title: SNP genotyping of Highland Wild dogs, New Guinea Singing Dogs, and a dingo.

city: Bethesda

first: Heidi

middle: G

last: Parker

state: MD

address: 50 South Dr. Rm 5347

department: CGB

institute: NHGRI

summary: SNP genotyping was used to determine if the free living Highland Wild dogs of Papua, Indonesia are the ansestors of captive New Guinea Singing Dogs.

overall_design: DNA was collected from free living Highland Wild dogs and dingo and captive New Guinea singing dogs. SNPs were genotyed using the Illumina CanineHD SNP chip. These SNPs were analyzed using distance measures, maximum likelihood, haplotype sharing and admixture tools to examine the genetic history of wild dogs.

first: Elaine

last: Ostrander

first: James

last: McIntyre

last: Davis

first: Suriani

last: Surbatki


title: Pharmacological Inhibition of PPARγ Reverses HIV Latency but Prevents Viral Production/Infectivity while Boosting Th17 Functions

status: Public on Mar 31 2020

city: Montréal

first: Jean-Philippe

last: Goulet

state: Québec

address: C.P. 6128, succursale Centre-ville

country: Canada

institute: Université de Montréal

type: Expression profiling by high throughput sequencing

summary: In addition to HIV-permissiveness factors, Th17-cells express PPARγ, a transcriptional repressor of specific genes including RORγt and HIV. Here, we investigated the effect of PPARγ pharmacological inhibition on HIV replication and Th17 functions. As predicted, T-cell receptor triggering in the presence of the PPARG antagonist T0070907 increased IL-17A production and cell-associated HIV-RNA levels in T-cells of HIV-infected ART-treated individuals. Unexpectedly, T0070907 inhibited HIV-RNA release/viral outgrowth ex vivo and transmitted/founder HIV replication in vitro. Whole genome RNA-sequencing revealed multiple genes/pathways modulated by T0070907, including those involved in HIV-permissiveness (e.g., CCR5, furin) versus HIV-restriction (e.g., TRIM22, BST2, miR29), as well as Th17-effector functions (e.g., RORγt, STAT3, BCL6, IL-17A/F, IL-21, IL-22, IL-26). Of note, T0070907 boosted IL-21, a cytokine exhibiting immune-regulatory and miR-29-mediated antiviral properties. miR-29 antagomir failed to restore HIV replication in T0070907-treated T-cells, indicative of a pleiotropic antiviral program triggered by PPARG antagonism.

overall_design: 8 patients, 2 conditions: DMSO, T007

first: Delphine

last: Planas

first: Yuwei

last: Zhang

first: Maria

middle: J

last: Ruiz

first: Laurence

middle: R

last: Marchand

first: Augustine

last: Fert

first: Tomas

last: Wiche Salinas

first: Huicheng

last: Chen

first: Annie

last: Gosselin

first: Jean-Pierre

last: Routy

first: Nicolas

last: Chomont

first: Petronela

last: Ancuta


title: DNA methylation analysis of HCT116 after knockdown of LIG1, UHRF1, or luciferase (control)

status: Public on Mar 26 2020

city: Grand Rapids

first: Scott

last: Rothbart

state: MI

address: 333 Bostwick Ave NE

department: Center for Epigenetics

country: USA

institute: Van Andel Research Institute

type: Methylation profiling by genome tiling array

summary: In HCT116 colorectal cancer cells, UHRF1, LIG1, or luciferase was knocked down by shRNA followed by selection with puromycin for 2 days. DNA was analyzed 12 days after viral transduction.

overall_design: Bisulphite converted DNA from the 3 samples were hybridised to the Illumina Infinium MethylationEPIC BeadChip.

first: Robert

last: Vaughan


title: EPR (BC030870) ChIRP-Seq analysis in NMuMG mouse mammary gland

status: Public on Mar 20 2020

city: Milano

first: gabriele

last: bucci

address: via olgettina 58

department: CTGB

country: Italy

institute: IRCCS Ospedale San Raffaele

summary: EPR, a lncRNA present in the chromatin fraction of NMuMG cells, controls proliferation and fate determination in mammary gland cells. We wanted to identify its genomic targets. We identified thousands of targets, many of them located in regulatory regions.

overall_design: Chromatin Isolation by RNA Purification (ChIRP) was performed according to the protocol published by Chu et al. (Mol.Cell 44, 667–678, 2011) in exponentially growing NMuMG cells. Two distinct pools (EVEN and ODD) of bio-TEG primers were utilized.

first: Roberto

last: Gherzi

first: Gabriele

last: Bucci


title: Acquired resistance to combined BET and CDK4/6 inhibition in triple-negative breast cancer

status: Public on Apr 08 2020

city: Boston

first: Kornelia

last: Polyak

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

type: Genome variation profiling by high throughput sequencing

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Chronic loss of STAG2 leads to altered chromatin structure contributing to deregulated transcription in AML

city: Belfast

first: Ken

last: Mills

address: 97 Lisburn Road

department: CCRCB

country: United Kingdom

institute: Queen's University Belfast

type: Genome binding/occupancy profiling by high throughput sequencing

summary: In this study, we use functional genomics to investigate the impact of chronic STAG2 loss on three-dimensional genome structure and transcriptional programming. We show that STAG1 partially functionally compensates for loss of STAG2 but that this leads to a shift in chromatin domain size with loss of smaller domain structure and the maintenance and formation of large domain interactions, leading to altered genome compartmentalization. Taken together this suggests differing functions for STAG1 and STAG2 containing cohesion complexes.  Additionally, the changes in genome structure driven by the chronic loss of STAG2 are linked with altered epigenetic marker deposition and changes in gene expression, including deregulation of the disease-relevant HOXA locus, which may contribute to disease development. Additionally, the altered genomic architecture driven by the chronic loss of STAG2 lead to altered MAPK signaling, resulting in increased sensitivity to MEK inhibition. This suggests that the altered genomic architecture induced by the chronic loss of STAG2 not only results in altered gene expression that may contribute to leukemogenesis but that this altered gene expression functionally affects cellular processes that may be therapeutically targeted in the future.

overall_design: Comparison of gene expression, chromatin binding, histone modification and genome interactions between WT and delta STAG2 OCI-AML3 cells.

first: James

middle: S

last: Smith

first: Stephanie

last: Craig

first: Fabio

last: Liberante

first: Katrina

middle: M

last: Lappin

first: Clare

last: Crean

first: Simon

last: McDade

first: Alexander

last: Thompson

middle: I

first: Kienan

last: Savage


title: Benzo[a]pyrene and dibenzo[def,p]chrysene in 3D primary human bronchial epithelial cells [RNA-seq]

status: Public on Mar 18 2020

city: Corvallis

first: Susan

middle: C.

last: Tilton

state: OR

address: 1007 ALS Bldg

department: AG Envr & Molec Toxicology

institute: Oregon State University

summary: In this study, we assess potential differences in mechanism of action for two PAHs, benzo[a]pyrene (BAP) and dibenzo-[def,p]chrysene (DBC), in a primary human 3D bronchial epithelial culture (HBEC) model based on short-term biosignatures identified from global transcriptional profiling.

overall_design: Fully differentiated bronchial epithelial cells (n=4 replicates) were treated with 500 µg/ml (19.80 nanomoles) benzo[a]pyrene (BAP), 10 µg/ml (0.35 nanomoles) dibenzo[def,p]chrysene (DBC) or acetone vehicle control for 48 hrs and isolated mRNA were sequenced on Illumina HiSeq 3000.

middle: C


title: Haploinsufficiency of RREB1 causes a Noonan-like syndrome via epigenetic reprogramming of RAS-MAPK pathway genes.

status: Public on Mar 13 2020

city: Toronto

first: Oliver

middle: A

last: Kent

state: ON

address: 101 College Street TMDT12-701

institute: University Health Network

summary: RREB1 is an epigenetic regulator of the RAS-MAPK pathway genes.

overall_design: RREB1-ChIP followed by sequencing in HEK293 cells.

first: Sujun

last: Chen

first: Hansen

last: He

last: Rottapel


title: Estrogen receptor β regulates skeletal muscle mass and muscle stem cell proliferation in young female mice

city: Tsukuba

first: Ryo

last: Fujita

state: Ibaraki

department: Transborder Medical Research Center

country: Japan

institute: University of Tsukuba

summary: The female sex hormone estrogens plays a critical role in maintaining muscle mass and muscle stem cell (MuSCs) functions. However, it is still unclear about downstream pathways of estrogens including its receptors that are expressed in both skeletal muscle tissue and MuSCs. To study the specific role of estrogen receptor β (ERβ), one of two main types of estrogen receptors, in skeletal muscle and MuSCs, we generated muscle-specific ERβ-knockout (mKO) mice and muscle stem cell-specific ERβ-knockout (scKO) mice. Here, we show that muscle-specific ERβ-deficient induced decreased muscle strength and fast-type muscle mass in young female mice. Furthermore, muscle stem cell-specific ERβ-deficient young female mice but not male exhibited impaired muscle regeneration ability after acute muscle injury, accompanied by a decreased proliferation rate of muscle stem cells. RNA sequencing analysis showed that the loss of ERβ in muscle stem cells changes the expression of cell cycle associated genes and niche component factors including laminin and collagen. Thus, our characterization of mKO and scKO mice indicate that the estrogen-ERβ pathway is a sex-specific regulatory mechanism that controls both skeletal muscle mass and the proliferation of muscle stem cell in females and could be of importance in a therapeutic context.

overall_design: mRNA profiles of primary satellite cells obtained from Control and ERβ cKO mice were generated by deep sequencing, in triplicate, using Illumina Miseq.

first: Yusuke

last: Ono


title: Genome-wide maps of chromatin state in saccharomyces cerevisiae

status: Public on Mar 12 2020

city: wuhan

first: Yu

last: Qi

state: Hubei

address: xujiapeng

department: College of life sciences

country: China

institute: Hubei university

summary: We report the application of single-molecule-based sequencing technology for high-throughput profiling of histone modifications in yeast. By obtaining  bases of sequence from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of saccharomuces cerevisiae.We find that H3T11 phosphorylationlysine is widely distributed in gene promoter region and chromosome telomere region

overall_design: Examination of H3T11 phosphorylation in yeast.


title: Comparison of miRNA between normal rat plasma exosomes and melatonin pretreated rat plasma exosomes

status: Public on Mar 27 2020

city: wenzhou

first: kankai

last: wang

address: wenzhou medical university

institute: wenzhou medical university

type: Non-coding RNA profiling by high throughput sequencing

summary: Stroke places a huge burden on society today, and great of studies were devoted for seeking safe and effective therapeutic strategy to improve the prognosis of stroke. Plasma exosome has exhibited its therapeutic potential against ischemia and reperfusion injury via ameliorating inflammation. To enhance therapeutic potential in patients with ischemic injury, we isolated exosomes from melatonin pretreated rat plasma and assessed the neurological protective effect in a rat model of focal cerebral ischemia. Treatment with melatonin enhanced plasma exosome therapeutic effect against ischemia induced inflammatory response and inflammasome mediated pyroptosis. In addition, we confirmed ischemic stroke induced pyroptotic cell death mainly occurred in microglia, while administration of melatonin treated exosome further effectively decreased infract volume and improved function recovery via regulation of TLR-4/NF-κB signaling pathway. Finally, the altered miRNAs profile in melatonin treated plasma exosomes demonstrated the regulatory mechanisms. This study suggests plasma exosome with melatonin pretreatment might be a more effective strategy for patients with ischemic brain injury. Further exploration of key molecules in plasma exosome may devote more therapeutic value for cerebral ischemic injury.

