title: Recombinant humant thrombomodulin treatment against endotoxemia-induced acute respiratory distress syndrome (ARDS).

city: Gifu

first: Hideshi

last: Okada

address: 1-1 Yanagido

department: Emergency and Disaster Medicine

institute: Gifu University Graduate School of Medicine

summary: We made LPS induced ARDS model mice, and determined the effect of recombinant human thrombomodulin against ARDS.

overall_design: Following 16-h starvation, mice were intraperitoneally injected with LPS (20 mg/kg; MilliporeSigma, Burlington, MA), and in some assays, with saline or recombinant human thrombomodulin (rhTM; Asahi Kasei Pharma Corporation, Tokyo, Japan) at 3 and 24 h post-LPS injection. Total RNA was extracted from mouse lung 30h after LPS injection.


title: Caloric Restriction Triggers Anti-tumor Immunity via a Mechanism Involving NK Cells and Transcription Factor Eomesdermin

status: Public on May 01 2020

city: Beijing

first: xiong

last: wei

address: qinghuayuan street

country: China

institute: Tsinghua University

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Our work argues that CR treatment enhances tumor-extrinsic anticancer effect by metabolic and transcriptional regulation of ILC-1 subpopulation and function

overall_design: RNA-Seq, ChIP-Seq, ATAC-Seq data were generated with CR treated or mock WT as well as Eomes KO mice NK cells

first: Xiong

last: Wei


title: RNA-sequencing of Wild-type and Bmal1 KO M1 macrophages

status: Public on Apr 30 2020

city: Boston

first: Chih-Hao

last: Lee

state: Massachusetts

address: 665 Huntington Avenue, Bld. 1, room 406

department: Molecular Metabolism

country: USA

institute: Harvard T.H. Chan School of Public Health

summary: The goal of this study was to determine role of the circadian regulator Bmal1 in metabolic regulation in pro-inflammatory ("M1") activating by bacterial lipopolysaccharide.

overall_design: Wild-type ("WT") and myeloid-specific Bmal1 KO ("M-BKO") bone marrow-derived macrophages were primed with interferon gamma overnight and treated without or with lipolysaccharide for another 8 hours to induce M1 activation. N=3 biological replicates.

first: Ryan

middle: K

last: Alexander


title: RNA expression profiling in G-CCE cells with a knock down of MMTR or overexpression of the full length, N-terminal or C-terminal of MMTR

city: Seoul

first: Chul Geun

last: Kim

address: wangsimni-ro 222

department: Life Science

country: South Korea

institute: Hanyang University

summary: The goal of this study is to compare total RNA expression profiles among wild type, MMTR knock down, and overexpression of full length, C-terminal and N-terminal in G-CCE cells at d0 and d3 after differentiation. All cell lines were maintained in DMEM supplemented with 15% heat-inactivated fetal bovine serum (FBS; Gibco, 16141079), 1X MEM Non-Essential Amino Acids Solution (Sigma-Aldrich, M7145), 300 μM monothioglycerol (Sigma-Aldrich, M6145), 1X penicillin/streptomycin, and 1000 U/ml Leukima inhibitory factor (LIF, Sigma-Aldrich, ESG1107) in 0.1% gelatin coated cell culture dishes. To induce differentiation of G-CCE cell lines, Leukemia inhibitory factor (LIF) was eliminated from the culture media for 3 days. Total RNA was amplified and purified using the Ambion Illumina RNA amplification kit (Ambion, AMIL1791) to yield biotinylated cRNA according to the manufacturer’s instructions. Briefly, 550 ng of total RNA was reverse-transcribed to cDNA using a T7 oligo(dT) primer.750 ng of labeled cRNA samples were hybridized to each Mouse WG-6 expression v.2 bead array for 16-18 h at 58°C, according to the manufacturer's instructions (Illumina). Detection of array signal was carried out using Amersham fluorolink streptavidin-Cy3 (Invitrogen, SA1010) following the bead array manual. Arrays were scanned with an Illumina bead array Reader confocal scanner

overall_design: Duplicated RNA expression profiles of wild type, MMTR knock down of MMTR or overexpression of the full length, N-terminal or C-terminal of MMTR in G-CCE cells  were anlayzed using Illumina BeadStudio v3.2 (Illumina). Background correction was performed using the Affymetrix Robust Multi-array Analysis background correction model, variance stabilization was performed using log2 scaling, and gene expression normalization was calculated with the quantile method implemented in the lumi package of R-Bioconductor.

first: C

middle: G


title: The small-molecule flunarizine in spinal muscular atrophy patient fibroblasts impacts on the Gemin components of the SMN complex and RNA-binding proteins relevant to motor neuron diseases

city: 91400 Orsay

first: Florent

last: Dumont

state: Ile de France

address: 17 avenue des sciences

country: France

institute: Université Paris-Saclay

summary: The deficiency of Survival motor neuron (SMN) protein causes the motor neuron disease spinal muscular atrophy (SMA). One of the cellular hallmarks of motor neuron diseases is the reduction in number of nuclear bodies (NBs) positive for the SMN protein. Owing to its ubiquitous expression, the consequences of SMN reduction can be studied in SMA patient fibroblasts. In previous studies, we described the beneficial effects of flunarizine on SMN-positive NBs both in fibroblasts of SMA patients and in spinal motor neurons of an SMA mouse model. Given that nuclear bodies are involved in RNA metabolism, here the goals are to make a proof-of-concept that genes modulated by flunarizine at the RNA levels can be identified and confirmed at the protein levels in SMA patient fibroblasts. Indeed, RNA-Seq analysis reveals that TXNIP is the most reduced by a 4-hr flunarizine treatment of SMA patient fibroblasts. This result is confirmed by RT-qPCR. Moreover, immunoblot analyses also shows a marked reduction of TXNIP at the protein levels in flunarizine-treated SMA fibroblasts.

overall_design:
Examination of components of the SMN complex and RNA molecules modulated by flunarizine in immortalized type I SMA patient fibroblasts

*** Submitter declares raw files were lost. ***

first: Suzie

last: Lefebvre

first: Franck

last: Letourneur


title: Optic atrophy 1 controls human neuronal development by preventing aberrant nuclear DNA methylation

city: Oslo

first: Adnan

last: Hashim

state: Oslo

address: NCMM - Forskningsparken, House 1, 3rd Floor - Gaustadalléen 21

department: NCMM (Centre for Molecular Medicine Norway)

country: Norway

institute: UiO (University of Oslo)

summary: Gene expression analysis was performed to investigate the role of OPA1 in human neuronal development.

overall_design: High throughput sequencing of RNA samples isolated from human embryonic stem cell derived neural progenitor cells and neurons. Sequencing was performed 150 bp paired-end in an HiSeq 3000 instrument

first: Judith

last: Staerk

first: Safak

last: Caglayan


title: The characterization of Mediator12 and 13 as conditional positive gene regulators in Arabidopsis

status: Public on Apr 29 2020

first: Qikun

last: Liu

state: Beijing

address: Haidian District, 5 Yiheyuan Rd., Zonghekeyan BLDG, Rm 502

department: School of Advanced Agricultural Sciences

institute: Peking University

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

overall_design: Refer to individual Series


title: The characterization of Mediator12 and 13 as conditional positive gene regulators in Arabidopsis [ChIP-seq]

summary: Mediator is a multi-protein complex which facilitates the initial steps of gene transcription. Mediator 12 (MED12) and MED13 are components of a module that reversibly associates with the core Mediator complex, and both positively and negatively regulates gene expression. Here, in an Arabidopsis mutant screen for factors required for morc1 de-repressed gene expression, we identified MED12 and MED13 as positive gene regulators, both of which contribute broadly to morc1 de-repressed gene expression. Both MED12 and MED13 are preferentially required for the expression of genes lacking active chromatin marks, a chromatin signature shared with morc1 re-activated loci. We further discovered that MED12 tends to interact with genes that are responsive to environmental stimuli, including light and radiation. We demonstrate that the light-induced transient gene expression depends on MED12, and is accompanied by a concomitant increase in MED12 enrichment during induction. In contrast, the steady-state expression level of these genes showed little dependence on MED12, suggesting that MED12 is primarily required to aid the expression of genes in transition from non-active to active states.

overall_design: The dataset contain 50 RNAseq samples, and 51 ChIPseq samples. Plants are of different genetic backgrounds, which include col-0, morc1 mutant, ddc mutant, med12 mutant, med13 mutant, med12/morc1 mutant, med13/morc1 mutant, med13/ddc mutant, and MED12-complementing line. Each sample has 3-4 biological replicates.

first: Sylvain

last: Bischof

first: Steven

middle: E

last: Jacobsen


title: The characterization of Mediator12 and 13 as conditional positive gene regulators in Arabidopsis [RNA-seq]


title: Global transcriptomic analysis of Arabidopsis thaliana ecotype Columbia-0 subjected to magnesium deficiency

city: Bunkyo-ku

first: Keitaro

last: Tanoi

state: Tokyo

address: 1-1-1 Yayoi

department: Graduate School of Agricultural and Life Sciences

country: Japan

institute: The University of Tokyo

summary: Magnesium (Mg) is essential for many biological processes in plant cells and its deficiency causes yield reduction in crop systems. Low Mg status reportedly impacts on photosynthesis, sucrose partitioning and biomass allocation. However, earlier responses to Mg deficiency are scarcely described. Generally, symptoms of nutrient deficiency appear in specific ages of leaves. Therefore, we hypothesised that transcriptional responses to Mg deficiency are different depending on the ages of leaves, and performed a global transcriptomic analysis in two types of leaves; source and sink leaves of the model plant species Arabidopsis thaliana to reveal the earlier responses to Mg deficiency. The global transcriptomic study revealed that short-term Mg deficiency triggers the expression of defence response genes in sink leaves. In roots, although short-term Mg deficiency enhanced the Mg2+ uptake from the environmnet, transcriptional levels of genes encoding putative Mg2+ transporters in roots were unchanged, suggesting non-transcriptional regulation of Mg2+ uptake in roots.

overall_design: mRNA was extracted from mature (source) and expanding (sink) leaves of control and Mg-deficient Arabidopsis at days 3, 5 and 8 of Mg deprivation treatment and roots at day 3. Three to six biological replicates were selected based on the quality of RNA.

first: Takaaki

last: Ogura

first: Natsuko

middle: I

last: Kobayashi

first: Yasunori

last: Ichihashi

first: Arisa

last: Shibata

first: Ken

last: Shirasu

first: Tomoko

middle: M

last: Nakanishi


title: Transcriptomes analysis of peripheral blood mononuclear cell revealed the immune heterogeneity of bTB at different stages

status: Public on Apr 28 2020

first: Ting

last: Xin

address: No.2 Yuanmingyuan West Road

institute: Institute of Animal Sciences, Chinese Academy of Agricultural Sciences

summary: We investigated peripheral blood mononuclear cell (PBMC) transcriptomes in naturally M. bovis-infected cattle. PBMCs isolated from cattle with different infection statuses (i.e., nested PCR-positive (bTB PCR-P), nested PCR-negative (bTB PCR-N) M. bovis-infected cattle and healthy cattle) were treated with bovine purified protein derivative of bovine tuberculin (PPD-B) or phosphate-buffered saline (PBS) for 6 h. By RNA-Seq, we compared the transcriptomes of PPD-B-stimulated and -unstimulated (PBS-treated) PBMCs between the three groups. Numerous differentially expressed genes were identified following pair-wise comparison of different groups, with or without PPD-B stimulation (adjusted p < 0.05). RNA-seq data was confirmed by validating 14 known genes with qRT–PCR. Finally, data analysis revealed the immune heterogeneity of bTB at different stages which can improve the understanding of the molecular mechanisms in bTB progression.

