overall_design: RNAseq for atino80 mutant in long-day condition, 2 genotypes with 2 replicates


title: Expression data from THP-1 cells treated with GSK3ß inhibitors

status: Public on Nov 30 2020

city: Duesseldorf

first: Karl

last: Koehrer

address: Universitaetsstr. 1

department: BMFZ

country: Germany

institute: University of Duesseldorf

summary:
The accumulation of amyloid-ß (Aß) peptides in the brain is a crucial step in the pathogenesis of Alzheimer`s disease (AD). Several studies indicate that microglia cells in the brain have the ability to internalize Aß by phagocytosis and might therefore play a protective role in AD. However, the mechanisms underlying Aß clearance remain unresolved. We have found that small molecule inhibitors of the ubiquitous glycogen synthase kinase 3ß (GSK3ß)  stimulate the uptake of Aß by human THP-1 monocytes and primary murine microglia cells.
To investigate how GSK3ß inhibitors might stimulate Aß uptake, we conducted microarray-based gene expression analyses of THP-1 cells after treatment with three different GSK3ß inhibitors. We identified a subset of genes similarly altered by all three inhibitors, including chemokines and surface receptors that have been linked to the regulation of microglial activation and phagocytosis.

overall_design: THP-1 monocytes differentiated into macrophages using PMA (Phorbol 12-myristate 13-acetate) were treated for 48h with three different GSK3ß inhibitors (5 µM CHIR99021, 10 µM SB216763, 1 µM Bio-Acetoxime) or DMSO vehicle. RNA was extracted for cDNA synthesis and hybridization on Affymetrix microarrays with two replicates per treatment condition.

first: Isabella

last: Ogorek

first: Sascha

last: Weggen

first: René

last: Deenen

last: Köhrer


title: SATB2-LEMD2 interaction links nuclear shape plasticity to regulation of cognition-related genes

status: Public on Nov 29 2020

city: Innsbruck

first: Galina

last: Apostolova

state: Tyrol

address: Innrain 66

department: Institute for Neuroscience

country: Austria

institute: Medical University Innsbruck

type: Expression profiling by high throughput sequencing

summary: SATB2, encoding a nuclear chromosomal scaffolding protein, is a schizophrenia risk gene and genetically associated with human intelligence. How SATB2 affects cognition at molecular level is currently unknown. Our data suggest that interactions between SATB2 and the inner nuclear membrane protein LEMD2 orchestrate gene expression programs in pyramidal neurons that are linked to cognitive ability and psychiatric disorder etiology. We show that LEMD2, a candidate component of the A-heterochromatin tether, binds to SATB2 and the two proteins exert overlapping cellular functions. SATB2 is essential for neuronal activity-triggered nuclear envelope plasticity, which requires LEMD2 as well as the ESCRT-III/VPS4 complex. LEMD2-depletion in cortical neurons, like SATB2 ablation, affects the expression of multiple neuronal activity-regulated genes. The gene-sets regulated by LEMD2 and SATB2 significantly overlap and the LEMD2 gene-set is enriched for SATB2-bound genes. In human genetic data, LEMD2-regulated genes are enriched for loss-of-function mutations reported in autism, intellectual disability and schizophrenia and are, like SATB2-regulated genes, associated with cognitive function.

overall_design: Analysis of transcriptome changes in LEMD2-depleted vs scrambled siRNA-transfected cortical neurons and in Satb2 knockout vs floxed cortical cultures upon stimulation with bicuculline or silencing with NBQX

first: Patrick

last: Feurle

first: Andreas

last: Abentung

last: Cera

first: Nico

last: Wahl

first: Georg

last: Dechant


title: Human PBMCs: Patients with HSPN vs. Patients with HSP

city: Koga-City

first: Takashi

last: Imai

state: Fukuoka

address: 1-1-1 Chidori

department: Pediatrics

country: Japan

institute: FUKUOKA HIGASHI MEDICAL CENTER

summary: Genes that were up-regulated in acute stage in HSPN patients compared with HSP patients, and that showed over 1.5-fold differences by the comparison between the two groups in the mean expression levels were selected.

overall_design: Gene expression in peripheral blood mononuclear cells (PBMCs) of HSPN patients was compared with HSP patients in acute stage.

first: Kei

last: Nishiyama

first: Kenji

last: Ueki

first: Ryoko

last: Unose

first: Tamami

last: Tanaka

first: Yoshitsugu

last: Kaku

first: Shouichi

last: Ohga


title: Histone H3K4 methyltransferase ATX1 positively regulates secondary wall biosynthesis in interfascicular fibers in Arabidopsis

city: Chongqing

first: Xianqiang

last: Wang

address: Tiansheng Road

country: China

institute: Southwest University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Secondary wall thickening in the sclerenchyma cells is strictly controlled by a complex network of transcription factors in vascular plant. However, little is known about the epigenetic mechanism regulating secondary cell wall biosynthesis. Genome-wide analysis revealed that the up-regulation of genes involved in secondary wall formation during stem development is largely coordinated by increasing level of H3K4 tri-methylation. In this study, we identified that ARABIDOPSIS HOMOLOG of TRITHORAX1 (ATX1), a H3K4-histone methyltransferase, positively regulates secondary wall deposition mainly through activating the expression of secondary wall NAC master switch genes, SECONDARY WALL-ASSOCIATED NAC DOMAIN PROTEIN1 (SND1) and NAC SECONDARY WALL THICKENING PROMOTING FACTOR1 (NST1).

overall_design: Examination of the difference of transcriptiomes and H3K4me3 modifications in the stem of wild type (Col) and atx1 mutant grown to 20cm. The stem is divided into four stages from top to bottom. Stage I 0-3cm, stage II 5-7cm, stage III 10-12cm, stage IV 18-20cm

first: Di

last: Fan

first: Keming

last: Luo


title: Inhibition of PRC2 activity by H3K36 methylation

status: Public on Nov 28 2020

city: Martinsried

first: Jürg

last: Müller

state: Bavaria

address: Am Klopferspitz

institute: Max Planck Institute of Biochemistry

summary: We provide evidence that Drosophila H3K36A and H3K36R mutant embryos as well as H3K36R mutant larvae show altered H3K36me2 and H3K27me3 ChIP-seq profiles.

overall_design: Analyis of H3K36me2 and H3K27me3 ChIP-seq profiles and read coverage across gene bodies in H3K36A and H3K36R mutant embryos and H3K36R larvae as compared to the corresponding wild-type references.