overall_design: Examination of miRNA differences in normal (n=3) and melatonin-treated (n=3) rat plasma exosomes

first: Kankai

last: Wang

first: Su

last: Yang


title: Comprehensive Analysis of the Translatome in High Fat Diet-Induced Liver Steatosis

status: Public on Mar 10 2020

city: Nanning

first: Lei

last: Zhou

state: Guangxi

address: Daxuedong Road, Xixiangtang District

department: College of Animal Science and Technology

institute: Guangxi University

summary: We performed translatome and transcriptome sequencing (RNC-seq and RNA-seq) on the livers of normal chow diet-, high-fat diet- and High-fat diet plus lycopene-fed mice.

overall_design: Total RNA and ribosome-bound RNA were extracted from the livers of normal chow diet- (control), high-fat diet- (HFD) and High-fat diet plus lycopene (HFD+LYC)-fed mice (three biological replicates per condition), and the polyA+ mRNA was sequenced using Illumina HiSeq X Ten sequencer. The reads were mapped to RefSeq RNA reference sequences and the expression level were quantified by rpkM calculation.

first: Zupeng

last: Luo

first: Hailong

last: Hu

first: Siqi

last: Liu

first: Zhiwang

last: Zhang

first: Yixing

last: Li


title: Microarray profiling analysis of lncRNAs expression in renal cell carcinoma cells

status: Public on Mar 15 2020

city: Shenyang

first: Yunhong

last: Zhan

address: No. 36 Sanhao Street

institute: Shengjing Hospital of China Medical University

summary: Despite sunitinib contributes to prolong the progression-free survival of metastatic renal cell carcinoma significantly, the universal presence of resistance limits the initial response rate and restricts durable responses. The mechanisms involved in sunitinib resistance vary and need further investigation. We found lncRNA CCAT1 overexpressed in sunitinib resistant cells while declined in the parental cells.  Moreover, lncRNA CCAT1 increased significantly in samples with resistance to sunitinib compared to those with responses to sunitinib. Impoverishment of CCAT1 suppressed cell growth and colony formation while triggered apoptosis. Inversely, the ectopic expression of c-Myc reversed the inhibition of cell growth and enhancement of apoptosis by sh-CCAT1. We also verified that anti-apoptosis protein Bcl-2 and Mcl-1 decreased along with the deregulation of CCAT1, whereas the expression of Bcl-2 and Mcl-1 restored in cells those were transfected sh-CCAT1 and c-Myc simultaneously. Apart from the in vitro experiments, we demonstrated that knockdown of CCAT1 boosted response to sunitinib by performing sunitinib-resistant ACHN mouse models. Briefly, lncRNA CCAT1 conferred renal cell carcinoma resistance to sunitinib in a c-Myc-dependent manner, providing novel target for improvement of sunitinib therapy.

overall_design: Three ACHN clones and three ACHN sunitinib-resistant clones were established in the present study. PCR arrays based LncRNA expression profiles were gained with nrStarTM Human Functional LncRNA PCR Array.


title: Human Breast Cancer cells: Control vs Treated with Palbociclib

status: Public on Apr 01 2020

city: Nanjing

first: kun

last: xu

address: 300 Guangzhou Road

institute: Department of Oncology, The First Affiliated Hospital of Nanjing Medical University

summary: Analysis miRNA profiling of breast cancer cells treated without or with palbociclib.Results provide insight into the molecular mechanisms involved in resistance to pabbociclib.

overall_design: Four breast cancer cell lines,MDA-MB-231, Hs578t, SK-BR-3 and MCF7 cells were treated with or without palbociclib.

first: Wenfei

last: Ji

first: Fang


title: RNA-seq of Stimulated/Recruited Renin Cells

status: Public on Mar 05 2020

city: Charlottesville

first: Omar

last: Guessoum

state: Va

address: MR4, 409 Lane Road

department: Biology

institute: University of Virginia

summary: This experiment was performed to study the expression profile of renin cells from mice subjected to homeostatic threat (hypotension). It was also used to compare expression of proliferation associated genes and tumor suppressors with existing cell line data.

overall_design: 2 Biological replicates with 2 technical replicates for a total of 4 samples.


title: Chromosomal instability associated with adverse outcome: a case report of patient with Nijmegen breakage syndrome and rapidly developed T-NHL with complex karyotype

status: Public on Apr 07 2020

city: Lublin

first: Monika

last: Szelest

address: ul. Antoniego Gębali 6

department: Laboratory of Genetic Diagnostics

country: Poland

institute: Medical University of Lublin

summary: Nijmegen breakage syndrome (NBS) is a rare genetic disorder inherited in an autosomal recessive pattern associated with an increased risk of developing lymphoproliferative disorders, mainly non-Hodgkin lymphoma (NHL) and acute lymphoblastic leukemia (ALL). This work presents a patient previously diagnosed with Nijmegen breakage syndrome who rapidly developed T-NHL despite of constant medical supervision. Cytogenetic karyotype and microarray tests revealed complex aberrations, indicating enhanced chromosomal instability.

overall_design: The microarray analyses were performed with the use of a CytoScan HD array. All laboratory procedures were carried out according to the manufacturers' protocols. The study was based on an analysis of scanned data files that was generated with the Chromosome Analysis Suite v 3.3 (ChAS, Thermo Fisher Scientific, Waltham, MA). Furthermore, the copy numbers of altered regions (CNAs) were calculated, and the data were normalized to a reference model (Thermo Fisher Scientific) of baseline reference intensities, NA 33 (hg19/CRCh37). The copy number states (CNS) and their breakpoints were determined with the use of the hidden Markov model (HMM) software package. The threshold levels of log2 ratio ≥0.5 and ≤0.5 were used for the categorization of the altered chromosomal regions as CNV gains and losses, respectively. The obtained data were analyzed based on two different criteria: genome-wide CNVs and leukaemia-associated region/gene-specific CNAs (leukaemia genes_all_20150505; Fullerton Overlap Map_hg19).

first: M

last: Włodarczyk

last: Lejman


title: Identification of miRNAs and Their targets in Colorectal Cancer (miRNA)

status: Public on Mar 02 2020

city: Shanghai

first: Fangbin

state: State...

address: Siping Road 1239

institute: Tongji University School of Medicine

summary: Background: Colorectal cancer (CRC) is one of the leading causes of cancer-related death worldwide. The roles of microRNAs (minRNAs) in mRNA destabilization and translational repression of this disease are well appreciated, their involvement in endonucleolytic cleavage of target mRNAs is poorly understood. Methods: High throughput small RNA sequencing was employed for the identification and profiling of miRNAs by six pairs of colorectal cancer tissues (CT) and their adjacent tissues (CN). GO (gene ontology) biological process analysis and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis was carried out to understand the role of regulated miRNAs in CRC. Results: Using high-throughput sequencing, we identified 1409 miRNAs in the CT and CN libraries, including 81 novel miRNAs. 420 conserved and eight novel differentially expressed miRNAs (DEmiRNAs) were identified by comparing the expression levels of CT libraries with CN libraries. Conclusions: Our findings may lead to a better understanding of the novel role of miRNA in the gene regulation of CRC.

overall_design: miRNA profiles of CRC were generated by deep sequencing using Illumina HiSeq2500

first: Yong

last: Dai


title: Dental cell type atlas reveals new stem and differentiated cell types in mouse and human teeth

status: Public on Feb 29 2020

city: New York

first: Ruslan

last: Soldatov

state: New York

address: 323 E 61st Street

department: Computational Oncology

institute: Memorial Sloan Kettering Cancer Center

summary: Reconstruction and engineering of human teeth are the tasks of utmost importance. Here we introduce detailed cellular atlas of the growing and non-growing mouse and human teeth including a condition with caries, which will enhance the field of dental engineering and lead to a better understanding of stem cell niche dynamics enabling tooth growth. We report previously unappreciated cellular complexity of the mouse incisor, including new spatially-restricted stem, progenitor and differentiated populations and compare this model system with the human adult, growing and caries-lesioned teeth. This comparison revealed specific parallelisms in mechanisms of dental growth in humans and mice.  Beyond the main mesenchymal and epithelial compartments, we demonstrate a surprising role of the immune system as a mediator of the epithelial-mesenchymal interactions required for proper development. Finally, our results brought new insights into the differentiation of cell lineages producing enamel and dentin, which should be of utmost importance for dental reconstructive engineering.

overall_design:
Analysis of cellular dynamics during homeostasis and maturation in human and mouse teeth using single-cell expression profiling

Please note that counts_SS2_16_257.txt (linked to the GSM4365617 records) was generated from both 'S2_16_257.PLP/YFP 3 days traced' and 'SS2_16_257.whole' samples, and the counts_SS2_17_014.txt (linked to the GSM4365621 records) from both 'SS2_17_014.Col2.3+' and 'SS2_17_014.DMP1+' samples.

first: Jan

last: Krivanek

first: Peter

middle: V

last: Kharchenko

first: Igor

last: Adameyko


title: Smooth muscle-derived progenitor cell myofibroblast differentiation through KLF4 downregulation promotes arterial remodeling and fibrosis

status: Public on Feb 20 2020

city: Aurora

first: Mary

last: Weiser-Evans

state: CO

address: 12700 East 19th Avenue, C281

department: Renal Diseases & Hypertension

institute: University of Colorado Anschutz Medical Campus

summary: Resident vascular adventitial SCA1(+) progenitor (AdvSca1) cells are essential in vascular development and injury. However, the heterogeneity of AdvSca1 cells presents a unique challenge in understanding signaling pathways orchestrating their behavior in homeostasis and injury responses. Using smooth muscle cell (SMC) lineage tracing models, we identified a subpopulation of AdvSca1 cells (AdvSca1-SM) originating from mature SMCs that undergo reprogramming in situ and exhibit a multipotent phenotype. Here we employed lineage tracing and RNA sequencing to define the signaling pathways regulating SMC-to-AdvSca1-SM cell reprogramming and AdvSca1-SM progenitor cell phenotype. Unbiased hierarchical clustering revealed that genes related to hedgehog/WNT/beta-catenin signaling are significantly enriched in AdvSca1-SM cells, emphasizing the importance of this signaling axis in the reprogramming event. Leveraging AdvSca1-SM-specific expression of Gli1, we generated Gli1-CreERT2-ROSA26-YFP reporter mice to selectively track AdvSca1-SM cells. We demonstrated that physiologically relevant vascular injury or AdvSca1-SM cell-specific Klf4 depletion facilitated the proliferation and differentiation of AdvSca1-SM cells to a pro-fibrotic myofibroblast phenotype rather than macrophages. Surprisingly, AdvSca1-SM cells selectively contributed to adventitial remodeling and fibrosis, but little to neointima formation. Together, these findings strongly support therapeutics aimed at preserving the AdvSca1-SM cell phenotype as a viable anti-fibrotic approach.

