city: Helsinki

first: Piet

last: Finckenberg

address: Haartmaninkatu 8

department: Medicum

institute: University of Helsinki

summary: Myocardial regeneration capacity declines during the first week after birth and is linked to the adaptation to oxidative metabolism. Utilizing this regenerative window, we characterized the transcriptomic changes in myocardial injury in 1-day-old regeneration-competent and 7-day-old regeneration-compromised mice. The mice were either sham-operated or received left anterior descending coronary artery ligation to induce myocardial infarction and acute ischemic heart failure. Myocardial tissue samples were collected after 3- and 21-day follow-up period. Whole transcriptome and miRNA NGS data was analyzed. We identified specific time-dependent transcription factors and networks contributing to both regeneration competence and failure.

overall_design: miRNA analysis of neonatal mice hearts after myocardial infarction performed at  postnatal days 1 or 7.

first: Esko

last: Kankuri

first: Maciej

last: Lalowski

first: Eero

last: Mervaala


title: Therapeutic Targeting Ewing Sarcoma through Inhibition of the FACT Complex (ChIP-Seq)

status: Public on Dec 31 2022

city: shanghai

first: Jialin

last: Mo

address: South Chongqing Road, Shanghai 200025. P.R. China

country: China

institute: Shanghai Jiao Tong University School of Medicine

type: Genome binding/occupancy profiling by high throughput sequencing

summary: EWS/ETS fusion transcription factors, most commonly EWSR1-FLI1, drive initiation and progression of Ewing sarcoma (EwS), a highly aggressive childhood cancer of bone and soft tissues. Even though direct targeting EWSR1-FLI1 is a formidable challenge, epigenetic or transcriptional modulators have been recently proved to be promising therapeutic targets for indirectly disrupting its expression and/or function. Here, we performed transcriptome and functional genomics dataset analyses, and combined with small molecule screening of EwS lines to identify novel epigenetic/transcriptional-targeted therapeutic strategies. SSRP1 and SUPT16H, two subunits of the Facilitates Chromatin Transcription (FACT) complex, are both found to be EWSR1-FLI1-induced essential oncogenes in EwS. The FACT-targeted drug CBL0137 exhibits potent therapeutic efficacy against multiple EwS preclinical models in vitro and in vivo. Mechanistically, the FACT complex and EWS-FLI1 form oncogenic positive feedback loop via mutual transcriptional regulation and activation, and cooperatively promote cell cycle/DNA replication process and IGF1R-PI3K-AKT-mTOR pathway to drive EwS oncogenesis. The FACT inhibitor drug CBL0137 effectively targets the EWSR1-FLI1-FACT circuit, resulting in transcriptional disruption of EWS-FLI1, SSRP1 and their downstream effector oncogenic signatures. Our study illustrates a crucial role of the FACT complex in facilitating the expression and function of EWSR1-FLI1 and demonstrates FACT inhibition as a novel therapeutic strategy against EwS via indirect targeting the oncogenic fusion TF, providing preclinical support for adding EwS to CBL0137’s future clinical trials.

overall_design: Briefly, 1~2 × 107 SKNMC cells were digested with Micrococcal Nuclease (New England Biolabs, M0247S) and sonicated for Chromatin IP experiment. Then 10 ug chromatin was immunoprecipitated with 10 uL of SSRP1 antibody (Cell Signaling Technology, 13421S), FLI1 antibody (Abcam, ab15289) or H3K27Ac antibody (Active Motif, AM39133,) and 50 uL Pierce™ ChIP-grade Protein A/G Magnetic Beads (Thermo Scientific, 26162). Immunoprecipitated DNA and INPUT DNA were then purified and sequenced by Romics, Shanghai, China. ChIP-seq data were first mapped against the human genome build hg19 using BowTie2 using the default settings. Then Model-based analysis of ChIP-seq (MACS2: v2.2.7.1) was used to identify peak regions of ChIP-seq enrichment comparing to input control with a q threshold of 0.05. Peak annotation and motifs finding was performed by HOMER Analysis. DeepTools was conducted to generate BigWig files and visualization. We explore Integrative Genome Viewer and WashU Epigenome Browse (http://epigenomegateway.wustl.edu/browser/) to visualize BigWig files on the hg19 genome track. Overlapped peaks were identified at least 20% intersected signal between two or three signal tracks.

first: Kezhe

last: Tan

first: Yu

last: Dong

first: Yujie

last: Tang


title: Transcriptome profiling of left ventricles from Wildtype and KDM5B knockout mice

city: Shanghai

first: Zhenzhen

last: Zhan

address: Jimo Road 150

department: Research Center for Translational Medicine

institute: Shanghai East Hospital, Tongji University School of Medicine,

summary: Myocardial fibrosis is the most common pathological feather of adverse ventricular remodeling, and persistent fibrotic extension decreases myocardial compliance, promotes the development of heart failure. Epigenetics has been considered to play a potent regulatory role in the development of excessive myocardial fibrosis. Although, the explicit mechanism of epigenetic regulation in myocardial fibrosis still needs to be fully elucidated.Transcriptome microarray analysis was used to screen differentially expressed genes in myocardial tissues from KDM5B KO and littermate control WT mice at day 7 after MI operation.

overall_design: 8-10-week-old male KDM5B KO mice and their corresponding WT mice were subjected to myocardial infarction by ligation of the left anterior descending coronary artery. At 7 days after myocardial infarction, the left ventricular samples were harvested  and total RNA was isolated for hybridization on agilent microarray. Each group contain with 2 replicates

first: Bo

last: Wang

first: Xingguang

last: Liu


title: Membrane palmitoylated protein 7 depletion effect on MDA-MB-231 cells

status: Public on Jan 01 2023

city: Foshan

first: Wanqin

last: Liao

state: Guangdong

address: 5# Hebin Road, Chancheng

institute: Foshan University

type: Expression profiling by high throughput sequencing

summary: Analysis of MDA-MB-231 cells depleted for membrane palmitoylated protein 7 (MPP7). MPP7 is a member of MPP subfamily of cell polarity-related proteins that function in cell junction and adhesion. Results provide insight into the identification of MPP7 target genes.

overall_design: MDA-MB-231 breast cancer cells were transduced with lentivirus expressing non-target control shRNA (shCON) or lentivirus expressing shRNA sequence targeting MPP7 (shMPP7). Total RNAs of shCON and shMPP7 groups were extracted and RNA-seq was performed to determine differentially expressed genes between shCON and shMPP7 groups.


title: MicroRNA-mediated downregulation of HMGB2 contributes to cellular senescence of microvascular endothelial cell

city: Seoul

first: Hye-ram

last: Jo

address: Nowon-ro 75, Nowon-gu

country: South Korea

institute: Korea Institute of Radiological & Medical Science

type: Non-coding RNA profiling by high throughput sequencing

summary: MicroRNA expression was profiled using small RNA sequencing in young and old human lung microvascular endothelial cells.

overall_design: Profiling microRNAs in young and old endothelial cells. Young endothelial cells were analyzed in duplicate and old endothelial cells were triplicate.

first: Jae-Hoon

last: Jeong


title: Whole transcriptome and miRNA analysis of neonatal mice hearts after myocardial infarction

country: Finland

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

overall_design: Refer to individual Series


title: Therapeutic Targeting Ewing Sarcoma through Inhibition of the FACT Complex


title: An organoid-based transplantation model reveals genetic interactions potentiating niche-independent gastric carcinogenesis

city: Chiba

first: Yoshitaka

last: Hippo

state: chiba

address: Nitona-cho 666-2

country: Japan

institute: Chiba Cancer Center Research Institute

summary: Despite distinct genetic aberrations introduced and diverse tumor histology, the derived tumor-derived organoids stereotypically exhibited cystic features. To clarify distinct genotype-dependent properties of p53-null tumor-derived organoids, seven tumor-derived organoids and organoids with pLKO.1 and shLuc were compared.

overall_design: The Trp53flox/flox mice-derived Ga organoids transduced with the control vector pLKO.1 and shLuc served as a reference for gene expression. seven tumor-derived organoids were analyzed.

first: Yoshiaki

last: Maru


title: Expression profiling and chromatin accessibility profiling of B cell subsets

city: Oullins

first: Fabrice

last: Chatonnet

address: 165 Chemin du Grand Revoyet

country: France

institute: INSERM


title: The transcription factor Zic4 promotes tentacle formation and prevents epithelial transdifferentiation in Hydra

city: Basel

first: Panagiotis

last: Papasaikas

address: Fabrikstrasse 24

country: Switzerland

institute: Friedrich Miescher Institute

summary:
Purpose: The mechanisms driving epithelial cell fate decisions to create differentiated body structures  (such as tentacles and basal disk) are not understood in Hydra. We explored the role of Wnt signaling targets Zic4 and Sp5 in this process.
Methods: RNA sequencing of differentiated body parts (tentacles) upon knockdowns of the candidate transcription factors. Comparison to existing datasets for body part identity and cell lineage.
Results: Upon Zic4 knockdown, tentacle battery cells transdifferentiate into the basal disk cells in a cell-cycle dependent manner. Similar results are obtained after the knockdown of Sp5, a positive regulator of Zic4 transcription, and their double knockdown enhances the phenotype.
Conclusions:We conclude that Zic4 acts as a master regulator to control the choice between two epidermal cell fates – battery cell and basal disk identity. It represses the basal disk specification, which appears to be the default epidermal epithelial differentiation trajectory. We also show evidence for transdifferentiation in Hydra.

overall_design: mRNA profiles of mock, Zic4 RNAi, Sp5 RNAi, and Zic4/Sp5 RNAi tentacles

first: Charisios

last: Tsiairis

first: Jaronslav

last: Ferenc


title: Phenotypic skewing of tumor-associated macrophages by cooperative actions of IL-6 and IL-4 in IFN-stimulated differentiating monocytes

city: Nanjing

first: Yuyan

last: Zhang

state: jiangsu

address: pukou 11

institute: Nanjing university

summary: I IFNs promote differentiating monocytes to differentiate into tumor-associated macrophages (TAMs) and limit the I IFNs anti-tumor effects.But how macrophage polarization is shaped by complex signals in the tumor microenvironment during IFN therapies is incompletely understood. Herein, it was discovered that I IFNs could stimulate transitional monocytes to secrete interleukins IL-4 and IL-6, which interact to influence target genes expression in primary mouse bone-marrow-derived macrophages (BMDMs).  To analyze the synergism mechanism, RNA seq was performed. Bone marrow derived macrophages were cultured under the 20ng/ml M-CSF for 7days, and treated with the indicated cytokine, samples were harvested for total RNAs and subjected to RNA sequencing analyses.

overall_design: BMDMs were stimulated with individual or combinatorial cytokines (IL-4 10 ng/ml, IL-4 10ng/ml+IL-6 40 ng/ml, IL-13 40 ng/ml, IL-13 40ng/ml+IL-6 40ng/ml) for 24 h,. each sample had three replicates. Total RNA was harvested at the indicated time, and then the RNA samples were subjected to RNA sequencing analyses.