first: Jacques

last: Bonnet


title: An inducible CRISPR-interference library for genetic interrogation of Saccharomyces cerevisiae biology

status: Public on Nov 27 2020

city: New York

first: Amir

last: Momen-Roknabadi

state: NY

address: 1150 St. Nicholas Ave Room 406

country: USA

institute: Colombia University

summary: Genome-scale CRISPR interference (CRISPRi) is widely utilized to study cellular processes in a variety of organisms. To date, a genome-wide CRISPRi library, optimized for targeting the Saccharomyces cerevisiae genome, has not been presented. Here, we have generated a comprehensive, inducible CRISPRi library, based on spacer design rules optimized for yeast. We have validated this library for genome-wide interrogation of gene function across a variety of applications, including accurate discovery of haploinsufficient genes and identification of enzymatic and regulatory genes involved in adenine and arginine biosynthesis. The comprehensive nature of the library also revealed refined spacer design parameters for transcriptional repression, including location, nucleosome occupancy and nucleotide features. CRISPRi screens using this library can identify genes and pathways with high precision and low false discovery rate across a variety of experimental conditions, enabling rapid and reliable genome-wide assessment of genetic function and interactions in S. cerevisiae.

sample_organism:
Escherichia coli
Saccharomyces cerevisiae

overall_design: We designed more than 51,000 gRNAs, with between 6-12 sequences per gene. As a negative control for gRNA activity, we introduced 500 synthetic randomly shuffled gRNAs with no matches in the yeast genome. We generated two independently cloned bacterial library replicates. The two bacterial biological replicates libraries were transformed into yeast.

first: Panos

last: Oikonomou

first: Maxwell

last: Zegans

first: Saeed

last: Tavazoie


title: Dual function of hPSC-derived pericyte-like cells in vascularization and fibrosis-related cardiac tissue remodeling in vitro

city: Hannover

first: Monika

last: Szepes

address: Carl-Neuberg Str. 1

department: Department of Cardiac, Thoracic, Transplantation and Vascular Surgery

institute: Hannover Medical School

summary: In the heart, cardiomyocytes (CMs) are coupled to capillary endothelial cells (EC), mural cells (e.g. pericytes) and fibroblasts (Fb) promoting structural and electrophysiological tissue maturation as well as vascular network formation. Here, an in vitro model is shown for the investigation of the role of ECs, cardiac pericyte-like cells (PC) and different Fb sources in hPSC-derived bioartificial cardiac tissue (BCT) formation and function. The hPSC-based CMs, ECs, and PCs were differentiated, purified, and characterized for cell-type specific marker expression and function. Differentiated hPSC-PCs were used with hPSC-ECs to generate BCTs and to address their effect on tissue morphology and electromechanical parameters compared to control tissues containing primary dermal or cardiac Fbs.

overall_design: The transcriptome of three bioartificial cardiac tissue (BCT) groups with hPSC-derived cardiomyocytes (CM), hPSC-derived endothelial cells (EC) and different fibroblast-like cell types was compared to the differentiated CM source and adult human ventricle. The fibroblast-like cell types included  human foreskin fbroblasts (group: CM+hFF+EC), human cardiac fibroblasts (group: CM+hCF+EC), and hPSC-derived cardiac pericyte-like cells (group: CM+PC+EC).

first: Anna

last: Melchert

first: Julia

last: Dahlmann

first: Jan

last: Hegermann

first: Christopher

last: Werlein

first: Danny

last: Jonigk

first: Axel

last: Haverich

first: Ulrich

last: Martin

first: Ruth

last: Olmer

first: Ina

last: Gruh


title: Expression data from mouse brain during development

city: Suita

first: Tokuichi

last: Iguchi

state: Osaka

address: 2-2 Yamada-oka

institute: Osaka University

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

overall_design: Refer to individual Series


title: Expression data from mouse pontine nucleus

summary:
During brain development, layer 5 neurons distributed across most areas of the neocortex innervate the pontine nuclei (basilar pons) by the initiation and extension of collateral branches interstitially along their corticospinally extending axons.
We used microarrays to compare gene expression profiles of pontine nucleus when axon collaterals towards the pontine nucleus start to extend (embryonic day 17.5 (E17.5) to postnatal day 1 (P1)), and/or throughout the development (E17.5-P14) in order to understand genetic programs that regulate axon collaterals formation.

overall_design: Pontine nucleus was dissected out from each developmental stage of the mouse brain and subjected to total RNA preparation and hybridization on Affymetrix microarrays.

first: Makoto

last: Sato


title: Mesenchymal transition and acquired therapy resistance of glioblastoma cells is connected to astrocyte reactivity (Affymetrix HTA 2.0 data set)

city: Uppsala

first: Bo

last: Segerman

address: Dag Hammarskjolds v 20

country: Sweden

institute: Uppsala University

summary: We show that Glioma initiating cells (GICs) can, through MES transition, enter a reactive-astrocyte-like cell state which is connected to increased therapy resistance

overall_design: Affymetrix HTA 2.0 array analyses were performed according to the manufacturer's directions on total RNA extracted from primary human astrocytes from cerebral cortex (ScienCell, San Diego) cultured acording to providers instructions.  3 bilogical replicates of IL1 stimulated cells (12-13 days) and corresponding control cells were analyzed. Affymetrix HTA 2.0 array analyses were also performed on a clonal malignant glioma.   3 bilogical replicate time series of IL1 stimulation (1-42 days) and corresponding control cells were analyzed.


title: Differentially expressed microRNAs in the mouse liver with T3 treatment

city: Shanghai

first: Dandan

last: Zhang

address: Dongan Road

institute: Fudan University

summary: An improved mechanistic understanding of the thyroid hormone (TH) action on bile acid (BA) synthetic pathway, the major route for cholesterol elimination, will facilitate the identification of novel therapeutic targets for hypercholesterolemia. Here, we show that hepatic miR-378 is positively regulated by TH. Transient overexpression of miR-378 in the liver of mice reduces the serum cholesterol levels, which is accompanied with an upregulation of key enzymes involved in the intrahepatic conversion of cholesterol to BAs. Importantly, transgenic mice with liver-specific and moderate overexpression of miR-378 also display a decrease in serum cholesterol levels accompanied with an enhanced BA synthesis and are resistant to diet-induced hypercholesterolemia. In contrast, mice lacking miR-378 exhibit an elevation of serum cholesterol levels accompanied with an impaired BA synthesis. Mechanistic studies reveal that hepatic miR-378 regulates BA synthesis and cholesterol homeostasis through its direct target gene MAFG, which is a transcriptional repressor of BA synthetic genes. We also show that miR-378 serves as an essential component in either incoherent or coherent feed-forward loop to confer robust and precise controls on BA synthesis in response to TH signalling. Together, we identify a previously undescribed miR-378-mediated mechanism underlying the cholesterol-lowering effect of TH. Our findings not only add a new dimension to our understanding the regulation of BA synthesis by TH, but also provide new therapeutic regimens to manage serum cholesterol levels

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus
Human alphaherpesvirus 1
Human betaherpesvirus 5
Murid betaherpesvirus 1
human gammaherpesvirus 4
JC polyomavirus
Human immunodeficiency virus 1
Murid gammaherpesvirus 4
Human gammaherpesvirus 8
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: Two groups: MMI and MMI+T3; one sample per group, and each sample is the pool of  livers of five mice treated the same.

