered gene modules. Strikingly, we found that KLF4 and SNAI2 have opposing effects on the pluripotency gene module, highlighting the power of our method to characterize the effects of genetic perturbations. From the fitness responses, we identified ETV2 as a driver of reprogramming towards an endothelial-like state.

sample_organism:
Homo sapiens
unidentified plasmid

platform_organism:
Homo sapiens
unidentified plasmid

overall_design: Pooled transcription factor overexpression screens with scRNA-seq in ~35,000 cells across ten screens: 61 pluripotency/lineage TFs in hPSC media with five replicates, endothelial media with one replicate, multilineage media with two replicates; MYC mutant overexpression in hPSC media with one replicate; KLF family TF overexpression in hPSC media with one replicate.

first: Parekh

last: Udit

first: Wu

last: Yan

first: Zhao

last: Dongxin

first: Worlikar

last: Atharv

first: Shah

last: Neha

first: Zhang

last: Kun

first: Mali

last: Prashant


title: Changes in H3K27ac following LPS stimulation in pharyngeal epithelial cells

city: Singapore

first: Lisa

last: Borghini

state: Singapore

address: 60 Biopolis Street, Genome, #02-01

department: Infectious Diseases

country: Singapore

institute: GIS

summary: We report changes in H3K27ac following LPS stimulation in Detroit 562 cells. We were able to identified LPS-increased H3K27ac regions which correlated with RELA binding as well as gene up-regulation.  This data set is relevant for airborne bacterial sensing as Detroit 562 cells are nasopharyngeal epithelial cells and LPS is a gram negative bacterial endotoxin.

overall_design: ChIP-seq for H3K27ac histone mark in Detroit 562 cells under no treatment control condition and after LPS stimulation, each condition in duplicates.


title: Differences in RNA expression between primary and metastatic colon tumor

city: Warszawa

first: Krzysztof

last: Goryca

address: Banacha 2c

department: CeNT

country: Poland

institute: Uniwersytet Warszawski

summary: Here, we report the genomic-scale characterization of metastatic colon cancer transcriptome. Fresh-frozen samples was used to asses differences between normal colon, primary colon tumor an liver metastasis.

overall_design: Total RNA was isolated from three location from each recruited patient: normal colon, colon tumor and metastatic lesion in liver.

first: Michal

last: Mikula

first: Agnieszka

last: Paziewska

first: Maria

last: Kulecka

first: Michalina

last: Dabrowska

first: Katarzyna

last: Paczkowska

first: Jerzy

last: Ostrowski


title: NFAT5 ChIP-seq in mouse bone marrow-derived macrophages (BMDM) [2016]

city: Barcelona

first: Cristina

last: Lopez-Rodriguez

address: Carrer Dr. Aiguader, 88

institute: Universitat Pompeu Fabra

summary: Chromatin from wild-type and NFAT5-deficient BMDM was immunoprecipitated with anti-NFAT5 antibodies and ultrasequenced to identify NFAT5 binding sites in steady state macrophages (BMDM)

overall_design: BMDM were generated by culturing bone marrow cell suspensions from wild-type and NFAT5-deficient mice in 25% (vol/vol) conditioned medium from M-CSF-producing L929 cells for 7 days.

last: Lopez Rodriguez

first: Luca

last: Cozzuto

first: Hector

last: Huerga Encabo


title: Non-invasive diagnosis of urothelial cancer in urine using DNA hypermethylation signatures

city: Tuebingen

first: Michael

middle: H.

last: Walter

address: Calwer Str. 7

department: Department of Medical Genetics

country: Germany

institute: University of Tuebingen

type: Methylation profiling by genome tiling array

summary: Methylation status of free DNA from urine from patients with urothelial tumor and healthy control patients were analysed

overall_design: Patients with histologically confirmed urothelial cancer vs healthy control donors

first: Christina

middle: U

last: Köhler

first: Heiko

last: Käfferlein


title: The Zmiz1-Notch1 interaction induces Myc expression to drive steady state and stress thymopoiesis

status: Public on Sep 21 2018

city: Ann Arbor

first: Richard

last: McEachin

state: United States

address: 2800 Plymouth Road

department: DCM&B

institute: University of Michigan

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

overall_design: Refer to individual Series


title: The Zmiz1-Notch1 interaction induces Myc expression to drive steady state and stress thymopoiesis [DN3]

summary: Notch1 signaling ramps up to very high levels in order to drive CD4-CD8- double-negative (DN) thymocytes to the CD4+CD8+ double-positive (DP) stage. During this important phase of T-cell development, which is known as the DN-DP transition, it is unclear whether the Notch1 complex simply strengthens its signal output as an isolated unit or recruits cofactors to amplify its signals. We previously showed that the PIAS-like coactivator Zmiz1 is a direct and context-dependent cofactor of Notch1 in T-cell leukemia. Using conditional knockout mouse models, we show that like inactivation of Notch, inactivation of Zmiz1 impaired the DN-DP transition under steady state and stress conditions. To determine mechanism, we performed RNA-Seq on sorted DN3 cells that were deprived of Zmiz1 signals either acutely (DeltaTamCre) or chronically (DeltaMxCre). To differentiate Notch1-independent from Notch1-dependent target genes, we also performed RNA-Seq on DN3 cells that were deprived of Notch1 signals using the anti-NRR Notch1 antibody. Our data suggests that Zmiz1 selectively amplifies a subset of Notch1 target genes in DN3 cells, such as Myc.

overall_design: RNA-Seq in murine DN3 thymocytes

first: Qing

last: Wang

first: Mark

last: Chiang

first: Rork

last: Kuick


title: CDK4 inhibition diminishes p53 activation by Mdm2-antagonists

status: Public on Sep 20 2018

city: Göttingen

first: Anusha

last: Sriraman

address: Justus-von-liebig Weg 11

department: Department of Molecular Oncology

institute: Georg-August University of Göttingen

summary: CDK4 inhibitors have reached clinical approval for cancer therapy. In parallel, the p53 antagonist Mdm2 remains an attractive target for anti-cancer therapy, including numerous clinical studies. The genes encoding Mdm2 and CDK4 are frequently co-amplified in human malignancies, most notably in liposarcomas, suggesting their combined targeting for therapy. Here we show, however, that small compounds that inhibit Mdm2 and CDK4 antagonize each other rather than synergize in their cytotoxicity towards sarcoma cells. CDK4 inhibition attenuates the induction of p53-responsive genes upon Mdm2 inhibition, and similar results were obtained when depleting Mdm2 and/or CDK4 with siRNA. CDK4 inhibitors also interfered with p53 activity in response to DNA damage. CDK4 inhibition did not reduce p53 binding or histone acetylation to promoters, but rather attenuated the subsequent recruitment of RNA polymerase II. The complexes of p53 and Mdm2, as well as CDK4 and Cyclin D1, physically associated with each other. Upon combined inhibition of Mdm2 and CDK4/6, the interaction of this complex was impaired. Thus, the CDK4-Cyclin D1 complex plays a key role in enabling the transcription of p53 target genes. Taken together, our results raise caution regarding the combination of CDK4 inhibitors with Mdm2 antagonists or conventional DNA-damaging chemotherapeutics in the clinics. Moreover, they suggest a hitherto unknown role for CDK4-cyclin D1 complex in sustaining p53 activity, possibly focusing p53-mediated transcription on actively proliferating cells.