first: Limin

last: Yang

first: Jianghuai


title: Transcriptome Analysis of Plasmodium CSP stable expressing or control A549 cells

city: Chongqing

first: Hong

last: Zheng

address: 30 Gaotanyan Street

institute: Army Medical University (Third Military Medical University)

summary: To investigate the potential effect of overexpression of Plasmodium yoelii cirumsporozoite protein on A549 cells. Control and CSP stable expression A549 cells were constructed by infected with pLenti vector and pLenti-CSP plasmids and cultured with HBSS for 24h. Total RNA from Control and CSP stable expression A549 cells was extracted using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol. RNA integrity was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). The samples with RNA Integrity Number (RIN) ≥ 7 were subjected to the subsequent analysis. The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. Then these libraries were sequenced on the Illumina sequencing platform (illumina novaseq6000) and 125bp/150bp paired-end reads were generated.

overall_design: mRNA profiles of Plasmodium CSP stable expressing or control A549 cells were generated by deep sequencing in quintuplicate, using illumina novaseq6000 platform.

first: Zheng

last: Hong

first: Lu

last: Xiao


title: New insight on enzymatic browning mechanism by comparative transcriptome analysis of romaine lettuce cultivars with different browning potentials

city: COLLEGE PARK

first: Xudong

last: Zhu

state: Maryland

address: 10300 Baltimore Ave.

country: USA

institute: USDA-ARS-BARC-FQL

summary: Enzymatic browning on the cut edge of lettuce significantly limits its quality and shelf life. To characterize its molecular mechanisms, we performed comparative transcriptome analysis of three Romaine lettuce cultivars, Parris Island Cos (PC) with low browning potential, Tall Guzmaine (TG) with high degree of browning and Clemente (CL), a medium degree of browning cultivar derived from TG x PC. Before cutting, the phenylpropanoid and oxidative stress genes, such as PAL1, MYB1 and PPO were up-regulated in PC as compared to TG, while the expressions of genes involved in auxin, cytokinin hormone signalings and defense, such as ARF, AHP and PTI in PC were higher than TG. The transcript levels of all these genes in CL were somewhere between TG and PC. On day 3 after cutting when browning was shown up in TG, the expression of these phenylpropanoid and oxidative stress genes were remarkably increased in all three cultivars, even though their levels in TG were still higher than those in PC and CI. In comparison, expressions of the hormone and defense genes were reduced in all three cultivars, but their levels in PC were higher than CI and TG. Exogenous application of IAA and 6-BA inhibited lettuce browning possibly by alleviating the burst of those browning related genes, such as PAL1 and PPO1. These results demonstrate that lettuce tissue browning is controlled by reduced growth hormone (mainly auxin) level and increased phenolics biosynthesis and oxidation. This study provides the useful knowledge and functional markers for lettuce breeders and industry to select low tissue browning cultivar and manage lettuce quality during storage and processing.

overall_design: These accessions are Parris Island Cos (PC), Tall Guzmaine (TG), and Clemente (CL).  The cultivars PC and TG are major ancestors  of romaine lettuce, and CL was selected from progeniesy of a cross between PC and TG. TG exhibited a relatively high degree of browning, PC possessed low browning potential and CL had medium browning potential. Immediately after harvesting, the lettuce was taken to a local distributor and stored in a 5°C cold room with forced air cooling. The cooled lettuce was transported via commercial refrigerated truck (2–4 °C) to the USDA facilities in Beltsville, MD within three days.  The lettuce was then stored at 5 °C for 24 h before sample preparation. On the day of sample preparation, wrapper leaves and stems were removed manually from each head of lettuce. Lettuce leaf midribs were obtained by carefully excising the green leaves. Representative samples were taken from all locations of each head. The ribs were then cut manually into 2.5-cm pieces using an paring knife. Then samples were stored  at 5 °C , and frozen on day 0, 2 and 3 in liquid nitrogen,

first: Tianbao


title: C. elegans L4 hypodermal SLAM-ITseq

city: Seville

first: Peter

last: Askjaer

address: UPO Carretera de Utrera km 1

country: Spain

institute: Centro Andaluz de Biología del Desarrollo

summary: To adapt SLAM-ITseq for Caenorhabditis elegans, we inserted a codon-optimized version of the Toxoplasma gondii UPRT gene downstream of a FRT-flanked mCh::his-58 cassette and under control of the strong and ubiquitous eft-3 promoter. We introduced a single copy of this construct into the C. elegans genome and crossed the resulting line with a dpy-7p::FLP driver. FLP-dependent expression of UPRT was confirmed by Western blotting (strain BN1190). As a proof of concept, we exposed animals to 4-TU from L3 to L4 stage and purified total RNA. RNA from animals without FLP expression was used to control for UPRT-independent labeling strain BN1158). RNA was alkylated with iodoacetamide, which leads to a T>C conversion of 4-TU-labeled positions during cDNA synthesis, and subjected to deep sequencing (see Materials and Methods). We confirmed that the presence of FLP and UPRT did not affect gene expression. Comparing the T>C conversion rate per gene revealed a significant increase in nematodes expressing UPRT in the hypodermis. Next, we performed a beta-binominal test to identify genes that were significantly labelled across all replicas, which retrieved 197 genes (p<0.003; FDR<0.1 after adjustment for multiple comparisons). Original SLAM-ITseq reference: Matsushima W, Herzog VA, Neumann T, Gapp K, Zuber J, Ameres SL, Miska EA (2018) SLAM-ITseq: sequencing cell type-specific transcriptomes without cell sorting. Development 145 (13). doi:10.1242/dev.164640

overall_design: Four replicas of control strain BN1158 (- FLP) and three replicas of strain BN1190 (+ FLP in hypodermis).

first: Adrián

last: Fragoso-Luna


title: Micro-RNA expression profile of BALB/c mouse glandular stomach in the early phase of Cryptosporidium muris infection

city: ZHENGZHOU CITY HENAN PROVINCE

first: Yankai

last: Chang

state: 河南

address: HENAN AGRICULTURAL UNIVERSITY, NO.15 ZHENGZHOU LONGZIHU, 河南省郑州市郑东新区龙子湖高校园区15号河南农业大学

institute: Henan Agricultural University

summary: Cryptosporidiosis is a zoonotic disease caused by infection with the oocyst of Cryptosporidium in human and animals. MicroRNA (miRNA) emerges as important player in regulating the innate immune response against parasitic infection. Here, we compared miRNA profiles of the glandular stomach of Cryptosporidium muris (C. muris) infected and un-infected BALB/c mice using microarray sequencing. A total of 10 miRNAs (including 3 upregulated and 7 downregulated miRNAs) with significant expression differences (|FC| ≥ 2 and P value test < 0.05) were screened after C. muris infected the glandular stomach of BALB/c mice for 8 hours. MiRWalk and miRDB online bioinformatics software were used to predict the target genes of differentially expressed miRNAs. Gene Ontology (GO) and KEGG enrichment analyses were performed for annotate the target genes. GO terms indicates that many are associated with the relevant generic transcription and ion transport. In addition, the KEGG analyses showed that the target genes were strictly related to a diverse types of tumor disease progression and the antipathogen immunity pathway. In the current study, we first reported the changes of miRNA expression profile in glandular stomach of BALB/c mice at the early phase of C. muris invasion. As such, dysregulation of miRNA expression profile may contribute to our understanding of the Cryptosporidiosis pathology. The result reported in this paper provide a new perspective into the miRNA regulatory mechanisms of Cryptosporidiosis, which may help to develop effective control strategies against Cryptosporidium.

overall_design: The experimental (three mice) and control groups (three mice) were sampled at 8 hours post-infection. The glandular stomach was collected from mice immediately euthanasia and washed with cold normal saline to remove the gastric content. Tissue samples were immediately placed into liquid nitrogen and stored at -80℃ for RNA extraction.

first: Longxian


title: Single cell transcriptome of human intrahepatic cholangiocarcinoma

first: Xiaoqiang

last: Chai

state: Shanghai

address: No.130 Dongan Road

department: Institutes of Biomedical Sciences

institute: Fudan University

summary: Intrahepatic cholangiocarcinoma (ICC) is the second most common malignancy within the liver, with a high degree of tumor heterogeneity and a very poor prognosis. In this study, single-cell transcriptome sequencing analysis was performed on 3 samples (1 plasma, 1 tumor and 1 paracancerous tissue) from an ICC patient with the aim of studying cell type variations in different tissue types.

overall_design: To investigate the distribution of bacterial transcription products in various cell types, we analyzed ICC scRNA-seq data. In this study, we obtained single cell RNA-seq data from a total of 3 tissue samples (1 tumor tissue, 1 paracancer tissue and 1 plasma tissue) from 1 ICC patient, yielding a total of 11357 cells for subsequent clustering analysis.

first: Jie

last: Wang

first: Huanping

last: Li

first: Jiabin

last: Cai


title: The influence of Burkholderia fungorum on the gene expression of human bile duct cancer cell line QBC939

summary: To investigate the effect of Burkholderia fungorum (BF) on cholangiocarcinoma cells, we treated the cell lines with bacterial supernatant and performed transcriptome sequencing. By transcriptome sequencing, we quantified the differentially expressed genes in control and experimental groups. The results of GO and KEGG functional enrichment analysis showed that the differentially expressed genes were mainly involved in some biological processes of metabolism and amino acid synthesis. We inferred that the transcriptome characterization can help us understand the relationship between bacterium and tumor cell metabolism.

overall_design: The examinations of mRNA profiles of control and BF supernatant-treated cell lines.


title: Flavivirus Capsid Proteins Facilitate Genome Compaction and Packaging

city: Singapore

first: Roland

middle: G

last: Huber

address: 30 Biopolis Street

department: Bioinformatics Institute (BII)

country: Singapore

institute: Agency for Science, Technology and Research (A*STAR)

summary: Dengue virus (DENV) and Zika virus (ZIKV) are single-stranded (+)-sense RNA viruses that infect humans and mosquitoes, posing a significant health risk in tropical and subtropical regions. Mature virions are composed of an icosahedral shell of envelope (E) and membrane (M) proteins circumscribing a lipid bilayer, which in turn contains a complex of the approximately 11 kb genomic RNA with capsid (C) proteins. Whereas the structure of the envelope is clearly defined, the structure of the packaged genome in complex with C proteins remains elusive. Here, we investigate the interactions of C proteins with viral RNA, in solution and inside mature virions, via footprinting and cross-linking experiments. We demonstrate that C protein interactions with DENV and ZIKV genomes saturate at an RNA:C protein ratio below 1:250, and that binding site lengths on the genome exhibit a bimodal distribution, suggesting that RNA-C protein complexes occur in singlets or pairs. We show that interaction sites are preferentially sites with low base pairing, as measured by previously measured SHAPE reactivity indicating structuredness. We found no preference for specific sequence motifs or nucleotide composition. However, RNA-C protein binding sites are strongly associated with long-range RNA-RNA interaction sites, particularly inside virions. This helps to explain the need of C protein for viral genome packaging: the protein could coordinate those key interactions, promoting proper packing of viral RNA. Such sites are thus possible targets for drug development strategies against these and related viruses.