overall_design: PBMCs mRNA profiles of nested PCR-positive  M. bovis-infected cattle, nested PCR-negative M. bovis-infected cattle and healthy cattle were generated by deep sequencing, in triplicate,  treated with PPD-B and PBS,  using an Illumina HiSeq 2000 system.

first: Lin

last: Jiang

first: Lichun

last: Fang


title: The transcriptional repressor Blimp-1/Prdm1 controls the maternal decidual response during pregnancy

city: Oxford

first: Arne

middle: Wyndham

last: Mould

state: Oxfordshire

address: Warneford Hospital

department: Psychiatry

country: United Kingdom

institute: Oxford University


title: ChIPseq analyses of BvgA in Bordetella pertussis

city: Lille

first: loic

last: coutte

address: 1 rue du Pr Calmette, U1019 INSERM

department: microbiology

institute: INSERM

summary: We examined the BvgA fixation on the genome of B. pertussis in different strains and culture conditions

overall_design: NextSeq 500 sequencine of ChIPseq samples obtained by the BvgA antibodies in different Bordetella pertussis strains and culture conditions

first: Coutte

last: Loic


title: Translational control of breast cancer plasticity

status: Public on Apr 27 2020

city: Edmonton

first: Laura

middle: Jiyoung

last: Lee

state: Alberta

address: 5-120 Katz Group Centre

department: Oncology

country: Canada

institute: University of Alberta

summary: Plasticity of neoplasia, whereby cancer cells attain stem-cell-like properties, is required for disease progression and represents a major therapeutic challenge. Hypoxia induces breast cancer cell plasticity and stem-cell-like phenotypes. Although this process is poorly understood, reports demonstrate that hypoxia induces the expression of stemness-factors including NANOG, SNAIL and NODAL. Moreover, both stem-cell-like phenotypes and elevated expression of stemness-factors have been linked to metastatic spread and chemoresistance. With the use of high through-put sequencing, we characterized the gene expression profiles of T47D breast cancer cells under normoxic and hypoxic conditions.

overall_design: Transcriptomic profiles of T47D breast cancer cells treated with hypoxia with normoixa controls were generated via high throughput sequencing. Three replicates were collected.

first: Michael

last: Jewer

first: Lynne-Marie

last: Postovit


title: GCN5 modulates salicylic acid homeostasis by regulating H3K14ac levels at the 5ʹ and 3ʹ ends of its target genes

city: Gif-sur-Yvette

first: Déborah

last: MANZA MIANZA

address: 630 Rue Noetzlin

institute: Institut des Sciences des Plantes - Paris Saclay

summary: The modification of histones by acetyl groups has a key role in the regulation of chromatin structure and transcription. The Arabidopsis thaliana histone acetyltransferase GCN5 regulates histone modifications as part of the Spt-Ada-Gcn5 Acetyltransferase (SAGA) transcriptional coactivator complex. GCN5 was previously shown to acetylate lysine 14 of histone 3 (H3K14ac) in the promoter regions of its target genes; however, its binding did not systematically correlate with gene activation and the mechanism by which GCN5 controls transcription thus remained unclear. To gain insight into GCN5 function, we fine-mapped its genome-wide binding sites and explored the effect of GCN5 loss-of-function on the expression of its target genes, finding that GCN5 has a dual role in the regulation of H3K14ac levels in their 5ʹ and 3ʹ ends. We found that the gcn5 mutation leads to a genome-wide reduction of H3K14ac in the 5ʹ end of some of the GCN5 targets, a phenomenon associated to   their down-regulated in the gcn5 mutant. By contrast, an increase of H3K14ac in the 3ʹ end was observed in GCN5 targets that are up-regulated in the gcn5 mutant, indicating that this protein plays a dual role in the control of H3K14ac levels and in the regulation of transcription. Furthermore, changes in H3K14ac levels in the gcn5 mutant correlated with changes in H3K9ac in a genome-wide fashion at both 5ʹ and 3ʹ ends, providing evidence for a molecular link between the deposition of these two histone modifications. Finally, we show that GCN5 participates in responses to biotic stress by repressing salicylic acid (SA) accumulation and SA-mediated immunity, highlighting the role of this protein in the regulation of the crosstalk between diverse developmental and stress-responsive physiological programs.

overall_design: Examination of 1 histone modification (H3K14ac) in two allelic mutants of GCN5 and wild-type control and target analysis of GCN5-GFP protein (2 replicates)

first: Soonkap

last: Kim

first: Sophie

last: Piquerez

first: Juan

middle: S

last: Ramirez-Prado

first: Alaguraj

last: Veluchamy

first: David

last: Latrasse

last: Manza-Mianza

first: Rim

last: Brik-Chaouche

first: Natalia

middle: Y

last: Rodriguez-Granados

first: Lorenzo

last: Concia

first: Thomas

last: Blein

first: Abdelhafid

last: Bendahmane

first: Catherine

last: Bergounioux

first: Martin

last: Crespi

first: Magdy

last: Mahfouz

first: Cécile

last: Raynaud

first: Heribert

last: Hirt

first: Vardis

last: Ntoukakis

first: Moussa

last: Benhamed


title: Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc-processing components during lymphangiogenesis

city: Huddinge

first: Lars

last: Muhl

address: Blickagången 6

department: MedH

country: Sweden

institute: Karolinska Institutet

summary: Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space, and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss-of-function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single-cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis

overall_design: single-cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single-cell RNA-sequencing

first: Guangxia

last: Wang

first: Yvonne

last: Padberg

last: Stehling

first: Christer

last: Betsholtz

first: Stefan

last: Schulte-Merker

first: Andreas

last: van Impel


title: Genome wide chromatin accessibilty changes associated with JUN expression in human normal and IPF lung fiborblasts

city: Stanford

first: Gerlinde

last: Wernig

state: CA

address: 265 Campus Drive

department: Pathology

institute: Institute for Regenerative Medicine and Stem Cell Research, Stanford University School of Medicine

summary: We found that JUN expression is increased in many human fibrotic diseases and that systemic induction of Jun in mice resulted in development of fibrosis of multiple organs. To identify the changes in chromatin accessibility associated with JUN, we worked with primary human fibrotic lung fibroblasts that have normal or Knock-out levels of JUN expression and performed ATAC-seq analysis in both of them. Meanwhile we also modified primary human normal lung fibroblasts with or without JUN over-expression induction, then processed ATAC-seq and ChIP-seq analysis.

overall_design: To confirm the key role of JUN in lung fibrosis process, chromatin accessibility and structure change profile in JUN gain-of-function and loss-of-function in primary human lung fibroblasts were evaluated by ATAC-seq and ChIP-seq using Nextseq 500.

first: Pablo

last: Domizi

first: Lu

last: Cui


title: Genome-wide open chromatin methylome profiles in colorectal cancer

status: Public on Apr 25 2020

city: Cheras

first: Nurul Syakima

last: Ab Mutalib

state: Kuala Lumpur

address: Jalan Yaacob Latiff

department: UKM Medical Molecular Biology Institute

country: Malaysia

institute: Universiti Kebangsaan Malaysia

summary: The methylome of open chromatins was investigated in colorectal cancer (CRC) to explore cancer-specific methylation and potential biomarkers. Epigenome-wide methylome of open chromatins was studied in colorectal cancer tissues using Infinium DNA MethylationEPIC assay. Differentially methylated regions were identified using the ChAMP Bioconductor. Our stringent analysis led to the discovery of 2187 significant differentially methylated open chromatins in CRCs. More hypomethylated probes were observed and the trend was similar across all chromosomes. Majority of hyper- and hypomethylated probes in open chromatin were in chromosome 1. Our unsupervised hierarchical clustering analysis showed that 40 significant differentially methylated open chromatins were able to segregate CRC from normal colonic tissues. Receiver operating characteristic analyses from the top 40 probes revealed several significant, highly discriminative, specific and sensitive probes such as OPLAH cg26256223, EYA4 cg01328892, and CCNA1 cg11513637, among others. OPLAH cg26256223 hypermethylation is associated with reduced gene expression in the CRC. This study reports many open chromatin loci with novel differential methylation statuses, some of which with the potential as candidate markers for diagnostic purposes.

overall_design: The Infinium DNA MethylationEPIC assay was performed on 24 CRC and normal adjacent colon from 12 patients according to the manufacturer’s specifications and the beadchips were scanned using iScan (Illumina, Inc., USA). The Illumina Infinium DNA MethylationEPIC assay examines the DNA methylation status of > 850,000 CpG dinucleotides distributed over the whole genome, including > 220,000 open chromatins.

first: Nurul

first: Muhiddin

last: Ishak

first: Rashidah

last: Baharudin

first: Learn

last: Lee

first: Nadiah

last: Abu


title: Integrative analysis of reference epigenomes in rice [ChIP-reChIP-seq]

city: Wuhan

first: Liang

last: Xie

state: Hubei

address: No.1,Shizishan Street

institute: Huazhong Agricultural University

summary: Approximately 73% of rice genomes were annotated with different epigenomic properties. Refinement of promoter regions using open chromatin and H3K4me3-marked regions provided insight into transcriptional regulation. Active and repressed histone modifications and the predicted enhancers varied largely across tissues, whereas inactive chromatin states were relatively stable. Further, we investigated the impact of genetic variants on epigenomic signals and gene expression. Together, these datasets constitute a resource for functional element annotation in rice and indicate the central role of epigenomic information in understanding transcriptional regulation.

overall_design: Here, we generated genome-wide profiling of five histone modifications and RNA polymerase II occupancy using an enhanced chromatin immunoprecipitation (eChIP) approach. By integrating chromatin accessibility, DNA methylation, and transcriptome datasets, we constructed comprehensive epigenome landscapes across various tissues

first: Lun

last: Zhao

first: Qing

last: Zhang


title: Intestinal gene expression analysis in response to maternal dietary resveratrol supplementation in pig

city: Harbin

first: Anshan

last: Shan

state: Heilongjiang

address: NO.600 Changjiang Street

department: Institute of Animal Nutrition

institute: Northeast Agricultural University

summary: Early weaning commonly results in gastrointestinal disorders, inflammation and diarrhea in infants and young animals. Resveratrol, a plant phenol, affords protection against inflammation and cancer.A porcine model was used to investigate the effects of maternal resveratrol supplementation on diarrhea, intestinal inflammation and intestinal morphology in offspring during weaning. The intestinal gene expression was measureed by RNA sequencing (RNA-seq) analysis. Results that weaning-associated intestinal inflammation and diarrhea in pig offspring were alleviated and intestinal morphology was improved by maternal resveratrol supplementation. In weaning piglets (21-day-old), RNA-seq showed that differentially expressed genes (DEGs) were enriched for T cell receptor, primary immunodeficiency, mitogen-activated protein kinase (MAPK) and Ras signaling pathway. In post-weaning piglets (28-day-old), RNA-seq showed that DEGs were enriched in the cytokine-cytokine receptor interaction pathway and pathways related to metabolism. This study provided insight into molecular mechanisms underlying the effects of maternal dietary resveratrol.

overall_design: Sows were bred with semen from a pool of Landrace boars and segregated into 2 dietary treatments 20 days after breeding as follows: 1) control sows were fed a corn-soybean meal basal diet (Con treatment), and 2) treatment sows were fed a basal diet supplemented with 300 mg/kg resveratrol for 20 days after breeding through gestation and lactation (Res treatment). After birth, piglets were cross-fostered within dietary treatment groups to standardize the litter size to range between 9 and 12 piglets. The piglets were weaned on day 21 of lactation. On the weaning day, the sows were removed from the piglets, while the piglets remained in the nursing pens for a week until day 28 to avoid the stress caused by a change in environment. The jejunum samples of weaning piglets (21-day-old) and post-weaning piglets (28-day-old) were collected for RNA-seq analysis. The weaning and post-weaning pigs from each treatment group were named Weaning-Con (W-Con), Weaning-Res (W-Res), Post-weaning-Con (PW-Con) and Post-weaning-Res (PW-Res), with a total of 12 samples with 3 biological replicates in each group for RNA-seq analysis.