first: Chao

last: Sun

first: Wei

last: Liu


title: The 3D Genomic Landscape of Differential Response to EGFR/HER2 Inhibition in Endocrine-Resistant Breast Cancer

status: Public on Dec 01 2020

city: Milwaukee

first: Victor

last: Jin

state: WI

address: 8701 Watertown Plank Rd

department: IHE

institute: Medical college of Wisconsin


title: Effects of cAMP supplementation on the transcriptome of Streptomyces coelicolor M1146 strain

first: Katsuaki

last: Nitta

address: Yamadaoka 2-1

summary: To identify unique gene expression in cAMP supplemented Streptomyces coelicolor M1146 strain. The genes with different gene expression might be key genes to understand the effects of cAMP supplementation on the transcriptome of Streptomyces coelicolor M1146.

overall_design: 3 time point, 1 strain, 1 condiitons: 0h, 1h and 2h after cAMP supplementation, 3 replicates

first: Franscesco

last: Del Carratore

first: Rainer

last: Breitling

first: Eriko

last: Takano


title: Effects of cAMP supplementation on the transcriptome of Streptomyces coelicolor M145 strain

summary: To identify unique gene expression in cAMP supplemented Streptomyces coelicolor M145 strain. The genes with different gene expression might be key genes to understand the effects of cAMP supplementation on the transcriptome of Streptomyces coelicolor M145.

overall_design: 1 time point, 1 strain, 2 condiitons: control and cAMP supplemented culture, 3 replicates


title: High-throughput sequencing and analysis of gene modification regulated by epigenetics modification in adult and old intracerebral hemorrhage rats. [ChIP-Seq]

city: wuhan

first: dong

last: chen

state: Hubei

address: GaoXin 2nd Road

institute: ablife

summary: Here we performed in depth epigenome sequencing and analysis to study the mechanism of high mortality rate of ICH in rat brain. It reveals a systematical transcription activation of mRNA genes enriched in inflammation and immune responses. These genes are clustered to specific genomic loci and regulated by repressive and activation chromatin markers. We show that epigenetic reprogramming responding to ICH in old rat brains differs greatly from that in the adult.

overall_design: Examination of 3 different histone modifications in adult (13 mon old) and old (22 mon old) ipsilateral and contralateral brain tissues，2 different histone modifications in old ipsilateral brain tissues with young plasma and old plasma treatment

first: Xiao-Yi

last: Xiong

first: Qing-Wu

last: Yang


title: Time-course transcriptome analysis of non-antibiotics producer and actinorhodin over-producing Streptomyces coelicolor strain

summary: To identify unique gene expression in higher antibiotics producing Streptomyces coelicolor strain, non-producer M1146 and the derivative strain M1146+ACT (M1146 with actinorhodin biosynthetic genes cluster) was choosen for comparative transcriptome analysis. The genes with different gene expression might be key genes important for antibiotics production.

overall_design: 10 time points, 2 strains: control (M1146) and M1146+ACT


title: Intrauterine inflammation-induced transcriptome changes in the mouse placenta

city: Philadelphia

first: Zhe

state: PA

address: Translational Research Lab

institute: University of Pennsylvania

summary: Placental insufficiency is implicated in the intrauterine infection-associated spontaneous preterm birth. Using a mouse model of LPS-induced intrauterine inflammation that leads to preterm delivery, RNA-seq study was performed in the placenta at gestational day 17 to assess the transcriptome changes.

overall_design: Examinatin of transcriptomes in 2 experimental conditions (LPS and control)

first: Yu-Chin

last: Lien

first: Rebecca

middle: A

last: Simmons

first: Guillermo

last: Barila

first: Amy

last: Green-Brown

first: Michal

last: Elovitz


title: Gene expression profiling of the vomeronasal organs in mice selectively bred for high voluntary wheel running activity and non-selected controls

status: Public on Nov 26 2020

city: Riverside

first: Sachiko

last: Haga-Yamanaka

state: CA

address: 900 University Ave.

department: Molecular, Cell and Systems Biology

institute: University of California, Riverside

summary: To examine the impact of selective breeding for voluntary wheel running activity on gene expression in the vomeronasal organ (VNO), RNAseq analysis was conducted in the VNO of 4 High Runner and 4 Control lines.

overall_design: For each of the 4 High Runner and 4 Control lines, total RNA samples were prepared, each consisting of the combined VNOs from 3 individual males or 3 individual females.

first: QuynhAnh

middle: T

last: Nguyen

first: David

last: Hillis

first: Sayako

last: Katada

first: Timothy

last: Harris

first: Crystal

last: Pontrello

first: Theodore

last: Garland Jr.


title: IRF-1 expressed in the early blastocyst inner cell mass of pigs enhances the pluripotency of induced pluripotent stem cells

city: Beijing

first: Jianyong

last: Han

address: 2rd, Yuanmingyuan West Road

department: State Key Laboratory of Agrobiotechnology

institute: China Agricultural University

summary: Naïve porcine stem cells is supposed to rely on the regulation of unique transcription factor in the early inner cell mass. The expression of Interferon regulatory factor 1 (IRF-1) were detected in aggregation in d6~7 somatic cell nuclear transfer blastocysts, which was supposed to regulate the pluripotency of naïve state. But IRF-1 is reported to be involved in the response to viral infections and initiate a rapid proinflammatory response, while the function of IRF-1 on pluripotency need to be explored. Then the heterogenicity of IRF-1 was associated with pluripotency in pig induced pluripotent cells and overexpression of IRF-1 promoted the gene expression profile of pluripotent genes as would be expected when cells approach the naïve state

overall_design: In order to determine how IRF-1 expression affects RNA expression, we performed high-throughput RNA sequencing on overexpression and WT cells. These data showed that overexpression of IRF-1 in pig induced pluripotent cells promoted the expression of pluripotency genes related to the naïve state and down-regulated genes related to differentiation processes. Then In order to detect the target genes of IRF-1, CHIP-seq was conducted using an anti-flag antibody and the chromatin of IRF-1-flag overexpressing cells. The captured genes were used to enrich for KEGG-pathways and the most enriched biological pathways were related to initiate immunity and adaptive immunity, as expected

first: Bingbo

last: Shi

first: Dengfeng

last: Gao


title: Estrogen-driven control of diabetogenic gene networks is associated with reduced levels of miR-224/452 circulating in extracellular vesicles [RNA-Seq]

city: Leiden

first: Roel

last: Bijkerk

address: Albinusdreef 2

department: Nephrology

country: Netherlands

institute: LUMC

summary: Women with diabetes have a higher prevalence of cardiovascular complications than men, suggesting that sex-steroid hormones like estrogen may impact on female health in diabetes. Here we demonstrate that estrogen suppletion and insulin resistance in male-to-female transgenders coincides with lower plasma levels of miR-224 and miR-452 carried in extracellular vesicles. Systemic silencing of miR-224 and miR-452 in mice triggered a prediabetic phenotype with higher plasma insulin levels, increased white adipose lipogenesis and less glucose uptake and mitochondrial respiration in brown adipose tissue. Consistent with a prediabetic metabolic state, RNA sequencing demonstrated differential expression of genes involved in lipogenesis in white adipose tissue and mitochondrial respiration and glucose uptake in brown adipose tissue. In vitro studies confirmed the estrogen-dependent lowering of miR-224 (brown adipocytes) and miR-452 (white adipocytes) and their impact on adipocyte-specific metabolic processes. Collectively, we identified novel estrogen-driven, post-transcriptional networks that could drive the progression to insulin resistance in transwomen and provide potential anti-diabetic therapeutic targets in women.