overall_design: Expression profiling by high throughput sequencing. 6 conditions were used for this experiment namely- DMSO, Nutlin, PD0332991 and the combination. SJSA cells were treated with Nutlin for 6 hours (Nutlin); PD0332991, a CDK4/6 inhibitor for a period of 24 or 30 hours (PD24, PD30), and combinations of Nutlin with PD0332991 at both time points (N+PD24 and N+PD30). DMSO is used as control. The libraries were performed in triplicates.

first: Matthias

last: Dobbelstein


title: Differential Effects of Partial and Complete Loss of TREM2 on Microglial Injury Response and Tauopathy

city: Los Angeles

first: Giovanni

last: Coppola

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA


title: Timing and order of the molecular events marking the onset of berry ripening in grapevine

city: San Pietro in Cariano

first: Marianna

last: Fasoli

state: Verona

address: Via della Pieve 70

department: Biotechnology

institute: University of Verona

summary: Grapevine (Vitis vinifera L.) is a model for the investigation of physiological and biochemical changes during the formation and ripening of non-climacteric fleshy fruits. However, the order and complexity of the molecular events during fruit development remain poorly understood. To identify the key molecular events controlling berry formation and ripening, we created a highly detailed transcriptomic and metabolomic map of berry development, based on samples collected every week from fruit-set to maturity in two grapevine genotypes for three consecutive years, resulting in 219 samples. Major transcriptomic changes were represented by coordinated waves of gene expression associated with early development, veraison (onset of ripening)/mid-ripening and late-ripening and were consistent across vintages. The two genotypes were clearly distinguished by metabolite profiles and transcriptional changes occurring primarily at the veraison/mid-ripening phase. Co-expression analysis identified a core network of transcripts as well as variations in the within-module connections representing varietal differences. By focusing on transcriptome rearrangements close to veraison, we identified two rapid and successive shared transitions involving genes whose expression profiles precisely locate the timing of the molecular reprogramming of berry development. Functional analyses of two transcription factors, markers of the first transition, suggested that they participate in a hierarchical cascade of gene activation at the onset of ripening. This study defined the initial transcriptional events that mark and trigger the onset of ripening and the molecular network that characterizes the whole process of berry development, providing a framework to model fruit development and maturation in grapevine.

overall_design: Grape berries were collected at ten-day intervals in 2012, and weekly in 2013 and 2014 beginning at fruit set until harvest (24.5 °Brix) at the same time of day (8:00 am). Samples were collected in randomized block designs along three rows for each cultivar: 8- and 6-vine blocks for Pinot noir and Cabernet Sauvignon respectively. Each sample entailed the collection of 26 clusters from each vine block. 60 berries, selected from 6 isolated clusters randomly selected from the vine blocks, were ground under liquid nitrogen. Seeds were removed in the grinding process. Frozen powder was aliquoted in 100mg and 400 mg samples for metabolite and RNA extractions respectively. Transcriptomic and metabolomic approaches were used to monitor the expression of all grapevine genes and to elucidate grape berry metabolome during development.

first: Chandra

last: Richter

first: Sara

last: Zenoni

first: Edoardo

last: Bertini

first: Nicola

last: Vitulo

first: Silvia

last: Dal Santo

first: Nick

last: Dokoozlian

first: Mario

last: Pezzotti

first: Giovanni Battista

last: Tornielli


title: TREM2 haploinsufficiency impairs microglia’s response to injury and exacerbates tau pathology in a tauopathy mouse model [RNA-Seq]

summary: Alzheimer's disease (AD), the most common form of dementia, is characterized by the abnormal accumulation of amyloid plaques and hyperphosphorylated tau aggregates, as well as microgliosis. The link between mutations in Triggering Receptor Expressed on Myeloid Cells 2 (TREM2), a microglia-expressed gene, and the increased risk for developing late-onset AD suggests a detrimental role for microglia in disease pathophyioslogy. Hemizygous TREM2 mutations are posited to increase risk for AD through loss-of-function haploinsufficiency. The effects of TREM2 haploinsufficiency on tau pathology and tau-associated deficits have not yet been characterized. Using in vivo imaging, we showed that TREM2 haploinsufficiency, but not complete loss of TREM2, resulted in a striking agedependent impairment in microglia’s response to injury without affecting baseline motility. This TREM2-dependent effect on microglial motility is consistent with transcriptomic alterations in cell motility uncovered with unbiased RNAsequencing analysis. Moreover, TREM2 haploinsufficiency, but not complete loss of TREM2, exacerbated phosphorylated tau pathology in transgenic mice expressing mutant human tau. In addition, TREM2 haploinsufficiency increased tau inclusions and tau-mediated inflammation without further exacerbating neuronal loss. Our findings demonstrate for the first time that TREM2 haploinsufficiency induces deficits in a tauopathy mouse model, supporting the notion that the hemizygous missense variant results in loss-of-function.

overall_design: Adult microglia were isolated from 3-5 month old TREM2+/+, TREM2+/- and TREM2-/- mice using CD11b magnetic beads, followed by total RNA isolation using an RNeasy kit (Qiagen).