sample_organism:
dengue virus type 1
Zika virus

platform_organism:
dengue virus type 1
Zika virus

overall_design: footprinting and crosslinking experiments of flavivirus RNA with flavivirus capsid proteins

first: Priscilla

middle: L

last: Boon

first: Ana

middle: S

last: Martins

first: Lim

last: Xin Ni

first: Francisco

middle: J

last: Enguita

first: Nuno

middle: C

last: Santos

first: Ivo

last: Bond

first: Yue

last: Wan


title: scONE-seq: A one-tube single-cell multi-omics method enables simultaneous dissection of genotype and phenotype heterogeneity from frozen tumor samples

city: Hong Kong

first: Angela

middle: Ruohao

last: WU

address: Clear water bay street

department: LIFS

institute: HKUST

summary: Both the genotypic and phenotypic cellular heterogeneity play important roles in normal tissue function as well as disease development. To be able to characterize these different forms of cellular heterogeneity in diverse types of samples, we developed scONE-seq, which enables simultaneous transcriptome and genome profiling in a one-tube reaction. We demonstrate the feasibility of scONE-seq by benchmarking it against existing methods using cell lines and lymphocytes from a healthy donor. Furthermore, we applied scONE-seq to a frozen years-old IDH1-mutant glioblastoma (GBM) sample and profiled over 1200 nuclei from a single sample, subsequently identifying a phenotypically normal-like tumor clone that was only distinguishable by superimposing paired clonal and transcriptomic data.

overall_design: Validate the scONE-seq method with cell lines, lymphcytes from PBMC, and a frozen glioblastoma sample.

first: Lei

last: Yu

last: Wu


title: Single-cell RNA-sequencing overviews global inflammatory response in in vitro organ cultured testes

city: Yokohama

first: Takahiro

last: Suzuki

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: Center for Integrative Medical Sciences

institute: RIKEN

summary: Background: Production of functional sperms from spermatogonial stem cells in vitro is important for understanding of biological mechanisms underlying physiological spermatogenesis and for treatment of male infertility. However, comparing with the in vivo testes, in vitro spermatogenesis is severely lower efficiency. Here we describe abnormalities occurring in early stage of in vitro spermatogenesis at single cell resolution.  Results: While spermatogenesis was similarly progressed between in vivo and in vitro-cultured testes, noticeable acute inflammatory response occurred right after in vitro culture of neonatal testes not only in immune cells but also non-immune testicular somatic cells. Inhibitor treatment revealed NLRP3 inflammasome signaling is key to the inflammation occurring in in vitro cultured testes We also found accumulation of damaged/dead germ cells in in vitro cultured testes, which may be due to dysfunction of sertoli cell phagocytosis.   Conclusion: Our data revealed tissue-wide sterile inflammation occurring in in vitro cultured testes, in which DAMPs - NLRP3 inflammasome axis may key element. Thus, these abnormal testicular microenvironments may be a cause of low spermatogenesis efficiency of in vitro spermatogenesis.

overall_design: Examination of single-cell transcriptomes in the in vivo testes and the in vitro cultured testes

first: Takeru

last: Abe

first: Haruka

last: Yabukami

first: Takehiko

last: Ogwa


title: Chromatin accessibility profiling of B cell subsets

first: Fabrice

last: Chatonnet

summary: Terminal B cell differentiation into antibody-secreting cells (ASC) is a critical process for adaptive immune responses. Although many efforts have been made in the recent years to decipher the cellular and molecular events sustaining this differentiation, both in mouse and human models, several key steps still need further elucidation. We used a combined RNA-seq and ATAC-seq approach to decipher the chromatin and gene expression events driving ASC differentiation from naive or memory B cells. Out goal with the dataset was to explore the divergent molecular properties of naive and memory B cells that sustain their differential abilities to differentiate into ASC.

overall_design: Four cell populations of peripheral blood and in vitro differentiating B cells were analyzed by ATAC-seq after cell sorting on 50,000 cells. No replicates.

first: Amandine

last: Pignarre

first: Gersende

last: Caron

first: Thierry

last: Fest


title: miRNA expression in LGCIN outcomes

city: New Orleans

first: Jennifer

middle: E.

last: Cameron

state: LA

address: 1901 Perdido St.

department: Microbiology, Immunology & Parasitology

institute: LSU Health Sciences Center

summary: The goal of this study was to investigate differential regulation of miRNA expression in the cervical tissue of women with low-grade cervical intraepithelial neoplasia (LGCIN, or low grade cervical dysplasia). We compared the miRNA expression profiles of women with LGCIN that progressed to high-grade CIN to the miRNA expression profiles of women with LGCIN that naturally resolved without medical intervention.

overall_design: Study design was case-control without matching. Retrospective chart review was performed to identify women with prior diagnosis of low-grade cervical dysplasia. Women were included if they met inclusion criteria as a Case (women with definitive diagnosis of high-grade dysplasia) or Control (women with significant clinical evidence of dysplasia resolution without medical intervention). Archived punch biopsy specimens with histology consistent with low-grade cervical intraepithelial neoplasia were tested for miRNA expression.  Analysis compared Case group to Control group.

middle: E

first: Ashley

last: Winters


title: DNA methylation patterns associated with cyanogenic cassava exposure and konzo in Sub-Saharan Africa

city: Washington,DC

first: Nino

last: Gustavo

state: Washington,DC,

address: Sheikh Zayed Campus,111 Michigan Avenue,

department: Center for Precision Medicine and Genomics Research

institute: Childrens National Hospital

type: Methylation profiling by genome tiling array

summary: Konzo, a disease characterized by sudden, irreversible spastic paraparesis, affecting up to 10% of the population in some regions of Sub-Saharan Africa during outbreaks and is strongly associated with dietary exposure to cyanogenic bitter cassava. The molecular mechanisms underlying the development of konzo, remain largely unknown. Here, through an analysis of 16 individuals with konzo and matched healthy controls from the same outbreak zones, we identified 117 differentially methylated loci involved in numerous biological processes that may identify cyanogenic- sensitive regions of the genome, providing the first study of epigenomic alterations associated with sub-lethal cyanide exposure and a clinical phenotype.

overall_design: DNA was extracted from 32 total blood samples that were collected and biobanked in 2011 (16 konzo cases, 16 controls; equal distribution of sex per cohort). Illumina Infinium EPIC BeadChip protocol was completed following manufacturer's specifications and DNA quality was determiend using Qubit Fluorometer. 300ng of DNA was bisulfite converted using Zymo DNA Methylation Lightning kit.

first: Kristen

last: Kocher

first: Surajit

last: Bhattacharya

first: Matthew

last: Bramble

first: Daniel

last: Okitundu-Luwa

first: D

middle: M

last: Ngoyi

first: Desire

last: Tshala-Katumbay

first: Eric

last: Vilain


title: Integrated single-cell sequencing reveals principles of epigenetic regulation of human gastrulation and germ cell development in a 3D organoid model

city: Santa Barbara

first: Alex

last: Chialastri

state: CA

address: 2002 BioEngineering Bldg, CNTR for Bioengineering

institute: University of California Santa Barbara

summary: The emergence of different cell types and the role of the epigenome in regulating transcription is a key yet understudied event during human gastrulation. Investigating these questions remain infeasible due to the lack of availability of embryos at these stages of development. Further, human gastrulation is marked by dynamic changes in cell states that are difficult to isolate at high purity, thereby making it challenging to map how epigenetic reprogramming impacts gene expression and cellular phenotypes. To overcome these limitations, we describe scMAT-seq, a high-throughput one-pot single-cell multiomics technology to simultaneously quantify DNA methylation, DNA accessibility and the transcriptome from the same cell. Applying scMAT-seq to 3D human gastruloids, we characterized the epigenetic landscape of major cell types corresponding to the germ layers and primordial germ cell-like cells (hPGCLC). As the identity of the progenitors that give rise to human PGCLCs remain unclear, we use this system to discover that the progenitors emerge from epiblast cells and show transient characteristics of both amniotic- and mesoderm-like cells, before getting specified towards hPGCLCs. Finally, as cells differentiate along different lineages during gastrulation, we surprisingly find that while changes in DNA accessibility are tightly correlated to both upregulated and downregulated genes, reorganization of gene body DNA methylation is strongly related to only genes that get downregulated, with genes that turn on displaying a lineage trajectory-dependent correlation with DNA methylation. Collectively, these results demonstrate that scMAT-seq is a high-throughput and sensitive approach to elucidate the epigenetic regulation of gene expression in complex systems such as human gastrulation that are marked by rapidly transitioning cell states.

overall_design: scMAT-seq profiles of HEK293T, H9, AICS-0024 cell lines. scMAT-seq profiles of differentiated AICS-0024 cells into mesoderm or 3D gastrulating organoids at 2 time points (20 or 48 hours).  scRNA-seq profiles of differentiated AICS-0024 cells into 3D gastrulating organoids at 1 time point (36 hr). scMA-seq of HEK293T cells. scMspJI seq of H9 cells. Bulk fully open chromatin MA-seq of H9 cells as a reference for unstructured genomic detection.

first: Eyal

last: Karzbrun

first: Aimal

middle: H

last: Khankhel

first: Monte

last: Radeke

first: Sebastian

last: Streichan

first: Siddharth

last: Dey


title: Identification of Early and Intermediate Biomarkers for Acute respiratory distress syndrome (ARDS) Mortality by Multi-Omic Approaches

city: Aurora

first: Ivana

last: Yang

state: CO

address: 1635 Aurora Ct

institute: University of Colorado

type: Methylation profiling by high throughput sequencing

summary: We compared the methylation profile between ARDS survivor v.s. non survivor

overall_design: Methylations for ARDS survivor and non-survivor

first: Nancy

last: Casanova

first: Shu-Yi

last: Liao


title: The transcriptomic and proteomic map of human primary cells

city: Rochester

first: Akhilesh

last: Pandey

state: Minnesota

address: 200 First Street SW

department: Laboratory Medicine and Pathology

institute: Mayo Clinic

summary: Molecular profiling of human primary cell types is essential for holistic understanding of human biology. Here we present a map of 28 human primary cell types with comprehensive measurements of expressed transcripts and proteins. Three major clusters of epithelial, endothelial, and mesenchymal cell types were observed both at transcriptome and proteome level along with discovery of several cell type specific proteins. Among them, we characterized the novel epithelial specific protein C1orf116 which was further validated with immunohistochemistry across various human tissues. Comprehensive proteome profiling across cell types allowed characterization of ten orphan proteins including TMEM252 and TM4SF18 which lacked protein level evidence. Exhaustive protein database search considering 27 biologically relevant post-translational modifications and 12 chemical modifications was performed, thanks to the increased performance of cloud-based search engine. This, for the first time, provided the catalog of post-translational modifications across cell types, which serve as a resource of PTMs for future studies. We characterized proteins such as protein EEF1A1with various types of PTMs and understudied PTMs including histidine methylation, and O-acetylation of serine. Interestingly, the unexpected higher frequency of dioxidation on tryptophan than that of methionine led us to characterize oxidative mitochondria complex subunit proteins modified through oxidative phosphorylation in mitochondria, which was mostly considered as chemical artifact so far. Overall, these indicated that considering various PTMs during protein database search from non-enriched samples could be routinely used in proteomics experiments. Further, protein database search strategy considering alternative translational start sites, splice junctions, and translational readthrough provided a unique opportunity to refine genome annotation with their proteomic evidence. We believe that our data with the large catalog of transcriptome and proteome of normal human primary cells provide a cornerstone for holistic understanding of cell biology.

overall_design:
Total RNA extracted from 28 human primary cell types are profiled by running on eight lanes of Illumina HiSeq 2500 to study gene expression
Please note that each processed data file was generated from all raw data (lane 1-lane 8) and is linked to the corresponding lane 1 sample records.