overall_design: RNA gene expression profile from mouse vascular smooth muscle cells (SMCs, 3 independent replicates), SMC-derived vascular AdvSca1 cells (AdvSca1-SM, 2 independent replicates) , and non-SMC-derived AdvSca1 cells (AdvSca1-MA, 2 independent replicates) sorted from aortae and carotid arteries of SMC lineage tracing mouse models, and AdvSca1-SM cells (3 independent replicates) from the aortae and carotid arteries of Gli1 lineage tracing mouse model. RNA gene expression profile of AdvSca1-SM cells sorted from injured (4 independent replicates) and uninjured (4 independent replicates) carotid arteries of SMC lineage tracing mouse model.

first: Sizhao

last: Lu

first: Austin

last: Jolly

first: Keith

last: Strand

first: Allison

last: Dubner

first: Marie

middle: F

last: Mutryn

first: Rebecca

last: Tucker

first: Karen

last: Moulton

first: Raphael

last: Nemenoff

first: Mark

middle: W

last: Majesky


title: Decoding the regulatory architecture of the maize leaf

status: Public on Mar 01 2020

city: Hong Hong

first: Silin

last: Zhong

address: Shatin, N.T.

department: School of Life Sciences

institute: CUHK

summary: Transcription factors (TF) binding is key to understanding and characterizing the effect of genetic variability on phenotypic differences. Here, we used a novel scalable ChIP-seq approach to annotate the regulatory landscape of the maize genome with binding data from 104 leaf TFs. TF binding regions co-localized with open chromatin regions, with ~70% of TF binding nearby genes. TF binding sites are evolutionarily conserved and show enrichment for GWAS-hits, cis-expression QTLs. Furthermore, the regulatory network shows characteristics of real-word networks such as scale-free topology and larger modularity than random graphs. Finally, machine-learning analyses reveal that sequence preferences are alike within TF families, and that TF co-localization is key for TF binding specificity. Our comprehensive TF-DNA interaction approach provides the starting point to decipher the gene regulatory system in plant leaves.

overall_design: ChIP-Seq for 104 maize leaf transcription factors. BioProject: PRJNA518749, SRA Study accession: SRP183225


title: RNA-Seq Analysis Illuminates the Early Stages of Plasmodium Liver infection

status: Public on Feb 22 2020

city: Chapel Hill

first: David

last: Corcoran

state: NC

address: 125 Mason Farm Rd

department: Genetics

institute: University of North Carolina at Chapel Hill

summary: The apicomplexan parasites Plasmodium spp. are the causative agents of malaria, a disease that poses a significant global health burden. Plasmodium spp. initiate infection of the human host by transforming and replicating within hepatocytes.  Yet, despite the liver stage being a critical step during infection, most transcriptomic studies have focused on more technically accessible stages of the Plasmodium life cycle, limiting our ability to target these parasites to prevent disease. We have conducted an extensive RNA-seq analysis of the Plasmodium berghei liver stage at high-resolution, covering early (2—18 hpi) and mid-stages (24—48 hpi) of the liver stage of infection. Our data revealed hundreds of genes are differentially expressed as early as 2 hours post-infection, and that multiple genes shown to be important for later infection may be upregulated as early as 12 hpi. Using hierarchical clustering along with co-expression analysis, we identified clusters functionally enriched for important liver-stage processes such as interactions with the host cell and redox homeostasis. Furthermore, some of these clusters were highly correlated to the expression of ApiAP2 transcription factors, while showing enrichment of mostly uncharacterized DNA binding motifs hinting at alternative uncharacterized targets during this stage. Our work represents a window into the previously undescribed transcriptome of the early LS upon host cell infection and offers a comprehensive view of the Plasmodium liver stage. Using the tractable organism P. berghei, our dataset provides a blueprint for future studies in the human-infective parasites, P. falciparum and P. vivax.

sample_organism:
Plasmodium berghei
Homo sapiens

platform_organism:
Plasmodium berghei
Homo sapiens

overall_design: Examination of Plasmodium berghei transcriptome in two hepatoma cell lines (HuH7/HepG2) over 8 time points (including time 0) with at least three replicates at each time point with a total of 34 samples from 0-48hpi.

first: Maria

last: Toro-Moreno

first: Kayla

last: Sylvester


title: Role of RBMX in the post-transcriptional control of homeotic genes

status: Public on Mar 04 2020

city: Trento

first: Erik

last: Dassi

state: TN

address: Via Sommarive, 9

department: CIBIO

institute: University of Trento

summary: Wild-type and RBMX-knockdown HEK293 cells where profiled at the transcriptome and translatome levels for the expression of 50 homeotic genes. Targeted RNA-seq libraries were built and sequenced on an Illumina MiSeq machine to allow for accurate gene expression quantification of this specific set of genes. To assess the binding of RBMX to the same set of mRNAs, RNA immunoprecipitation was also performed on HIS-HA tagged  RBMX expressing HEK293 cells.

overall_design: 5 biological samples per condition are used for the RIP samples, 5 per condition for the knock-down samples. A total of 32 samples were sequenced.


title: Platform effects on regeneration by pulmonary basal cells as evaluated by single-cell RNA sequencing [RNA-seq]

city: New Haven

last: Greaney

state: CT

address: 10 Amistad St

department: Biomedical Engineering

institute: Yale University

summary: Cell-based therapies have shown promise for treating myriad chronic pulmonary diseases through direct application of epithelial progenitors or by way of engineered tissue grafts or whole organs. To elucidate environmental effects on epithelial regenerative outcomes in vitro, we isolated and cultured a population of pharmacologically expanded basal cells (peBC) from rat tracheas. At peak basal marker expression we simultaneously split peBC into four in vitro platforms – organoid, air-liquid interface (ALI), engineered trachea, and engineered lung. Following differentiation, these samples were evaluated using single-cell RNA sequencing (scRNAseq) and computational pipelines were developed to compare samples both globally and at the population level. A sample of native rat tracheal epithelium was also evaluated by scRNAseq as a control for engineered epithelium. Overall this work identifies platform-specific effects that support the use of engineered models to achieve the most physiologic differential outcomes in pulmonary epithelial regenerative applications.

overall_design: Native rat tracheal epithelium characterization, characterization of basal cells under pharmacologic expansion at three passages, differentiation of peBC on four in vitro culture platforms

first: Taylor

last: Adams

first: Micha

last: Brickman Raredon


title: Platform effects on regeneration by pulmonary basal cells as evaluated by single-cell RNA sequencing

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

overall_design: Refer to individual Series


title: Discovery and validation of urinary molecular signature of early sepsis (discovery cohort)

city: Gainesville

first: Azra

last: Bihorac

state: FL

address: 1600 SW Archer Road

department: Medicine

institute: University of Florida

summary: Sepsis remains a diagnostic challenge with no gold-standard test. Urine provides a readily available, non-invasive biofluid with significant diagnostic potential. Urinary gene expression has been previously used for diagnosis and prognosis of urological malignancies and transplant allograft rejections, but remains unutilized for sepsis diagnosis. In this study, the authors use urinary gene expression profiles to both diagnose sepsis and characterize its pathophysiology. By using differential expression augmented with machine learning ensembles, the authors identify a collection of cellular mRNA from 239 genes in patient urine which show exceptional power in classifying septic patients from those with chronic systemic disease in both internal and independent external validation cohorts. Functional analysis indexes the disrupted biological pathways in early sepsis and additionally reveals key molecular networks driving its pathogenesis. This study serves a pioneering step towards expanding the clinical potential of urinary molecular profiles for application to systemic diseases.

overall_design: Urine was collected from 145 sepsis patients within 12 hours of sepsis onset. Urine was collected from 32 patients set to undergo vascular surgery within 4 hours before surgical incision.

first: Sabyasachi

last: Bandyopadhyay

first: Nicholas

last: Lysak

first: Lasith

last: Adhikari

first: Tezcan

last: Ozrazgat-Baslanti

first: Laura

last: Turizo

first: Larysa

last: Sautina

first: Rajesh

last: Mohandas

last: Lopez

first: Ricardo

last: Ungaro

first: Ying-Chih

last: Peng

first: Ferdous

last: Kadri

first: Parisa

last: Rashidi

first: Philip

last: Efron

first: Scott

last: Brakenridge

first: Lyle

last: Moldawer

first: Frederick

last: Moore

first: Henry

last: Baker

last: Segal


title: Discovery and validation of urinary molecular signature of early sepsis (validation cohort)

first: Azra

last: Bihorac

last: Bandyopadhyay

last: Lysak

first: Maria

first: Mark


title: Coding transcriptome analyses reveal altered functions underlying immunotolerance of PEG-fused rat sciatic nerve allografts

status: Public on Feb 19 2020

city: Austin

first: Tyler

middle: Aaron

last: Smith

state: TX

address: 2415 Speedway

department: Neuroscience

institute: The University of Texas at Austin

summary:
Purpose: Current methods to repair ablation-type peripheral nerve injuries (PNIs) using peripheral nerve allografts (PNAs) often result in poor functional recovery due to immunological rejection as well as slow and inaccurate outgrowth of regenerating axon sprouts.  In contrast, ablation-type PNIs repaired by PNAs using a multistep protocol, in which one step uses the membrane fusogen polyethylene glycol (PEG), permanently restore sciatic-mediated behaviors within weeks.  Axons and cells within the PNA remain viable, even though outbred host and donor tissues are neither immunosuppressed nor tissue matched.  PEG-fused PNAs exhibit significantly reduced T cell and macrophage infiltration, apoptosis, and expression of major histocompatibility complex I/II.  In this study, we analyzed the coding transcriptome of PEG-fused PNAs to determine possible mechanisms underlying immunosuppression.
Methods: Ablation-type sciatic PNIs in adult Sprague Dawley rats were repaired using PNAs and a PEG-fusion protocol combined with neurorrhaphy.  Electrophysiological and behavioral recovery tests confirmed successful PEG-fusion of PNAs.  RNA sequencing analyzed differential expression profiles of protein-coding genes between PEG-fused PNAs and NC PNAs (not treated with PEG) at 14d PO, along with Unoperated nerves.  Sequencing results were validated by Quantitative Reverse Transcription PCR (RT-qPCR).
Results: PEG-fused PNAs display significant downregulation of a great many gene transcripts associated with innate and adaptive allorejection responses.  Many Schwann cell-associated transcripts are upregulated, and many cellular processes such as extracellular matrix remodeling, cell and tissue development are particularly enriched.  Transcripts encoding several potentially immunosuppressive proteins (e.g. Thrombospondins 1 and 2) are upregulated in PEG-fused PNAs.
Conclusions: This study is the first to characterize the coding transcriptome of PEG-fused PNAs, and identifies possible links between alterations of the extracellular matrix and suppression of the allorejection response.  The results establish a molecular-basis to  understand mechanisms underlying PEG-mediated immunosuppression.

overall_design: PEG-fused sciatic nerve PNAs (n=3 animals) and NC sciatic nerve PNAs (n=3 animals) from outbred female Sprague Dawley rats were excised and sampled at 14d PO.  Both treatment groups were compared to Unoperated Control sciatic nerves (n=2 animals).  DNase I-treated Total RNA was extracted and poly-A-enriched libraries were prepared and then sequenced via HiSeq 3000 (Illumina).  Initial analyses were conducted sequentially by FastQC, Tophat2, HTSeq-count and DESeq2 software.  Subsequently, analyses of gene ontology (GO) biological processes, protein families, pathways, and protein-protein interaction analyses were performed.  Validation of RNAseq results for selected transcripts was performed via RT-qPCR.