first: Faten

middle: A

last: Sayed

first: Maria

last: Telpoukhovskaia

first: Yaqiao

last: Li

first: Yungui

last: Zhou

first: David

last: Le

first: Axel

last: Hauduc

first: Connor

last: Ludwig

first: Fuying

last: Gao

first: Claire

last: Clelland

first: Lihong

last: Zhan

first: Dimitrios

last: Davalos

first: Katerina

last: Akassoglou

first: Li

last: Gan


title: Gene expression profiling of HCCLM3 cells: Control ASO vs SCARNA13 ASO

status: Public on Sep 19 2018

city: Chengdu

first: Tian

last: Lan

state: Sichuan

address: No. 37 of Guoxue Lane

department: Department of Liver Surgery & Liver Transplantation

institute: West China Hospital

summary: Understanding the roles of ncRNAs in tumorigenesis and metastasis would establish avenues for the identification of diagnostic and therapeutic targets. We observed that lncRNA SNHG10 and its derived SCARNA13 were concomitantly upregulated in hepatocellular carcinoma (HCC) pulmonary metastases and associated with poor prognosis. Mechanistically, SCARNA13, modulated by SNHG10, facilitated the cell cycle and epithelial-mesenchymal transition (EMT) of HCC cells by promoting SOX9. SNHG10 served as a sponge for miR-150-5p and interacted with RPL4 mRNA to increase the expression and activity of c-Myb. Reciprocally, upregulated and hyperactivated c-Myb enhanced SNHG10 and SCARNA13 expression through regulating SNHG10 promoter activity, forming a positive feedback loop and continuously stimulating SCARNA13 expression. Our findings characterized a complex epigenetic cause of HCC with clinical implications.

overall_design: To identify candidate downstream factors of SCARNA13, RNA-seq analysis was implemented for HCCLM3 cells with or without SCARNA13 knockdown.

first: T

first: X

last: Yan

first: L

last: Xu

first: H

last: Liao


title: Gene expression profiling of xenografts generated by lung metastasis screening models and HCCLM3 cells


title: Gene expression profiling of xenografts generated by lung metastasis screening models

overall_design: To identify ncRNAs involved in HCC metastasis, we grafted Hep3B and SK-Hep1 cells into nude mice and performed a screen of lung metastasis based on orthotopic implanted models in vivo. RNA-seq was conducted to compare the expression profiles between xenografts and parental HCC cells.


title: Cyprinus carpio RNA-seq in multiple tissues

city: Leiden

first: Christiaan

last: Henkel

address: Sylviusweg 72

department: Institute of Biology

institute: University Leiden

summary: We report RNA-seq data of several tissue types in the european common carp.

overall_design: RNA-seq data on several tissues in carp

first: Herman

last: Spaink


title: CNS lymphatic drainage and neuroinflammation are regulated by meningeal lymphatic vasculature

status: Public on Sep 18 2018

city: Charlottesville

first: Christopher

last: Overall

state: Virginia

address: 409 Lane Road

department: Neuroscience

institute: University of Virginia

summary: Neuroinflammatory diseases, such as multiple sclerosis, are characterized by invasion of the brain by autoreactive T cells. The mechanism for how T cells acquire their encephalitogenic phenotype and trigger disease remains, however, unclear. The existence of lymphatic vessels in the meninges indicates a relevant link between the CNS and peripheral immune system, perhaps affecting autoimmunity. Here we demonstrate that meningeal lymphatics fulfill two critical criteria: they assist in the drainage of cerebrospinal fluid components and enable immune cells to enter draining lymph nodes in a CCR7-dependent manner. Unlike other tissues, meningeal lymphatic endothelial cells do not undergo expansion during inflammation, and they express a unique transcriptional signature. Notably, the ablation of meningeal lymphatics diminishes pathology and reduces the inflammatory response of brain-reactive T cells during an animal model of multiple sclerosis. Our findings demonstrate that meningeal lymphatics govern inflammatory processes and immune surveillance of the CNS and pose a valuable target for therapeutic intervention.

overall_design: Lymphatic endothelial cells (LECs) were isolated from meninges, diaphragm and skin of adult male C57Bl6 mice. Cells were sorted according to the following phenotype: CD45-CD31+PDPN+

first: Antoine

last: Louveau

first: Jasmin

last: Herz

first: Maria

middle: N

last: Alme

first: Andrea

middle: F

last: Salvador

first: Michael

middle: Q

last: Dong

first: Kenneth

middle: E

last: Viar

first: Grace

last: Herod

first: James

last: Knopp

first: Joshua

last: Setliff

first: Alexander

last: Lupi

first: Sandro

last: Da Mesquita

first: Elizabeth

last: Frost

first: Alban

last: Gaultier

first: Tajie

middle: H

last: Harris

first: Rui

last: Cao

first: Song

last: Hu

first: John

middle: R

last: Lukens

first: Igor

last: Smirnov

first: Guillermo

last: Oliver

first: Jonathan

last: Kipnis


title: Protein kinase D1 deletion in adipocytes enhances energy dissipation and protects against adiposity

city: Wuerzburg

first: Martin

last: Eilers

address: Am Hubland

department: Chair for Biochemistry and Molecular Biology

institute: University of Wuerzburg

summary: DAG-activated Pkd1 promotes triglyceride accumulation in adipocytes; Pkd1 promotes lipogenesis and suppresses mitochondrial function in adipocytes in an AMPK-dependent manner; Pkd1 suppresses expression of genes characteristic for beige adipocytes; Deletion of Pkd1 in adipocytes protects mice from diet-induced obesity, T2D and liver steatosis.

overall_design: Gene expression changes in subcutaneous adipose tissue of mice after deletion of Pkd1.

first: Mona

last: Löffler

last: Mayer

last: Trujillo

first: Carsten

middle: P

last: Ade

first: Till

last: Karwen

first: Sudha

last: Janaki-Raman

first: Anja

last: Slotta

first: Rabih

last: El-Merahbi

first: Angel

last: Loza Valdes

first: Manuela

last: Erk

first: Nuria

last: Matesanz

first: Jorge

middle: L

last: Torres

first: Miguel

last: Marcos

first: Guadalupe

last: Sabio

first: Almut

last: Schulze

first: Grzegorz

last: Sumara


title: Super-enhancer-driven CCAT1 is co-activated by SOX2 and TP63 and promotes squamous cancer from esophagus, head and neck and lung [ChIP-seq]

status: Public on Sep 17 2018

first: Phillip

last: Koeffler

address: 14 Medical Drive

institute: Cancer Science Institute

summary: Squamous cell carcinomas (SCCs) are aggressive malignancies. Previous report demonstrated that the transcription factors TP63 and SOX2 exhibited overlapping genomic occupancy in SCCs. Our recent study have identified TP63 and SOX2 as super-enhancer-associated genes. However, functional consequences of their frequent co-localization at super-enhancers region remains unexplored. Here, ChIP-seq result indicated TP63 and SOX2 co-occupied peaks are significantly located the super enhancer region compare with unique of TP63 and SOX2 signaling, and combined RNA-seq analyses of different types of SCCs reveal that TP63 and SOX2 cooperatively regulate expression of the super-enhancer-associated the long non-coding RNA (lncRNA) gene, CCAT1. CCAT1 is highly expressed in SCCs compared to either other tumor types or normal tissues. CCAT1 expression strongly correlates with expression levels of TP63 and SOX2. Silencing of CCAT1 significantly reduces cellular growth both in vitro and in vivo, phenotyping the effect of silencing either TP63 or SOX2. Furthermore, ChIP-Seq and luciferase reporter assays demonstrate TP63 and SOX2 co-occupy the promoter and super-enhancer regions of CCAT1. Interaction of CCAT1 with TP63 and SOX2 are validated by RNA immunoprecipitation. In addition, ChIRP analysis suggests that CCAT1 regulates EGFR expression by binding to the super-enhancer of EGFR. Further investigations shows that CCAT1 activates both the MEK/ERK1/2 and PI3K/AKT signaling pathways through up-regulation of EGFR. In conclusion, CCAT1 is driven by master transcription factors TP63 and SOX2 and is recruited to the super-enhancer of EGFR, promoting SCC tumorigenesis through activation of the MEK/ERK1/2 and PI3K/AKT signaling pathways. These studies help to explain the pathogenesis of SCC and aids in providing novel therapeutic strategy.