first: Pandey

last: Akhilesh


title: Efficient Elimination of Acute Myeloid Leukaemia Cells through Inhibition of KDM4A

city: Glasgow

first: Tae Ju

last: Park

address: 21 Shelley Rd

country: United Kingdom

institute: Paul O' Gorman Leukaemia Research Centre

summary: We previously identified an essential role for the H3K9me3 histone demethylase, KDM4A, in maintaining AML cell survival, with genetic depletion by shRNA of KDM4A inducing leukaemic cell death with little effect on normal haematopoiesis. We hypothesised KDM4A inhibition may represent a novel and effective strategy to treat AML. To address this, we provided proof-of-principle for the use of KDM4 inhibitors (KDM4Ai) and fully characterised their functional potential in AML cells and identified the epigenetic mechanisms underpinning the essential role of KDM4A activity in THP-1 cells using both ChIP-seq and RNA-seq, delineating and functionally validating the epigenomic network regulated  by KDM4A, showing that selective loss of KDM4A is sufficient to induce apoptosis in a broad spectrum of human AML cells. This detrimental phenotype results from a global accumulation of H3K9me3 and H3K27me3 at KDM4A targeted genomic loci thereby causing down-regulation of a KDM4A-PAF1 controlled transcriptional program essential for leukemogenesis, distinct from that of KDM4C.

overall_design: Preliminary data collection identified the best concentration and most appropriate timepoint for harvest of THP-1 cells treated with 30μM IOX1 (Tocris, #4464), 50μM IOX1, 100μM IOX1 alongside DMSO as a vehicle control in triplicate. Cells were grown in R10 with a final concentration of 0.1% vehicle across all samples. RNA-seq libraries were produced using the TruSeq stranded mRNA kit (Illumina) and single-end sequenced using the Illumina NextSeq 500 platform. For ChIP-seq, DNA was purified using Diagenode's iPure kit v2 and libraries made using the TruSeq ChIP Library Preparation Kit according to the manufacturer's instructions.

last: Massett

first: Laura

last: Monaghan


title: Profiling ERRb-target genes in mouse ES cells

city: Koto-ku

first: Tomoyoshi

last: Nakadai

state: Tokyo

institute: Cancer Institute of JFCR

summary:
We found ERRb activates the transcription through two molecular pathways, which are interaction to AF2-region binding PGC-1a/cofactors and general transcription factor TFIIH. To analyze the significance of these pathways in cells, we first identified ERRb-target genes in ES cells.
Estrogen-related receptors (ERRa/b/g) are orphan nuclear receptors that function in a number of energy-demanding physiological processes, as well as in development and stem cell maintenance, but mechanisms underlying target gene activation are largely unknown. Here, reconstituted biochemical assays that manifest ERR-dependent transcription have revealed two complementary mechanisms. On chromatin templates ERR-dependent transcription is dependent on interactions with cell-specific coactivator PGC-1a, which in turn recruits the ubiquitous p300 and MED1/Mediator coactivators. The N-terminal half of PGC-1a is necessary and sufficient for these interactions and for transcription both in vitro and in vivo. On DNA templates, ERRs activate transcription with just the normal complement of general initiation factors in a manner dependent upon interaction of the ERR DNA-binding domain with the p52 subunit of initiation factor TFIIH. Importantly, the PGC-1a and TFIIH interactions are both essential for ERRb/g functions in maintaining embryonic stem cell pluripotency through regulation of target gene transcription.

overall_design: ERRb gene in mouse ES cell line K3 was knockout. Then, was transduced with lentivirus expressing ERRb (KO/ERRb-wt)

first: Keiichi

last: Ito

first: Robert

last: Roeder


title: Transcriptome analysis of gene expression in young and aged oocyte samples (RNA-Seq)

city: Beijing

first: Wenjie

last: Shu

address: Taiping Road 27

institute: Beijing Institute of Radiation Medicine

summary: The purpose of this study are to compare transcriptome profiling (RNA-seq) data in young and aged oocytes,and to evaluate the transcriptome alterataions after rapamycin treatment in aged oocytes. The sequencing libraries from young, aged and rapa-treated oocytes were generated according to protocols of Smart-seq2.Then cDNA libraries were checked on a Bioanalyzer instrument (Agilent) and the passed samples were finally sequenced by Illumina novaseq for 150-bp paired-end reads. RNA-seq data were aligned to the mouse genome mm10 using STAR 2-pass mode with the annotations of Ensembl version 90 and parameter ‘--outFilterMismatchNmax 6’. SAMtools was used to extract uniquely mapped reads with mapping quality more than or equal to 20. The number of reads mapped to each gene was counted using the HTSeq python package with the ‘union’ overlap resolution mode and –stranded = no. The expressions of genes were quantified as RPKM by edgeR . Genes with RPKM more than 1 in at least three control samples were considered as expressed. Only expressed genes were kept for the subsequent analysis. Differentially expressed genes were identified by DESeq2 using two criteria: fold change of expression should be higher than 2 and the adjusted p-value should be lower than 0.05. Enriched GO terms were obtained with P-value less than 0.05 from DAVID.The analysis of data revealed a total of 454 genes were significant differentially expressed during oocyte aging,of which, 242 genes were upregulated and 212 downregulated in aged oocytes.GO enrichment analysis showed that some of gene expressions were related to oxidation-reduction process, cell cycle, translation and mitochondrial functions. However, gene expression analysis revealed only 4 differently expressed genes between oocyte from rapa-treated and reproductively aged mice.

overall_design: Total 9 samples from 4-week-old control, 48-week-old aged and 48-week-old (about 12 months) rapa-treated oocytes in 3 separate experiments, each sample contained about 10 oocytes.


title: Sensing of miRNA/ssDNA hybrid by AGO2 for Enhancing Gene Transcription

city: Shanghai

first: Ying

last: Liang

address: Room 416, West Building 13, Dong'an Road 130, Xuhui District

summary: We found that AGO2 suspends the formation of miRNA-single stranded (ss) DNA hybrid due to the high affinity interaction of AGO2-miRNA, being different from canonical miRNA guidance of AGO2 loading for mRNA. By this mechanism, we demonstrated that NamiRNA miR-1246 could promote MMP1 gene transcription to induce osteosarcoma cell metastasis. The observed metastasis features can be also extended to the transmission of miR-1246 enriched and carried by extracellular vesicles (EVs) to induce metastasis phenotypes of benign osteosarcoma cells. Collectively, we reveal that AGO2 senses and stabilizes miRNA-enhancer hybrids/loops to activate global gene expression and elucidate EV-carried miR-1246 plays important biological function to facilitate tumor metastasis.

overall_design: 1). Examination of H3K27ac and H3K4me1 histone modifications  and AGO2 enrichment alterations in MNNG cells after overexpressing miR-1246; 2). mRNA profiles of  MNNG cells after overexpressing miR-1246

first: Qingping

last: Zou

first: Wei

last: Li

first: Wenqiang

last: Yu


title: Single-cell profiling unravels bone marrow stromal remodeling driven by leptin receptor-expressing mesenchymal precursors in myelofibrosis

city: New York

first: Lei

last: Ding

state: NY

department: Rehabilitation & Regenerative Medicine

institute: Columbia University Irving Medical Center

summary: In order to comprehensively characterize the cellular constituents of the bone marrow microenvironment in primary myelofibrosis, single-cell RNA sequencing was performed on bone marrow stromal cells isolated from mice transplanted with MPLW515L-transduced hematopoietic cells.

overall_design: We profiled non-hematopoietic bone marrow cells from Lepr-Cre; tdTomato recipient mice transplanted with hematopoietic cells transduced with MPLW515L or empty vector retrovirus. Following onset of fulminant disease at 30-35 days after transplantation, bone marrow stromal cells were enriched by FACS using negative markers (CD45, Ter119, MPLW515L-GFP, SYTOX Green) to exclude hematopoietic/dead cells and a positive live cell marker (Calcein Violet-AM) to exclude tissue debris. Single cells isolated by FACS were profiled using droplet-based scRNA-seq (10x Genomics). We analyzed 4 MPLW515L mice (2 were pooled together for a total of 3 samples) and 2 empty vector control mice (pooled together into 1 sample). After data filtering and exclusion of contaminating hematopoietic cells (mostly erythroid progenitors), we ended up with 1,765 control cells and 2,184 MPLW515L cells, which were used for our downstream analyses.


title: Genome-wide maps of DNA methylome during oocyte aging and its transgenerational  inheritance

summary: The goals of this study are to compare genome-wide DNA methylation levels  in young and aged oocytes,and to investigate the transgenerational inheritance of methylome profiles in oocytes during natural aging. We apply a novel protocol of rapamycin to overcome the DNA methylation drift associated with oocyte aging. 8-week-old female mice were injected intraperitoneally with rapamycin or vehicle for 40 weeks. At the end of the experiment, females (48 weeks, F0) were paired with  young adult (~4 mo old) males to produce F1 offspring (OF1 and ORaF1). An F2 generation (OF2 and ORaF2) resulted from mating F1 female at 44~48 weeks of age  with  young adult males. To generate YF1 and YF2 as normal control (offspring of young mother), we mated females (~8 weeks) with young adult males. Then we collect oocytes (F0,F1 and F2 generations)，sperm ( F1 and F2 generations) and hippocampus (F1 female offspring)  from different groups to  investigate the transgenerational inheritance of DNA methylome profiles associated with oocyte aging by the single cell whole-genome methylation sequencing (sc-WGBS). We found that oocytes from aged mother exhibited increased DNA methylation levels in CpG sites. Maternal aging related methylome changes can be inherited transgenerationally though oocyte to the germ line of F1 and F2 offspring. The application of rapamycin during the course of oocyte aging could  reverse these DNA methylation alterations, and it can ameliorate several neurobehavioral aging trails that were in observed in aged oocyte offspring. WGBS-seq on DNA from hippocampal tissue revealed a number of differentially methylated (P<0.05) genes in OF1 and ORaF1 compared with YF1, and some of the enriched pathways were associated with aging process, such as PI3K-Akt signaling pathway (akin to transcriptional alterations above), MAPK signaling and Ras signaling pathway .

overall_design: Total 47 samples from F0, F1 and F2 generations.  9 samples from F0 mother(4-week-old as young control, 48-week-old and 48-week-old rapa-treated oocytes),  7 samples from F1 oocytes (YF1,oocytes from young mother; OF1,oocytes from aged mother; ORaF1,oocytes from rapa-treated aged mother),  7 samples from F2 oocytes (YF2, oocytes from YF1; OF2, oocytes from OF1; ORaF2, oocytes form ORaF1),   6 samples from F1 sperm( OF1,sperm from aged mother; ORaF1,sperm from rapa-treated aged mother),  9 samples from F2 sperm(  YF2, sperm from YF1; OF2, sperm from OF1; ORaF2, sperm form ORaF1),each group consists of 3 separate experiments, each sample contained about 15 oocytes. 9 hippocampus samples from F1 famale offspring(YF1, hippocampus from young mother; OF1, hippocampus from aged mother;ORaF1, hippocampus from rapa-treated mother), each group consists of 3 separate hippocampus from different offspring.

first: Jing

first: Xiaowei

last: Dou


title: Down-regulation of FABP5 suppresses the proliferation and induces apoptosis in gastric cancer cells through Hippo signaling pathway

first: Ji

last: Dong

address: Yiheyuan 5#

institute: Peking University

summary: We used RNA-seq to study the function of FABP5 in gastric cancer cells (AGS and MGC803). Down-regulation of FABP5 suppressed cell proliferation, cell migration and invasion, and induced cell apoptosis. Bioinformatics analysis revealed that Hippo signaling pathway was related to FABP5 in GC cells.Our data suggested that FABP5 might act as a potential target associated with Hippo signaling pathway for GC treatment.