overall_design: Total RNA obtained from WAT and BAT from mice that were treated with scramblemir, miR-224 inhibitor or mir-452 inhibitor

first: Barend

last: Florijn

first: Anton

last: Jan van Zonneveld


title: Transcriptome mapping of Enterococcus faecalis and Enterococcus faecium

status: Public on Nov 25 2020

city: Würzburg

first: Lars

last: Barquist

state: Bayern

address: Josef-Schneider-Straße 2 / Bau D15

department: Institute for Molecular Infection Biology

institute: Universität Würzburg

summary: The enterococci comprise a genus of 49 low-GC content Gram-positive commensal species within the Firmicutes phylum that are known to occupy diverse habitats, notably the gastrointestinal core microbiota of nearly every phylum, including human. Of particular clinical relevance are two rogue species of enterococci, Enterococcus faecalis and the distantly related Enterococcus faecium, standing among the nefarious multi-drug resistant and hospital-acquired pathogens. Despite increasing evidence for RNA-based regulation in the enterococci, including regulation of virulence factors, their transcriptome structure and arsenal of regulatory small sRNAs (sRNAs) are not thoroughly understood. Using dRNA-seq, we have mapped at single-nucleotide resolution the primary transcriptomes of E. faecalis V583 and E. faecium AUS0004. We identified 2517 and 2771 transcription start sites (TSS) in E. faecalis and E. faecium, respectively. Based on the identified TSS, we created a global map of s70 promoter motifs. We also revealed features of 5’ and 3’UTRs across the genomes. The transcriptome maps also predicted 150 and 128 sRNA candidates in E. faecalis and E. faecium, respectively, some of which have been identified in previous studies and many of which are new. Finally, we validated several of the predicted sRNAs by Northern Blot in biologically relevant conditions. Comprehensive TSS mapping of two representative strains will provide a valuable resource for the continued development of RNA biology in the Enterococci.

sample_organism:
Enterococcus faecalis V583
Enterococcus faecium Aus0004

overall_design: Differential RNA-seq at late exponential growth phase.

first: Elisabeth

middle: E

last: Hansen


title: MicroRNA expression profiles in different tissues from normolipidemic hamster and high-fat diet induced hyperlipidemic hamster (Mesocricetus auratus)

city: Bucharest

first: Loredan

middle: Stefan

last: Niculescu

address: 8, B. P. Hasdeu Street

department: Lipidomics

country: Romania

institute: Institute of Cellular Biology and Pathology "Nicolae Simionescu"

summary: Hyperlipidemia is one of high risk factors for cardiovascular disease (CVD), whose regulation is known to be mediated also by microRNA-mediated mechanisms. Therefore, the analysis of transcriptomics data would gain insights into the molecular mechanisms implicating microRNAs (miRNAs) behind the atherogenic hyperlipidemia. The goal of our study was to profile the specific miRNAs expression associated with atherogenic hyperlipidemia. To this aim, we performed miRNAs microarray analysis for different tissues (liver, left ventricle of the heart, small intestine and blood mononuclear cells) obtained from the experimental model of high-fat diet induced hyperlipidemic hamsters (Mesocricetus auratus). The microarray data were obtained using miRCURY LNA microRNA arrays 7 th generation platform with miRBase 19 (Exiqon, Denmark), using total RNA isolated from hyperlipidemic (HL) and normolipidemic (NL) hamsters? tissues and blood cells. The animals were fed for 12 weeks either standard rodent chow supplemented with 3% cholesterol and 15% unsalted butter (HL) or standard rodent chow (NL), with free access to food and water.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: MicroRNA microarray analysis was performed for the liver (LIV), the small intestine (INT), the left ventricle of the heart (LVH) and blood circulating mononuclear cells (BMC) collected from 12-week high-fat diet induced hyperlipidemic (HL) hamsters and normal chow fed normolipidemic (NL) hamsters (Mesocricetus auratus).

middle: S

first: Lu

last: Zhang

first: Camelia

last: Stancu

first: Anca

middle: V

last: Sima


title: Early commitment in the steady state programs antigen specific CD4+ T cells for subsequent effector differentiation

status: Public on Nov 24 2020

city: Saint Louis

first: Daniel

last: Hawiger

state: Missouri

address: 1100 South  Grand Boulevard

department: Molecular Microbiology and Immunology

institute: Saint Louis University


title: Infection of human Nasal Epithelial Cells with SARS-CoV-2 and a 382-nt deletion isolate lacking ORF8 reveals similar viral kinetics and host transcriptional profiles

city: Singapore

first: Wharton

middle: O Yinn

last: Chan

address: 8 College Road

department: Emerging Infectious Disease

country: Singapore

institute: Duke NUS Medical School

summary: Gene expression profile of human Nasal Epithelial Cells infected with SARS-CoV-2 and a 382-nt deletion strain, for the indicated time periods

overall_design: Examination of effects of two different SARS-CoV2 strains on NECs over time (0,8,24,72 hpi)

first: Akshamal

middle: M

last: Gamage

first: Kai

last: Tan

middle: O

first: Jing

last: Liu

first: Chee

middle: W

first: Yew

middle: K

last: Ong

first: Mark

last: Thong

first: Anand

last: Andiappan

first: Danielle

last: Anderson

first: De

middle: Y

last: Wang

first: Lin-Fa


title: Early commitment in the steady state programs antigen specific CD4+ T cells for subsequent effector differentiation [12hRNA]

summary: RNA expression in CD4 positive naïve and dendritic cell-activated T cells

overall_design: RNA expression in 12hr in vitro restimulated antigen-specific T cells expressing different levels of Hopx that were pre-activated by dendritic cells in vivo

first: Adeleye

last: Opejin

first: Alexey

last: Surnov


title: Molecular mechanism of EPC1-PHF1 fusion protein  (ChIP-seq Homo Sapiens)

city: Quebec City

first: Deepthi

last: Sudarshan

state: Quebec

address: 9 Rue Mc Mahon

country: Canada

institute: Université Laval

summary: In this study, we characterize the fusion protein produced by the EPC1-PHF1 translocation in Low Grade Endometrial Stromal Sarcoma (LG-ESS) and Ossifying FibroMyxoid Tumors (OFMT). We express the fusion protein and necessary controls in K562 Cells. The fusion protein assembles a mega-complex harboring both NuA4/TIP60 and PRC2 subunits and enzymatic activities and leads to mislocalization of chromatin marks in the genome, linked to aberrant gene expression.