first: Cameron

middle: L

last: Ghergherehchi

first: Haley

middle: O

last: Tucker

first: George

middle: D

last: Bittner


title: JMJD1A inhibits proliferation and aggressiveness of gastric cancer by up-regulating RUNX3

status: Public on Feb 12 2020

city: ShenYang

first: Ke

last: Ning

state: LiaoNing

address: PuHe street No.77

institute: China Medial University

summary: The histone demethylase JMJD1A（Jumoji domain containing 1A） is overexpressed in multiple cancers and promotes cancer progression. However, the role and mechanism of JMJD1A in gastric cancer remains poorly understood.Here, we found that JMJD1A could suppress gastric cancer cell proliferation, migration, invasion and xenograft tumor growth. Using RNA sequencing, we identified RUNX3 as a novel target gene of JMJD1A.

overall_design: Examination the total RNA change of JMJD1A depletion in SGC-7901 cells

first: Yangguang

last: Shao


title: Characterizing adult cochlear supporting cell transcriptional diversity using single-cell RNA-Seq: Validation in the adult mouse and translational implications for the adult human cochlea

city: Bethesda

first: Michael

last: Hoa

state: MD

address: 35 Convent Dr, Rm 1F-226

institute: National Institutes on Deafness and Other Communication Disorders, NIH

summary:
Characterizing adult cochlear supporting cell transcriptional diversity using scRNA-Seq
Hearing loss is a significant disability that impacts 432 million people worldwide. A significant proportion of these individuals are dissatisfied with or do not have access to available treatment options which include hearing aids and cochlear implants. An alternative approach to restore hearing would be to regenerate lost cells, including hair cells in the adult cochlea. Such therapy would require restoration of the organ of Corti’s complex architecture, necessitating regeneration of both mature hair cells and supporting cells. We characterize the first single-cell adult cochlear supporting cell transcriptomes with the goals of: (1) demonstrating their transcriptional distinctiveness from perinatal cochlear supporting cells, (2) providing a metric for future attempts at regenerating mature cochlear supporting cells by identifying both cell type-specific and regional-specific expression, and (3) identify cell cycle gene expression present in adult supporting cells at the single cell level which may establish a basis for targeting cell cycle regulation pathways to force these cells out of quiescence.

overall_design:
FACS-purified P60 and P120 Lfng-EGFP cochlear supporting cells scRNA-Seq on Fluidigm C1 platform

Grant information: ZIA DC000088-05

first: Matthew

last: Kelley


title: Discovery and validation of urinary molecular signature of early sepsis


title: A mevalonate bypass system facilitates elucidation of apicoplast biology in malaria parasites

status: Public on Feb 11 2020

city: Baltimore

first: Anne

middle: E.

last: Jedlicka

address: 615 N. Wolfe street

department: Molecular Microbiology and Immunology

institute: Johns Hopkins University, School of Public Health

summary: Malaria parasites rely on a plastid organelle for survival during the blood stages of infection. However, the entire organelle is dispensable as long as the isoprenoid precursor isopentenyl pyrophosphate (IPP) is supplemented in the culture medium. We engineered parasites to produce isoprenoid precursors from a mevalonate-dependent pathway, creating a parasite line that replicates normally after the loss of the apicoplast organelle. We show that carbon-labeled mevalonate is specifically incorporated into isoprenoid products, opening new avenues for researching this essential class of metabolites in malaria parasites. We also show that essential apicoplast proteins, such as the enzyme target of the drug fosmidomycin, can be deleted in this mevalonate bypass parasite line, providing a method to determine the roles of other important apicoplast-resident proteins. Several antibacterial drugs kill malaria parasites because they target basic processes, such as transcription, in the organelle. We used metabolomic and transcriptomic methods to characterize parasite metabolism after azithromycin treatment triggered loss of the apicoplast. These results provide insight into the effects of apicoplast-disrupting drugs, several of which have been used to treat malaria infections in humans. Overall, the mevalonate bypass system provides a way to probe essential aspects of apicoplast biology and study the effects of drugs that target apicoplast processes.

overall_design: Apicoplast negative PfMev parasites were cultured for 48 hours with samples taken every eight hours for transcriptomics and processed in quadruplicate, except for Time 24 Apicoplast Rep 1 and Time 0 Apicoplast Rep 4. Nf54 attB parasites without treatment were cultured for 48 hours with samples taken every eight hours and processed in quadruplicate, except for Time 48 Control which is in triplicate.

first: Russel

last: Swift

first: Krithika

last: Rajaram

first: Hans

last: Liu

first: Amanda

last: Dziedzic

first: Aleah

last: Roberts

first: Krista

last: Matthews

first: Hugo

last: Jhun

first: Namandje

middle: N

last: Bumpus

first: Shivendra

last: Tewari

first: Anders

last: Wallqvist

first: Sean

last: Prigge


title: Identifying the translatome of mouse NEBD – stage oocytes via SSP-profiling; a novel polysome fractionation method

city: Ceske Budejovice

first: Lenka

last: Gahurova

address: Branisovska 1760

department: Department of molecular biology and genetics

country: Czech Republic

institute: University of South Bohemia

summary: Meiotic maturation of oocyte relies on pre-synthesized maternal mRNA, the translation of which is highly coordinated in space and time. Here, we provide a detailed polysome profiling protocol utilising small SW55Ti ultracentrifugation tubes with a volume of 5 ml. This newly optimized method, named Scarce Sample Polysome Profiling (SSP-profiling), is suitable for both scarce and conventional sample sizes and is compatible with downstream RNA-seq to identify polysome associated transcripts. Utilising SSP-profiling we have assayed the translatome of mouse oocytes at the onset of nuclear envelope breakdown (NEBD); a developmental stage that has thus far remained unexplored. Our analyses have identified 1778 transcripts with moderate to strong polysome occupancy, including abundantly represented mRNAs encoding mitochondrial and ribosomal proteins, proteoasomal components, glycolytic and amino acids synthetic enzymes, proteins involved in cytoskeleton organization plus RNA-binding and translation initiation factors. In addition to transcripts encoding known players of meiotic progression, we have also identified several mRNAs encoding proteins of unknown function. Polysome profiles generated using SSP-profiling were more than comparable to those developed using existing conventional approaches, being demonstrably superior in their resolution, reproducibility, versatility, speed of derivation and downstream protocol applicability.

overall_design: 4 replicates of RNAseq datasets from polysomal (P) and non-polysomal (NP) fractions

first: Tomas

last: Masek

first: Andrej

last: Susor

first: Edgar

last: del Llano

first: Michal

last: Kubelka

first: Alexander

last: Bruce

first: Martin

last: Pospisek


title: Pro-neuronal activity of Myod1 due to promiscuous binding [ATAC-seq]

status: Public on Feb 03 2020

city: Singapore

first: Qian Yi

last: Lee

address: Biopolis Drive

department: R&D

country: Singapore

institute: Nuevocor

summary: Basic helix-loop-helix (bHLH) pioneer transcription factors Myod1 and Ascl1 are biochemically related but produce fundamentally different outcomes when expressed in fibroblasts: Myod1 produces muscle cells and Ascl1 induces neurons. Here, we sought to investigate the molecular mechanisms explaining the differential activity. Surprisingly, we found a large overlap in the overall binding patterns of Ascl1 and Myod1 in fibroblasts, with both transcription factors accessing both neuronal and myogenic targets. We also observed similar changes in chromatin accessibility and transcriptional activation.  Yet, Myod1 predominantly induced a muscle program and Ascl1 a neuronal program. We found that differences in binding affinity at key targets resulted in largely distinct reprogramming outcomes. Accordingly, exchanging Myod1’s C-terminal protein-protein interacting domain and DNA-binding basic domain with those of Ascl1 induces an Ascl1-like binding and converts Myod1 into a pro-neuronal factor. Finally, we found that co-expression of Myod1 with the transcriptional repressor Myt1l inhibits induction of the muscle program and yields functional neuronal cells. Our findings are compatible with the notion that pioneer factor activity is associated with high-affinity protein-DNA and suggest that promiscuous binding of pioneer factors can induce unspecific lineage features which need to be kept in check by co-factor interactions.

overall_design: ATAC-seq was performed on MEF+Myod1 48hr post-dox induction. New data was analyzed together with existing data on MEF alone, MEF+rtTA and MEF+Ascl1 (GSE101397) to determine differences in chromatin accessibility in MEFs when overexpressing either Myod1 or Ascl1

first: Qian

middle: Y

first: Moritz

last: Mall

first: Michael

last: Kareta

first: Orly

last: Wapinski

first: Rui

last: Li

first: Howard

last: Chang

first: Marius

last: Wernig


title: Pro-neuronal activity of Myod1 due to promiscuous binding [FLAG ChIP-seq mESC]

overall_design: FLAG ChIP-seq was performed 48hr post-dox induction on: mESC+rtTA (control), mESC+flagAscl1, mESC+flagMyod1.


title: Pro-neuronal activity of Myod1 due to promiscuous binding [RNA-seq]

overall_design: RNA-seq was performed on MEF+flagMyod1 48hr post-dox induction.


title: Pro-neuronal activity of Myod1 due to promiscuous binding


title: Pro-neuronal activity of Myod1 due to promiscuous binding [H3K27ac ChIP-seq]

overall_design: H3K27ac ChIP-seq was performed 48hr post-dox induction on: MEF alone (control), MEF+rtTA (control), MEF+flagAscl1 and MEF+flagMyod1.


title: RNA sequencing of Escherichia coli Nissle 1917 after HOCl stress

status: Public on Jan 23 2020

city: Birmingham

first: Rhea

last: Derke

state: Alabama

department: Microbiology

institute: University of Alabama at Birmingham

summary: RNA sequencing of Escherichia coli Nissle 1917 before and after HOCl treatment was perfomed to identify pathways that may be important in responding to oxidative stress caused by reachive chlorine species (RCS).

overall_design: Samples: 0 mins, 15 mins, and 30 mins post HOCl treatment (0.4 mM in MOPS minimal media). N= 3 for each sample type.

first: Micheal

middle: J

last: Gray


title: Pro-neuronal activity of Myod1 due to promiscuous binding [FLAG ChIP-seq]

overall_design: FLAG ChIP-seq was performed 48hr post-dox induction on: MEF+rtTA (control), MEF+flagAscl1, MEF+flagMyod1, MEF+flagMyod1+Myt1l and MEF+flagMyod1(Ascl1-basic+C-term) domain swap.

middle: S


title: Genome-wide maps of RNA Pol III subunits POLR3C, POLR3G, and PLOR3GL in ES-E14TG2a and primary MEF cells

status: Public on Jan 22 2020

city: Taipei

first: Wei-Yi

last: Chen

address: No. 155, Sec 2, Linong St.