overall_design: ChIP sequencing of H3K27Ac histone modifications,  TP63, and SOX2  binding occupancies in Esophageal Squamous Cell Carcinoma cell lines

first: Yan-Yi

last: Jiang

first: De-Chen

last: Lin

first: Yuan


title: Super-enhancer-driven CCAT1 is co-activated by SOX2 and TP63 and promotes squamous cancer from esophagus, head and neck and lung [RNA-seq]

overall_design: Gene Expression profile was measured following shRNA mediated knock down of TP63, SOX2, and CCAT1 in Esophageal Squamous Carcinoma Cell lines


title: Banana sRNAome and degradome identify microRNAs functioning in differential responses to temperature stress

city: GUANGZHOU

first: HONG

last: ZHU

state: GUANGDONG

address: 723 XINGKE RD.TIANHE DISDRICT

institute: SOUTH CHINA BOTANICAL GARDEN,CHINESE ACADEMY OF SCIENCES

summary: We report the high-throughput profiling of miRNAs in banana. By deep sequencing and computational and molecular analyses, we identify 113 known and 26 banana-specific miRNAs and we characterize their expression pattern under cold and heat stress. We find that 42 banana miRNAs are temperature-responsive. By degradome sequencing, we identify 60 targets for known miRNAs and half of these targets are regulated by 15 temperature-responsive miRNAs. The correlative expression patterns between several miRNAs and their target genes are further validated via qRT-PCR. Our results provide a foundation for understanding the miRNA-dependent temperature stress response in banana and the characterized correlations between miRNAs and their responses to cold or heat stress could serve as markers in the breeding programs or tools for biotechnological approaches for improving temperature stress tolerance of banana.

overall_design: Examination of miRNAs in banana peel tissue subjected to cold and heat stress.

first: Hong

last: Zhu


title: Dynamic remodeling of translation programs drives hepatocyte proliferation during liver regeneration

city: Urbana

first: Sushant

last: Bangru

state: Illinois

address: 600 S Mathews Avenue

department: Biochemistry

institute: University of Illinois, Urbana-Champaign

summary: During liver regeneration, most new hepatocytes arise from pre-existing ones; yet, the underlying mechanisms that drive these cells from quiescence to proliferation remain poorly defined. By using high-resolution transcriptome profiling of polysome fractions from purified hepatocytes isolated from quiescent and toxin-injured adult mouse livers,we uncover the mRNA transcripts regulated during liver regeneration. The translational remodeling modulates protein levels of a set of splicing factors including Epithelial splicing regulatory protein 2 (ESRP2), which activates an early postnatal splicing program in regenerating hepatocytes as well as metabolic genes.

overall_design: Hepatocytes were isolated in presence of Cycloheximide (CHX) from normal fed mice and DDC fed (4 week) mice. Polysomal fractions were separated over sucrose gradient and RNA was isolated from the three fractions Monosome (1 ribosome), Light polysome (2-4 ribosomes) and Heavy polysomes (>5).  Isolated RNA was subject to polyA selection and sequenced on an Illumina platform.

first: Auinash

last: Kalsotra

first: Waqar

last: Arif


title: Dynamic remodeling of mRNA splicing and translation programs drives hepatocyte proliferation during liver regeneration

summary: During liver regeneration, most new hepatocytes arise from pre-existing ones; yet, the underlying mechanisms that drive these cells from quiescence to proliferation remain poorly defined. By using high-resolution transcriptome profiling of purified hepatocytes isolated from quiescent and toxin-injured adult mouse livers,we uncover an overlap of regenerative response with developmental transcriptome programming. The translational remodeling modulates protein levels ofa set of splicing factors including Epithelial splicing regulatory protein 2 (ESRP2), which activates an early postnatal splicing program in regenerating hepatocytes. We find that regeneration-regulated exons are enriched within unstructured regions of proteins and frequently harbor amino-acid residues that can be post-translationally modified to influence protein-protein interactions.

overall_design: Hepatocytes were isolated from normal fed mice and DDC fed (4 week) mice. Additionally, hepatocytes were isolated from E18 livers wherein livers from approx. 8 E18 embryos were pooled to prepeare hepatocytes. From all samples total RNA was isolated and after polyA selection sequenced on an Illumina platform.


title: IL-7 receptor blockade in human PBMC

city: Nantes

first: Richard

last: Danger

address: 30 Boulevard Jean Monnet

institute: CHU Nantes - INSERM- Nantes Universite

summary: Targeting the expansion and survival of pathogenic memory immune cells is a promising therapy to prevent chronic autoimmune attacks. Interleukin-7 receptor α chain (IL-7Rα) genetic variation were repeatedly associated with susceptibility of several chronic autoimmune and inflammatory diseases. Interleukin-7 (IL-7) is as a critical survival factor for the maintenance of mature T lymphocytes and numerous studies in rodent suggest targeting the IL-7/IL-7Rα pathway holds promise for the treatment of autoimmune diseases or transplant rejection. In this study, we evaluated agonist and antagonist properties of different anti-IL7Rα mAbs recognizing different type of epitope. To determine if agonist/antagonist anti-IL7Rα mAbs could deliver effective agonist signals capable of modifying human T cells, we analyzed by RNA-based-next-generation sequencing (RNA-SEQ) the transcriptome of human PBMC incubated during 3,5 hours with a site-1 (IgG4 #1 or IgG1 #2) or site-1/2b (IgG4) mAbs in the presence or not of exogenous human IL-7 (5 ng/ml). Altogether, transcriptional analysis confirmed that, while site-1 and site-1/2b anti-human IL-7Rα mAbs shared similar antagonist properties, the two site-1 mAbs induced significant human PBMC transcriptional modification compatible with T-cell activation and inflammatory responses associated by the MAPK/ERK pathway.