overall_design: Here, we performed RNA-Seq analysis of silencing FABP5 and negative control in gastric cancer cell lines (AGS and MGC803 ).

first: Wendong

last: Wang

first: Xinglong

last: Wu

first: Xin

last: Zhou

last: Fu

first: Fuchou

last: Tang


title: Expression data from the dermis of human stretched scars and patient-matched healthy dermis from occipital scalps

city: London

first: Magdalena

last: Plotczyk

address: Royal School of Mines, Prince Consort Road

department: Bioengineering

institute: Imperial College London

summary: It is well accepted that elevated mechanical tension of the skin surrounding a healing wound stimulates a fibrotic cascade of events and contributes to an increased size of scars. A laxity paradox in the field of hair transplantation describes a phenomenon opposing this view. During Strip Follicular Unit Transplantation (Strip FUT), surgeons remove a strip of scalp skin (approximately 5 cm x 10 cm, depending on the number of hair follicles required) from the occipital scalp, which is then used to harvest hair follicles that will be transplanted into the balding frontal scalp. Most patients with normal scalp skin laxity heal with narrow normotrophic scars, while a small number of patients (14%) with very loose scalp skin, and so low residual skin tension, heal with post operating scar widening (4 - 12 mm). These scars, referred to as stretched scars in the hair transplantation field, often require revision surgery or secondary hair grafting into the scar. We hypothesise that stretched scars present a unique transcriptional signature different from other types of scars. To determine the gene expression profile of stretched scars, we used Affymetrix microarrays to perform profiling of fibrotic dermis and the surrounding patient-matched healthy dermis.

overall_design: We collected full-thickness skin samples from 3 patients who had their stretched scars excised for aesthetic reasons. The samples were approximately 1 cm x 2 cm and consisted of mature (at least 4 years old) and wide (at least 5 mm) scars and the surrounding healthy skin. All scars formed post-surgically on occipital scalps after excision of skin needed for harvesting hair follicles during a Follicular Unit Transplantation (FUT) surgery. The scar and healthy dermis were dissected from 20 µm-thick sections of the sample and RNA was isolated using RNeasy Plus Mini Kit (Qiagen). RNA was used to synthesize first-strand complementary DNA (cDNA) using Nugen Ovation V2. This was then converted to double-stranded cDNA, and used as a template for in vitro transcription to generate cRNA using the Nugen Encore Biotin Module. The cRNA was then transferred for hybridization and scanning onto the GeneChip™ Human Genome U133 Plus 2.0 Array. Transcriptomic Analysis Console (TAC) was used to perform a one-way ANOVA on the dataset to identify 442 transcripts that were significantly (P < 0.01) and differentially (fold change <- 1.5 or > 1.5) regulated between the dermis of stretched scars and the surrounding healthy skin. We used Ingenuity Pathway Analysis (IPA) to find the diseases & functions that these differentially expressed genes were involved in and define transcripts of proteins that are expressed extracellularly.

first: Claire

middle: A

last: Higgins

first: Greg

last: Williams


title: Tumor secretome and VEGF-C induce opposite transcriptomic changes in lymphatic endothelial cells

city: Liège

first: Bernard

last: Staumont

address: Avenue de l'Hôpital 11

country: Belgium

institute: University of Liège

summary: Within the tumor microenvironment, lymphatic endothelial cells (LEC) contribute to the remodeling and the formation of lymphatic vessels involved in the transport of metastatic and immune cells. Displaying an increasingly recognized plasticity and heterogeneity, tumor-associated LEC are expected to exert additional functions in the primary tumor environment. Using RNA sequencing data, we analyzed the transcriptomic changes induced in LEC in response to two different stimuli from the tumor microenvironment, i.e. vascular endothelial growth factor C (VEGF-C) and the tumor secretome of malignant cells. This analysis revealed that these two stimuli exert contrasting effects leading to distinct transcriptomic switches: a stimulation of pro-inflammatory factors (“secretory transcriptome”) induced by the tumor secretome versus an upregulation of cell cycle-associated pathways (“lymphangiogenic transcriptome”) induced by VEGF-C. These data help to better understand the phenotypic reprogramming of LEC caused by their interaction with tumor cells and pro-lymphangiogenic factors, opening the door for further investigations to decipher the diversity of LEC subpopulations and their diverse roles in lymphangiogenic conditions and the tumor microenvironment.

overall_design: RNA profiling of lymphatic endothelial cells (LEC) stimulated with: (i) conditioned medium of LEC themselves (naive LEC/control; 3 samples), (ii) conditioned medium of HaCaT-II-4 tumor cells (teLEC, 4 samples) , or (iii) VEGF-C at 400 ng/ml (VEGF-LEC, 4 samples)

first: Marie

last: Ebroin

first: Marc

last: Joiret

first: Liesbet

last: Geris

first: Agnès

last: Noël


title: Yap1 ChIP-seq in Pten/Smad4-deficient mouse prostate cancer cells

city: Houston

first: Guocan

state: TX

address: 1515 Holcombe Blvd, T7.3900

institute: MD Anderson Cancer Center

summary: Yap1 is a critical transcription coactivator in the Hippo pathways. However, its target genes are not well defined in prostate cancer cells. To determine the downstream transcriptional targets and pathways of Yap1 in Pten/Smad4-defiicent mouse prostate cancer cells, ChIP-seq was performed in the Pten/Smad4-deficient mouse prostate cancer cells.

overall_design: ChIP-seq was performed in Pten/Smad4-deficient mouse prostate cancer cells.

first: Zheng

middle: D

last: Lan

first: Ming


title: Cas9 interactions with host RNAs and transposable elements impair neurodevelopment

city: Guangzhou City

first: Denghui

last: Chen

address: No. 74 Zhongshan 2nd Road

department: Zhongshan School of Medicine

institute: Sun Yat-sen University

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

overall_design: Refer to individual Series


title: Cas9 interactions with host RNAs and transposable elements impair neurodevelopment (irCLIP-seq)

summary: The CRISPR (clustered regulatory interspaced short palindromic repeats)/ Cas9 (CRISPR-associated protein 9) system-based precise genome editing has revolutionized biomedical studies. As the CRISPR/Cas9 system has been also recently considered to permanently cure genetic diseases via human germline genome editing, a careful risk assessment of this genome engineering tool is required in human early development. Here we perform comprehensive analysis to evaluate the potential impact of Cas9 in human early embryogenesis. We find that even in the absence of synthetic guide RNA, Cas9 can be still guided by endogenous RNAs, and cut the genome of human embryonic cells at low frequency, and the resulting DNA damage induces the intrinsic immune response. Moreover, Cas9 interferes with the spliceosome, and with the suppressor machinery (e.g. L1TD1, APOBEC3G and PIWIL4) of LINE-1 (L1) retrotransposition. Even the transient presence of Cas9 in human embryonic cells induces robust de novo L1 retrotransposition that exacerbates DNA damage, and results in compromised neurodevelopment. Besides the ethical issues, these inevitable and detrimental Cas9-associated impacts on human embryonic development raise such serious safety concerns as to question the clinical use of human germline genome editing.

overall_design: We first established a hESC line that expressed Cas9 (fused with FLAG) under doxycycline treatment and then performed irCLIP-seq experiments of Cas9. Two replicate Cas9 irCLIP libraries were sequenced.

first: Yuanglang

last: Hu

first: Ruiqi

last: Li

first: Chuanbo

last: Sun

first: Mingzhu

last: Yang

first: Hanwen

last: Yu

first: Jichang


title: A Heated tobacco product ‘IQOS’ exposure enhances apoptosis and emphysema in mice lungs

city: Hongo

first: Naoko

last: Nitta

state: Bunkyo-ku

department: Respiratory medicine

institute: Juntendo university

summary: To assess the mechanism which caused emphysema in the IQOS group, we performed microarray analysis using homogenate lung tissue that were exposed to fresh air, IQOS aerosol, or cigarette smoke for 6 months. In microarray-based analysis, gene expressions to the air group were different in the IQOS and CS group, and apoptosis-related pathways were enhanced in the IQOS  group. Apoptosis-related protein (cytochrome c, cleaved caspase-3, and cleaved PARP1) expression in the IQOS group were higher than air group in homogenete lungs. More single-stranded DNA and TUNEL positive alveolar cells were found in the IQOS group than control significantly.

overall_design: Twelve-week-old C57BL6/J male mice were divided into 3 groups; air-exposed, IQOS aerosol-exposed, and CS-exposed group, and exposed for 6 months. Microarray analysis and pathway analysis using whole lung specimens were performed to determine gene-expression profiles.

middle: N

last: Arano

first: Tadashi

last: Sato

first: Moegi

last: Komura

first: Hitomi

last: Yoshikawa

first: Yohei

last: Suzuki

first: Aki

last: Mitsui

first: Eriko

last: Kuwasaki

first: Fumiyuki

last: Takahashi

first: Yuzo

last: Kodama

first: Kuniaki

last: Seyama

first: Kazuhisa


title: Dissecting gonadal cell lineage specification and sex determination during human development using a single-cell transcriptomics approach

first: Rui

last: WANG

address: No.5 Yiheyuan Road, Haidian District

department: Biodynamics Optical Imaging Center (BIOPIC)

summary: Gonadal somatic cells are the main players in gonad development and are important for sex determination and germ cell development. Here, using a time-series scRNA-seq strategy, we analyzed the fetal germ cells (FGCs) and gonadal somatic cells in human embryos and fetuses. Clustering analysis of testes and ovaries revealed several novel cell subsets, including POU5F1+SPARC+ FGCs and KRT19+ somatic cells. Furthermore, our data indicated that DLK1+ cells may be the progenitors of steroidogenic cell lineages in both sexes and that TAC1+ cells may be the progenitors of granulosa cells in females. Intriguingly, the testosterone synthesis function transitioned from fetal Sertoli cells to adult Leydig cells in a step-wise manner. Moreover, interactions between gonadal somatic cells were systematically explored and verified in our study. In detail, we observed that Sertoli cells interacted with Leydig cells through DHH-PTCH1 and PDGFA-PDGFRA/PDGFRB ligand-receptor gene pairs. More importantly, we identified cell type-specific developmental defects of both FGCs and gonadal somatic cells in a Turner syndrome embryo (45, XO). Our work provides a blueprint of the complex yet highly ordered development and interactions of human FGCs and gonadal microenvironment cells.

overall_design:
To further expand our understanding of the specification of gonadal somatic cells and sex differentiation in humans, we performed large-scale single-cell RNA sequencing (scRNA-seq) of gonadal cells in both sexes in a time series spanning gonad development from 6W to as late as 23W of gestation. In total, we obtained 56,399 gonadal cells from 16 embryos.