department: Institute of Biochemistry and Molecular Biology

country: Taiwan

institute: National Yang Ming Chiao Tung University

summary: Mammalian cells contain two isoforms of RNA Polymerase III (Pol III) that differ in only a single subunit, with POLR3G in one form and the related POLR3GL in the other form. Previous research indicates that POLR3G and POLR3GL are differentially expressed, with POLR3G expression being largely restricted to embryonic stem cells (ESCs) and tumor cells in contrast to the ubiquitously expressed POLR3GL. To date, the functional differences between these two subunits remain largely unexplored, especially in vivo. Here, we show that POLR3G and POLR3GL containing Pol III complexes bind the same target genes and assume the same functions both in vitro and in vivo and, to a certain degree, can compensate for each other in vivo. Moreover, an observed defect in the differentiation ability of POLR3G knockout ESCs can be rescued by exogenous expression of POLR3GL. Interestingly, POLR3G knockout mice die at a very early embryonic stage, whereas POLR3GL knockout mice complete embryonic development without noticeable defects but die at about 3 weeks after birth with signs of both general growth defects and potential cerebellum-related neuronal defects. The different phenotypes of the knockout mice likely reflect differential expression levels of POLR3G and POLR3GL across developmental stages and between tissues and insufficient amounts of total Pol III in vivo.

overall_design: Genome-wide binding/occupancy profiling of RNA Pol II and RNA Pol III subunits POLR3C, POLR3G, and POLR3GL by ChIP-seq in ES-E14TG2a and primary MEF cells

first: Xiaoling

last: Wang

first: Rebert

middle: G

last: Roeder


title: Histone Exchange is Associated with Activator Function at Transcribed Promoters and with Repression at Histone Loci

status: Public on Jan 09 2020

city: Geneva

first: Julien

last: Soudet

address: 30 quai Ansermet

department: BICEL

country: Switzerland

institute: Université de Genève

summary: Transcription in eukaryotes correlates with major chromatin changes, including the replacement of old nucleosomal histones by new histones at the promoters of genes. The role of these histone exchange events in transcription remains unclear. In particular, the causal relationship between histone exchange and activator binding, preinitiation complex (PIC) assembly, and/or subsequent transcription remains unclear. Here, we provide evidence that histone exchange at gene promoters is not simply a consequence of PIC assembly or transcription but instead is mediated by activators. We further show that not all activators up-regulate gene expression by inducing histone turnover. Thus, histone exchange does not simply correlate with transcriptional activity, but instead reflects the mode of action of the activator. Last, we show that histone turnover is not only associated with activator function but also plays a role in transcriptional repression at the histone loci.

overall_design: ChIP-seq of newly incorporated HA-tagged H3 and total H3 in G1-phase synchronized cells upon depletion of TBP

first: Sari

last: Kassem

first: Paolo

last: Ferrari

first: Amanda

last: Hughes

first: Oliver

last: Rando

first: Michel

last: Strubin


title: Genomic Landscape and Therapeutic Targets of Adenosquamous Carcinoma of the Pancreas [ATAC-seq]

status: Public on Jan 14 2020

city: Scottsdale

first: michael

middle: thomas

last: barrett

state: Arizona

address: 13400 east shea boulevard

institute: mayo clinic arizona

summary: We applied DNA content flow cytometry to a series of adenosquamous cancer of the pancreas (ASCP) tumor samples and patient derived xenografts (PDXs). We interrogated purified sorted tumor fractions from each sample with whole genome copy number variant (CNV) and whole exome sequencing (WES) analyses. These identified a variety of somatic genomic lesions targeting chromatin regulators in ASCP genomes that were superimposed on well characterized genomic lesions including mutations in KRAS and TP53, homozygous deletion of CDKN2A, and amplification of c-MYC, that are common in PDACs. Furthermore, a comparison of ATAC-seq profiles of ASCP and pancreatic ductal adenocarcinoma (PDAC) genomes using flow sorted PDX models distinguished genes with accessible chromatin in ASCP genomes including the lysine methyltransferase SMYD2, the pancreatic cancer stem cell driver RORγ, and a FGFR1-ERLIN2 fusion associated with focal CNVs in both genes. Organoids derived from these models were used to screen compounds of interest. Notably a FGFR inhibitor had significant activity against the FGFR1-ERLIN2 fusion positive PDX.

overall_design: Patient derived xenografts were flow sorted using DNA content to purify human tumor nuclei for downstream genomic and epigenomic analyses including ATAC-seq

first: Elizabeth

last: Lenkiewicz

first: Smriti

last: Malasi

first: Martin

last: Fernandez-Zapico

first: Derek

last: Cridebring

first: Tara

last: Hogenson

first: Mitesh

last: Borad

first: Kendall

last: Chambers

first: Nirakar

last: Rajbhandari

first: Tannishtha

last: Reya

first: Yuning

last: Xiong

first: Jeong-Heon

last: Lee

first: Zhenqing

last: Ye

first: Huihuang

last: Yan

first: Tamas

last: Ordog

first: Matthew

last: Hernandez

first: Jennifer

last: Leiting

first: Mark

last: Truty

first: Daniel

last: Von Hoff

middle: T

last: Barrett


title: Respiratory syncytial virus (RSV) F subunit vaccine with adjuvants affect immunity in BALB/c mice

status: Public on Jan 15 2020

city: Changchun

first: yu

last: zheng

address: 2699 Qianjin Street

department: Jilin University

institute: National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun

summary: Purpers: To verify the effect of adjuvants (Alhydrogel, AS02, AS03) on immunity of  BALB/c mice induced by RSV-F subunit vaccine at the level of gene expression. Methodes:Four groups ((1) RSV-F, (2) RSV-F + Alhydrogel, (3) RSV-F + AS02, and (4) RSV-F + AS03) were analyzed in the transcriptome sequencing experiment. On days 0 and 14,  vaccines were administered intramuscularly into the thigh muscle. 14 days after the last vaccination, blood samples from three  BALB/c mice in each group were collected. RNA degradation and contamination were assayed. Concentration were measured using a Qubit RNA Assay Kit and a Qubit 2.0 Fluorometer. RNA integrity was assessed using an RNA Nano 6000 Assay Kit and a Bioanalyzer 2100 system. 3 μg RNA per qualified sample was used as input material for RNA library preparation. Sequencing libraries were generated using a NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs, US), and unique index codes were added to each sample. Result: We obtained sample gene expression information. The subsequent differentially expressed gene GO and KEGG enrichment analysis result suggested that AS02 regulates immune balance by activating TLR-4 and promotes Th1-type immune responses.

overall_design: Total RNA transcriptome sequencing of four groups administered intramuscularly  RSV-F subunit vaccine with or without adjuvants

first: Yu

last: Zheng

first: Yong

last: Zhang


title: Acquisition of Cancer Stem Cell Properties in Osteosarcoma Cells by Defined Factors

city: Kobe-City

first: Shuichi

last: Fujiwara

institute: Kobe University

summary: Cancer stem cells (CSCs) are proposed to be unique subsets of clones within a tumor, attributed with tumor progression, resistance to chemotherapy, and metastases. However, little is known about the molecular mechanisms regulating the acquisition and maintenance of CSC properties in cancers, especially in rare cancers, such as osteosarcoma (OS). In this study, we generated OS cells with CSC properties following transduction of defined factors. This method enabled us to obtain abundant OS CSC material. The results of our study could facilitate a better understanding of the mechanisms of OS progression, and aid in the development of new therapies targeting CSCs in patients with OS.

overall_design: We used microarray analysis to identify changes in the expression of genes between the different cell groups.

first: Teruya

last: Kawamoto

first: Yohei

last: Kawakami

first: Yasufumi

last: Koterazawa

first: Hitomi

last: Hara

first: Toshiyuki

last: Takemori

first: Kazumichi

last: Kitayama

first: Shunsuke

last: Yahiro

first: Tomoyuki

last: Matsumoto

first: Takehiko

last: Matsushita

first: Takahiro

last: Niikura

first: Michiyo

last: Koyanagi

first: Toshihiro

last: Akisue

first: Takashi

last: Aoi

first: Ryosuke

last: Kuroda


title: Comprehensive transcriptome analysis regarding CDR1AS expression

status: Public on Jan 07 2020

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary: We determined the gene expression changes by URB597, a fatty acid amide hydrolase inhibitor, treatment.

overall_design: URB597 inhibits MICA shedding via an indirect mechanism. To determine the gene expression changes dependent on this inhibition, we used DMSO treated cells and URB597 treated cells for the cDNA microarrya analyses.

first: K

last: Sekiba

first: M

last: Otsuka

last: Koike


title: An integrative view of the regulatory and transcriptional landscapes in mouse hematopoiesis [ChIP-seq]

city: University Park

first: Ross

last: Hardison

state: PA

address: 303 Wartik Lab

institute: Pennsylvania State University

summary: Thousands of epigenomic datasets have been generated in the past decade, but it is difficult for  researchers to effectively utilize all the data relevant to their projects. Systematic integrative  analysis can help meet this need, and the VISION project was established for ValIdated  Systematic IntegratiON of epigenomic data in hematopoiesis. Here, we systematically  integrated extensive data recording epigenetic features and transcriptomes from many sources,  including individual laboratories and consortia, to produce a comprehensive view of the  regulatory landscape of differentiating hematopoietic cell types in mouse. By employing IDEAS  as our Integrative and Discriminative Epigenome Annotation System, we identified and  assigned epigenetic states simultaneously along chromosomes and across cell types, precisely  and comprehensively. Combining nuclease accessibility and epigenetic states produced a set of  over 200,000 candidate cis-regulatory elements (cCREs) that efficiently capture enhancers and  promoters. The transitions in epigenetic states of these cCREs across cell types provided  insights into mechanisms of regulation, including decreases in numbers of active cCREs during  differentiation of most lineages, transitions from poised to active or inactive states, and shifts in  nuclease accessibility of CTCF-bound elements. Regression modeling of epigenetic states at  cCREs and gene expression produced a versatile resource to improve selection of cCREs  potentially regulating target genes. These resources are available from our VISION website  (usevision.org) to aid research in genomics and hematopoiesis.

overall_design: One sample along with two input controls

first: Guanjue

last: Xiang

first: Cheryl

last: Keller

first: Elisabeth

last: Heuston

first: Belinda

middle: M

last: Giardine

first: Lin

last: An

first: Alexander

middle: Q

last: Wixom

first: Amber

last: Miller

first: April

last: Cockburn

first: Michael

middle: E

last: Sauria

first: Kathryn

last: Weaver

first: Jens

last: Lichtenberg

first: Berthold

last: Göttgens

first: Qunhua

last: Li

first: David

last: Bodine

first: Shaun

last: Mahony

first: James

last: Taylor

first: Gerd

last: Blobel

first: Mitchell

last: Weiss

first: Yong

last: Cheng

first: Feng

last: Yue

first: Jim

last: Hughes

first: Douglas

middle: R

last: Higgs

first: Yu

last: Zhang

middle: C


title: Cyclin K interacts with β-catenin to induce Cyclin D1 expression and facilitate tumorigenesis and radioresistance in lung cancer

city: Hubei,China

first: Yao

last: Guojun

address: Hubei,China

institute: Hua Zhong University of science and technology

summary:
Rationale: Radioresistance remains the major cause of local relapse and distant metastasis in lung cancer. However, the underlying molecular mechanisms remain poorly defined. This study aimed to investigate the role and regulatory mechanism of Cyclin K in lung cancer radioresistance.
Methods: Expression levels of Cyclin K were measured by immunohistochemistry in human lung cancer tissues and adjacent normal lung tissues. Cell growth and proliferation, neutral comet and foci formation assays, G2/M checkpoint and a xenograft mouse model were used for functional analyses. Gene expression was examined by RNA sequencing and quantitative real-time PCR. Protein-protein interaction was assessed by immunoprecipitation and GST pull-down assays.
Results: We report that Cyclin K is frequently overexpressed and correlates with poor prognosis in lung cancer patients. Functionally, we demonstrate that Cyclin K depletion results in reduced proliferation, defective G2/M checkpoint and enhanced radiosensitivity in lung cancer. Mechanistically, we reveal that Cyclin K interacts with and promotes the stabilization of β-catenin, thereby upregulating the expression of Cyclin D1. More importantly, we show that Cyclin D1 is the major effector that mediates the biological functions of Cyclin K in lung cancer.
Conclusions: These findings suggest that Cyclin K positively modulates the β-catenin/Cyclin D1 axis to promote tumorigenesis and radioresistance in lung cancer, indicating that Cyclin K may represent a novel attractive biomarker for lung cancer radiotherapy.