first: Qingwei

last: Meng


title: Integrative analysis of reference epigenomes in rice [RNA-seq]


title: Histone variant H2A.Z regulates nucleosome unwrapping and CTCF binding in mouse ES cells

city: Shenzhen

first: Zengqi

last: Wen

state: Guangdong

address: No 66, Gongchang Road, Guangming District

department: School of Medicine

institute: Sun Yat-sen University

summary: Nucleosome is the basic structural unit of chromatin, and its dynamics plays critical roles in the regulation of genome functions. However, how the nucleosome structure is regulated by histone variants in vivo is still largely uncharacterized. Here, by employing Micrococcal nuclease (MNase) digestion of crosslinked chromatin followed by chromatin immunoprecipitation (ChIP) and paired-end sequencing (MNase-X-ChIP-seq), we mapped genome-wide unwrapping states of nucleosomes containing histone variant H2A.Z in mouse embryonic stem (ES) cells. We found that H2A.Z is enriched with unwrapped nucleosomes. Interestingly, the function of +1 H2A.Z nucleosome in transcriptional regulation is correlated with the unwrapping states. We further showed that H2A.Z nucleosomes adjacent the CTCF binding sites (CBS) may adopt an open conformation. We confirmed the unwrapping state of H2A.Z nucleosomes under native condition by re-ChIP of H2A.Z after CTCF CUT&RUN in mouse ES cells. Importantly, we found that depletion of H2A.Z results in increased CTCF binding, indicating dynamic competition between the unwrapped H2A.Z nucleosomal intermediates and CTCF at the CBS. Taken together, our results showed that histone variant H2A.Z regulates transcription and CTCF binding through modulating the nucleosome unwrapping.

overall_design: Chromatin was first crosslinked with formaldehyde, then digested with MNase and solubilized by minimal sonication. After Chromatin immunoprecipitation (ChIP), the ChIPed DNA was subjected to paired-end sequencing without size selection. The read pairs were mapped to the mouse reference genome (mm9) using Bowtie2, and only read pairs with mapping quality higher than 10 (mapq > 10) were retained for further analyses. We counted the frequency of the length of ChIPed DNA fragments per base pair from 0 to 200 bp to analyze the fragment length profiles of histones.


title: Sequencing to determine the effect of neuronal IL-1b receptor knockout on the stress effect of paired fighting social defeat in mice

status: Public on Apr 24 2020

city: Columbus

first: Damon

middle: Joseph

last: DiSabato

state: OH

address: 460 Medical Center Drive

institute: The Ohio State University

summary: Chronic stress contributes to the development of psychiatric disorders including anxiety and depression. Several inflammatory-related effects of stress are associated with increased interleukin-1 (IL-1) signaling within the central nervous system and are mediated by IL-1 receptor 1 (IL-1R1) on several distinct cell types. Neuronal IL-1R1 is prominently expressed on the neurons of the dentate gyrus, but its role in mediating behavioral responses to stress is unknown. We hypothesize that IL-1 acts on this subset of hippocampal neurons to influence cognitive and mood alterations with stress. Here, mice subjected to psychosocial stress showed reduced social interaction and impaired working memory, and these deficits were prevented by global IL-1R1 knockout. Selective deletion of IL-1R1 in glutamatergic neurons (nIL-1R1-/-), abundant in the hippocampus wherein the inflammatory-influenced effects were observed, abrogated the stress-induced deficits in social interaction and working memory. RNA-sequencing of microdissected hippocampi revealed that stress increased several canonical pathways (TREM1, NF-κ, complement, IL-6 signaling) and upstream regulators (INFγ, IL-1β, NF-κB, MYD88) associated with inflammation. The inductions of TREM1 signaling, complement, and leukocyte extravasation with stress were reversed by nIL-1R1-/-. Collectively, we show that stress-dependent IL-1R1 signaling in hippocampal neurons represents a novel mechanism by which inflammation is perpetuated and social interactivity and working memory are modulated.

overall_design: 2x2 design: control v. stress groups; WT and nIL-1R1 knockout genotypes

middle: J

first: Daniel

middle: P

last: Nemeth

first: Xiaoyu

last: Liu

first: Kristina

last: Witcher

first: Shane

last: O'Neil

first: Braedan

last: Oliver

first: Chelsea

last: Bray

first: John

middle: F

last: Sheridan

first: Jonathan

last: Godbout

first: Ning

last: Quan


title: Developmental trajectory of pre-hematopoietic stem cell formation from endothelium (scRNA-seq data set)

city: San Francisco

first: Qin

last: Zhu

address: 600 Minnesota Street

institute: UCSF

summary: To examine the cell and molecular transitions between endothelial (E), hemogenic endothelial (HE), and intra-arterial clusters (IAC) cells, and the heterogeneity of hematopoietic stem and progenitor cells (HSPCs) within the IACs, we profiled ~40,000 cells from the caudal arteries (dorsal aorta, umbilical, vitelline arteries) of embryonic day (E) 9.5 to 11.5 mouse embryos by single-cell RNA sequencing (scRNA-Seq). We identified a developmental bottleneck in endothelial to hematopoietic transition (EHT) and heterogeneity within the IAC population.

overall_design: Single cell RNA-Seq profiles of cells involved in endothelial to hematopoietic transition (EHT) from mouse embryos at embryonic day 9.5, 10.5, 11.5 and functional HSCs at E14.5.

first: Kai

last: Tan

first: Nancy

middle: A

last: Speck


title: A genome-scale map of DNA methylation turnover identifies site-specific dependencies of DNMT and Tet activity

city: Basel

first: Dirk

last: Schuebeler

address: Fabrikstrasse 24

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

type: Methylation profiling by high throughput sequencing

summary: DNA methylation is considered a stable epigenetic mark, yet methylation patterns can vary during differentiation and in diseases such as cancer. Local levels of DNA methylation result from opposing enzymatic activities, the rates of which remain largely unknown. Here we developed a theoretical and experimental framework enabling us to infer methylation and demethylation rates at 860,404 CpGs in the mouse genome.  Surprisingly, enzymatic rates can vary as much as two orders of magnitude between CpGs with identical steady-state measurements. Unexpectedly, de novo and maintenance methylation activity is reduced at transcription factor binding sites, while methylation turnover is elevated in transcribed gene bodies. Furthermore, we show that TET activity contributes substantially more than passive demethylation to establishing low methylation levels at distal enhancers. Taken together, our work unveils the first genome-scale map of methylation kinetics, revealing highly variable and context specific activity for the DNA methylation machinery.

overall_design: Analysis of DNA methylation dynamics in mouse embryonic stem cells

first: Paul

last: Ginno

first: Dimos

last: Gaidatzis

first: Angelika

last: Feldmann

last: Schübeler


title: The landscape of human m6A methylation

city: Guangzhou

first: Rui

last: Zhang

address: No. 135, Xingang Xi Road

summary: We compiled a comprehensive list of human m6A sites in cerebellum, frontal cortex, heart, kidney, liver, lung, muscle,spleen and testis.

overall_design: m6A-seq of mRNA from multiple human tissues. Replicate of each tissue is also included.

first: Hui

first: Xinrui

last: Shi

first: Tao

last: Huang


title: Lupus milieu favors the conversion of self-reactive CD8 T cells to IL-17 producing double negative T cells

city: Boston

first: George

middle: C

last: Tsokos

address: CLS-928, 3 Blackfan Circle

department: Rheumatology/BIDMC

institute: Harvard Medical School

summary: Mature double negative (DN) T cells are αβ T cells lacking CD4/CD8 coreceptors and expanded in patients with systemic lupus erythematosus (SLE). It is not known whether they display a narrow or expander TCR repertoire.

overall_design: Examination of TCR repertoire of CD4, CD8 and DN T cells from lupus prone MRL/lpr mouse

first: Hao

last: Li


title: Gene expression profile in Caco-2 cells upon co-treatment with lovastatin and selective AHR ligands

status: Public on Apr 23 2020

city: University Park

first: Gary

last: Perdew

state: PA

address: 309 LSB

department: Veterinary and Biomedical Sciences

institute: Pennsylvania State University

summary: We report high-throughput profiling of gene expression from human colon adenocarcinoma Caco-2 line. We profile mRNA in lovastatin-treated cells, and examine the effect of AHR ligands, SGA360 or SGA315. This study provides a framework for understanding transcriptional changes caused by SGA360 or SGA315 during upon lovastatin use.

overall_design: Examination of gene expression in Caco-2 cells under lovastatin treatment and in the presence of AHR ligands.

first: Gulsum

last: Muku

first: Ann

last: Kusnadi

first: Guray

last: Kuzu

first: Rachel

last: Tanos

first: Iain

last: Murray

first: Krishne

last: Gowda

first: Shantu

last: Amin

middle: H


title: Gene expression profile in human cumulus cells (CCs) during long-term in vitro culture

status: Public on Apr 22 2020

city: Poznań

first: Marcin

last: Ruciński

state: Wielkopolska

address: Święcickiego 6

department: Histology and Embryology

country: Poland

institute: Poznań University of Medical Sciences

summary:
In the ovarian follicle, maturation of the oocyte increases in the presence of somatic cells called cumulus cells (CCs). These cells form a direct barrier between the oocyte and external environment. Thanks to bidirectional communication, they have a direct impact on the oocyte, its quality and development potential. Understanding the genetic profile of CCs appears to be important in elucidating the physiology of oocytes. In this work, CCs were subjected to in vitro long-term culture. RNA was collected after 1, 7, 15 and 30 days of culture. Expression microarrays were used for analysis, which allowed to identify groups of genes characteristic for particular cellular processes.
In this study, we demonstrated the gene expression profile of long time primary cultured human cumulus cells.

overall_design: Human cumulus cells (CCs) were obtained from patients, aged 25-40 years, mean age 33.67 years ± 1.46 [SEM; standard error of the mean],, with diagnosed infertility. The cells were harvested after 24h, 7 days, 15 days and 30 days after begining of culture and submited to RNA isolation and microarray analisys.

first: Błażej

last: Chermuła

first: Wiesława

last: Kranc

first: Karol

last: Jopek

first: Maciej

last: Brązert

first: Piotr

last: Celichowski

first: Joanna

last: Budna-Tukan

first: Leszek

last: Pawelczyk

first: Małgorzata

last: Bruska

first: Bartosz

last: Kempisty


title: Regulation of histone H3 by the ubiquitin-conjugating enzyme UBE2K determines neurogenesis of human embryonic stem cells [ChIP-Seq]

city: Cologne

first: David

last: Vilchez

state: NRW

address: Joseph Stelzmann Strasse, 26

country: Germany

institute: CECAD - Cluster of Excellence

summary: We find that loss of UBE2K leads to accumulation of histone leading to increase in overall load for epigenetic marks and thus hindering differentiation.Our results provide a novel link between ubiquitination, histone regulation and hESC differentiation into neurons. To test whether UBE2K knockdown also induces enrichment of H3K9me3 marks at specific genes, we performed chromatin immunoprecipitation (ChIP)-sequencing assays of hESCs using an antibody to H3K9me3.

overall_design: We performed chromatin immunoprecipitation (ChIP)-sequencing using H3K9me3 antibody (Abcam, #8898, reported suitable for ChIP) comparing H9 hESCs expressing non-targeting (NT) shRNA with H9 hESCs expressing UBE2K shRNA.