overall_design: Human PBMC from seven independant healthy volunteers were incubated during 3,5 hours with a site-1 (IgG4 #1 or IgG1 #2) or site-1/2b (IgG4) mAbs  in the presence or not of exogenous human IL-7 (5 ng/ml).

first: Lyssia

last: Belarif

first: Caroline

last: Mary

first: Lola

last: Jacquemont

first: Nicolas

last: Degauque

last: Poirier


title: Super-enhancer-driven CCAT1 is co-activated by SOX2 and TP63 and promotes squamous cancer from esophagus, head and neck and lung


title: Targeted sequencing by a CRISPR-assistant target enrichment-sequencing (CATE-seq)

status: Public on Sep 15 2018

city: Nanjing

first: Xu

last: Xinhui

address: Sipailou 2#

institute: SEU

summary: Targeted sequencing of genome is essential to the basic biological research and biomedicine. Therefore, various targeted enrichment methods have been developed for this end, in which various hybridization-based methods have been most widely used. However, the current hybridization-based methods (both on solid or in solution) are still restricted by the intrinsic shortcomings of nucleic acid hybridization. In this study, by combining an engineered dCas9-sgRNA with widely used magnetic isolation, we developed a new strategy to enrich target genomic DNAs in high efficiency. In this strategy, target DNA was firstly specifically recognized and bound by a complex of dCas9 and capture sgRNA (csgRNA). The DNA-dCas9-csgRNA complex was then captured on magnetic beads through the annealing of elongated 3′ end of csgRNA with single-stranded capture oligonucleotides coupled on streptavidin-coated magnetic beads. We thus named the strategy as CRISPR-assistant target enrichment (CATE). The enriched DNAs can be analyzed by the next generation sequencing (NGS). We thus named the technique as CATE-seq. Used the technique, we successfully enriched 35 target exons of 6 genes in 6 cell lines by using 54 csgRNA. We found that the target genomic DNA fragments such as exons could be efficiently enriched and analyzed by CATE-seq. The technique has several significant advantages over the current hybridization-based methods, including high simplicity, specificity, sensitivity, and throughput. This study therefore provides a new powerful tool for targeted sequencing.

overall_design: we developed a new dCas9/sgRNA-based target enrichment technique by combining dCas9-sgRNA with magnetic separation. The 3′ end of sgRNA was redesigned to add a short capture sequence in complementary with a single-stranded capture oligonucleotide coupled on magnetic beads. The special sgRNA was named as capture sgRNA (csgRNA). The single-stranded capture oligonucleotides is anchored on the surface of magnetic beads by biotin-streptavidin interaction, in which the single-stranded capture oligonucleotide was modified by biotin and streptavidin was coated on the surface of magnetic beads. In order to enrich target DNA fragments from an input DNA library, the input DNA library was firstly incubated with the dCas9-csgRNA to form DNA-dCas9-csgRNA complex, which were them captured by the capture oligonucleotides-coupled magnetic beads via annealing of capture sequence of csgRNA with capture oligonucleotides. The captured DNA-dCas9-csgRNA complex can be easily isolated from input DNA library by a magnetic separation. The enriched DNA can be analyzed by next-generation sequencing. We named this technique as CATE-seq. We used this technique successfully enriched 35 exons of 6 genes in 6 cell lines, indicating the feasibility, reliability, specificity, and simplicity of the new target enrichment sequencing technique.

first: Xinhui

last: Xu

first: Qiang

last: Xia

first: Jinke

last: Wang


title: Genomic and transcriptomic responses to partial hepatectomy in the mouse liver (RNA-Seq)

status: Public on Sep 16 2018

city: Copenhagen

first: Leonor

last: Rib

address: Ole Maaløes Vej 5

country: Denmark

institute: University of Copenhagen

overall_design: C57/BL6 12-14 week old male mice were housed and entrained for two weeks on a  12 hrs on/12 hrs off feeding and dark-light cycle with food access between ZT12 and ZT24 (ZT0 is defined as  the time when the lights are turned on and ZT12 as the time when the lights are turned off). Negative control, sham control and post-PH liver samples were collected.

first: Dominic

last: Villeneuve

first: Viviane

last: Praz

first: Nouria

last: Hernandez

last: Guex

first: Herr

last: Winship


title: Transcriptome analysis of AGS cells infected with Helicobacter pylori P12

city: Berlin

first: Frithjof

last: Glowinski

state: Berlin

address: Chariteplatz 1

department: Molecular Biology

institute: MPI for Infection Biology

overall_design: Cultured AGS cells infected with wildtype H. pylori P12 for 2,5 h. 3 biological replicates (non-infected vs. infected)

first: Konstantin

last: Okonechnikov

first: Fernando

last: Garcia-Alcalde

first: Thomas

last: Meyer


title: Differential m6A, m6Am, and m1A Demethylation Mediated by FTO in Cell Nucleus and Cytoplasm

status: Public on Sep 14 2018

city: Chicago

first: zhike

last: lu

address: 5801 South Ellis Avenue

department: department of chemistry

institute: University of Chicago

summary: FTO, the first RNA demethylase discovered, mediates the demethylation of N6-methyladenosine (m6A), installed internally on messenger RNA, and N6,2′-O-dimethyladenosine (m6Am), occurring at the +1 position from the 5’ cap. Despite extensive recent research on FTO, its physiological impact on cellular processes has yet to be fully elucidated. Here, we demonstrate that the cellular distribution of FTO is distinct among different cell lines, which critically affects the access of FTO to different RNA substrates. FTO binds multiple RNA substrates, including mRNA, U6 RNA, and tRNA. It mainly targets internal m6A when located in the cell nucleus and preferentially demethylates m6Am when residing in the cytoplasm. The expression levels of transcripts containing internal m6A are associated with the alteration of the FTO more so than transcripts containing m6Am. We also discover that N1-methyladenosine (m1A) in tRNA is a main substrate of FTO, with the FTO-catalyzed demethylation of target tRNAs repressing protein synthesis. Collectively, FTO-mediated RNA demethylation affects both mRNA level and translation through distinct pathways.

overall_design: Profile the binding RNA of ALKBH1 by CLIP-seq in 3T3-L1 cells transfected with FLAG-tagged FTO. RNA-seq in HeLa cells transfected with FTO siRNA or control siRNA

first: Zhike

last: Lu

first: Fange

last: Liu

first: Jiangbo

last: Wei

first: Chuan

last: He


title: Cortical gene expression profiles in the forebrain-specific Foxp1 conditional knockout (cKO) mice at P0 and P7.