overall_design: Analysis of control and Cyclin K-siRNA lung cell lines obtained from 3 independent samples each.

first: Gang

last: Wu

first: Shuangbing

last: Xu

first: Guojun

last: Yao

first: Jing

last: Tang


title: Dissecting Expression Profiles of Gastric Precancerous Lesions and Early Gastric Cancer to Explore Crucial Molecules in Intestinal-type Gastric Cancer Tumorigenesis

status: Public on Mar 15 2020

city: Beijing

first: Yajing

state: Beijing

address: no.17 Panjiayuan Nanli

institute: Peking Union Medical College

summary: To investigate the changes in molecular expression, biological processes, stemness, immune microenvironment, tumor hallmark activities and co-expression relationships during intestinal-type gastric cancer carcinogenesis and to excavate the prognostic information contained in the carcinogenesis process. RNA expression profiles of ninety-four gastroscope biopsy samples with different stages of precancerous lesions or early gastric cancers and their paired controls were detected by Agilent Microarray.

first: Chengli


title: Differently expressed genes of the heart from sham and 5/6 nephrectomy mice

status: Public on Jan 04 2020

city: Chongqing

first: Yinghui

last: Huang

address: Shapingba

institute: Army medical university

summary: To examine genome wide transcriptional changes in the heart of 5/6 nephrectomy CKD mice, we performed microarray analysis using the Affymetrix Clariom S array.

overall_design: Mice were divided into two groups: sham (mice underwent laparotomy without kidney operation) and 5/6 nephrectomy CKD mice. n=3 mice per group.


title: Age Attenuates the Transcriptional Changes that Occur with Sleep in the Medial Prefrontal Cortex

status: Public on Jan 03 2020

city: Philadelphia

first: Allan

middle: I

last: Pack

address: 125 South 31st St

institute: University of Pennsylvania

summary: Sleep abnormalities are common with aging. Studies show that sleep plays important roles in brain functions, and loss of sleep is associated with increased risks for neurological diseases. In this study, we used next generation RNA-sequencing to explore effects of age on transcriptome changes between sleep and sleep deprivation in medial prefrontal cortex. Old mice showed a 30% reduction in the number of genes significantly altered between sleep/wake, and, in general, had smaller magnitudes of changes in differentially expressed genes compared to young. Gene ontology analysis revealed differential age-effects on certain pathways. Compared to young mice, many of the wake-active functions were similarly induced by sleep deprivation in old mice, whereas many of the sleep-active pathways were attenuated in old mice. We found similar magnitude of changes in a number of synaptic homeostasis genes (Fos, Arc, and Bdnf) induced by sleep deprivation, suggesting intact synaptic upscaling during extended wakefulness with aging. However, sleep-activated processes, such as DNA repair, synaptogenesis, and axon guidance, were sensitive to the effect of aging. Old mice expressed elevated levels of immune-related genes  when compared to young mice, and enrichment analysis using cell-type specific markers indicated up-regulation of microglia and oligodendrocyte genes in old mice. Moreover, gene sets of the two cell types showed age-specific sleep/wake regulation. This study indicates alteration of molecular changes with sleep in old mice.

overall_design: Medial prefrontal cortex of spontaneous sleep (SS) and sleep deprived (SD) young (2-4month) and old (18-20month) mice; SD were performed for 3, 6, 9, 12 hours since lights-on (7am) and compared to time-matched SS mice slept for >=75% of last hour before sacrifice. Mice were also randomly selected at ZT0 (baseline).

first: Xiaofeng

last: Guo

first: Brendan

last: Keenan

first: Dimitra

last: Sarantopoulou

first: Jie

last: Lian

first: Diane

last: Lim

first: Gregory

last: Grant


title: Genome-wide distribution of proteins ZAF1 and dCTCF in Drosophila embryos

status: Public on Jan 01 2020

city: Moscow

first: Natalia

last: Klimenko

address: 34/5 Vavilova Street

country: Russia

institute: Institute of Gene Biology (IGB) of the Russian Academy of Sciences

summary: Recently, the concept has arisen that a special class of architectural proteins exists, which are responsible not only for global chromosome architecture but also for the local regulation of enhancer–promoter interactions. Here, we describe a new architectural protein, with a total size of only 375 aa, which contains an N-terminal zinc finger-associated domain (ZAD) and a cluster of five C2H2 domains at the C-terminus. This new protein, named ZAD and Architectural Function 1 protein (ZAF1 protein), is weakly and ubiquitously expressed, with the highest expression levels observed in oocytes and embryos. The cluster of C2H2 domains recognizes a specific 15-bp consensus site, located predominantly in promotors, near transcription start sites. The expression of ZAF1 by a tissue-specific promoter led to the complete blocking of the eye enhancer when clusters of ZAF1 binding sites flanked the eye enhancer in transgenic lines, suggesting that the loop formed by the ZAF1 protein leads to insulation. The ZAF1 protein also supported long-range interactions between the yeast GAL4 activator and the white promoter in transgenic Drosophila lines. A mutant protein lacking the ZAD failed to block the eye enhancer or to support distance interactions in transgenic lines. Taken together, these results suggest that ZAF1 is a minimal architectural protein that can be used to create a convenient model for studying the mechanisms of distance interactions.

overall_design: ChIP-seq signal of the ZAF1 (two replicates) and dCTCF (one replicate) architectural/insulator proteins occupancy in whole embryo during embryonic development at 0-12h after egg-laying.

first: O

last: Maksimenko

first: N


title: Dysregulation of Lung Biology of Healthy Never Smokers Following Acute Inhalation of E-Cigarette Vapors

city: New York

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

summary: Little is known about the health risks to humans associated with smoking or “vaping” electronic cigarettes (EC). Based on the knowledge that the adverse effects of cigarette smoking are observed in the dysregulation of lung biology long before clinical abnormalities manifest, we assessed the hypothesis that acute exposure to EC vapors, with or without nicotine, modifies the biology of the lung of healthy never smokers. No significant changes in clinical parameters were observed following this brief exposure to EC vapors. However, marked changes were observed in the transcriptome of small airway epithelium and alveolar macrophage compared to baseline for both exposure groups with and without nicotine, and the group inhaling the nicotine containing vapors had elevated plasma endothelial microparticle levels. While additional studies are needed to ascertain long-term health risks of EC, this study provides preliminary in vivo data suggesting that EC vapors likely dysregulates normal human lung homeostasis, at least at the biologic level.

overall_design: Ten healthy never-smokers, with no history of exposure to any tobacco products or electronic cigarettes (EC), were assessed at baseline on day 1 with a questionnaire, chest X-ray, lung function, plasma levels of endothelial microparticles, and bronchoscopy with brushings to sample the small airway epithelium (10th–12th order bronchi) and bronchoalveolar lavage to obtain alveolar macrophages. One week later, subjects were trained how to use EC, and then inhaled 10 puffs of “Blu” brand EC, waited 30 min, then inhaled another 10 puffs. Of the n=10 subjects, n=7 were randomized to EC with nicotine and n=3 to EC without nicotine. Within 2 hr post-EC exposure, they were assessed with questionnaires, lung function, plasma EMP levels and repeat bronchoscopy with brushing and lavage.

first: Michelle

last: Staudt

first: Jacqueline

last: Salit

first: Robert

last: Kaner

first: Charleen

last: Hollman

first: Ronald

last: Crystal


title: Novel heart specific long non-coding RNAs contribute to pathogenesis of Arrhythmogenic Cardiomyopathy [ARVC patients' heart RV]

city: Houston

first: Jia

last: Li

state: Texas

address: 2121 W HOLCOMBE BLVD

department: CEDP

institute: Guangzhou Medical University

summary: Arrhythmogenic cardiomyopathy (AC) is an inherited cardiomyopathy characterized by fibrofatty replacement predominantly involved in right ventricle and clinically by ventricular arrhythmias.In this study, we set out to characterize the cardiac novel long-noncoding RNAs using deep RNA sequencing data from human heart tissues. Particularly, we identified AC specific novel lncRNAs that contribute to AC pathophysiology by comparing the lncRNAs transcripts of nine AC explanted hearts (RV), five non-diseased donor hearts (RV), four non-AC failing hearts (dilated cardiomyopathy, RV). To dissect the roles of novel lncRNAs in ARVC from LV, we also include six non-diseased donor hearts (LV) and six ARVC explanted hearts (LV) in the analysis. In the identified novel AC lncRNAs, a large part of them are derived from enhancer regions and acting as cis- elements to potentially regulate lipogenesis or lipid metabolism related genes. Finally, we validated several of these AC specific novel lncRNAs and their potential targets in independent patient samples. Collectively, we identified high-confidence AC specific novel lncRNAs from human samples and suggest their potential roles as cis- elements in AC pathology. Further study of these novel AC lncRNAs could provide new opportunities for diagnosis and therapeutic intervention.

overall_design: RNAseq for ARVC patients' heart RV

first: Liang

last: Zhang

first: Deqiang

last: Sun

first: Jiangping

last: Song

first: Shengshou

last: Hu


title: Characterization of the Endometrial Transcriptome in Early Diestrus Influencing Pregnancy Establishment in Dairy Cattle after Transfer of In-Vitro Produced Embryos

status: Public on Dec 31 2019

city: Kongens Lyngby

first: Haja

last: Kadarmideen

address: Richard Petersens Plads, Building 324

department: Department of Applied Mathematics and Computer Science

country: Denmark

institute: Technical University of Denmark

summary: In this study, we sequenced the RNA content of endometrial biopsies from Holstein cows at day 6-8 to identify candidate genes and describe biological mechanisms for endometrium receptivity and pregnancy establishment upon transfer of IVP embryos.

overall_design: 23 RNA-Seq profiles of endometrial biopsies collected from 23 Holstein cows on day 6-8 in dioestrus. In the same animals one in vitro produced embryo was transferred on day 6-8 in the following cycle. The pregnancy status was determined after slaughter on day 26-47.