first: Azra

last: Fatima

first: Dilber

last: Irmak

first: Alireza

last: Noormohammadi

first: Markus

last: Rinschen

first: Wojciech

last: Pokrzywa

first: Orsolya

last: Leidecker

first: Christina

last: Schindler

first: Víctor

last: Sánchez-Gaya

first: Isabel

last: Saez

first: Prerana

last: Wagle

first: Thorsten

last: Hoppe

first: Alvaro

last: Rada-Iglesias


title: Regulation of histone H3 by the ubiquitin-conjugating enzyme UBE2K determines neurogenesis of human embryonic stem cells [RNA-Seq]

overall_design: We performed RNAseq in pluripotent stem cells  to examine how changes in Ube2k levels change transcript levels. We have 6 samples in total:  3 replicate H9 ES cells expressing Nt shRNA +  3 replicates of H9 ES cells expressing Ube2k  shRNA#1


title: Colibactin DNA damage signature indicates mutational impact in colorectal cancer

city: Berlin

first: Thomas

last: Meyer

address: Chariteplatz 1

department: Molecular Biology

institute: Max Planck Institute for Infection Biology

summary: Colibactin, a potent genotoxin of Escherichia coli, causes DNA double strand breaks (DSBs). We investigated if colibactin creates a particular DNA damage signature in infected human cells. Genomic contexts of colibactin-induced DSBs were enriched for a distinct AT-rich hexameric sequence motif. A survey of somatic mutations at the colibactin target sites of several thousand cancer genomes revealed significant enrichment of the motif in colorectal cancers. Moreover, the exact break point location corresponded with mutational hot spots in these cancers corresponding to a distinct trinucleotide signature. This work provides evidence for a role of colibactin in the etiology of human cancer.

overall_design: Genome-wide and unbiased profiling of DNA double-strand breaks upon colibactin-positive (pks+)  and colibactin-negative (pks-) E.coli infection, as well as upon etoposide treatment and no-treatment using Breaks Labeling in Situ and Sequencing (BLISS)

first: Paulina

last: Dziubanska-Kusibab

first: Hilmar

last: Berger

first: Britta

last: Bouwman

first: Amina

last: Iftekhar


title: Transcriptome-wide Organization of Subcellular Microenvironments Revealed by ATLAS-Seq

city: Gainesville

first: Eric

last: Wang

state: FL

address: 2033 Mowry Road

department: Molecular Genetics and Microbiology

institute: University of Florida

summary: Subcellular organization of RNAs and proteins is critical for cell function, but we still lack global maps and conceptual frameworks for how these molecules are localized in cells and tissues. Here we introduce ATLAS-Seq, which generates transcriptomes and proteomes from detergent-free tissue lysates fractionated across a sucrose gradient. Proteomic analysis of fractions confirmed separation of subcellular compartments. Unexpectedly, RNAs tended to co-sediment with other RNAs in similar protein complexes, cellular compartments, or biological functions. With the exception of those encoding secreted proteins, most RNAs sedimented differently than their encoded protein counterparts. To identify RNA binding proteins potentially driving these patterns, we correlated their sedimentation profiles to all RNAs, confirming known interactions and predicting new associations. Hundreds of alternative RNA isoforms exhibited distinct sedimentation patterns across the gradient, despite sharing most of their coding sequence. These observations suggest that transcriptomes can be organized into networks of co-segregating mRNAs encoding functionally related proteins, and provide insights into the establishment and maintenance of subcellular organization.

overall_design: RNA profiles of 10-50% sucrose gradients from two wild type FVB mice (gradient1 and gradient2) were generated by deep sequencing, using an Illumina NextSeq

first: Danielle

last: Adekunle

middle: T


title: The role of lncRNA Lassie in endothelial cells

status: Public on Apr 21 2020

city: Amsterdam

first: Reinier

last: Boon

address: De Boelelaan 1117

country: Netherlands

institute: Amsterdam UMC

summary: The vascular endothelium forms a physical barrier between blood and the surrounding tissue. Its constant exposure to haemodynamic shear stress controls endothelial barrier function which is of major importance for vascular homeostasis. The role of long non-coding RNAs (lncRNAs) in this process remains elusive.   Here we identify the shear stress-induced lncRNA LASSIE (linc00520) as a stabilizer of adherens junctions (AJs) in endothelial cells (ECs), that is indispensable for normal endothelial barrier function and shear stress sensing. Silencing of LASSIE in ECs resulted in impaired cell survival, loss of cell-cell contacts and failure to align in the direction of flow. RNA affinity purification followed by mass spectrometry identified several junction proteins associated with LASSIE, including the endothelial adhesion protein PECAM-1 and intermediate filament (IF) protein nestin. Proteomic analysis of VE-cadherin-associated proteins showed that LASSIE silencing reduces VE-cadherin interaction with nestin and microtubule (MT)-associated cytoskeletal proteins. We confirmed that LASSIE silencing results in a decreased connection between VE-Cadherin and the cytoskeleton, resulting in loss of barrier function and shear stress sensing.  Together, this study identifies the shear stress-induced lncRNA LASSIE as a critical link between AJs and the IF cytoskeleton, which is indispensable for normal EC junction stabilization and shear stress sensing.

overall_design: 3 replicates human umbilical vein endothelial cells were transfected with control gapmeRs and, in parallel, 3 replicates human umbilical vein endothelial cells were transfected with gapmeRs targeting lncRNA Lassie

first: Laura

last: Stanicek


title: Regulation of histone H3 by the ubiquitin-conjugating enzyme UBE2K determines neurogenesis of human embryonic stem cells

first: David

last: Vilchez

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

overall_design: Refer to individual Series


title: Truncation of mutant huntingtin in knock-in mice via CRISPR-Cas9 uncovers exon1 huntingtin as a key pathogenic form

first: Su

last: Yang

address: Huangpu Avenue

institute: Jinan University

summary: It remains unknown how polyglutamine expansion in widely expressed proteins can cause selective neurodegeneration. In Huntington’s disease (HD), proteolytic processing generates toxic N-terminal huntingtin (HTT) fragments that preferentially kill striatal neurons. Considerable efforts have been devoted to investigating how HTT is cleaved and whether blocking its cleavage is therapeutically beneficial.  However, using CRISPR-Cas9 to truncate full-length mutant Htt in HD140Q knock-in (KI) mice, we found that exon1 Htt is stably present in the brain, regardless of truncation sites in full-length Htt.  This N-terminal Htt led to similar HD phenotypes and age-dependent Htt accumulation in striatum in different KI mice. Exon1 Htt is constantly generated but its selective accumulation in the striatum is caused by the age-dependent expression of striatum-enriched HspBP1, a chaperone inhibitory protein. Our findings suggest that tissue-specific chaperone function accounts for the selective neuropathology in HD and highlight therapeutic importance in regulating this function.

overall_design:
We performed RNAseq analysis using striatal tissues from WT, KI-96, KI-571 and KI-FL mice, which are different lines of HD KI mice.
KI-FL expresses full-length mutant Huntingtin, KI-571 expresses an N-terminal Huntingtin fragment, KI-96 expresses an N-terminal Huntingtin fragment shorter than KI-571.

Please note that the processed data columns T1_1 to T1_4 (in the processed_count_matrix.txt) should be disregarded.

first: Xiao-Jiang

last: Li


title: Genomewide nucleotide-resolution mapping of single-strand breaks and lesions by GLOE-Seq [MMS treatment]

city: Mainz

first: Helle

last: Ulrich

state: Germany

address: Ackermannweg 4

institute: Institute of Molecular Biology

summary: Numerous methods are available for the mapping of DNA lesions ranging from double-strand breaks (DSBs) to incorporated ribonucleotides. We now present a technology based on the Genomewide Ligation of 3’-OH Ends (GLOE-Seq) and an associated computational pipeline designed for single-stranded breaks (SSBs), but versatile enough to be applied to any lesion that is convertible into a free 3’-OH terminus. We demonstrate its applicability to the mapping of Okazaki fragments without prior size selection and detect biases and asymmetries in the distribution of spontaneous SSBs in budding yeast and human DNA.

overall_design: VI. Genomewide mapping of lesions in DNA following MMS damage in yeast GLOE-Seq was applied to samples of yeast genomic DNA isolated from cells challenged or not with 0.02% MMS, after treatment with hAAG and APE1 for conversion of alkylated bases to nicks. To map the endogenous repair intermediates, the same samples were not subjected to hAAG/APE1 treatment. Two replicates were used per condition.

first: Annie

last: Sriramachandran

first: Giuseppe

last: Petrosino

first: María

last: Méndez-Lago

first: Axel

last: Schäfer

first: Liliana

last: Batista-Nascimento

first: Nicola

last: Zilio

middle: D


title: Genomewide nucleotide-resolution mapping of single-strand breaks and lesions by GLOE-Seq [Human_Ligase_inactivation]

overall_design: V. Analysis of Okazaki fragments and global DNA single-strand breaks in human cells   DNA ligase-competent and -compromised HCT116 cells were subjected to GLOE-Seq analysis in two replicates each. Ligase-competent cells were used to map the genomewide distribution of DNA single-strand breaks. Cells with inactivated DNA Ligase 1 and 3 were used to map the distribution of Okazaki fragments.


title: Organ of Corti size is governed by Yap/Tead-mediated progenitor self-renewal

city: Los Angeles

first: Neil

last: Segil

address: 1425 san pablo st, BCC 503K

department: BCC

institute: University of Southern California

summary: We report on gene expression, chromatin accessibility, active histone marks distribution, and Tead DNA-binding in proliferating and postmitotic organ of Corti progenitor cells.

overall_design: Examination of gene expression (RNA-seq), chromatin accessibility (ATAC), histone modifications (CUT&RUN), and Tead-binding (CUT&RUN) in 2 cell types.

first: Ksenia

last: Gnedeva


title: single cell RNA-seq analysis of ovarian cancer ascites

city: Rehovot

first: Itay

last: Tirosh

address: Herzl 234

country: Israel

institute: WEIZMANN INSTITUTE OF SCIENCE

summary: To understand the cellular diversity within malignant ascites, we profiled ~11,000 single cells from 22 samples by Smartseq2 and by 10x.

overall_design:
Ascites samples were either depleted of CD45+ cells and profiled by 10x or sorted by EPCAM+CD24+ and profiled by SmartSeq2
Note from Submitter: We have difficulties in approving raw data submission of data from clinical patient samples to GEO or dbGAP and are therefore submitting at this point only the processed data and the metadata.  In parallel with the process of granting approval for raw data submission to dbGAP we are also using another repository to which we are allowed to deposit raw data (DUOS@broadinstitute.org).


title: Genome-wide nucleotide-resolution mapping of DNA replication patterns, single-strand breaks and lesions by GLOE-Seq

sample_organism:
Saccharomyces cerevisiae
Homo sapiens

platform_organism:
Saccharomyces cerevisiae
Homo sapiens


title: Genomewide nucleotide-resolution mapping of single-strand breaks and lesions by GLOE-Seq [UV treatment]

overall_design: III. Genomewide mapping of UV-induced pyrimidine dimers in yeast   GLOE-Seq was applied to samples of yeast genomic DNA isolated from unirradiated and UV-irradiated cultures (20 or 120 J/m2) after treatment with Endonuclease V and APE1 for conversion of the UV lesions to nicks. Control samples were not subjected to Endonuclease V/APE1 treatment. Two replicates were used per condition.


title: Genomewide nucleotide-resolution mapping of single-strand breaks and lesions by GLOE-Seq [CDC9 inactivation]

overall_design: IV. Mapping of Okazaki fragments in yeast   GLOE-Seq was applied to genomic DNA isolated from budding yeast under conditions of Cdc9 inactivation. A sample from a wild-type (ligase-competent) strain served as control.