**The raw files have been uploaded to the Genome Sequence Archive (GSA) database (accession number HRA000344).

last: Wang

first: Xixi

last: Liu

first: Li


title: Expression data from 87 complex sarcomas

city: Bordeaux

first: ELodie

last: Darbo

address: 229 cours de l'Argonne

department: INSERM

institute: University of Bordeaux

summary:
Based on the transcriptome analysis of 555 sarcomas, we identified a group of tightly clustered leiomyosarcomas (LMS) due to their gene expression homogeneity. We named them “hLMS” and the other LMS “oLMS”. We derived a transcriptional signature able to identify each group and used it to classify patients from two independent cohorts. In all cohorts, hLMS were preferentially carried by women, located in the internal trunk, highly differentiated, and similarly altered at the genomic level. Based on integrative bioinformatic analysis, we show that hLMS originate from vascular smooth muscle cells presenting both contractile and synthetic characteristics, while oLMS could derive from fibroblasts. We found strong MYOCD expression to be an hLMS-specific driver and show that the MYOCD/SRF axis is essential only for hLMS survival. Identification of hLMS could become standard clinical practice, leading to the development of specific effective treatments with MYOCD/SRF inhibitors.
These 87 samples from leiomyosarcoma primary tumors were analysed on Affymetrix and Agilent platforms and both datasets were used to define genes with consistent expression between the platforms. These genes were then selected in other datasets from the two plaforms before combination and normalization.

overall_design: 87 Complex Sarcomas hybridized to Agilent-014850 Whole Human Genome Microarray 4x44K G4112F

first: Frédéric

last: Chibon


title: The hepatocyte insulin receptor is required to program rhythmic gene expression and the liver clock

city: Toulouse

first: Hervé

last: Guillou

address: 180 Chemin de Tournefeuille

department: ToxAlim

institute: INRAE


title: miRNA expression data from 39 leiomyosarcomas [miRNA-seq]

summary: Based on the transcriptome analysis of 555 sarcomas, we identified a group of tightly clustered leiomyosarcomas (LMS) due to their gene expression homogeneity. We named them “hLMS” and the other LMS “oLMS”. We derived a transcriptional signature able to identify each group and used it to classify patients from two independent cohorts. In all cohorts, hLMS were preferentially carried by women, located in the internal trunk, highly differentiated, and similarly altered at the genomic level. Particularly, miRNA from 39 leiomyosarcomas (LMS) classified as homogeneous and other LMS according to a mRNA transcriptional signature were sequenced, mapped to mature miRNA sequences  and analysed in order to evaluate miRNA impact on LMS biology and oncology. Based on integrative bioinformatic analysis, we show that hLMS originate from vascular smooth muscle cells presenting both contractile and synthetic characteristics, while oLMS could derive from fibroblasts. We found strong MYOCD expression to be an hLMS-specific driver and show that the MYOCD/SRF axis is essential only for hLMS survival. Identification of hLMS could become standard clinical practice, leading to the development of specific effective treatments with MYOCD/SRF inhibitors.

overall_design: miRNA from 39 leiomyosarcomas were sequenced wih HiSeq2500

first: Frederic


title: Expression data from 50 mixoid liposarcomas

summary: Based on the transcriptome analysis of 555 sarcomas, we identified a group of tightly clustered leiomyosarcomas (LMS) due to their gene expression homogeneity. We named them “hLMS” and the other LMS “oLMS”. We derived a transcriptional signature able to identify each group and used it to classify patients from two independent cohorts. In all cohorts, hLMS were preferentially carried by women, located in the internal trunk, highly differentiated, and similarly altered at the genomic level. Based on integrative bioinformatic analysis, we show that hLMS originate from vascular smooth muscle cells presenting both contractile and synthetic characteristics, while oLMS could derive from fibroblasts. We found strong MYOCD expression to be an hLMS-specific driver and show that the MYOCD/SRF axis is essential only for hLMS survival. Identification of hLMS could become standard clinical practice, leading to the development of specific effective treatments with MYOCD/SRF inhibitors.

overall_design: 50 mixoid liposarcomas hybridized to Agilent-014850 Whole Human Genome Microarray 4x44K G4112F

first: F


title: Transcriptomic profiling of human senescent cells in the setting of alpha-lipoic acid intervention

first: Yu

last: Sun

address: 320 Yueyang Rd, Life Sciences Building A #1508

department: Shanghai Institute of Nutrition and Health

institute: Chinese Academy of Sciences

summary: Aging and age-related pathologies can be delayed by specifically targeting the senescence-associated secretory phenotype (SASP), a hallmark feature of senescent cells. Achieving the goal using small molecule inhibitors would have a tremendous impact on the quality of lifespan and burden of age-related chronic diseases. We report the potential of alpha lipoic acid (ALA), a naturally existing antioxidant, in targeting senescent cells via induction of programmed cell death. This study demonstrates the impact of alpha-lipoic acid as a medicinal compound on the expression profile of senescent cells and provides a strong rationale for its future use in geriatric medicine.

overall_design: Examination of in vitro efficacy of alpha-lipoic acid, a non-sedating antioxidant with evidence of efficacy in the medication of symptomatic diabetic neuropathy that has not been evaluated in the setting of fibromyalgia treatment, in treating human senescent cells. This assay was performed beyond previous studies reporting alpha-lipoic acid's antioxidant and anti-inflammatory effects as a traditional herbal medicine, as well as its efficacy in improvement of inflammatory diseases and diabetes.

first: Liu

last: Han


title: Reinforcement of DNA methylation in CHH context through  RNA-directed DNA methylation ensures sexual reproduction in rice

city: Nanjing

first: Lili

address: Weigang No.1

institute: Nanjing Agricultural University


title: Reinforcement of DNA methylation in CHH context through RNA-directed DNA methylation ensures sexual reproduction in rice [sRNA-seq]

summary: DNA methylation is an important epigenetic mark that regulates the expression of genes and transposons. RNA-directed DNA methylation (RdDM) is the main molecular pathway responsible for de novo DNA methylation in plants. Although the mechanism of RdDM has been well understood in Arabidopsis, mutations in RdDM genes cause no visible developmental defects in Arabidopsis. Here, we isolated and cloned Five Elements Mountain 1 (FEM1), which encodes RNA-dependent RNA polymerase 2 in rice. Mutation in OsRDR2 abolished the accumulation of 24-nt small interfering RNAs, and consequently substantially decreased genome-wide CHH methylation levels. Moreover, male and female reproductive development was disturbed, which led to the sterility of osrdr2 mutants. We discovered that OsRDR2-dependent DNA methylation likely regulates the expression of multiple key genes involved in stamen development and meiosis. In wild-type (WT) plants but not in osrdr2 mutants, genome-wide CHH DNA methylation levels were greater in panicles, stamens, and pistils than in seedlings. The global increase of methylation in reproductive organs of the WT was mainly explained by the enhancement of RdDM activity including OsRDR2 activity. Our results, which revealed a global increase in DNA methylation through enhancement of RdDM activity in reproductive organs, demonstrate the crucial role of OsRDR2 in the sexual reproduction of rice.

overall_design: small RNA sequencing data

first: Dong-Lei

last: Yang


title: microRNA Expression Study of chicken CD3-28-4+ intraepithelial lymphocyte natural killer cells infected with very virulent Infectious Bursal Disease Virus

city: Serdang

first: Boo

last: Sook Yee

state: Selangor

address: Universiti Putra Malaysia

department: Institute of Bioscience

country: Malaysia

institute: Universiti Putra Malaysia

summary:
Infectious bursal disease is an acute immunosuppressive viral disease which significantly affect the economic in poultry industrial. Infectious bursal disease virus (IBDV) infection was known to destroy B lymphocytes, activate macrophage and T lymphocytes, but there are limited studies on the impact of IBDV infection on chicken intraepithelial Natural killer (IEL-NK) cells.
The main objective of this study is to determine the innate immune response of chicken IEL-NK cells towards very virulent IBDV (vvIBDV) infection. Specific pathogen free (SPF) chickens were infected with vvIBDV for 0, 1 and 3 dpi. The IEL-NK cells were isolated and enriched from total IEL cells using the 28.4+ antibodies. The microRNA sequencing was conducted in MiSeq system and approximately 1.6 to 3.6 million single reads generated per sample. The differential expression analysis was performed on the miRNA-Seq data. there are 35 and 16 sRNAs were differentially expressed at 1 and 3 dpi, respectively. The SNORD101, gga-miR-222a and gga-miR-221-3p were up-regulated on Day 1 and 3 whereas gga-miR-30a-50, gga-miR-142-5p, gga-miR-32-5p and gga-miR-146b-5p were down-regulated on both days.
gga-miR-217-5p and gga-miR-222b-5p with the highest fold change were involved in the regulation of tumor growth and apoptosis by targeting the MAPK signaling pathway. The vvIBDV replication was suppressed by overexpression of gga-miR-21 at 3 dpi. Some of the miRNAs were up-regulated with unknown reasons but the same findings were showed in other publications such as gga-miR-3538 and gga-miR-2954 which were up-regulated after being infected by other viruses, but the roles of these miRNA are not clear.

overall_design: The miRNA-Seq data for 3 groups of samples (uninfected chicken, chicken infected by vvIBDV for 1 day and chicken infected by vvIBDV for 3 days) in triplicate was generated using MiSeq

last: Yee

first: Yeap

last: Keong


title: Expression data from the dermis of human established scars before and after hair follicle transplantation

first: Magdalena

last: Plotczyk

summary: Human hair follicles undergo repetitive cycles of growth throughout their lifetime. During the hair follicle cycle, functional and structural changes occur within the surrounding skin environment. However, skin that experienced a deep injury lacks cycling hair follicles and turns into a mass of unremodelled scar tissue. We hypothesise that re-introducing cycling hair follicles into human scars will stimulate skin remodelling improving fibrotic tissue. To determine the transcriptional events underlying remodelling of scar dermis after hair follicle transplantation, we used Affymetrix microarrays to perform profiling of scar dermis before (0 mo), and at three time points after hair transplantation transplantation: 2, 4, and 6 months.

overall_design: During the study, 3 mm punch biopsies were taken from the scar dermis from each patient at four time points: prior to transplantation (time point 0 mo), then again at 2, 4, and 6 months after hair follicle transplantation. The scar dermis was dissected from 20 µm-thick sections of the biopsies and RNA was isolated using RNeasy Plus Mini Kit (Qiagen). RNA was used to synthesize first-strand complementary DNA (cDNA) using Nugen Ovation V2. This was then converted to double-stranded cDNA, and used as a template for in vitro transcription to generate cRNA using the Nugen Encore Biotin Module. The cRNA was then transferred for hybridization and scanning onto the GeneChip™ Human Genome U133 Plus 2.0 Array. Transcriptomic Analysis Console (TAC) was used to perform a one-way ANOVA on the dataset to identify 719 transcripts that were significantly (P < 0.01) and differentially (fold change <- 1.5 or > 1.5) regulated the four time points (0 mo, 2 mo, 4 mo, 6 mo). We used Ingenuity Pathway Analysis (IPA) to find the upstream regulators of the transcriptomic changes in human scars after hair follicle transplantation at three time points: after 2, 4, and 6 months.

first: Claire

last: Higgins

first: Colin

last: Boyle

first: Francisco

last: Jiménez Acosta


title: Effect of LPS on gene expression and the role of Lamin-A

city: Zurich

first: giancarlo

last: russo

state: Schweiz

address: winterthurerstrasse 190

department: Functional Genomics Center Zurich

institute: ETH/University of Zurich

summary: We report here the RNA-Seq data for WT_BMDMs_Untreated, WT_BMDMs_LPS Treated, LAMIN-A-KO_BMDMs_Untreated and Lamin-A--KO_BMDMs_LPS Treated

overall_design: Examination of effect of LPS on gene expression and the role of Lamin-A

first: N

last: Jaiin


title: An integrative analysis of genome-wide methylation and expression in ameloblastoma

city: Bangkok

first: Nakarin

last: Kitkumthorn

address: Yothi

country: Thailand

institute: Mahidol University

summary: We integrate methylation array data and RNA Seq data to identify genes controlled by DNA methylation

overall_design: Genomic DNA was extracted from fresh frozen tissue using standard phenol chloroform and was later converted by sodium bisulfite treatment using an EZ DNA Methylation-GoldTM Kit (Zymo Research, Irvine, CA, USA) according to the manufacturer’s instructions.