overall_design: ChIP-sequencing of FLAG, H4 penta acetyl (H4K5ac, H4K8ac, H4K12ac, H4K16ac, H4K20ac) and H3K27me3 in K562 cells expressing FLAG tagged EPC1-PHF1 fusion protein or EPC1(1-581) or PHF1 or tag only.

first: Eric

middle: R

last: Paquet

first: Jacques

last: Côté


first: Daniel

type: Non-coding RNA profiling by high throughput sequencing

overall_design: RNA expression in antigen-specific T cells expressing different levels of Hopx that were activated by dendritic cells was compared to expression in naïve T cells


title: Gene expression data from mesenchymal cells

status: Public on Nov 21 2020

city: Ann Arbor

first: Vibha

middle: N.

last: Lama

state: Michigan

address: 1150 W. Medical Center Drive

department: Internal Medicine

institute: University of Michigan

summary: Understanding the trancriptional role of FOXF1 in mesenchymal activation

overall_design: Mesenchymal cells cultured from the cell pellet fraction of bronchoalveolar lavage fluid were subjected to RNAi-mediated FOXF1 silencing

middle: N


title: Transcriptional Remodeling Patterns in Murine Dendritic Cells Infected with Paracoccidioides brasiliensis: More Is Not Necessarily Better

city: Brasília

first: Fabián

middle: Andrés

last: Hurtado Erazo

state: DF

address: Campus universitário Darcy Ribeiro. Asa Norte

department: University of Brasília Medical School

country: Brazil

institute: University of Brasília

summary: Examination and comparison of the transcriptional profile of bone marrow derived dendritic cells (BMDCs) in response to infection by the fungus Paracoccidioides brasiliensis in resistant/susceptible mice

overall_design: Total RNA of BMDCs from A/J (resistant) and B10.A (susceptible) mice strains after 6 hours exposure to P. brasiliensis plus their BMDCs controls. All samples have three replicates.

first: Calliandra

last: de-Souza-Silva

last: Hurtado

first: Aldo

middle: H

last: Tavares

first: Getúlio

middle: P

last: de Oliveira-Jr

first: Taina

last: Raiol

first: Christiane

last: Nishibe

last: Paiva-Agustinho

first: Nalvo

middle: F

last: Almeida

first: André

last: Nicola

first: Anamélia

last: Lorenzetti-Bocca

first: Patrícia

last: Albuquerque

first: Ildinete

last: Silva-Pereira


title: The Deubiquitylase Ubp15 Couples Transcription to mRNA Export

status: Public on Nov 23 2020

city: Montreal

first: Francois

last: Robert

state: QC

address: 110 av des Pins Ouest

institute: IRCM

type: Genome binding/occupancy profiling by genome tiling array

summary: The nuclear export of messenger RNAs (mRNAs) is intimately coupled to their synthesis. pre-mRNAs assemble into dynamic ribonucleoparticles as they are being transcribed, processed and exported. The role of ubiquitylation in this process is increasingly recognized as the ubiquitylation of many key players have been shown to affect mRNA nuclear export. While a few E3 ligases have been shown to regulate nuclear export, evidence for deubiquitylases is currently lacking. Here, we identified the deubiquitylase Ubp15 as a regulator of nuclear export in Saccharomyces cerevisiae. Ubp15 interacts both with RNA polymerase II and with the nuclear pore complex, and its deletion reverts the nuclear export defect of mutants of the E3 ligase Rsp5. The deletion of UBP15 leads to hyper-ubiquitylation of the main nuclear export receptor Mex67 and affects its association with THO, a complex coupling transcription to mRNA processing and involved in the recruitment of mRNA export factors to nascent transcripts. Collectively, our data support a role for Ubp15 in coupling transcription to mRNA export.

overall_design: We profiled RNAPII (Rpb3) in WT, ubp15Δ, dst1Δ and ubp15Δ/dst1Δ cells treated or not with 100 µg/mL of 6-azauracil for 60 min in yeast Saccharomyces cerevisiae by ChIP-chip on tiling arrays. All ChIP samples were labeled with Cy5 and hybridized against Input DNA (labeled with Cy3). The microarrays used were described before (Jeronimo and Robert, 2014). The data were normalized using the Limma Loess method, and replicates were combined as described previously (Ren et al. 2000, Science 290(5500):2306-9). The data were subjected to one round of smoothing using a Gaussian sliding window with a standard deviation of 100 bp to generate data points in 10-bp intervals (Guillemette et al. 2005, PLoS Biol 3(12):e384). Each experiment was done in duplicate, except for the Rpb3 ChIP in non-treated ubp15Δ/dst1Δ cells.

first: Fanny

last: Eyboulet

first: Célia

last: Jeronimo

first: François


title: Whole-transcriptome RNA-seq analysis of zebrafish microglia subpopulations

city: HK

first: Zilong

last: WEN

address: Academic Bld., HKUST, Clearwater Bay, Kowloon

department: Division of Life Science

country: Hong Kong

institute: Hong Kong University of Science and Technology

summary: We generate whole-transcriptome RNA-seq profiles of microglia subpopulations in the adult zebrafish brain (4-month-old) to study their heterogeneity. Cells were isolated as ccl34b.1+mpeg1+ populations or ccl34b.1-mpeg1+ populations from the whole brain of double transgenic TgBAC(ccl34b.1:eGFP);Tg(mpeg1:DsRedx) fish. ccl34b.1+mpeg1+ and ccl34b.1-mpeg1+ microglia were grouped into two distinct clusters in the Principal component analysis (PCA), and we identified substantial differentially-expressed genes between these two microglial populations using the DESeq2 package. To further unveil their differential roles during inflammation, we injected E. coli into the brain ventricles of adult zebrafish and isolated both populations for whole-transcriptome RNA-seq. This RNA-seq profile provides valuable information for dissecting their respective functions in vivo.

overall_design:
WT experiment: 5 fish in total; each fish sorted 100 ccl34b.1+mpeg1+ cells and 100 ccl34b.1-mpeg1+ cells with 3 technical replicates; 1 technical replicate processed for RNA-seq based on the cDNA quality.
E. coli injection experiment: 9 fish in total; 2 control fish, 4 pbs injected fish, 3 E. coli injected fish; each fish sorted 100 ccl34b.1+mpeg1+ cells and 100 ccl34b.1-mpeg1+ cells with 3 technical replicates; 1 technical replicate processed for RNA-seq based on the cDNA quality.