first: Gianluca

last: Mazzoni

first: Hanne

last: Skovsgaard Pedersen

first: Maria

middle: B

last: Rabaglino

first: Poul

last: Hyttel

first: Henrik

last: Callesen


title: Conserved Arabidopsis response to oviposition and crude egg extract treatment

city: Lausanne

first: Philippe

last: Reymond

address: Biophore building

department: Department of Plant Molecular Biology

institute: University of Lausanne

summary: Although a seemingly harmless developmental stage of herbivores, insect eggs trigger efficient plant defenses that include necrosis, callus formation, accumulation of ovicidal compounds and release of volatiles to attract egg predators. The large white butterfly Pieris brassicae deposits batches of 20-30 eggs onto Arabidopsis leaves, causing a large transcriptional reprograming that is drastically distinct from the expression profile triggered by larval feeding. Also, P. brassicae eggs induce localized cell death, accumulation of reactive oxygen species (ROS) and salicylic acid (SA), and expression of PTI-related genes, suggesting that egg-associated molecular patterns (EAMPs) activate a response that is similar to the response induced by microbial pathogens. We previously reported that a crude P. brassicae egg extract (EE, soluble fraction from crushed eggs) induced similar responses as oviposition, including ROS and SA accumulation, cell death and defense gene induction. In order to compare oviposition and EE treatment at the transcriptome level, we analyzed changes in transcipt abundance with P. brassicae EE or after natural oviposition. After 5 days, hundreds of genes were significantly upregulated by each treatment and their induction was highly similar between treatments. This conserved transcriptomic signature thus strongly supports our previous observations that oviposition and EE treatment trigger comparable responses in Arabidopsis.

overall_design: For experiments with natural oviposition, 15 plants were placed in a 60 x 60 x 60 cm tent containing approximately 30 Pieris brassicae butterflies. After 24 h, four plants containing one egg batch on two leaves were placed in a growth chamber for 4 days. Just before hatching, eggs were gently removed with a forceps. For egg extract application, 2 x 2 µl of egg extract were spotted under the surface of each of two leaves of each treated plant. Four plants were treated with egg extract for 5 days. Treated or oviposited leaves were harvested and quickly stored in liquid N2. Untreated plants were used as controls. Total RNA from 3 biologically independent experiments was extracted using an RNeasy® plant mini kit (Qiagen). DNase treatment was added to the protocol. For cDNA synthesis, RNA samples were purified by NaAC 3M and EtOH precipitation. Library were synthetized from 500 ng of purified total RNA using the TrueSeq stranded mRNA kit (Illumina). RNA and library quality was assessed with a fragment analyzer from Advanced Analytical. Library were sequenced with the Illumina HiSeq 2500 sequencer at the Genomic Technologies Facility platform of the University of Lausanne (LGTF) (http://www.unil.ch/gtf/en/home.html).

first: Olivier

last: Hilfiker


title: Zebrafish whole brain single cell RNA-seq of nr1d1:VNP fish

status: Public on Dec 29 2019

city: Shanghai

first: Haifang

last: Wang

address: NO 320, Yue Yang Road

institute: Institute of Neuroscience

summary: we report a transgenic zebrafish line using destabilized fluorescent protein, Venus-NLS-PEST (VNP), driven by the promoter of a key circadian clock gene, nr1d1. This system allows us to monitor the development of single-cell circadian rhythm in live zebrafish larva in a cell-type specific manner. To identify the cell types expressing nr1d1:VNP in the whole brain, we conducted single cell RNA-seq (scRNA-seq) of ~15,000 cells dissociated from the brain of Tg(nr1d1:VNP) larval fish at 6.5dpf. Among them, 6514 cells were identified with number of genes > 500 and used for the following analysis. 26 cells clusters were classified from scRNAseq, and manually annotated by comparing the marker genes with the adult zebrfiash whole brain single cell RNA-seq data. The mRNA of nr1d1:VNP was enriched in photoreceptors in pineal gland, granule cells and purkinje cells in cerebellum, habenula cells as well as non-neuron cell.

overall_design: To identify the cell types expressing nr1d1:VNP in the whole brain, we conducted single cell RNA-seq (scRNA-seq) of ~15,000 cells dissociated from the brain of Tg(nr1d1:VNP) larval fish at 6.5dpf using 10X genomics.

first: Jun

last: Yan


title: DNA methylation data from renal cancer patient-derived xenograft tumor treated with temsirolimus or vehicle

city: Kyoto

first: Hiromasa

last: sakamoto

address: 54 Shogoinkawahara-cho, Sakyo-ku,

institute: Kyoto University Graduate School of Medicine

summary: We kept a primary xenograft models (KURC;Kyoto University Renal Cancer-3) derived from human renal cell carcinoma tissues, and 10 mg/kg of temsirolimus or vehicle was intraperitoneally administered.We performed DNA methylation analysis to compare the methylation profile of temsirolimus-treated primary xenograft tumors with that of vehicle-treated.

overall_design: We kept a patient-derived xenograft models (KURC3) derived from human renal cell carcinoma tissues. Ten mg/kg temsirolimus or vehicle only was intraperitoneally administered once a week.Once xenograft tumors had developed sufficiently, they were removed and transplanted into other SCID mice. Two weeks later, temsirolimus was re-administered to these mice, and this was repeated until tumors became completely resistant to temsirolimus  KURC3 developed resistance to temsirolimus. DNA methylation profiling was performed for two KURC3 xenograft tumors using the Infinium HumanMethylation450 BeadChip array (Illumina Inc.).

first: H

last: Sakamoto


title: Interaction of Va and Vc in somatic cell reprogramming

status: Public on Dec 17 2019

city: Guangzhou

first: Zheng

last: Hui

address: Kaiyuan Avenue 190

institute: GIBH

summary: Since VitaminA and VitaminC are pleiotropic vitamins, and both can promote reprogramming, we want to know the relationship between them. We use serum-free N2B27(B27 minus Va) medium to generate iPS with OKSM virus infecting OG2 MEF, and collect  mRNA at day7 under 10nM and 1uM Va with or without Vc. We found tha both Va and Vc promote reprogramming, and the genes upregulated  by Va and Va had overlpped more than 80%.

overall_design: To detecn the interaction of Va and Vc in MEFs during reprogramming, we collect iPS samples at day7 with Va or Vc in the medium and process with RNA-seq.

first: Mengdan

first: Hui

last: Zheng


title: Novel heart specific long non-coding RNAs contribute to pathogenesis of Arrhythmogenic Cardiomyopathy

first: Jia

last: Li

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

overall_design: Refer to individual Series


title: Expression data from renal cancer patient-derived xenograft tumor treated with temsirolimus or vehicle

summary: We kept 2 types of primary xenograft models (KURC;Kyoto University Renal Cancer-1,3) derived from human renal cell carcinoma tissues, and 10 mg/kg of temsirolimus or vehicle was intraperitoneally administered.We performed microarray analysis to compare the gene expression profile of temsirolimus-treated primary xenograft tumors with that of vehicle-treated.

overall_design: Total RNA was extracted from KURC1,3 xenograft tumors treated with temsirolimus or vehicle. Ten mg/kg of temsirolimus was intraperitoneally administered once a week, and KURC1 kept sensitive and KURC3 developed resistance to temsirolimus.


title: Translational profiling of RBMX-overexpressed HEK293 cells

status: Public on Dec 01 2019

city: Trento

first: Erik

last: Dassi

address: Via Sommarive, 9

institute: University of Trento

summary: Wild-type and RBMX-overexpressed HEK293 cells where profiled at the transcriptome and translatome levels through polysomal profiling. Paired-end RNA-seq libraries were built and sequenced on  an Illumina HiSeq 2000 machine to allow for accurate gene expression quantification and alternative splicing isoforms detection.

overall_design: 3 biological samples per condition are used. A total of 12 samples were used: 3 are the wild-type total RNA, 3 are the wild-type polysomal RNA, 3 are the RBMX-overexpressed total RNA and 3 are the RBMX-overexpressed polysomal RNA.


title: Coordination and assembly of protein complexes encoded across mitochondrial and nuclear genomes is assisted by mtCLPXP in Arabidopsis thaliana

status: Public on Dec 13 2019

city: Crawley

first: Jakob

last: Petereit

state: WA

address: 35 Stirling Highway

country: Australia

institute: ARC Centre of Excellence in Plant Energy Biology

summary: Protein homeostasis in eukaryotic organelles and their progenitor prokaryotes is regulated by a series of ATP-dependent proteases including the caseinolytic protease complex (ClpXP).  In chloroplasts, ClpXP has essential roles in organelle biogenesis and maintenance , but the significance of the plant mitochondrial ClpXP remains unknown and factors that aid coordination of nuclear and mitochondrial encoded subunits for complex assembly in mitochondria await discovery.  In this study, we generated knock-out lines of the single copy mitochondrial Clp protease subunit, CLPP2, in Arabidopsis thaliana. They have higher abundance of transcripts from mitochondrial genes encoding OXPHOS protein complexes, while transcripts for nuclear genes encoding other subunits of the same complexes showed no change in transcript abundance. In contrast, the protein abundance of specific nuclear-encoded subunits in OXPHOS complexes I and V increased in knockouts, without accumulation of mitochondrial-encoded counterparts in the same complex. Protein complexes mainly or wholly encoded in the nucleus were unaffected. Analysis of protein import, assembly and function of Complex I revealed that while function was retained, protein homeostasis was disrupted through slower assembly, leading to accumulation of soluble subcomplexes of nuclear-encoded subunits after import.  It is proposed that CLPP contributes to the mitochondrial protein degradation network through supporting coordination and assembly of protein complexes encoded across mitochondrial and nuclear genomes.

overall_design: Overall we analysed 9 samples of Arabidopsis thaliana total RNA extracts by high throughput RNA sequencing. The samples were 3 replicates of WT (Wild type - Arabidopsis ecotype Columbio-0, used at control), clpp2-1 (knock-out mutant 1 of the mitochondrial CLPP2 protease (AT5G23140)) and clpp2-2 (knock-out 2 of the mitochondrial CLPP2 potease). Both mutations were produced from Arabidopsis ecotype Columbia-0.  Replicates are indicated by the numbering after the underscore.

first: Shaobai

last: Huang


title: Investigation of molecular events underlying the miR192-mediated modulation of inflammatory response

status: Public on Nov 18 2019

first: Satoshi

last: Kondo

address: 10-1 tebiro 6-chome

summary: To understand the molecular mechanism underlying the miR192-mediated modulation of inflammatory response, we have employed whole genome microarray expression profiling of bone-marrow derived macrophages transfected with miR192. In order to distingish the effect of miR192 on inflammatory response from the effecct of IL-6, RNA was isolated from miR192-transfected and R848-stimulated macrophages in the presence or absence of anti-IL-6 Ab during the culture.

overall_design: The differential gene expressions in mouse bone marrow-derived macrophages transfected with control mimic vs miR192 mimic, tin the presence of control Ab or anti-IL-6 Ab during the in vitro culture. Macrophages in each condition were stimulated with TLR7/8 ligand, R848.

first: Hirotake

last: Tsukamoto

first: Hiroyuki

last: Oshiumi


title: ChIP-seq and R-ChIP-seq following BET bromodomain protein loss in HeLa cells

status: Public on Dec 11 2019

city: Durham

first: Drake

last: Edwards

address: 11 Pilatus Dr

department: Radiation Oncology

institute: Duke University

summary: We report that treatment of HeLa cells with 2 hours of 100nM dBET6, which degrades BET bromodomain proteins, leads to global increases of RNA:DNA hybrids (R-loops) and DNA damage (γH2AX). R-loop occupancy was determined using a mutant version of RNase H1 (D210N) which binds to, but cannot resolve, R-loops.