title: Identification of ETV4-responsive genes in NSCLC cells

city: Shijiazhuang

first: Lingxiao

last: Xing

state: Hebei

address: No.361 East Zhongshan Road

institute: Hebei Medical University

summary: H1703, H1299, and H358T cells treated with or without si-ETV4 were used to screen the global profiling of human long-noncoding RNAs (lncRNAs) and protein-coding transcripts.

overall_design: To identify the molecular mechanism underlying the ETV4-mediated increase in cancer growth and progression, we performed human microarray analyses to compare protein-coding transcripts levels in H1703, H1299, and H358T cells treated with or without si-ETV4.


title: ChIP Seq of influenza specific primary, memory and secondary CD4+ T cells [In Vivo]

city: Vancouver

first: Martin

last: Hirst

state: British Columbia

address: 2125 East Mall

department: Microbiology and Immunology

country: Canada

institute: University of British Columbia

summary: Immune responses to infection involve a careful balance: too weak a response allows pathogen replication; too strong risks immunopathology. The immunoregulatory cytokine IL-10 is a key factor in this balance, but the impact of IL-10 is context-dependent and current understanding of the factors that regulate IL-10 is incomplete. In this study, we demonstrated that the infection induced cytokine IL-27 promotes IL-10 expression in CD4+ T cells by directing epigenetic changes in H3K4me3, H3K27me3, H3K4me1 and H3K27Ac modifications at the Il10 locus. We showed that primary activation of antigen-specific CD4+ T cells, in the context of murine influenza infection, led to the long-term remodelling of the epigenetic landscape at both the Il10 promoter and a distinct active enhancer element ~ 25 kb upstream of the TSS. Intact IL-27 signalling was an essential requirement for these persistent epigenetic changes in memory CD4+ Tcells. We identified CREB1 as a transcription factor binding the Il10 active enhancer, and we showed that the ability of IL-27 to promote IL-10 expression was dependent on the histone acetyl transferase activity of the CREB1 complex member, p300. Together our data provide mechanistic insight into the action of IL-27 in regulating an immune response. We suggest that infection-induced cytokine signals direct epigenetic changes that moderate cytokine output in response to T cell receptor stimulation, regulating immune activity at sites of infection.

overall_design: 20 samples; naïve B6, primary (Day 10), memory (Day 35), secondary (Day 6)

first: Alireza

last: Lorzadeh

first: Nicolette

last: Fonseca

first: Michelle

last: Moksa

first: Misha

last: Bilenky

first: Stephen

last: Redpath

first: Amy

last: Shergold

first: Aria

last: Jazdarahee

first: Billy

last: Zhao

first: Georgia

middle: P

last: Wright


title: Transcriptome and alternative splicing analyses of aged gastrocnemius.

city: Boston

first: Ronald

last: Neppl

state: MA

address: 60 Fenwood Rd.

department: Orthopedic Surgery

institute: Brigham and Women's Hospital, Harvard Medical School

summary: We used a high read depth (>75 million reads per sample) RNA sequencing to determine how the expression and splicing of genes change with advancing age.

overall_design: Paired end whole transcriptome profiles were generated from mouse gastrocnemius muscles, in duplicate, at 3, 12, 24, and 30 months of age

first: Linh

middle: K

last: Chu

first: Eun-Joo

last: Lee


title: Reinforcement of DNA methylation in CHH context through RNA-directed DNA methylation ensures sexual reproduction in rice [RNA-seq]

first: Lili

last: Wang

overall_design: Transcriptome sequencing

first: Dong-Lei

last: Yang


title: ChIP Seq of influenza specific primary, memory and secondary CD4+ T cells [InVitro]

overall_design: 36 samples;  naïve VertX, naïve VertX TCCR, in vitro VertX, in vitro VertX TCCR


title: Expression array of DNMT1 inhibitor treated 3 AML cell lines

city: Collegeville

first: Shawn

middle: W

last: Foley

state: PA

address: 1250 S. Collegeville Rd

department: Oncology

institute: GlaxoSmithKline

summary:
Genome wide demethylation by DNMT1 inhibitor GSK3484862 results in up-regulation of epigenetically-silenced genes
Differential expression was perfomed for each cell line following DNMT1 inhibitor or vehicle treatment. Differentially epressed gene lists were submitted to gene set enrichment analysis (GSEA) to identify consistently changed pathways.

overall_design: Three AML cell lines were treated for 96 hours in biological duplicate with 0.1% DMSO, DNMT1 specific inhibitor 1 µM GSK3484862, or an inactive compound  GSK3510477 before isolating RNA, labeling, and hybridizing to Affymetrix GeneChip® Human Genome U1331 Plus 2.0 arrays.

first: Melissa

middle: B

last: Pappalardi

first: Michael

middle: T

last: McCabe

first: Wendy

last: Kellner

first: Kathryn

last: Keenan


title: ChIP Seq of influenza specific primary, memory and secondary CD4+ T cells

first: Martin

last: Hirst

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

overall_design: Refer to individual Series


title: The roles of Zbtb11 in embryonic stem cell proliferation and survival

first: Vlad

middle: Cezar

last: Seitan

address: Guy's Hospital

department: Medical & Molecular Genetics

institute: King's College London

summary:
Zbtb11 is a transcription factor conserved in vertebrates. Mutations in its human gene cause a form of inherited intellectual disablity, while in zebrafish Zbtb11 mutations lead to impaired hematopoesis and neruonal development.
To determine the genes regulated by Zbtb11 we generated an inducible KO ES cell line (Zbtb11 lox/lox, Rosa26 ERt2-Cre) that allows the rapid depletion of Zbtb11 upon treatment with 4-hydroxytamoxyfen (4OHT). We subsequently performed RNA-seq in Zbtb11 KO and control cells to determine differentially expressed genes.
Upon Zbtb11 deletion 310 genes changed expression. Integration of the RNA-seq data with Zbtb11 ChIP-seq data (GEO series GSE125047) allowed us to distinguish between genes directly regulated by Zbtb11 and indirect changes. 204 differentially expressed genes were bound by Zbtb11, while 106 did not have Zbtb11 binding sites. Directly regulated genes were significantly enriched in genes with mitochondrial functions, while indirectly controlled genes were enriched for p53 targets. In agreement with these findings Zbtb11 KO led to impaired respiration, proliferation arrest and cell death.

overall_design: RNA-seq to determine differentially expressed genes upon induction of Zbtb11 KO. Directional RNA-seq was performed to compare transcripts in Zbtb11 lox/lox, Rosa26 ERt2-Cre mouse ES cells treated with 4-hydroxytamoxifen (4OHT) (Zbtb11 KO) or ethanol (EtOH) (control) for 72 hours. To control for non-specific effects of 4OHT on gene expression, we also compared EtOH-treated Zbtb11 lox/lox, Rosa26 ERt2-Cre cells with 4OHT-treated Zbtb11 wt/wt, Rosa26 wt cells.

first: Brooke

last: Wilson

first: Alan

last: Hodgkinson


title: Reinforcement of DNA methylation in CHH context through RNA-directed DNA methylation ensures sexual reproduction in rice [Bisulfite-seq]

overall_design: whole genome wide DNA methylation data by bisulfite sequencing


title: H2A.W is essential for silencing of whole genome heterochromatin in Arabidopsis

city: Taipei

first: Paoyang

last: Chen

state: Taiwan

address: 128 Sec. 2, Academia Rd, Nankang, Taipei 11529 Taiwan, R.O.C.

country: Taiwan

institute: Academia Sinica

summary: Heterochromatin of flowering plants is occupied by histone variant H2A.W and marked by DNA and H3K9 methylation. The relative impact of these heterochromatic features on activity of Transposable Elements (TEs) remains largely unknown. We obtained mutants deficient for H2A.W and key components controlling each of the key heterochromatic pathway in Arabidopsis and observed that knock out of individual pathway does not affect in a major manner TEs activity. However, when we combine the loss of H2A.W with any of the other heterochromatin controller we observe synergistic effects on heterochromatin compaction as well TEs activity. H2A.W appears to control expression of all TEs while each other heterochromatin controller target distinct subsets of TEs. We also observe an impact of linker histone H1. We propose that H2A.W acts together with several components of heterochromatin to prevents activity of distinct sets of TEs activity and chromatin architecture. Synergistic action with H2A.W is more prominent specifically in pathways controlled by the plant specific DNA chromomethyltransferases, CMT2 and CMT3.

overall_design: To study the role of H2A.W in the regulation of whole genome heterochromatin in Arabidopsis, we used high-throughput RNA-Seq and BS-seq approaches to investigate key mutants and double mutants potentially involved in RdDM pathways and chromatin structures.  The samples include WT, and mutants of h2aw, h1 double, h2aw/h1 quadruple, kyp6, h2aw/kyp6, nrpd2a, h2aw/nrpd2a, drm2-2-55103, h2aw_drm2-2-55105, cmt2-3, h2aw/cmt2-3

first: Ramesh

last: Yelagandula

first: Archana

last: Allishe

first: Jui-Hsien

last: Lu

first: Pao-Yang

first: Fredric

last: Berger


title: Next Generation Sequencing Facilitates Quantitative Analysis and Comparisions of Bone Marrow, Blood and Tumor-infiltrating Neutrophils

city: Singapore

first: Kaibo

last: Duan

address: 8A Biomedical Grove, Immunos Building, Level 4

institute: Singapore Immunology Network

summary: We report that tumor-infiltrating neutrophils are significantly different from their bone marrow and circulating neutrophils counterparts. We generated a heatmap clustering of the differentially expressed genes between the neutrophils from the three compartments, and identified four distinct gene clusters. Notably, genes in cluster 1 were down-regulated in tumor neutrophils, and comprised of genes involved in the adaptive immune response (GO:0002250). By contrast, genes in cluster 4 were up-regulated in tumor neutrophils, and consisted of genes involved in chemokine-mediated signalling pathway (GO:0070098) and positive regulation of cellular metabolic process (GO:0031325). We observed several cellular metabolic processes were up-regulated, suggesting a change in the metabolic signature of neutrophils that infiltrate the tumor. In conclusion, the distinct metabolic signature led us to hypothesize that the pronounced glycolytic profile of tumor-infiltrating neutrophils mediates pro-tumoral activity and PDAC progression.

overall_design: Examination of differential neutrophil populations in tumor-bearing mice

first: Je Lin

last: Sieow

first: Siew Cheng

last: Wong


title: Expression array of DNMT1 inhibitor treated AML cell lines

first: Shawn

last: Foley

summary: Genome wide demethylation by DNMT1 inhibitor GSK3484862 results in up-regulation of epigenetically-silenced genes. Differential expression was perfomed for each cell line following DNMT1 inhibitor or vehicle treatment. Differentially epressed gene lists were submitted to gene set enrichment analysis (GSEA) to identify consistently changed pathways.

overall_design: Seven AML cell lines were treated for 96 hours in biological duplicate with 0.1% DMSO or 1 µM GSK3484862 before isolating RNA, labeling, and hybridizing to Affymetrix GeneChip® Human Genome U1331 Plus 2.0 arrays.