first: Shuting

last: Wu

first: Linh

middle: T

last: Nguyen

first: Jin

last: Xu

last: Wen


title: An epoxide hydrolase inhibitor reduces   neuroinflammation in a mouse model of Alzheimer’s disease

status: Public on Nov 20 2020

city: Houston

first: Hui

last: Zheng

state: TX

address: 1 Baylor Plaza

department: Huffington Center on Aging

institute: Baylor College of Medicine

summary: Neuroinflammation has been increasingly recognized to play a critical role in Alzheimer’s disease (AD). The epoxy fatty acids (EpFAs) are derivatives of the arachidonic acid metabolism pathway and have anti-inflammatory activities. However, their efficacy is limited due to their rapid hydrolysis by the soluble epoxide hydrolase (sEH). We report that sEH is predominantly expressed in astrocytes and its concentrations are elevated in postmortem brain tissue from AD patients and in the 5xFAD -amyloid mouse model of AD. The amount of sEH expressed in AD mouse brains correlated with a reduction in brain EpFA concentrations. Using a specific small molecule sEH inhibitor, 1-trifluoromethoxyphenyl-3-(1-propionylpiperidin-4-yl) urea (TPPU), we report that TPPU treatment protected AD mice against LPS-induced inflammation in vivo. Long-term administration of TPPU to the 5xFAD mouse model via drinking water reversed microglia and astrocyte reactivity and immune pathway dysregulation. This was associated with reduced β-amyloid pathology and improved synaptic integrity and cognitive function on two behavioral tests. Importantly, TPPU treatment correlated with an increase in EpFA concentrations in the brains of 5xFAD mice, demonstrating brain penetration and target engagement. These findings support further investigation of TPPU as a potential therapeutic agent for the treatment of AD.

overall_design: Total 3 experimental groups: Non-transgenic (N-tg) Vehicle, Tg (5xFAD) Vehicle, and Tg-TPPU. 4 mice in each group

first: Anamitra

last: Ghosh


title: Early commitment in the steady state programs antigen specific CD4+ T cells for subsequent effector differentiation [ChIP]

first: Daniel

last: Hawiger

summary: Epigenetic profile of CD4 positive naïve and dendritic cell-activated T cells

overall_design: Chromatin methylation and acetylation in antigen-specific T cells expressing different levels of Hopx that were activated by dendritic cells was compared to naïve T cells

first: Adeleye

last: Opejin

first: Alexey

last: Surnov


title: Characterisation of human PSC-derived cardiovascular cell types

city: Hannover

first: Monika

last: Szepes

address: Carl-Neuberg Str. 1

institute: Hannover Medical School

summary: Vascularization and maturation options for cardiac tissue engineered structures are currently intensively investigated. Therefore, the generation  and characterisation of all cardiovascular cell types from  human pluripotent stem cells (hPSC; either induced -iPSC- or embryonic -hESC) are of particular interest. In our group, differentiation and selection methods were described for obtaining highly pure hPSC-derived cardiomyocytes (CM; selected for αMHC), endothelial cells (EC; selected for CD31) and PDGFRβ expressing cardiac pericyte-like cells (PC). With the purpose of identifying cell type-related mechanisms in co-culture and tissue formation, gene expression profile of hPSC-derived CM, ECs, and PCs was compared to their undifferentiated progeny (hPSC) as well as to primary pericytes (hPC-PL) and fibroblasts (HFF).

overall_design: To characterize the generated cell types, samples from 3 differentiations per cell type were compared in a microarray analysis with each other, their undifferentiated origin, and 2 samples of primary hPC-PL and HFF.

first: Anna

last: Melchert

first: Julia

last: Dahlmann

first: Ulrich

last: Martin

first: Ruth

last: Olmer

first: Ina

last: Gruh


title: A microRNA cluster in the DLK1-DIO3 imprinted region on chromosome 14q32.2 in hepatoblastoma

city: Sapporo

first: Shohei

last: Honda

department: Department of Gastroenterological surgery I

institute: Hokkaido University Hospital

summary:
Using array-based expression analysis on formalin-fixed paraffin-embedded tissues, we aimed to identify miRNA signatures that can discriminate between lung metastatic tumors, primary tumors (fetal and embryonal subtypes) and nontumorous surrounding livers.
A large cluster of microRNAs and snoRNAs located within the 14q32.2 DLK1-DIO3 region showed a strikingly upregulated expression pattern in HB tumors, especially metastatic tumors, compared to normal liver tissues.

overall_design: Here we examined microRNAs and snoRNAs profiles related to different type of hepatoblastoma tumor cells, using array-based expression analysis.

first: Aniruddha

last: Chatterjee

middle: L

last: Leichter

first: Michael

last: Eccles


title: Transcriptome of ZFP36L1-sufficient and ZFP36L1-deficient Fo B cells

city: Cambridge

first: Louise

last: Matheson

address: Babraham Research Campus

department: Laboratory of Lymphocyte Signalling and Development

country: United Kingdom

institute: The Babraham Institute

summary: High-throughput sequencing analysis of transcriptome from LPS-activated B cells from Lymph node of Zfp36l1(fl/fl) and Zfp36l1(fl/fl) x Cd79a(Cre/+) mice

overall_design: The RNA-seq libraries were prepared using ARTseq Ribosome Profiling Kit, ten libraries were pooled and sequenced on two lanes of HiSeq 2500, after quality control both FASTQ files for each sample were concatenated and mapped as one.

first: Alexander

last: Saveliev

middle: S

first: Martin

last: Turner


title: Growing Trichoderma reseei on a mix of carbon sources reveals links between development and cellulase production

status: Public on Nov 19 2020

city: PARIS

first: Stephane

last: Le Crom

address: 46 rue Ulm

department: Genomic Core Facility

country: France

institute: IBENS

summary: Study of the impact of the carbon source (various mixture of glucose and lactose) on the cellulase production.

overall_design: T. reseei RUT-C30 (ATCC 56765) was cultivated on various mixtures of glucose and lactose were used for the cellulase production phase in fed-batch mode (after an initial growth phase on glucose in batch mode). RNA extraction was performed 24 h and 48 h after analysis was carried out thanks to RNAseq experiments. two to six biological replicates were used

first: A

last: Pirayre

first: F

last: Bidard


title: Comparison of the PU.1 transcriptional regulome and interactome in human and mouse dendritic cells

city: Oviedo

first: Patricia

last: Martínez-Botía

state: Asturias

address: Avda/ Roma s/n

country: Spain

institute: Instituto de Investigación Sanitaria del principado de Asturias

summary: Dendritic cells (DCs) are key immune modulators, and are able to mount immune responses or tolerance. DC differentiation and activation imply a plethora of molecular and cellular responses, including transcriptional changes. PU.1 is a highly expressed transcription factor in DCs, and coordinates relevant aspects of DC biology. Due to their role as immune regulators, DCs pose as a promising immunotherapy tool. However, some of their functional features, such as survival, activation or migration, are compromised due to the limitations to simulate in vitro the physiological DC differentiation process. A better knowledge of transcriptional programs would allow the identification of potential targets for manipulation with the aim of obtaining “qualified” DCs for immunotherapy purposes. Most of the current knowledge regarding DC biology derives from studies using mouse models, which not always find a parallel in human. In the present study we dissect the PU.1 transcriptional regulome and interactome in mouse and human DCs, in the steady state (ST) or LPS-activated. The PU.1 transcriptional regulome was identified by performing PU.1 chromatin immunoprecipitation followed by high throughput sequencing, and pairing these data with RNA-sequencing data. The PU.1 interactome was identified by performing PU.1 immunoprecipitation followed by mass spectrometry analysis. Our results portray PU.1 as a pivotal factor that plays an important role in the regulation of genes required for proper DC activation and function, and assures the repression of non-lineage genes. The interspecies differences between human and mouse DCs are surprisingly substantial, highlighting the need to study the biology of human DCs.