title: Genomewide nucleotide-resolution mapping of single-strand breaks and lesions by GLOE-Seq [HO endonuclease]

overall_design: II. Mapping of 3'-ends of an HO-induced double-strand break   GLOE-Seq was used to map the 3'-ends of a DNA double-strand break introduced into the budding yeast genome by galactose-induction of the HO endonuclease. Samples from raffinose-grown cells served as controls. Two replicates were used per condition.


title: Expression data from HepG2-NTCP and Huh-106 cell lines

city: Strasbourg

first: Thomas

last: Baumert

address: 3 Rue Koeberle

institute: INSERM U1110

summary:
Microarray data to compare the gene expression in HepG2-NTCP and Huh-106 cell lines
Knowledge of HBV virus-host interactions is still limited. Here, we performed a genome-wide gain-of-function screen using weakly permissive Huh-106 cells to uncover novel HBV host factors.

overall_design: RNA was isolated from two different cell lines (HepG2-NTCP and Huh-106) performed in triplicates using Promega Relia Prep kit

first: Eloi

last: Verrier


title: Genomewide nucleotide-resolution mapping of single-strand breaks and lesions by GLOE-Seq [digestion]

overall_design: I. Method validation with yeast genomic DNA   GLOE-Seq was validated by mapping DNA single- and double-strand breaks generated by restriction or nicking endonucleases in yeast genomic DNA. The sensitivity of the method was assessed by dilution of nicked with untreated DNA at defined ratios. Benchmarking against other methods was performed by direct comparison to samples prepared by following the EndoSeq protocol. The genomewide distribution of single-strand breaks was analysed in samples of undigested genomic DNA, using control samples of randomly fragmented DNA for comparison. Two replicates were used per conditions, except for Nb.BsrDI-treated DNA (4 replicates) and EndoSeq samples (1 replicate).


title: Investigation on different small RNA expression of TT19 suppressors under anthocyanin induction condition (AIC) using Small RNA-seq

status: Public on Apr 20 2020

city: East Lansing

first: Erich

last: Grotewold

state: MI

address: 603 Wilson Road

institute: Michigan State University

type: Non-coding RNA profiling by high throughput sequencing

summary:
To investigate the functions of TRANSPARENT TESTA 19 (TT19) on anthocyanin accumulation and stabilization using forward genetic screening approach. EMS mutagenized tt19 mutant to screen tt19 mutant suppressors that could restore the anthocyanin accumulation and the causative mutations were identified as point mutations in the RDR6/SGS3/DCL4 siRNA biogenesis pathway using whole genome re-sequencing. The idea for RNA-Seq and small RNA-Seq analysis is to illustrate the connection between siRNA biogenesis, TT19, and anthocyanin restoration.

RNA's of 4 Arabidopsis lines (col-0, tt19 and two TT19 suppressors, all in  triplicate) which were under AIC (3% sucrose shaking four days under 24h light) for four days was extracted. Small RNA libraries were prepared by BGI company and sequenced using BGISEQ-500 as 50SE.

overall_design: The RNA of 12 samples from 4 Arabidopsis lines (col-0, tt19 and two TT19 suppressors,all in triplicate) was extracted from seedlings which had been under AIC for four days. An analysis of the small RNAs differential expression among col-0, tt19, and TT19 suppressors was performed.

last: Jiang


title: Investigation on different gene expression of TT19 suppressors under anthocyanin inducing conditions (AIC) using RNA-seq

summary: 24 samples of total RNA of 8 Arabidopsis lines (col-0, tt19, and six tt19 suppressors in triplicate) which were under AIC (shaking in 3% sucrose for four days under 24hrs of light)  was extracted. mRNA libraries were prepared by BGI company and sequenced BGISEQ-500 as 100PE.

overall_design:
24 samples of total RNAs from  8 Arabidopsis lines (col-0, tt19, and six tt19 suppressors with triplicate) which were under AIC for  four days was extracted. The gene differential expression among col-0, tt19, and tt19 suppressors was examined.
8 total genotypes: Col-0 is used as  wild type or control; tt19 is a T-DNA insertion line SALK_105779 (under Col-0 background) that knockout TT19 (At5g17220) function; and the six tt19 mutant suppressors are EMS mutagenized point mutation under tt19 background (which is SALK_105779 in Col-0).


title: Substrate Specificity of the TRAMP Nuclear Surveillance Complexes

city: Edinburgh

first: Clementine

last: Delan-Forino

address: Michael Swann Building 5.1, King's Buildings, Mayfield Road

institute: University of Edinburgh - WTCCB

summary: During nuclear surveillance, the RNA exosome functions together with the TRAMP complexes, which include the RNA helicase Mtr4 together with a RNA binding protein (Air1 or Air2) and a poly(A) polymerase (Trf4 or Trf5). To better determine how RNA substrates are targeted, we analyzed protein and RNA interactions by TRAMP components. Mass spectrometry identified three distinct TRAMP complexes formed in vivo. These complexes preferentially assemble on different classes of transcripts. Unexpectedly, on many substrates, including pre-rRNAs and pre-mRNAs, specificity was apparently conferred by Trf4 and Trf5. Clustering of mRNAs by TRAMP association showed co-enrichment for mRNAs with functionally related products, supporting the significance of surveillance in regulating gene expression. Comparison of the binding sites of TRAMP components with multiple nuclear RNA binding proteins revealed preferential colocalization of subsets of factors. On pre-mRNAs, ∆trf5 deletion caused reduced Mtr4 binding and RNA accumulation of Trf5 top targets.

overall_design: Cooperation of TRAMP cofactors was study combining CRAC and RNAseq approach. CRAC Samples were tagged (HTP for all except Sample4 which carry an Flag-Prescission-HIs6). Duplicate CRAC experiements were carried out on each protein. RNAseq was carried out on wt and ∆trf5 stains (4 and 3 repaeats respectively) using Lexogen SENSE mRNA kit standard protocol

first: Christos

last: Spanos

first: Juri

last: Rapsilber

last: Tollervey


title: Malaria parasites regulate intraerythrocytic development duration via serpentine receptor 10 to coordinate with host rhythms

city: Thuwal

first: AMIT

middle: KUMAR

last: SUBUDHI

state: Thuwal

address: Level4, Builiding, 2, KAUST

department: BESE

country: Saudi Arabia

institute: King Abdullah University of Science and Technology

summary: The intra-erythrocytic developmental cycle (IDC) of malaria parasites is synchronized with the time-of-day hosts feed, but the mechanism underpinning this coordination is unknown. Combining in vivo and in vitro approaches using rodent and human malaria parasites, we reveal that: (i) 57% of P. chabaudi genes exhibit 24 h “circadian” periodicity in expression; (ii) 58% of these genes lose rhythmicity when the IDC is out-of-synchrony with host rhythms; (iii) 6% of P. falciparum genes show circadian expression under free-running conditions; (iv) Serpentine receptor 10 (SR10) is circadian and disrupting it in rodent models shortens the IDC by 2-3 hours; (v) diverse processes, including DNA replication, the ubiquitin and proteasome pathways, are affected by disruption of SR10 and loss of coordination with host rhythms. Our results reveal that malaria parasites are at least in part responsible for scheduling their IDC, explaining the fitness benefits of coordination with host rhythms.

overall_design: Plasmodium falciparum II3 strain was maintained at 37°C, 5% O2 and 5% CO2 in AB+ human RBCs in RPMI 1640 medium containing Albumax II (Invitrogen) supplemented with 2mM L- glutamine. Culture medium was changed in every two days to avoid providing unknown 24 hour rhythmic cues that might be present in the culture medium. Cultures were routinely monitored by Giemsa’s solution-stained thin blood smears and synchronized by treating the cultures with 5% sorbitol (w/v) to kill any late stage asexual stages.  For time-series experiment mature segmented schizonts were isolated by centrifugation over cushions of 70% (v/v) isotonic Percoll (GE healthcare Life Sciences), washed twice with RPMI 1640 without Albumax and allowed to invade fresh RBCs for about two hours in a shaker maintained at 37°C . Following invasion, remaining schizonts were removed from the culture by overlaying the culture over cushions of 70% (v/v) isotonic Precool (GE healthcare Life Sciences). Pellet containing ~ two hours early ring stage infected RBCs and uninfected RBCs was then treated with 5% sorbitol (w/v) to kill the contaminating mature schizonts. Culture containing highly synchronous early ring stage parasites was then split into six-well plates. Over the course of 48 h, 1-2  mL of infected RBC culture was collected every two hours, media was removed by centrifugation for two minutes at 900g, and cells were lysed by adding 1 mL of TRIzol and immediately stored at -80°C deep freezer. The T0 time point was considered to be three hours after addition of Percoll cushion isolated segmented mature schizonts to the fresh RBCs.

first: Subudhi

last: Kumar

first: O

last: Aidan

first: Ramaprasad

last: Abhinay

first: Abkallo

last: Hussein

first: Kaushik

last: Abhinav

first: Ansari

middle: R

last: Hifzur

first: Mohamed

last: Alyaa

first: Rached

middle: B

last: Fathia

first: Kaneko

last: Osamu

first: Culleton

last: Richard

first: Reece

last: Sarah

first: Pain

last: Arnab


title: WT vs TNFAIP8 knockout enterocyte single cell RNA-Seq

city: Philadelphia

first: Michael

last: Gonzalez

state: Pennsylvania

address: 3535 Market St

department: Translational Medicine and Human Genetics

institute: University of Pennsylvania

summary: We compare wild type and TNFAIP8 ileal enterocytes by single cell RNA-Seq and find loss of TNFAIP8 results in increased numbers of Lgr5+ stem cells, goblet cells, and partially differentiated cells by gene signature analysis

overall_design: Examination of cell populations in WT vs TNFAIP8-/- ileums by single cell RNA-seq

first: Jason

last: Goldsmith

middle: V


title: Single cell analysis of murine fibroblasts identifies neonatal to adult switching that regulates cardiomyocyte maturation

city: Durham

first: Li

last: Wang

address: 111 T.W. Alexander Dr

institute: NIH

summary: Cardiac maturation lays the foundation for postnatal heart development and disease, yet little is known about the contributions of the microenvironment to cardiomyocyte maturation. By integrating single-cell RNA-sequencing data of mouse hearts at multiple postnatal stages, we construct cellular interactomes and regulatory signaling networks. Here we report switching of fibroblast subtypes from a neonatal to adult state and this drives cardiomyocyte maturation. Molecular and functional maturation of neonatal mouse cardiomyocytes and human embryonic stem cell-derived cardiomyocytes are considerably enhanced upon coculture with corresponding adult cardiac fibroblasts. Further, single-cell analysis of in vivo and in vitro cardiomyocyte maturation trajectories identify highly conserved signaling pathways, pharmacological targeting of which substantially delays cardiomyocyte maturation in postnatal hearts, and markedly enhances cardiomyocyte proliferation and improves cardiac function in infarcted hearts. Together, we identify cardiac fibroblasts as a key constituent in the microenvironment promoting cardiomyocyte maturation, providing insights into how the manipulation of cardiomyocyte maturity may impact on disease development and regeneration.

overall_design: Single cell RNASeq at multiple postnatal stages.

first: Fang

last: Yao

first: Zheng

last: Li


title: A critical role of fibroblast in cardiac maturation as revealed by single-cell RNA-Sequencing

summary: The mammalian postnatal heart undergoes orchestrated and systematic changes to culminate in functional maturation, yet little is known about the cellular and molecular foundations underlying these processes. Here, we reported a critical role of fibroblast in cardiac maturation as revealed by single-cell RNA-Sequencing, both in vivo and in vitro.We also identified the key ligands secreted by fibroblast that are involved in the regulation of cardiac maturation.