city: Dallas

first: Genevieve

last: Konopka

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

summary: Examination of 2 different developmental time points (P0 and P7) in the cortex of control and Foxp1 cKO mice.

first: Noriyoshi

last: Usui

first: Daniel

last: Araujo

first: Ashwinikumar

last: Kulkarni


title: Role of BET proteins in YAP/TAZ-dependent transcription [RNA-seq 1]

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

institute: University of Padova

summary: We performed RNA-seq experiments to identify YAP/TAZ target genes in triple negative breast cancer cells, and evaluate the relevance of BET proteins for their expression.

overall_design: Transcriptional profiling by RNA-seq of MDA-MB-231 cells transfected with YAP/TAZ siRNA, BRD(2-3-4) siRNAs, or treated with the BET inhibitor JQ1.

first: Mattia

last: Forcato

first: Giusy

last: Battilana

first: Francesca

last: Zanconato

first: Michelangelo

last: Cordenonsi

first: Stefano

last: Piccolo


title: Expression data from WT and rtcR, rtcB, and rsr mutant strains of Salmonella enterica serovar Typhimurium strain 14028S with and without 3mM mitomycin C

city: Athens

first: Anna

last: Karls

state: GA

address: 120 Cedar St

department: Microbiology

institute: Univeristy of Georgia

summary: We have shown that mitomycin C induces expression of the rsr-yrlBA-rtcBA operon in Salmonella Typhimurium in a manner that is dependent on the activator for this operon, RtcR.  As such, treatment with mitomycin C generates the ligand or other cellular conditions that activate RtcR and likely generates the substrates on which the components of this RNA repair operon act.  We performed an RNA-seq analysis on WT cells and cells with components of the RNA repair operon, or the activator of the operon, deleted with and without mitomycin C.  Changes in the transcriptome during mitomycin C between cells that do and do not express the RNA repair system were assessed.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium

overall_design: Data for 24 samples is provided.  Three biological replicates of the WT strain and rtcR, rtcB, and rsr mutant strains each with and without mitomycin C are included.

first: Christine

last: Hartman

first: David

middle: J

last: Samuels


title: Genomic and transcriptomic responses to partial hepatectomy in the mouse liver (ChIP-Seq)

first: Leonor

last: Rib

first: Dominic

last: Villeneuve

first: Viviane

last: Praz

first: Nouria

last: Hernandez

first: Nicolas

last: Guex

first: Herr

last: Winship


title: Role of BET proteins in YAP/TAZ-dependent transcription [ChIP-seq]

summary: We performed ChIP-seq experiments to investigate the role of BET proteins in YAP/TAZ transcriptional activity.

overall_design: BRD4, RNA pol II and H3K122ac ChIP-seq in MDA-MB-231 cells treated with vehicle (DMSO) or JQ1, or depleted of YAP/TAZ.


title: Interplay between Nsd1 and PRC2 demarcates regions of H3K27me2 and H3K27me3

city: Milan

first: Sri Ganesh

last: Jammula

address: Via Adamello 16

institute: IFOM-IEO

summary: The core Polycomb Repressor Complex 2 (PRC2) is composed of Ezh1/2, Suz12, Eed and is responsible for mediating both H3K27me2 and H3K27me3. However, the mechanisms by which PRC2 demarcates these two repressive modifications in the genome are unknown. In a functional screen, we identified the H3K36 dimethyltransferase Nsd1 as a modulator of PRC2-mediated di- and trimethylation of H3K27. ChIP-Seq analysis following the depletion of Nsd1 revealed a global reduction in H3K36me2 and an increase in H3K27me3 at sites previously marked by H3K27me2. We show that the H3K36me2 at H3K27me2 marks co-occupy regions and provide evidence that the presence of H3K36me2 functions to restrict the spatial distribution of Polycomb mediated H3K27me3 domains.

overall_design: Immuno-precipitation of formaldehyde cross-linked chromatin prepared from mouse embryonic stem cells transduced with shRNA targeting Nsd1 (pLKO.TRC1shNsd1.1 and pLKO.TRC1shNsd1.2) and non-targeting control shRNA (pLKO.TRC1shLuciferase). For H3K27me3, ChIP with spike-in using Drosophila melanogaster chromatin was performed.

first: Gundula

last: Streubel

first: Sri

middle: G

first: Adrian

last: Bracken

first: Diego

last: Pasini


title: Genomic and transcriptomic responses to partial hepatectomy in the mouse liver

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

overall_design: Refer to individual Series


title: Genome-wide mapping of histone marks at single-nucleosome resolution

city: La Jolla

first: Marcelo

last: Rivas

state: CA

address: 9500 Gilman Drive, MC 0412

department: Bioengineering

institute: University of California San Diego

summary: Histone post-translational modifications (PTM) encode much of genome's regulatory information. However, regular chromatin immunoprecipitation followed by sequencing (ChIP-seq) protocols trace histone PTM to genomic regions spanning several nucleosomes, making it difficult to study how different histone PTM combine within individual nucleosomes to regulate the genome. Here, we devised computational and statistical methods to map H3K4me3, H3K27Ac, H3K9me3, and H3K27me3 to individual nucleosomes using MNase digestion of chromatin coupled with ChIP-seq. A significant number of nucleosomes were marked by two or more of histone marks. Nucleosomes marked simultaneously by H3K4me3 and H3K27me3 were prevalent among bivalent domains compared to the genomic background whereas nucleosomes having the repressive marks H3K27me3 and H3K9me3 were enriched at the transcription staring site of highly active genes only if they were also co-localized with the activating mark H3K27Ac. Inclusion of alternatively spliced exons on the final mRNA is correlated with nucleosomes marked by H3K4me3, H3K27Ac, and H3K27me3, but is largely unaffected by nucleosomes marked by H3K9me3. Together, these findings reveal that combinatorial patterns of histone PTM within individual nucleosomes are fundamental to encode regulatory information.

overall_design: Four histone marks (H3K4me3, H3K27Ac, H3K27me3, and H3K9me3) were mapped at single-nucleosome resolution on mouse embryonic stem cells.