overall_design: Human monocyte-derived dendritic cells (moDCs) from the PBMC fraction of the blood from healthy donors were stimulated with LPS or unstimulated (under steady state), 2 biological replicates each

first: M

last: Scheenstra

first: P

first: L

last: Gutiérrez


title: Molecular patterns of isolated tubulitis differ from tubulitis with interstitial inflammation in early indication biopsies of kidney allografts

city: Praha 4

first: Petra

last: Hruba

address: Videnska 1958

department: Transplant Laboratory

country: Czech Republic

institute: Institute for Clinical and Experimental Medicine

summary: Banff 2019 update of kidney allograft pathology excluded isolated tubulitis without interstitial inflammation (ISO-T) from category of borderline (suspicious) for acute T cell-mediated rejection due to its proposed benign clinical outcome. However, molecular assessment of ISO-T has not been explored yet.  ISO-T or interstitial inflammation with tubulitis (I+T) were diagnosed in indication biopsies within first 14 postoperative days. Molecular patterns of ISO-T was compared to I+T either by using RNA sequencing (n=16) or by Molecular Microscope Diagnostic System (MMDx, n=51).   In ISO-T group, RNA sequencing showed lower expression of genes related to interferon-y (p=1.5 *10-16), cytokine signaling (p=2.1 *10-20) and inflammatory response (p=1.0*10-13) than in I+T groups. Increased transcripts in I+T group had significant overlap with previously described pathogenesis-based transcript sets associated with T cell-mediated rejection (TCMR), cytotoxic and effector T cell transcripts. In ISO-T, MMDx classified biopsies as no-rejection in 25/32 (78%) while in I+T in 12/19 (63%). ISO-T had significantly lower MMDx scores for interstitial inflammation (p=0.014), tubulitis (p=0.035) and TCMR (p=0.016) compared to I+T.   Less inflammatory molecular signals of isolated tubulitis suggest its benign phenotype also on molecular level.

overall_design: To compare expression profiles of kidney allografts between isolated tubulitis without interstitial inflammation (ISO-T) and interstitial inflammation with tubulitis (I+T) by RNAseq.

first: Katellyn

last: Madill-Thomsen

first: Martina

last: Mackova

first: Jiri

last: Klema

first: Jana

last: Maluskova

first: Ludek

last: Voska

first: Alena

last: Parikova

first: Janka

last: Slatinska

first: Philip

last: Halloran

first: Ondrej

last: Viklicky


title: Reawakening of Dormant Tumor Cells by Modified Lipids derived from Stress Activated Neutrophils

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

summary: Tumor recurrence years after seemingly successful treatment of primary tumors is one of the major causes of mortality in cancer patients. Reactivation of dormant tumor cells is largely responsible for this phenomenon. Using models of lung and ovarian cancer, we found a specific mechanism that may govern this process mediated by stress and neutrophils. Stress hormones cause rapid release of S100A8/A9 proteins by neutrophils. S100A8/A9 induce activation of myeloperoxidase resulting in accumulation of oxidized lipids. These lipids up-regulate fibroblast growth factor pathway in tumor cells causing tumor cell exit from the dormancy and formation of tumor lesions. Higher serum levels of S100A8/A9 were associated with shorter time to recurrence in patients with lung cancer after complete tumor resection. Targeting of S100A8/A9 or β2 adrenergic receptors abrogated stress induced reactivation of dormant tumor cells. These observations demonstrate a mechanism linking stress, and specific neutrophils activation with early recurrence in cancer.

overall_design: RNA-seq for parental (KRP) and reactivated (KRP.react) by S100A8/9 cells

first: Dmitry

last: Gabrilovich

first: Michela

last: Perego


title: miRNA expression data from MCF-7, LCC2 and LCC9 cells

status: Public on Nov 18 2020

city: Suzhou

first: Min

last: Jiang

state: Jiangsu

address: No. 188, Shi Zi Road

institute: The First Affiliated Hospital of Soochow University

summary: Acquired resistance to tamoxifen and fulvestrant is a challenging clinical problem in the treatment of hormone receptor-positive breast cancer patients. Non-coding RNAs (ncRNAs) could contribute to endocrine resistance but their specific roles in tamoxifen and fulvestrant resistance are not fully understood.

overall_design:
We performed microarray analysis of endocrine therapy sensitive (MCF-7), tamoxifen-resistant (LCC2), and dual tamoxifen and fulvestrant-resistant (LCC9) breast cancer cells.
MCF-7, LCC2 and LCC9 cells were lysed to extract RNAs for microarray analysis.


title: circRNA expression data from MCF-7, LCC2 and LCC9 cells


title: lncRNA and mRNA expression data from MCF-7, LCC2 and LCC9 cells

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


title: Transcriptomic Analysis reveals responses to Cycloastragenol in Arabidopsis thaliana

city: ISTANBUL

first: Wissem

last: Mhiri

address: DAVUTPASA MAH. DAVUTPASA CADDESI ESENLER

department: chemistry

country: Turkey

institute: Yildiz technial university

summary: Purpose: we aimed to demonstrate the effects of Cycloastragenol on the different plant signaling mechanisms and analyze genome-wide transcriptional responses in order to demonstrate its potential as a new key molecule to help plants overcome different environmental stresses. Methods: RNA-seq was employed to assess transcriptional profiles in treated and non-treated A. thaliana calli. We sequenced two cDNA libraries developed from A. thaliana (wild type Col-0) calli treated with 1µM Cycloatragenol and without. The sequence reads that was filtered, were mapped, aligned and then compared to the reference annotation (the known genes of A. thaliana genome) using Cufflinks tools. Clean data was analyzed using CPC software and results were validated by qRT-PCR using TaqMan and SYBER green assays. Results: We mapped around 63 and 70 million sequence reads from, respectively, control and CAG-treated samples. After filtration and mapping about 21 thousands genes corresponding to an average of 34 thousands transcripts, for each sample were identified. 1045 genes showed differential expression between control and treated sample with a p value < 0.05. Seven genes, which have been chosen randomly, were validated with qRT-PCR. RNA-seq data had a linear relationship with qRT-PCR for a goodness of fit (R2) of 0.959.