overall_design: RNA-Seq of mouse neonatal cardiomyocytes co-cultured with neonatal fibroblasts or adult fibroblasts; Single cell RNA-Seq of co-culture system of cardiomyocytes and fibroblasts

first: Yin


title: Prp5-Spt8/Spt3 Interaction Mediates a Reciprocal Coupling between Splicing and Transcription

status: Public on Apr 17 2020

city: Shanghai

first: Zhan

last: Ding

address: FengLin 300

institute: CAS Center for Excellence in Molecular Plant Science

summary: Transcription and pre-mRNA splicing are coupled to promote gene expression and regulation. However, mechanisms by which transcription and splicing influence each other are still under investigation. The ATPase Prp5p is required for pre-spliceosome assembly and splicing proofreading at the branch-point region. From an open UV mutagenesis screen for genetic suppressors of prp5 defects and subsequent targeted testing, we identify components of the TBP-binding module of the Spt–Ada–Gcn5 Acetyltransferase (SAGA) complex, Spt8p and Spt3p. Spt8Δ and spt3Δ rescue the cold-sensitivity of prp5-GAR allele, and prp5 mutants restore growth of spt8Δ and spt3Δ strains on 6-azauracil. By chromatin immunoprecipitation (ChIP), we find that prp5 alleles decrease recruitment of RNA polymerase II (Pol II) to an intron-containing gene, which is rescued by spt8Δ. Further ChIP-seq reveals that global effects on Pol II-binding is mutually rescued by prp5 mutant and spt8Δ. Inhibited splicing caused by prp5-GAR is also restored by spt8Δ. In vitro assay indicates that Prp5p directly interacts with Spt8p, but not Spt3p. We demonstrate that Prp5p’s splicing proofreading is modulated by Spt8p and Spt3p. Therefore, this study reveals that interactions between the TBP-binding module of SAGA and the spliceosomal ATPase Prp5p mediate a balance between transcription initiation/elongation and pre-spliceosome assembly.

overall_design: Examining the Pol II profile in WT and Spt8Δ strains with Prp5-WT or Prp5-GAR mutation at 16°C and 30°C

first: Wei

last: Shao

first: Charles

last: Query

first: Yong-Zhen

last: Xu


title: Malaria parasites regulate intraerythrocytic development duration via serpentine receptor 10 to coordinate with host rhythms [Dataset1]

first: AMIT

last: SUBUDHI

summary: The intra-erythrocytic developmental cycle (IDC) of malaria parasites is synchronized with the time-of-day hosts feed, but the mechanism underpinning this coordination is unknown. Combining in vivo and in vitro approaches using rodent and human malaria parasites, we reveal that: (i) 57% of P. chabaudi genes exhibit 24 h “circadian” periodicity in expression; (ii) 58% of these genes lose rhythmicity when the IDC is out-of-synchrony with host rhythms; (iii) 9% of P. falciparum genes show circadian expression under free-running conditions; (iv) Serpentine receptor 10 (SR10) is circadian and disrupting it in rodent models shortens the IDC by 2-3 hours; (v) diverse processes, including DNA replication, the ubiquitin and proteasome pathways, are affected by disruption of SR10 and loss of coordination with host rhythms. Our results reveal that malaria parasites are at least in part responsible for scheduling their IDC, explaining the fitness benefits of coordination with host rhythms.

overall_design: Ring stage sr10KO (clone A and B) and wild type P. chabaudi parasites were sub-inoculated into groups of four CBA mice each (1 x 106 parasitized RBCs per mouse) by intravenous injection at 20:30 hrs, day 0. Starting at 20:30 hrs on day 2 post-infection, blood smears were taken for both groups every three hours for 48 hrs producing a total of 17 time points. 20µl of blood were also collected via tail snip at these time points, washed in PBS and immediately treated with 500 uL TRIzol reagent and stored shortly at 4°C and for long term at -80°C. Total RNA was isolated from TRIzol treated samples according to the manufacturer’s instructions (Life Technologies). Strand-specific mRNA libraries were prepared from total RNA using TruSeq Stranded mRNA Sample Prep Kit LS (Illumina) according to the manufacturer’s instructions. Briefly, at least 100ng of total RNA was used as starting material to prepare the libraries. PolyA+ mRNA molecules were purified from total RNA using oligo-T attached magnetic beads. First strand synthesis was performed using random primers followed by second strand synthesis where dUTP were incorporated in place of dTTP to achieve strand-specificity. Ends of the double stranded cDNA molecules were adaptor ligated and the libraries amplified by PCR for 15 cycles. Libraries were sequenced on Illumina HiSeq 4000 platform with paired-end 100/150bp read chemistry according to manufacturer’s instructions. Data from 14 timepoints were anlyzed further

first: Amit

middle: K

last: Subudhi

first: Aidan

last: O’Donnell

first: Arnab

last: Pain

first: Richard

last: Culleton

first: Abhinay

last: Ramaprasad

first: Sarah

middle: E

last: Reece

first: Hussein

middle: M

last: Abkallo


title: Investigation on different gene and small RNA expression of TT19 suppressors under anthocyanin inducing conditions (AIC)

first: Erich

last: Grotewold

overall_design: Refer to individual Series


title: AGO-bound Mature miRNAs with an Exposed 3’ end are Oligo-uridylated by TUTs and Subsequently Degraded by DIS3L2

city: Frederick

first: Shuo

last: Gu

state: MD

address: 1050 Boyles Str. Building 560 Room 11-6B

institute: National Cancer Institute

summary: microRNAs (miRNAs) associating with Argonaute proteins (AGOs) regulate gene expression in mammals. miRNA 3' ends are subject to frequent sequence modifications, which have been proposed to affect miRNA stability. However, the underlying mechanism is not well understood. Here, by genetic and biochemical studies as well as deep sequencing analyses, we find that AGO mutations disrupting miRNA 3' binding are sufficient to trigger extensive miRNA 3’ modifications in HEK293T cells and in cancer patients. Comparing these modifications in TUT4, TUT7 and DIS3L2 knockout cells, we find that TUT7 is more robust than TUT4 in oligo-uridylating mature miRNAs, which in turn leads to their degradation by the DIS3L2 exonuclease. Our findings indicate a decay machinery removing AGO-associated miRNAs with an exposed 3' end. A set of endogenous miRNAs including miR-7 are targeted by this machinery presumably due to target-directed miRNA degradation.

overall_design: HEK293T cells and various KO cells with or without ectopic expression of miRNAs were subjected miRNA-Seq and isomiR profile analyses.

first: Acong

last: Yang

first: Xavier

last: Bofill-De Ros


title: Centromere locations and structure in Candida parapsilosis.

city: Dublin

first: Geraldine

last: Butler

address: Belfield, Dublin 4

department: School of Biomolecular and Biomedical Science

country: Ireland

institute: UCD Conway Institute

summary: Investigation of centromeres in the pathogenic yeast Candida parapsilosis, shows that the location of two centromeres are polymorphic within this species. The centromeres consist of large inverted repeats (IRs), surrounding unique sequences. New (neo) centromeres have emerged in one C. parapsilosis isolate even though the original CEN location is undamaged. The neocentromeres do not contain IRs, and have no obvious sequence features.

overall_design: Regions in the genome where the variant histone H3 (Cse4) binds in Candida parapsilosis were identified by chromatin immunoprecipitation (ChIP). Three copies of a 9 amino acid epitope from Human influenza hemagglutinin (HA), were introduced near the N terminus of both Cse4 alleles using CRISPR-Cas9 editing together with a synthetic repair template. The epitope was introduced into Cse4 twice independently in two different strains – C. parapsilosis CLIB214, which is the type strain, and C. parapsilosis 90-137, originally isolated from orbital tissue. We analysed ChIP signals per chromosome in the immunoprecipitated Cse4-HA strains, control input chromatin and control un-tagged strains, generating 10 samples.

first: Mihaela

last: Ola

first: Caoimhe

last: O'Brien

first: Aisling

middle: Y

last: Coughlan

first: Qinxi

last: Ma

first: Paul

last: Donovan

first: Kenneth

last: Wolfe


title: Malaria parasites regulate intraerythrocytic development duration via serpentine receptor 10 to coordinate with host rhythms [Dataset2]

first: AMIT

last: SUBUDHI

overall_design: Hosts were 6-8 weeks old female MF1 mice housed in groups of five at 21°C with food and drinking water supplemented with 0.05 % para-aminobenzoic acid (PABA, to supplement parasite growth) provided ad libitum. All experimental infections were initiated by intravenous injection of 1 x 107 P. chabaudi (clone AS) parasitized red blood cells. Parasites at ring stage were collected at ZT0.5 (08:00 GMT) from donor mice housed in standard LD light conditions (Lights ON 07:30; Lights OFF 19:30 GMT) and immediately used to infect two groups of experimental mice. One group (termed “matched”) were entrained to the same photoperiod as the donor mice, generating infections in which parasite and host rhythms were in the same phase. The other group (termed “mismatched”) were entrained to reverse light (Lights OFF 07:30 and Lights ON 19:30 GMT) resulting in infections in which the parasite is out of phase with the host by 12 hours. Samples were collected every three hours, over a period of 30 hours, from 09:00 GMT on day 4 to 15:00 GMT on day 5 post infection. This corresponds to a starting time of ZT1.5 for matched, and ZT13.5 for mismatched infections.

first: Amit

last: Subudhi

first: J

last: O’Donnell


title: Gut-Resident IL10+CX3CR1hi Macrophages Induce Tertiary Lymphoid Structures and IgA Response in Situ

city: Corvallis

first: Andrey

last: Morgun

state: OR

address: 1601 SW Jefferson Way

institute: Oregon State University

summary: Gut resident IL10+CX3CR1hi macrophages drive development of mucosal tertiary lymphoid structures that serve as ectopic site of the IgA response to enteric infection.

overall_design: RNA-seq data was obtained from different cell populations sorted from LB of control mice and mice infected with Salmonella enterica (SL1344) (day 5)

first: Milena

last: Bogunovic

first: Balázs

last: Koscsó


title: The Ccr4-Not complex monitors the translating ribosome for codon optimality

status: Public on Apr 16 2020

city: Tokyo

first: Yoshitaka

last: Matsuo

address: 4-6-1, Shirokanedai, Minato-Ku

department: IMSUT

institute: The University of Tokyo,

summary: Control of messenger RNA (mRNA) decay rate is intimately connected to translation elongation, but the spatial coordination of these events is poorly understood. The Ccr4-Not complex initiates mRNA decay through deadenylation and activation of decapping. We used a combination of cryo–electron microscopy, ribosome profiling, and mRNA stability assays to examine the recruitment of Ccr4-Not to the ribosome via specific interaction of the Not5 subunit with the ribosomal E-site in Saccharomyces cerevisiae. This interaction occurred when the ribosome lacked accommodated A-site transfer RNA, indicative of low codon optimality. Loss of the interaction resulted in the inability of the mRNA degradation machinery to sense codon optimality. Our findings elucidate a physical link between the Ccr4-Not complex and the ribosome and provide mechanistic insight into the coupling of decoding efficiency with mRNA stability.

overall_design: 2 replicates in 2 different strains.