first: Melissa


title: Expression data of mRNA from kidney of SD rats with chronic exposure to cadmium

city: Guangzhou

first: Guanghai

last: Wang

address: Shatainan Road 1023

department: School of Public Health

institute: Southern Medical University

summary:
Cadmium accumulation in kidney results in an irreversible chronic toxicity, but the underlying mechanisms are not clear. Transcriptomics assay may provide insight for the involved complex molecular networks.
We used Affymetrix RTA arrays to detail the global gene expression profile of kidney tissues of SD rats with chronic exposure to Cadmium, and identified distinct classes of cadmium exposure related mRNA and pathways.

overall_design: The rat kidney was harvested at 3 points of time in terms of period of cadmium exposure (1 day, 6 weeks, 12 weeks) for RNA extraction and hybridization on Affymetrix mRNA arrays.

first: GuangHai

first: YaoTang

last: Deng

first: Ke

last: Huang

first: Fei

last: Zou


title: Cerebellar abiotrophy in working Kelpies with a later clinical onset

city: CAMPERDOWN

first: Annie

last: Pan

state: NSW

address: Reagent Crescent

department: School of Life and Environmental Sciences

country: Australia

institute: University of Sydney

summary: Australian working Kelpie dogs are known to be affected with an autosomal recessive form of inherited cerebellar ataxia (cerebellar abiotrophy, CA) that is characterised by a degeneration of Purkinje and granule cells in the cerebellar cortex. The clinical signs of CA include cerebellar ataxia, head tremor, motor in-coordination, wide based stance and high stepping gait, with varied clinical onset age. The clinical and pathological features are similar to cerebellar ataxias in humans. The genome-wide association study on a group of working Kelpies affected with the later onset form of CA identified a region on chromosome 9 to be strongly associated with the disease phenotype. Homozygosity analysis and whole genome sequencing identified a missense single nucleotide polymorphism, that segregated with the CA phenotype.

overall_design:
9 cases and 154 healthy controls
Please note that the .ped file contains the total 172 sample data including the additional 9 control sample data (306-311, 316-18 whose raw data is unavailable).

middle: Y

first: Claire

last: Wade

first: Rosanne

last: Taylor

first: Peter

last: Williamson


title: Delivery of a tissue derived extracellular matrix gel modulates early fibro-adipogenic cell behavior and improves recovery following both acute and chronic disuse muscle injury.

status: Public on Dec 30 2022

city: Fayetteville

first: Jeffrey

last: Wolchok

address: 1 University of Arkansas

institute: University of Arkansas

summary:
To evaluate decellularized skeletal muscle extracellular matrix hydrogel effectiveness in treating shoulder cuff tears using a rabbit (RI) model. Male New Zealand white rabbits had supraspinatus tendon severed and were housed for 12 weeks, after which they had tendon reattached and half of rabbits also received an extracellular matrix gel injection.
We then performed gene expression profiling analysis using data obtained from RNA-seq from rabbit supraspinatus muscles (n=5 for repair+gel treatment, n=5 for repair only treatment , n=4 for injured control) at 2 weeks post and (n=5 for repair+gel treatment, n=5 for repair only treatment , n=5 for uninjured control) at 12 weeks post treatment

overall_design: Comparative gene expression profiling analysis of RNA-seq data from rabbit supraspinatus muscle tissues between uninjured, injured, repair only and repair+gel treatment

first: Tai

last: Huynh

first: Chris

last: Slavin


title: Microarray mRNA expression profiling in Stat5b knockdown pancreatic beta cell line

city: Thiruvananthapuram

first: Malini

last: Laloraya

state: Kerala

address: Thycaud PO, Poojappura

department: Department of Molecular Reproduction,

country: India

institute: Rajiv Gandhi Centre for Biotechnology,

summary: Stat5b gene is located at IDD4 type 1 diabetes susceptibility interval, and is mutated in NOD mice. This mutation has been linked to diabetes with strong association with autoimmune aetiology. We have treated MIN6 pancreatic beta cell line with Stat5b siRNA and analyzed the differential expression profile in control siRNA treated versus Stat5b siRNA treated cells in an effort to understand the role of Stat5b in diabetes.

overall_design: MIN6 cells were treated with control siRNA or Stat5b siRNA for 72 hours, followed by prolactin stimulation.  The cells were trypsinized and total RNA isolated using miRNeasy Mini Kit (Qiagen). The mRNA differential expression was compared using Illumina microarray platform.

first: Annu

last: Joseph


title: DNA methylation profiling for CCD-18Co cells stably transfected with an artificial P16 DNA methyltransferase (P16-Dnmt)

city: Beijing

first: Baozhen

last: Zhang

address: Fuchenglu No.52

department: Dept Aetiology

country: China

institute: Peking University Cancer Hospital and Institute

summary:
Differential methylation between human normal fibroblast cell CCD-18Co transfected with P16-Dnmt or pTRIPZ control vector was identified using Illumina HumanMethylation 850K array.
The genome-wide methylation detection experiment was carried out by CapitalBio Technology Company.

overall_design: Bisulphite converted DNA from the 4 samples were hybridised to the Illumina Infinium 850k Human Methylation Beadchip.

first: Dajun


title: Identification and Bioinformatic Analysis of CircRNAs in the Plasma of Patients with Very Severe Chronic Obstructive Pulmonary Disease

city: Hefei

first: Yichuan

last: Ding

state: Anhui

address: No. 81 Meishan Road

institute: Anhui Medical University

summary: The differential expression of circular RNAs (circRNAs) in individuals with very severe chronic obstructive pulmonary disease (COPD) and healthy individuals was screened using microarray technology. The related functions and mechanisms were analyzed using bioinformatic methods to explore the potential of target circRNAs as biomarkers of COPD and provide insights for future pathogenesis.

overall_design: Blood samples from three patients with very severe COPD and three healthy controls were randomly selected.

first: Sihui

last: Tang


title: Transcriptomic and methylation analysis of susceptible and tolerant grape genotypes following P. viticola infection

city: Lisbon

first: Vanessa

last: Azevedo

address: Campo Grande

department: Plant Biology Department

country: Portugal

institute: Biosystems & Integrative Sciences Institute

summary:
Downy mildew, caused by the biotrophic oomycete Plasmopara viticola, is one of the most economically significant grapevine diseases worldwide. Current strategies to cope with this threat rely on the massive use of phytochemical compounds during each cultivation season. The economic costs and negative environmental impact associated with these applications increased the urge to search for alternative strategies for sustainable disease control. Improved knowledge on plant mechanisms able to counteract pathogen infection may allow the development of alternative strategies of plant protection.
Epigenetic regulation, in particular DNA methylation, is emerging as a key factor in the context of plant-pathogen interactions, associated with the expression modulation of defense genes. To improve our understanding of the genetic and epigenetic mechanisms underpinning grapevine response to P. viticola, we studied the modulation of both 5-mC methylation and gene expression at 6 and 24 hours post-infection (hpi). Leaves of two table grape genotypes (Vitis vinifera), selected by breeding activities for their contrasting level of susceptibility to pathogen, were analysed. Following pathogen infection, we found variations in the 5-mC methylation level and in the gene expression profile. The results indicate a genotypic-specific response to pathogen infection. The tolerant genotype (N23/018) at 6 hpi exhibits a lower methylation level compared to the susceptible one (N20/20), and its shows an early modulation (at 6 hpi) of defense and epigenetic-related genes during P. viticola infection. These data suggest that the timing of response is an important mechanism to efficiently counteract the pathogen attack.

overall_design: Two grapevine genotypes were analysed at two timepoints (6 and 24hpi) comparing 2 treatments (mock and inoculated). Each RNA sample was a pool of  three biological replicates.

first: Loretta

last: Daddiego

first: Maria

middle: F

last: Cardone

first: Giorgio

last: Perrella

first: Lisete

last: Sousa

first: Rita

last: Santos

first: Rui

last: Malhó

first: Carlo

last: Bergamini

first: Antonio

last: Marsico

first: Andreia

last: Figueiredo

first: Fiammetta

last: Alagna


title: Functional study of Rbbp5 in preimplantation embryos

first: Jie

state: Beijing

address: Tsinghua University

department: Basic Medical Sciences, School of Medicine

institute: Tsinghua University

summary: We performed RNA-sequencing, ChIP-sequncing and Brif-sequencing on Rbbp5 knockout (KO) and wild-type (WT) mouse ICM and E5.0 epiblast. Our results showed that Rbbp5 KO lead to significant reduction of H3K4me3 modification at early blastocyst stage. The change in H3K4me3 landscape occured before the transcriptome change.  Moreover, Rbbp5 KO specifically affected epiblast lineages the most at late blastocyst stage and the KO embryos died at E5.5.

overall_design: Single-cell RNA-seq of wild-type (WT) and Rbbp5 knock-out (KO) E3.5 ICM, E4.5  epiblast, E4.5 primitive endoderm, E4.5 trophectoderm and E5.5  epiblast. H3K4me3 ChIP-seq of WT and Rbbp5 KO E3.5 ICM and E5.5 epiblast. ATAC-seq of E3.5 WT and Rbbp5 KO ICM. Brif-seq analysis of DNA methylome of WT and Rbbp5 KO single E4.5 epiblast cells.

first: Peizhe

last: Wang


title: RNA expression profiles in bile

city: Houston

first: exRNA

last: BRL

address: One Baylor Plaza

department: Molecular & Human Genetics - Milosavljevic

institute: Baylor College of Medicine

summary: Compare small RNA expression in bile from normal vs. cancer patients and using different kits.

overall_design: The study sought to characterize the extracellular RNA in human bile samples. Samples were collected from biliary tubes placed at the time of surgery.

first: Tushar

last: Patel

first: Irene

last: Yan


title: Analysis of microRNAs in response to cycloastragenol treatment by small RNA sequencing in Arabidopsis thaliana

city: ISTANBUL

first: Wissem

last: Mhiri

address: DAVUTPASA MAH. DAVUTPASA CADDESI ESENLER

department: chemistry

country: Turkey

institute: Yildiz technial university

summary: Purpose:we aimed to demonstrate the effects of cycloastragenol on the different plant signaling mechanisms and analyze microRNAomic responses in order to demonstrate its potential as a new key molecule to help plants overcome different environmental stresses. Methods: smallRNA-seq was employed to give a quantitative profile of microRNA expression and to identify new micro RNAs and  in treated and non-treated A. thaliana calli. We sequenced two cDNA libraries developed from A. thaliana (wild type Col-0) calli, one non-treated and the other is treated with 1µM cycloatragenol. Reads were filtered, mapped, aligned and then compared to the reference annotation (miRBase database). Clean data was analyzed using different software in order to  identify differentilly expressed miRNAs and their target genes. Results were validated by qRT-PCR using TaqMan and SYBER green assays. Results: We mapped more than 31 and 30 million tags from, respectively, control and CAG-treated samples. After filtration and mapping, a total of 273 known micro RNAs, 298 novels expressed miRNAs and 6160 target genes were identified, among which a total of 119 miRNAs and 961 target genes showed differential expression between control and treated sample with a p value < 0.05. Nine miRNAs, which have been chosen randomly, were validated with qRT-PCR. SmallRNA-seq data had a linear relationship with qRT-PCR for a goodness of fit (R2) of 0.938.

overall_design: Small RNAs response to cycloastragenol of two samples (Control and 1µM) and an elucidation of the differentially expressed sRNAs in Arabidopsis calli (developed in three biological repetitions for each sample)

first: W

first: Ö

last: Çakır

first: N

last: Turgut-Kara

first: B

last: Nalbantoğlu