last: Rivas-Astroza

first: Shu

last: Xiao

first: Xiaoyi

last: Cao

first: Sheng

last: Zhong


title: Retinoic acid regulation of bone marrow-derived LCs

city: West Lafayette

first: Chang

last: Kim

state: IN

address: 725 Harrison St

department: Comparative Pathobiology

institute: Purdue

summary: This study investigates the impact of retinoic acid on Langerhans cell gene expression

overall_design: There are three groups of cells: wild type cultured LCs, Rara KO cultured LCs, and retinoic acid-treated LCs

first: Seika

last: Hashimoto-Hill

first: Suji

last: Im


title: Stem cell intrinsic nutrient sensing regulating diet dependent intestinal adaptation

status: Public on Sep 13 2018

city: Helsinki

first: Krista

last: Kokki

address: Viikinkaari 9, Biocenter 1, Institute of Biotechnology P.O.Box. 56

department: Department of Biosciences (Genetics)

country: Finland

institute: University of Helsinki

summary: The intestine is an organ with exceptionally high rate of cell turnover and perturbations in this process can lead to disease such as cancer or intestinal atrophy. Nutrition is a key factor regulating the intestinal cell turnover and has a profound impact on intestinal volume and cellular architecture. However, how the intestinal equilibrium is maintained in fluctuating dietary conditions is insufficiently understood. By utilizing the Drosophila midgut as a model, we reveal a novel nutrient sensing mechanism coupling stem cell metabolism with stem cell extrinsic growth signal. Our results show that intestinal stem cells (ISCs) employ the hexosamine biosynthesis pathway (HBP) to monitor nutritional status and energy metabolism. Elevated activity of the HBP promotes Warburg effect-like metabolic reprogramming, which is required for the reactivation of ISCs from calorie restriction-induced quiescence. Furthermore, the HBP activity is an essential facilitator for insulin signaling-induced intestinal growth. In conclusion, intestinal stem cell intrinsic nutrient sensing regulates metabolic pathway activities, and defines the stem cell responsiveness to niche-derived growth signals.

overall_design: Intestinal mRNA profiles of 7 days old mated females of UAS-mCD8::GFP, hsFLP; tub-GAL4/+; FRT82B tub-GAL80/FRT82B genotype kept in calorie-restriction +/- 0.1M D-acetylglucosamine for 24h.

first: Jaakko

last: Mattila

first: Ville

last: Hietakangas

first: Michael

last: Boutros


title: INDUCER OF CBF EXPRESSION 1 is a male fertility regulator impacting anther dehydration in Arabidopsis

city: Shanghai

first: Juan

last: Lin

address: 2005 Songhu Road

institute: Fudan University

summary: Our results show that ICE1 controls plant male fertility via impacting anther dehydration. The loss-of-function mutation in ICE1 gene in Arabidopsis caused anther indehiscence and decreased pollen viability as well as germination rate. Further analysis revealed that the anthers in the mutant of ICE1 (ice1-2) had the structure of stomium, though the epidermis did not shrink to dehisce. The anther indehiscence and influenced pollen viability as well as germination in ice1-2 were due to abnormal anther dehydration, for most of anthers dehisced with drought treatment and pollen grains from those dehydrated anthers had similar viability and germination rates compared with wild type. Accordingly, the sterility of ice1-2 could be rescued by ambient dehydration treatments. Likewise, the stomatal differentiation of ice1-2 anther epidermis was disrupted in a different manner compared with that in leaves. ICE1 specifically bound to MYC-recognition elements in the promoter of FAMA, a key regulator of guard cell differentiation, to activate FAMA expression. Transcriptome profiling in the anther tissues further exhibited ICE1-modulated genes associated with water transport and ion exchange in the anther. Together, this work reveals the key role of ICE1 in male fertility control and establishes a regulatory network mediated by ICE1 for stomata development and water movement in the anther.

overall_design: mRNA profiles of wild type (Col-0) and ice1-2 -/- Arabidopsis were generated by deep sequencing, in triplicate.

first: Donghui

last: Wei

first: Hu

last: Chen

first: Ye

last: Zheng


title: genome-wide mapping of FoxA target sites in human bladder cancer cells (RT4)

city: Cincinnati

first: Joo-Seop

last: Park

address: 3333 Burnet Avenue

institute: Cincinnati Children's Hospital Medical Center

summary: In order to identify direct target genes of FoxA1 in RT4 cells, we carried out genome-wide mapping of FoxA1.

overall_design: RT4 cells were cultured in McCoy 5A medium with 10% FBS. RT4 cells were crosslinked with 1% PFA and FoxA1 ChIP was performed by using anti-FoxA1 antibody (abcam, ab5089). Sequencing libraries were generated using Rubicon ThruPLEX DNA-Seq kit. Sequecning was performed using the Illumina HiSeq2500.

first: Eunah

last: Chung


title: Mixed-Effects Association of Single Cells Identifies an Expanded Effector CD4+ T Cell Subset in Rheumatoid Arthritis

city: Boston

first: Ilya

last: Korsunsky

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Brigham and Women's Hospital

summary: High dimensional single-cell analyses have improved the ability to resolve complex mixtures of cells from human disease samples; however, identifying disease-associated cell types or cell states in patient samples remains challenging due to technical and inter-individual variation. Here we present Mixed-Effects modeling of Associations of Single Cells (MASC), a reverse single cell association strategy for testing whether case-control status influences the membership of single cells in any of multiple cellular subsets while accounting for technical confounders and biological variation. Applying MASC to mass cytometry analyses of CD4+ T cells from the blood of rheumatoid arthritis (RA) patients and controls revealed a significantly expanded population of CD4+ T cells, identified as CD27- HLA-DR+ effector memory cells, in RA patients. The frequency of CD27- HLA-DR+ cells was similarly elevated in blood samples from a second RA patient cohort, and CD27- HLA-DR+ cell frequency decreased in RA patients who responded to immunosuppressive therapy. Mass cytometry and flow cytometry analyses indicated that CD27- HLA-DR+ cells were associated with RA. Compared to peripheral blood, synovial fluid and synovial tissue samples from RA patients contained ~5-fold higher frequencies of CD27- HLA-DR+ cells, which comprised ~10% of synovial CD4+ T cells. CD27- HLA-DR+ cells expressed a distinctive effector memory transcriptomic program with Th1- and cytotoxicity-associated features, and produced abundant IFNg and granzyme A protein upon stimulation. Thus MASC identified the expansion of a unique effector memory CD4+ T cell population in RA. We propose that MASC is a broadly applicable method to identify disease-associated cell populations in high-dimensional single cell data.

overall_design:
Transcriptional characterization of 7 CD4+ T Cell populations: Central Memory T cells (TCM), Naïve T cells (TN), Regulatory T cells (TReg), DR+27+ Effector T cells (DR+27+), DR+27- Effector T Cells (DR+27-), DR-27+ Effector T Cells (DR-27+), and DR-27- Effector T Cells (DR-27-)

***The submitter declares that the raw data will be made available in dbGaP (https://www.ncbi.nlm.nih.gov/gap) due to patient privacy concerns.