first: Robert

last: Buschauer

first: Takato

last: Sugiyama

first: Ying

last: Chen

first: Najwa

last: Alhusaini

first: Thomas

last: Sweet

first: Ken

last: Ikeuchi

first: Jingdong

last: Cheng

first: Yasuko

last: Matsuki

first: Risa

last: Nobuta

first: Andrea

last: Gilmozzi

first: Otto

last: Berninghausen

first: Petr

last: Tesina

last: Becker

first: Jeff

last: Coller

first: Toshifumi

last: Inada

first: Roland

last: Beckmann


last: Matsuo

overall_design: 2 replicates in 2 different strains

first: Ying-Hsin


title: Effect of Dermatophagoides farinae extract and calcitriol on canine primary sublingual epithelial cells

status: Public on Apr 14 2020

city: Merelbeke

first: Michael

last: Pelst

address: Salisburylaan 133

country: Belgium

institute: Ghent University

summary: Application of allergens onto the sublingual epithelium is used to desensitize allergic individuals, a treatment known as sublingual immunotherapy. However, the response of sublingual epithelial cells to house dust mite allergen and potential tolerance-promoting adjuvants such as Toll-like receptor ligands and calcitriol has not been investigated. In order to study this, primary sublingual epithelial cells were isolated from dogs and cultured in vitro. After 24h incubation with Dermatophagoides farinae extract, TLR2 ligands (FSL-1, heat-killed Listeria monocytogenes, Pam3CSK4), a TLR3 ligand (poly I:C), a TLR4 ligand (LPS) and calcitriol (1,25-dihydroxyvitamin D3), viability of the cells was analyzed using an MTT test and their secretion of IL-6, IL-10, CXCL8 and TGF-β1 was measured by ELISA. Additionally, to evaluate its potential effect as an adjuvant, sublingual epithelial cells were incubated with calcitriol in combination with D. farinae extract followed by measurement of CXCL8 secretion. Furthermore, the effect of D. farinae and calcitriol on the transcriptome was assessed by RNA-sequencing. The viability of the sublingual epithelial cells was significantly decreased by poly I:C, but not by the other stimuli. CXCL8 secretion was significantly increased by D. farinae extract and all TLR ligands apart from LPS. Calcitriol significantly decreased CXCL8 secretion and co-administration with D. farinae extract reduced CXCL8 concentrations to levels seen in unstimulated sublingual epithelial cells. Although detectable, TGF-β1 secretion could not be modulated by any of the stimuli. IL-6 and IL-10 could not be detected at the protein nor at the mRNA level. It can be concluded that D. farinae extract and TLR ligands augment the secretion of the pro-inflammatory chemokine CXCL8, which might interfere with sublingual desensitization. On the other hand, CXCL8 secretion was reduced by co-application of calcitriol and D. farinae extract. Calcitriol therefore seems to be a suitable candidate to be used as adjuvant during sublingual immunotherapy.

overall_design: 5 biological replicates were analysed which were all subjected to 4 different conditions

first: Yannick

last: Gansemans


title: A functional link between miR-200a and ELK3 regulates the metastatic nature of breast cancer

city: Seongnam-si

first: Joo Dong

last: Park

state: Gyeonggi-do

address: 335, Pangyo-ro

department: Biomedical Science

institute: CHA University

summary: The ectopic expression of miR-200a impaired the migration and invasion of TNBC cells by reducing the expression level of the ELK3 mRNA. An analysis of differentially expressed genes showed that the control group - and miR-200a plus ELK3 group had similar genetic signatures that differed from that of the miR-200a alone group.

overall_design: the gene expression profiles of wild-type MDA-MB 231 cells with those that were transfected with miR-200a alone or miR-200a plus a plasmid expressing wild-type ELK3

first: Hyung-Keun

last: Kim

first: Joo


title: RNA-seq of WT and Stat3 cKO neural progenitors

city: SHENZHEN

first: Yixun

last: Su

state: GUANGDONG

address: 628 Zhenyuan Road

department: Research center

country: China

institute: The Seventh Affiliated Hospital, Sun Yat-sen University

summary: To identify STAT3-regulated genes during neural progenitor development.

overall_design: Neural progenitors were isolated from WT and STAT3 conditional KO (Nes-cre driven) brains at embryonic day 11 and 14. Cells were cultured in suspension for 3 days before total RNA isolation.

first: Chenju

last: Yi

first: Yi

last: Zhou


title: NRP histone chaperones promote the removal of histone variant H2A.Z

first: Zhenhui

last: Zhong

address: 610 Charles E Young Dr East

department: Department of Molecular, Cell and Developmental Biology

country: USA

institute: University of California, Los Angeles

summary: In eukaryotes, DNA wraps around histones to form nucleosomes, which are compacted into chromatin. DNA-templated processes, including transcription, require chromatin disassembly and reassembly mediated by histone chaperones. Additionally, distinct histone variants can replace core histones to regulate chromatin structure and function. Although replacement of H2A with the evolutionarily conserved H2A.Z via the SWR1 histone chaperone complex has been extensively studied, in plants little is known about how a reduction of H2A.Z levels can be achieved in plants. Here, we show that NRP proteins cause a decrease of H2A.Z-containing nucleosomes in Arabidopsis under standard growing conditions. nrp1-1 nrp2-2 double mutants show an over-accumulation of H2A.Z genome-wide, especially at heterochromatic regions normally H2A.Z-depleted in wild-type plants. Our work suggests that NRP proteins regulate gene expression by counteracting SWR1, thereby preventing excessive accumulation of H2A.Z.

overall_design: In Arabidopsis, NRP proteins have been implicated in several biological processes, including cell-cycle control, root meristem formation, heat tolerance, DNA repair, somatic homologous recombination, and genome defense under genotoxic stress. NRP proteins are localized mainly in the nucleus and bind H2A, H2B, H3, and H4 histones. However, a molecular mechanism for these proteins has not been clearly established.

first: Israel

last: Ausin


title: Hi-C profiling of B-cell progenitors from Erg KO and WT mice

city: Parkville

first: Gordon

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

summary: Hi-C was used to examine long range chromatin interactions in B cell progenitors in the presence and absence of the Erg transcription factor. Specifically, OP9 cultured B220+ B-cell progenitors derived from the bone marrow of Rag1CreT/+;ErgΔ/Δ mice and from Rag1CreT/+ and Rag1Cre+/+;Erg fl/fl  control mice were isolated and DNA interactions were profiled by in situ Hi-C.

overall_design: Hi-C profiling was performed for two biological replicates of progenitor B-cells from each of the three mouse genotypes: Rag1CreT/+;ErgΔ/Δ, Rag1CreT/+ and Rag1Cre+/+;Erg fl/fl.

first: Hannah

last: Coughlan

first: Ashley

last: Ng


title: Variation of human neural stem cells generating organizer states in vitro before committing to cortical excitatory or inhibitory neuronal fates

status: Public on Apr 15 2020

city: New haven

first: Nenad

last: Sestan

state: CT

address: 333 Cedar street

department: Neuroscience

institute: Yale University

summary: Systematic analysis of the earliest patterning events that generate the major neuronal trajectories of the human telencephalon.

overall_design: single-cell RNA-sequencing profiling of E77 and E78 macaque Visual cortex (V1)

first: Nicola

last: Micali

first: Shaojie

last: Ma


title: Immune-Related Gene Expressions in EOC using Nanostring analysis

status: Public on Apr 10 2020

city: BUSAN

first: Kyungbin

address: 179, Gudeok-ro

country: South Korea

institute: Pusan National University Hospital

summary: Gene expression of HGSC according to chemotherapeutic response was analyzed using Nanostring nCounter PanCancer Immune Profiling Panel.

overall_design: All 12 EOCs patients were divided into chemosensitive (6 cases) and chemoresistant (6 cases) groups and difference of gene expression between the groups was analyzed using customized 770 gene NanoString Panel.

first: Kyung Un

last: Choi


title: A multiple reporter protein tolerant mouse model

status: Public on Apr 12 2020

city: Amsterdam

first: Kaspar

last: Bresser

address: Plesmanlaan 125

department: Hematopoeisis

institute: Sanquin

summary: We report the generation of a novel mouse strain that is immunologically tolerant to exogenously introduced reporter proteins ('Tol' strain). As a control, we test whether any transcriptomic changes can be observed between the Tol strain and wild-type littermate. This is tested for thymus, cerebrum and cerebellum.

overall_design: Examination of transcriptomes of 3 different tissues from mice from 2 genotypes.

first: K

first: F

last: Dijkgraaf

first: Ton

middle: N

last: Schumacher


title: The role of Erg in B cell development (RNA-Seq)

city: Melbourne

first: Melissa

last: Davis

state: Victoria

address: 1G Royal Parade

department: Bioinformatics Division

summary: RNA-seq of pre-proB, proB and preB populations from Ergfl/fl bone marrow, pre-proB cell population from Rag1CreT/+;ErgΔ/Δ bone marrow

overall_design: Two biological replicates of each primary B-cell progenitor population were purified from bone marrow of the specified genotypes using flow cytometry sorting. Transcriptomic profiling was undertaken on purified populations.

first: Soroor

last: Hediyeh-Zadeh


title: The role of Erg in B cell development (ChIP-Seq)

summary: ChIP-seq of B-cell progenitors and Rag1CreT/+;ErgΔ/Δ thymocytes for Erg transcription factor

overall_design: ChIP-seq for Erg on B220+ purified B-cell progenitors isolated after culture on OP9 stromal cells with IL7, SCF and FL and Rag1CreT/+;ErgΔ/Δ thymocytes


title: Single cell transcriptomics reveals opioid usage evokes widespread suppression of antiviral gene program

city: Boston

first: Christine

last: Cheng

state: Massachusetts

address: 24 Cummington Mall

institute: Boston University

summary: We report scRNA-seq of in vitro morphine treated PBMCs reveals suppression of anti-viral genes in various immune cell types.

overall_design: PBMCs were treated in vitro with morphine for 24 hours, followed by LPS stimulation for 3 hours in vitro. We have used an antibody-based cell hashing technique to multiplex samples in droplet based scRNA-seq.

first: Tanya

last: Karagiannis

first: John

last: Cleary Jr


title: Dynamic landscapes and regulome of mRNA structure during zebrafish early embryogenesis

city: Beijing

first: Jinsong

last: Zhang

state: Beijing

department: Life Science

institute: Tsinghua University

summary: We resolved the RNA secondary structure during zebrafish early embryogenesis based on  in vivo click selective 2'-hydroxyl acylation and profiling experiment (icSHAPE). We analyzed the RNA structure dynamics among different development stages.  Also, we studied which factors regulate maternal gene decay by RNA structure switch.

overall_design: icSHAPE of 12 samples from zebrafish embryos at six different early development stages and 4 samples from Elavl1a deficient zebrafish embryos at sphere and shield stages, including two treated with DMSO as control and two treated with NAIN3 for each stage or condition. RNA-seq of 6 samples from zebrafish embryos at 2, 4, 6 h.p.f. and 4 samples from Elavl1a deficient zebrafish embryos at 4 and 6 h.p.f. including two biological replicates. iCLIP-seq of 4 samples from flag-elavl1a mRNA injected zebrafish embryos at 4 and 6 h.p.f. including two biological replicates.