overall_design: Examination of γH2AX and R-loop levels following BET bromodomain protein loss in HeLa cells

first: Scott

last: Floyd


title: De novo formation in maize from irradiated materials

status: Public on Dec 21 2019

city: Wuhan

first: Handong

last: Su

state: Hubei

address: No.1,Shizishan Street · Hongshan District

institute: Huazhong Agricultural University

summary: In maize (Zea mays), irradiation can produce many variants with varying centromeric DNA sequences. We found de novo centromeres in F3-152 and F3-600, which has no canonical centromeric repeat sequences. This centromere is derived from a 1520-kb and 188-kb region on the arm of chromosome 10 and 3. Our results suggest that de novo centromere formation is more common than previously thought and can persist on chromosomal fragments without a canonical centromere providing implications for karyotype evolution.

overall_design: ChIP-seq was carried out with anti-CENH3 antibodies using material from young leaves in B73, F3-152 and F3-600.

first: Fangpu

last: Han


title: IRF4 in skeletal muscle regulates exercise capacity via PTG/glycogen pathway

status: Public on Nov 19 2019

city: LOS ANGELES

first: Xingxing

last: Kong

state: CA

address: UCLA PEDIATRICS, 10833 LE CONTE AVE, CHS-MARION DAVIES CHILDREN CTR

institute: UCLA

summary: Exercise-induced fatigue and exhaustion have been an interesting area for many physiologists.Muscle glycogen is critical forphysical performance. However, how glycogen depletion is manipulated during exercise is not very clear. Our aim here is to assess the impact of interferon regulatory factor 4 (IRF4) on skeletal muscle glycogen and subsequent regulation ofexercise capacity. Skeletal muscle-specific IRF4 knockout mice show normal body weight and insulin sensitivity, but better exercise capacity and increased glycogen content with unaltered triglyceride levels compared to control mice on chow diet. In contrast, mice overexpression of IRF4 display decreased exercise capacity and lower glycogen content. Mechanistically, IRF4 regulates glycogen-associated regulatory subunit protein targeting to glycogen (PTG) to manipulate glucose metabolism. Knockdown of PTG can reverse the effects imposed by the absence of IRF4in vivo. Our studies reveal a regulatory pathway including IRF4/PTG/glycogen synthesis that controlling exercise capacity.

overall_design: Examination of different gene expression in skeletal muscle of muscle-specific IRF4 knockout mice and control mice.

first: Tiemin

last: Liu


title: ATAC-seq profile of mouse palatal epithelium at E14.5

status: Public on Nov 06 2019

city: Iowa City

first: Robert

last: Cornell

state: Iowa

address: 1-400 D Bowen Science Bldg. 51 Newton Road

department: Anatomy and Cell Biology

institute: University of Iowa

summary: To profile nucleosome free regions of moust palatal epithelium at E14.5, we performed ATAC-seq for isolated palatal epithelium and mesenchyme cells.

overall_design: We digested the mouse embryonic palate at E14.5 with 0.25% trypsin-EDTA (Life Technologies) at 4°C for 10 minutes, after which the reaction was stopped using trypsin Inhibitor (Life Technologies). Under a dissecting microscope, the epithelium was isolated for ATAC-seq by gently peeling using microforceps. The remaining tissue, comprised largely of mesenchymal cells, was also collected for control samples.  For each biological replicates, 20000 cells from 3 different mouse embryos were used. Three biological replicates were sequenced using HiSeq X Ten.

first: Huan

middle: A


title: Genome wide analysis of PAX2 chromatin interaction in MCF-7 cell

status: Public on Nov 08 2019

city: Oslo

first: Shixiong

last: Wang

address: Gaustadalléen 21

department: Centre for Molecular Medicine Norway

country: Norway

institute: University of Oslo

summary: The aim of the study is to understand the role of the transcription factor PAX2 in estrogen receptor positive breast cancer cell line by using ChIP-seq. MCF-7-PAX2 stable cells were cultured in full media and treated with doxycycline (50ng/ml) for 16 hours to induce overexpression of PAX2-HA protein. Then cells were treated with 4-OH-tamoxifen (1μM) for 6 hours. All 3 treatments (Veh, Dox, DoxTam) were performed in duplicates. After treatments, cells were collected for ChIP experiment with HA antibody. ChIP-seq libraries were sequenced and data analysis showed almost no binding in Veh treatment, indicating low backgroud and good quality of the data. PAX transcription factor motif were enriched in PAX2 peaks, indicating the reliability of the data. When crossing the ChIP-seq data with genes regulated by PAX2 in MCF-7, we could observe high level binding of PAX2 to prmoters of PAX2 up-regulated genes and the center of intergenic transcripts induced by PAX2, suggesting the role of PAX2 in regulating transcription activation.

overall_design: PAX2 genome interaction mapping in MCF-7 cells treated with doxycycline (50ng/ml) alone, or in combination with tamoxifen (1uM). Whole experiment include 2 replicates of each treatments, a Veh control (no PAX2-HA overexpression), and input samples.

first: Igor

last: Chernukhin

first: Jason

last: Carroll

first: Antoni

last: Hurtado


title: An integrative view of the regulatory and transcriptional landscapes in mouse hematopoiesis

status: Public on Jan 08 2020

city: University Park

first: Ross

last: Hardison

address: 303 Wartik Lab

institute: Pennsylvania State University


title: Pre-eclampsia TAC-seq

status: Public on Nov 25 2019

city: Tartu

first: Hindrek

last: Teder

address: Tiigi 61b

country: Estonia

institute: The Competence Centre on Health Technologies

summary: The etiology of preeclampsia, a hypertensive disorder of human pregnancy, remains unknown. We  addressed fetal sex selection and the suggestive role of fetal HLA-G and related genes, regulating  maternal immune responses, in preeclampsia pathogenesis.  We assessed birth sex ratios, weights, and seasonality of preeclampsia among 1.79 million births  in Finland. We studied haplotypes of HLA-G 3’ untranslated region (UTR), regulating HLA-G  expression, in 1000 Genomes series and in a preeclampsia cohort (n=1249). We quantified  placental (n=163) mRNA expression of 136 genes, studied HLA-G and IFNα protein expression by  immunohistochemistry, and measured maternal and fetal circulating IFNα levels by ELISA.  Population-level data showed loss of male fetuses as a characteristic of preeclampsia. As a  potential contributor to immune-mediated loss, we found balancing selection at HLA-G 3’UTR  modulating sex ratio, and association of HLA-G 3’UTR haplotypes with placental HLA-G expression.  HLA-G and its receptors were downregulated in preeclampsia placentas, and surprisingly,  interferon alpha-1 (IFNA1) was highly upregulated. IFNA1 and HLA-G distinguished preeclampsia  better than placental FLT1 expression. Fetal but not maternal circulating IFNα, produced by  trophoblasts, showed association with maternal hypertension and fetal growth restriction.  We uncover the link between placental HLA-G expression and human birth sex ratio. We propose  that preeclampsia shares, through reduced HLA-G mediated immunotolerance, the mechanism  needed to fight placental viral infections and malaria in evolution. IFNα upregulation in  preeclampsia placenta, together with its known actions upstream of inflammatory genes,  encourages testing IFNα inhibitors and especially the pregnancy-approved antimalarial  hydroxichloroquine in treatment of preeclampsia.

overall_design: 163 samples in total in 5 libraries (SATU1, SATU2, SATU3, SATU4, SATU5). 169 targets in total including 162 biomarker genes (136 remaining after QC) and 7 ERCC RNA Spike-In controls.

first: Kaarel

last: Krjutškov


title: Genes altered in expression by Cisplatin treatment in lung cancer cell lines

status: Public on Nov 05 2019

city: Gyeonggi-do

first: Hyonchol

last: Jang

address: 323, Ilsan-ro, Ilsandong-gu, Goyang-si

country: South Korea

institute: National Cancer Center

summary: Genes altered by Cisplatin treatment and long term-cultured in lung cancer cell lines

overall_design: mRNA expression profiles of the lung cancer of Homo sapiens were examined by Illumina package bcl2fastq v1.8.4.

first: Kim

middle: H

last: Yeon


title: Human oral epithelial cell line HIOEC

status: Public on Nov 02 2019


title: Strand specific Sequencing of myr-Akt1 induced transcriptomes in NSCLC cell lines

status: Public on Nov 01 2019

first: Han

last: Tian

state: Guangdong

address: No.74, Zhongshan Er Road

department: Zhongshan School of Medicine

institute: Sun Yat-sen University

summary: To identify the genes significantly regulated by Akt1 activation in NSCLC, myr-Akt1 stable over-expressed A549, HCC827 cells and control vector cells were constructed. The transcriptomes were analyzed by rRNA-depleted strand specific RNA-seq, and LINC01546 was identified significantly up-regulated in myr-Akt1 A549 and HCC827 cells, as compared to vector cells.

overall_design: Transcriptomes profiles of A549-myr-Akt1, A549-vector, HCC827-myr-Akt1 and HCC827-vecotr were generated by Illumina NovaSeq 6000.

first: Xingui

last: Wu

first: Junchao

last: Cai


title: Effects of a nutritional supplement in older individuals subject to ten days of complete bed rest.

city: Orlando

first: Rick

last: Vega

address: 303 E. Princeton

institute: AdventHealth

summary: Older individuals subjected to complete bed rest for 10 days were randomized to a complete nutritional supplement with or without hydroxymethyl butyrate (HMB). Muscle biopsies from the vastus lateralis were obtained immediately prior and at the conclusion of the bed rest. RNA-sequencing was performed to determine the gene expression changes associated with bed rest. Marked decrease in the expression of genes associated with mitochondrial energy metabolism including fatty acid oxidation, TCA cycle and the electron transport chain was observed with bed rest. These effects were partly mitigated in the subjects provided the nutritional supplement with HMB.

overall_design: RNA-sequencing was performed on 5 individual subjects in both the placebo and HMB groups before and after 10 days of complete bed rest.

last: Standley

first: Giovanna

last: Distefano

first: Michelle

last: Trevino

first: Daniel

middle: P

last: Kelly

first: Bret

last: Goodpaster

first: Paul

last: Coen


title: H3K27Ac ChIP-seq profile of human oral epithelial cell line HIOEC

first: Robert

last: Cornell

summary: To identify the active enhancers and promoters in human oral epithelial cell line, we performed H3K27Ac ChIP-seq for HIOEC cell line.

overall_design: HIOEC cells were maintained in culture medium supplemented with 1.2mM Ca2+ for 3 days, and then were disassociated with 0.25% trypsin-EDTA. For each replicates, 500000 HIOEC cells were harvested for H3K27Ac ChIP-seq library preparation. Three independent biological replicates were performed.

first: Huan

last: Liu


title: G-CSF in vitro treatment modulates adipose derived stem cell and mononuclear cells derived umbilical cord blood functions.

status: Public on Oct 25 2019

city: La Plata

first: Martin

middle: Carlos

last: Abba

state: Buenos Aires

country: Argentina

institute: School of Medical Sciences - UNLP

summary: The purpose of this study was to evaluate the transcriptomics changes in adipose derived mesenchymal stem cells (ADSC) and an in vitro model of umbilical cord blood cells (UCB) exposed to biosimilar and innovative G-CSF (Granulocyte-colony stimulating factor) for the comparison of molecular targets impacted by both drugs.

overall_design: The institutional Ethics Committee of the Hospital Militar Central approved this study under the code 2013-049 (Bogotá – Colombia) and all samples were obtained with written informed consent.

first: Mabel

last: Avila-Portillo