first: Chamith

last: Fonseka


title: Genome-wide identification of transcripts associated with SNHG10 by ChIRP-seq

status: Public on Sep 12 2018

city: Chengdu

first: Tian

last: Lan

address: No. 37 of Guoxue Lane

institute: West China Hospital

summary: Understanding the roles of ncRNAs in tumorigenesis and metastasis would establish avenues for the identification of diagnostic and therapeutic targets. We observed that lncRNA SNHG10 and its derived SCARNA13 were concomitantly upregulated in hepatocellular carcinoma (HCC) pulmonary metastases and associated with poor prognosis. Mechanistically, SCARNA13, modulated by SNHG10, facilitated the cell cycle and epithelial-mesenchymal transition (EMT) of HCC cells by promoting SOX9. SNHG10 served as a sponge for miR-150-5p and interacted with RPL4 mRNA to increase the expression and activity of c-Myb. Reciprocally, upregulated and hyperactivated c-Myb enhanced SNHG10 and SCARNA13 expression through regulating SNHG10 promoter activity, forming a positive feedback loop and continuously stimulating SCARNA13 expression. Our findings characterized a complex epigenetic cause of HCC with clinical implications.

overall_design: To identify mRNA species bound by SNHG10, we performed an ChIRP to pull down endogenous mRNAs associated with the SNHG10 and sequenced the retrieved RNA.

first: T

first: X

last: Yan

first: L

last: Xu

first: H

last: Liao


title: High-resolution liver cancer genomic profiling links etiology, epigenetic and mutation signatures

city: Melbourne

first: Assam

last: El-Osta

address: 75 Commercial Road

country: Australia

institute: Baker Heart and Diabetes Institute


title: High-resolution liver cancer genomic profiling links etiology, epigenetic and mutation signatures [RNA-Seq]

summary:
Purpose: This study unravel the mechanisms that link viral infection and cancer
Methods:Human HCC cell line and HCC liver FFPE samples from HCC patients from three etiology groups- HBV, HCV infection, or neither were taken to explore their genomic DNA in two aspects: The HCC genomic mutations within the exons of 224 candidate genes, frequently mutated in HCC, using SureSelect™ Target Enrichment System kit and the transient response of liver cells to HCV infection, in genome wide histone modifications and gene expression, as demonstrated by ChIP-Seq and RNA-Seq.
Results:Mutational signature was explored by high-resolution targeted sequencing that detected low-frequency passenger mutations in 64 HCC samples from three etiology groups – HBV, HCV, or other. We identified novel distinct etiology-dependent regional mutations signatures. To explore the link between genomic signature and genome wide chromatin organization we studied the epigenetic changes occur following HCV infection. We demonstrated that HCV infection induces epigenetic changes that persist as "epigenetic signature" following virus eradication and reprogram host gene expression. High mutation rate associated with HCV etiology correlated with HCV-induced changes in epigenetic markers leading to closed chromatin.
Conclusions:We present a new link between cancer causing mutagenesis, and increase in liver cancer predisposition in chronic HCV-infected individuals. The sequential events begin with HCV-specific epigenetic signature that in turn dictates a unique HCV-specific somatic mutational profile in HCC

overall_design: Huh-7.5 cells were infected with HCV and ChIP-seq (at least 3 biological replicates were conducted.) and RNA-seq (6 biological replicates ) were done, all compared to non infected cells

first: Meital

last: Gal-Tanamy

first: Izhak

last: Haviv


title: Next Generation Sequencing Analysis of gene expression profile in Dgcr8 conditional KO embryonic hearts

city: Beijing

first: Jie

state: Beijing

address: Tsinghua University

department: Basic Medical Sciences, School of Medicine

institute: Tsinghua University

summary:
Purpose: To compare the transcriptome of wild type and Mesp1Cre+/Dgcr8-/-  embryonic heart at embryonic stage E8.5 and E9.5
Methods: For mRNA analysis of embryonic heart during development, total RNA of E8.5 and E9.5 heart were extracted with TRIZOL, and 100ng total RNA was reverse transcribed and amplified by Smart-seq 2 protocol as described (Picelli et al., 2014). Duplicated biological samples were analyzed using Illumina HiSeq2500, Clean reads were mapped to mouse genome (mm9) using BWA software.
Results: Genes significantly differentially expressed in the CKO cardiac tube at E9.5 compared with wild type were identified.
Conclusions: Dgcr8 CKO caused important gene expression changes in E9.5 embryonic heart tube

overall_design: Perform RNA-seq of wild type and Mesp1Cre+/Dgcr8-/- embryonic heart at embryonic stage E8.5 and E9.5


title: Next Generation Sequencing Analysis of gene expression profile in E9.5 Mesp1Cre/+/Dgcr8-/- embryonic heart cells transfected with NC miRNA and miR-541 mimics

summary:
Purpose: To compare the E9.5 Dgcr8 conditional knockout embryonic heart cells transfected with NC miRNA and miR-541 mimics
Methods: In vitro cultured E9.5 Dgcr8 conditional KO  heart cells transfected with miR-541-5p and NC miRNA were extracted with TRIZOL 48hrs after transfection, and 10ng total RNA was reverse transcribed and amplified by Smart-seq2 protocol as described (Picelli et al., 2014). Duplicated biological samples were analyzed using Illumina HiSeqX10, Clean reads were mapped to mouse genome (mm9) using BWA software.
Results: Genes differentially expressed in  E9.5 Dgcr8 cKO embryonic heart cells transfected with NC miRNA and miR-541 were identified.
Conclusions: miRNA-541 significantly changes the gene expression profiles of E9.5 Dgcr8 cKO embryonic heart cells and promote the cardiac function

overall_design: Perform RNAseq of E9.5 Dgcr8 cKO embryonic heart cells transfected with NC miRNA and miR-541 mimics


title: High-resolution liver cancer genomic profiling links etiology, epigenetic and mutation signatures [ChIP-Seq]


title: Next Generation Sequencing Analysis of miRNA expression profile in E9.5 mouse embryonic heart

summary:
Purpose: To identify miRNA expresssion profiles in E9.5 mouse embryonic heart
Methods: Total RNA of E9.5 heart were extracted with TRIZOL, miRNA deep sequencing were performed in using Illumina Hiseq 2500, SE50 (RIBOBIO, http://www.ribobio.com/), producing over 10 million reads from each sample. Clean reads were mapped to mouse genome (mm9), using miRDeep2
Results: MiRNAs that were highly expressed in E9.5 embryonic heart were identified
Conclusions: Results provide insight into the role of miRNAs function in E9.5 embryonic heart development

overall_design: Perform miRNA sequencing in wild type E9.5 mouse embryonic heart