first: Boyang

last: Shi

first: Jian

last: Heng

first: Jing

last: Gong

first: Feng

last: Liu

first: Qiangfeng

first: Yun-gui

last: Yang


title: The Mi-2 nucleosome remodeler and the Rpd3 histone deacetylase are involved in piRNA-guided heterochromatin formation

first: Kaoru

last: Sato

address: 35-2 Sakae-cho, Itabashi-ku

country: Japan

institute: Tokyo Metropolitan Institute of Gerontology

summary: In eukaryotes, trimethylation of lysine 9 on histone H3 (H3K9) is associated with transcriptional silencing of transposable elements (TEs). In drosophila ovaries, this heterochromatic repressive mark is thought to be deposited by SetDB1 on TE genomic loci after the initial recognition of nascent transcripts by PIWI-interacting RNAs (piRNAs) loaded on the Piwi protein. Here, we show that the nucleosome remodeler Mi-2, in complex with its partner MEP-1, forms a subunit that is transiently associated, in a MEP-1 C-terminus-dependent manner, with known Piwi interactors, including a recently reported SUMO ligase Su(var)2-10. Together with the histone deacetylase Rpd3, this module is involved in the piRNA-dependent TE silencing, correlated with H3K9 deacetylation and trimethylation. Therefore. drosophila piRNA-mediated transcriptional silencing involves three epigenetic effectors, a remodeler, Mi-2, an eraser, Rpd3 and a writer, SetDB1, in addition to the Su(var)2-10 SUMO ligase.

overall_design: Transcriptome-wide examination of gene expression changes  in Piwi, Mi-2, Rpd3-depleted OSCs. Knockdowns of Piwi, Mi-2, and Rpd3 were treated for 4 days in OSCs. siEGFP was used as a control. Isolated total RNAs were analyzed by deep sequencing using Illumina HiSeq 2500. Sequences were mapped to dm6 Drosophila genome, and then FPKMs were calculated.  Upon depletion of Mi-2 and Rpd3 in OSCs, Piwi-targeted transposons were derepressed.

first: Bruno

last: Mugat

first: Simon

last: Nicot

first: Carolina

last: Varela-Chavez

first: Christophe

last: Jourdan

first: Eugenia

last: Basyuk

first: François

last: Juge

first: Mikiko

last: Siomi

first: Alain

last: Pélisson

first: Séverine

last: Chambeyron


title: High-resolution single cell RNAseq of ALK3-expressing human pancreatic ductal cells

city: Miami

first: Juan

last: Domínguez-Bendala

address: 1450 NW 10th Ave Miami

department: Department of Surgery

institute: Diabetes Research Institute, University of Miami, Miller School of Medicine

summary: Purpose: We demonstrate here that human pancreatic ductal cells within the exocrine pancreas have multiple cell type populations. Flow cytometry and live-cell sorting of ALK3bright+ cells enabled transcriptomics analysis at the single cell level. Methods: Live CD90-/ALK3bright+ cells from 3 non-diabetic human donors were sorted and cryopreserved. After cryopreservation and dead cell removal, we performed single-cell cDNA library construction using the 10X Genomics microfluidics platform, utilizing the chromium single cell 3’ v2 chemistry kit. Single cell libraries were sequenced on an Illumina sequencing platform with 10X Genomics recommended parameters. After sequencing, data was converted to filtered read counts via the 10X Genomics Cellranger v3.0.2 software. Filtered gene counts were then utilized for downstream analysis using the Seurat scRNAseq analysis package. Conclusions: Our research presents the first detailed analysis at the single-cell level of ALK3-expressing ductal cells isolated from the human exocrine pancreas. This study reveals heterogeneity across the human ductal compartment, with certain sub-populations of ductal cells exhibiting progenitor-like characteristics. These data also demonstrate plasticity across the exocrine pancreas, which is donor-dependent. Overall, this study furthers our understanding of pancreatic biology at the single cell level.

overall_design: Single cell RNA sequencing analysis of human exocrine pancreas-derived CD90-/ALK3bright+ cells.

first: Fahd

last: Qadir

last: Dominguez-Bendala

first: Ricardo

middle: L

last: Pastori


title: Dynamics of the 4D genome during in vivo lineage specification and differentiation

status: Public on Apr 13 2020

city: Oxford

first: A Marieke

last: Oudelaar

address: John Radcliffe Hospital

department: MRC Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

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

overall_design: Refer to individual Series


title: KAT3-dependent acetylation of cell type-specific genes maintains neuronal identity in the adult mouse brain

city: Sant Joan d'Alacant

first: Angel

last: Barco

state: Alicante

address: Av. Santiago Ramón y Cajal

country: Spain

institute: Instituto de Neurociencias (UMH-CSIC)

summary: The acquisition of neuronal identity requires the coordinated action of transcription factors and chromatin-modifying enzymes. However, little is known about the mechanisms that are responsible for maintaining neuronal identity throughout life. The paralogous lysine acetyltransferases CBP and p300 are both essential during development, but their specific function in postmitotic neurons remains unclear. Here, we show that when both KATs are simultaneously knocked out in excitatory neurons of the mouse adult brain, the mice express a rapidly progressing neurological phenotype. This phenotype is associated with a loss of physiological, morphological and transcriptional features defining excitatory neuron identity. This correlates with a dramatic loss of H3K27 acetylation and occupancy by pro-neural transcription factors at neuron-specific genes and enhancers. Restoring CBP expression or lysine acetylation restitutes neuronal-specific gene expression. These experiments demonstrate that CBP and p300 are jointly necessary for maintaining neuronal identity and function by preserving correct chromatin acetylation levels in the adult brain.

overall_design:
ChIP-seq for CBP and p300 in the hippocampus of inducible and forebrain excitatory neuron-restricted knockouts for Crebbp (CBP-ifKO), Ep300 (p300-ifKO or both proteins (dKAT3-ifKO), and their controls.
mRNA-seq in the hippocampus of dKAT3-ifKOs and controls.
ATAC-seq in forebrain excitatory neurons of dKAT3-ifKOs and controls.
ChIP-seq for H3K27ac and H3K9,14ac in the hippocampus of dKAT3-ifKOs and controls.
Single nucleus (sn)RNA-seq in the hippocampus of dKAT3-ifKOs and controls.

first: Michal

last: Lipinski

first: Rafael

last: Viana

last: Galera

last: Barco Guerrero


title: Expression profile of select glucose and lipid metabolic genes mediated by STIM1 knockout, or STIM1 knockout plus Snail1 overexpression in SMMC7721 cells

status: Public on Apr 07 2020

city: Chongqing

first: Huakan

last: Zhao

state: State...

address: Xinqiao Street 183, Shapingba district

department: Clinical Medicine Research Center

institute: Xinqiao Hospital, Third Military Medical University

summary: To investigate the altered glucose and lipid metabolism genes after STIM1 knockout (STIM1 KO) or STIM1 knockout plus Snail1 OE (STIM1 KO+Snail1 OE) in SMMC7721 cells. STIM1 KO-SMMC7721 cells were constructed by CRISPR/Cas9, and STIM1 KO+Snail1 OE-SMMC7721 cells was established via lentiviral Infection of Snail1 overexpression in STIM1 KO-SMMC7721 cells. The cells mentioned above were cultured in DMEM supplemented with 10% (v/v) FBS at 37 °C in 5% CO2. When the cells grow to 60~70% confluent, total RNA was extracted by using Trizol (TAKARA, Japan). Reverse transcription was performed from 1μg total RNA using PrimeScript™ RT reagent Kit with gDNA Eraser (TAKARA), Quantitative real-time PCR were performed (CFX386, BioRad) with 40 cycles at 95 °C for 10 seconds, 59 °C for 20 seconds and 72 °C for 30 seconds.

overall_design: In the study presented here, Widetype (WT)-, STIM1 knockout (STIM1 KO)- and STIM1 knockout  plus STIM1 overexpression (STIM1 KO+Snail1 OE)-SMMC7721 cells were used to acquire expression profiles of a total of 48 unique genes related to glucose and lipid metabolism.

first: Yongsheng

last: Li


title: Circadian clock regulation of developmental time in the kidney

status: Public on Apr 11 2020

city: New York

first: Rosemary

last: Sampogna

state: NY

department: Medicine

institute: Columbia University

summary: We report the emergence of an endogenous circadian clock in mouse fetal kidney that regulates organogenesis. We detect circadian rhythms both in vivo with transcriptional profiling and ex vivo by bioluminescence. High-resolution structural analysis of embryonic explants reveals that global or local clock disruption results in defects that resemble human congenital abnormalities of the kidney. The onset of fetal rhythms strongly correlates with the timing of a distinct transition in branching and growth rates during a gestational window of high fetal growth demands. Defects in clock mutants typically have been attributed to accelerated aging, however, our study establishes a role for the fetal circadian clock as a developmental timer that regulates the pathways that control organogenesis, branching rate and nephron number, and thus plays a fundamental role in kidney development.

overall_design: Examination of RNA-seq time series of developing fetal mouse kidnes from embryonic ages E18 to E20.5 (inclusive)


title: The role of Erg in B cell development (ATAC-Seq)

first: Melissa

last: Davis

summary: ATAC-seq of pre-proB, proB and preB populations from Ergfl/fl bone marrow, pre-proB cell population from Rag1CreT/+;ErgΔ/Δ bone marrow, and pre-proB, proB and preB populations from from Rag1CreT/+;ErgΔ/Δ;IgHVH10tar bone marrow.

overall_design: ATAC-seq of sorted B-cell progenitor populations from specified genotypes was performed.

first: Ashley

middle: P

last: Ng

first: Soroor

last: Hediyeh-Zadeh


title: Effect of Ephrin-A5 DNA Nanocalipers stimulation of EphA2 receptor signaling in U3013 cell line

city: Solna

first: Toon

last: Verheyen

address: Tomtebodavägen 16

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

summary: Ligand binding induces extensive spatial reorganization and clustering of the EphA2 receptor at the cell membrane. It has previously been shown that the nanoscale spatial distribution of ligands modulates EphA2 receptor reorganization, activation and the invasive properties of cancer cells. However, the mechanisms by which cells transduce ligand nanoscale spatial distribution signals have not been elucidated. Here we used DNA origami nanocalipers to control the positions of ephrin-A5 ligands at the nanoscale and investigated the transcriptional responses following ligand binding. Using mRNA sequencing, we determined the transcriptional profiles of glioblastoma cells treated with nanocalipers presenting a single ephrin-A5 dimer or two dimers spaced 14, 40 or 100 nm apart. We observed divergent transcriptional responses to ephrin-A5 nano-organization, with ephrin-A5 dimers spaced 40 or 100 nm apart showing the highest levels of differential expressed genes compared to treatment with n  anocalipers that do not present ephrin-A5. These findings show that the nanoscale organization of ephrin-A5 modulates transcriptional responses to EphA2 activation.

overall_design: Here, we compare differently spaced Ephrin-A5 dimers on DNA nanocalipers and the effect they have on the U3013 transcriptome when stimulating the EphA2 receptor

first: T


title: Ephrin-A5 modulates transcriptional responses to EphA2 activation


title: Effect of IgG-clustered Ephrin-A5 stimulation on EphA2 signaling in MDA-MB-231 and U3013 cell lines

overall_design: Comparing the transcriptional response of cell lines MDA-MB-231 and U3013 when stimulating the cells either with IgG (ctrl) or with IgG-clustered Ephrin-A5 (treatment) for 30 min.


title: RNA-Seq analysis of skeletal muscles of mice with chronic or acute infections of LCMV Armstrong and LCMV clone 13

status: Public on Apr 08 2020

city: Heidelberg

first: Guoliang

last: Cui

address: Im Neuenheimer Feld 280

institute: German cancer research center (DKFZ)

summary: Chronic but not acute infections cause cachexia, characterized by bodyweight reduction and muscle loss. The underlying mechanisms remain incompletely understood. It is also not clear if muscle, in turn, regulates antiviral immune responses. In this study, we use two infection mouse models, one is acute and the other is chronic (described in PMID6332167 and PMID17950003), to study the global transcript profiles in muscles during infections.

overall_design: To understand the global gene expression profiles in muscle during acute and chronic infections, we harvest quadriceps muscle from C57BL/6 mice infected with LCMV Armstrong and LCMV clone 13, followed by RNA extraction and  RNA sequencing (RNA-seq) analysis.

first: Jingxia

last: Wu