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

first: W

first: Ö

last: Çakır

first: N

last: Turgut-Kara

first: B

last: Nalbantoğlu

first: M

last: Ceylan


title: lncRNA, mRNA, miRNA and circRNA expression data from MCF-7, LCC2 and LCC9 cells

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

platform_organism:
Homo sapiens
synthetic construct

overall_design: Refer to individual Series


title: Identification of a human gut-derived LEAP2 fragment as a novel insulin secretagogue

city: Hørsholm

first: Martin

middle: Rønn

last: Madsen

state: Please Select

address: Hørsholm Kongevej 11

department: Computation Biology

country: Denmark

institute: Gubra

summary: The mechanisms underlying Roux-en-Y gastric bypass (RYGB) surgery-induced weight loss and the immediate postoperative beneficial metabolic effects associated with the operation remain uncertain. We aimed to identify novel gut-derived peptides with therapeutic potential in obesity and/or diabetes by determining genome-wide expression patterns in isolated human small intestinal enteroendocrine cells (EECs) obtained from 20 obese subjects undergoing RYGB and again three months later by upper enteroscopy. RYGB increased expression levels of the inverse ghrelin receptor agonist, liver-enriched antimicrobial peptide 2 (LEAP2), and a secreted endogenous LEAP2 fragment (LEAP238-47) demonstrated insulinotropic properties in vitro, promoting an increase in insulin release comparable to the gut hormone glucagon-like peptide 1. LEAP238-47 showed reciprocal effects on growth hormone secretagogue receptor (GHSR) activity, suggesting that the insulinotropic action of the peptide may be directly linked to attenuation of tonic GHSR activity. The fragment was infused to healthy human individuals, but compared to placebo, no glucoregulatory effect was observed in the chosen dose. In conclusion, small intestinal LEAP2 expression was upregulated after RYGB; and the fragment LEAP238-47 showed a strong in vitro insulinotropic effect, but failed to elicit glucoregulatory effects when infused in healthy human subjects.

overall_design: Global transcriptome profiling of gut segments from patients undergoing RYGB surgery.

first: Christoffer

middle: A

last: Hagemann

first: Chen

last: Zhang

first: Henrik

last: Hansen

first: Tina

last: Jorsal

first: Kristoffer

last: Rigbolt

first: Natasha

middle: C

last: Bergmann

first: Sebastian

last: Heimbürger

first: Mechthilde

last: Falkenhahn

first: Stefan

last: Theis

first: Kristin

last: Breitschopf

first: Stephanie

last: Holm

first: Morten

last: Hedegaard

first: Mikkel

last: Christensen

last: Vilsbøll

first: Birgitte

last: Holst

first: Niels

last: Vrang

first: Jacob

last: Jelsing

first: Filip

last: Knop


title: H3K27M in Gliomas Causes a One-step Decrease in H3K27 Methylation and Reduced Spreading Within the Constraints of H3K36 Methylation [RNA-seq]

status: Public on Nov 17 2020

city: Santiago de Compostela

first: Carmen

last: Rivas

address: Avda Barcelona

department: CIMUS

institute: Universidad de Santiago de Compostela

summary: The discovery of H3K27M mutations in pediatric gliomas marked a new chapter in cancer epigenetics. Numerous studies have investigated the effect of this mutation on H3K27 trimethylation, but only recently have we started to realize its additional effects on the epigenome. Here, we use isogenic glioma H3K27M(+/-) cell lines to investigate H3K27 methylation and its interaction with H3K36 and H3K9 modifications. We describe a “Step Down” effect of H3K27M on the distribution of H3K27 methylation: me3 is reduced to me2, me2 is reduced to me1, while H3K36me2/3 delineate the boundaries for the spread of H3K27me marks. We also observe a replacement of H3K27me2/3 silencing by H3K9me3. Using a computational simulation, we explain our observations by reduced effectiveness of PRC2 and constraints imposed on deposition of H3K27me by antagonistic H3K36 modifications. Our work further elucidates the effect of H3K27M in gliomas, as well as general principles of deposition of H3K27 methylation.

overall_design: WGBS, RNA-seq, and ChIP-seq for histone H3 post-translational modifications in high-grade glioma cell lines.

first: Ashot

last: Harutyunyan

first: Haifen

last: Chen

first: Tianyuan

last: Lu

first: Cynthia

last: Horth

first: Hamid

last: Nikbakht

first: Brian

last: Krug

first: Caterina

last: Russo

first: Eric

last: Bareke

first: Dylan

middle: M

last: Marchione

first: Mariel

last: Coradin

first: Benjamin

last: Garcia

first: Nada

last: Jabado

first: Jacek

last: Majewski


title: H3K27M in Gliomas Causes a One-step Decrease in H3K27 Methylation and Reduced Spreading Within the Constraints of H3K36 Methylation [WGBS]

type: Methylation profiling by high throughput sequencing


title: H3K27M in Gliomas Causes a One-step Decrease in H3K27 Methylation and Reduced Spreading Within the Constraints of H3K36 Methylation [ChIP-seq]


title: Next Generation Sequencing of Transcriptomes in SKOV3 and rhCCL20-treated SKOV3 cells

city: Shanghai

first: Wan

last: Liu

address: 160 Pujian Road

department: Department of Obstetrics and Gynecology, Ren Ji hospital

institute: School of Medicine, Shanghai Jiao Tong University

summary: The goals of this study are to compare the transcriptome differences between SKOV3 and rhCCL20-treated SKOV3 cells and identify the defferential expressed genes regulated by rhCCL20 in SKOV3 cells. We treated SKOV3 cells with 5% trehalose (control group) and rhCCL20 protein dissolved in 5% trehalose (experimental group) in vitro. The cells were collected 24 hours after treatment and used for RNA-sequencing.

overall_design: Examination of mRNA profiles of SKOV3 and rhCCL20-treated SKOV3 cells

first: Ning

last: Zhang

first: Wen

last: Di


title: H3K27M in Gliomas Causes a One-step Decrease in H3K27 Methylation and Reduced Spreading Within the Constraints of H3K36 Methylation

first: Carmen

last: Rivas


title: Classification and functional identification by gene expression patterns from various muscle tissues in a single livestock

city: Daejeon

first: Ho-yeon

last: Lee

address: 125, Gwahak-ro, Yuseong-gu

country: South Korea

institute: KRIBB

summary:
Purpose : The RNA-seq data of 18 skeletal muscle tissues obtained from one Jejunal were sequenced. In this study, we aimed to group multiple tissues by unsupervised clustering of tissues based on expression pattern alone, and to find the criteria for dividing the classified tissues and the causative genes.
Method : The raw counts obtained from the STAR 2 pass alignment were obtained. The log2 normalization value of raw counts of each sample is classified by hierarchical clustering. The eighteen samples were classified into two groups of nine each. Differential expression analysis of each group through R package DESeq2 revealed a total of 1104 Differentially expressed genes (DEGs).
Result and Conclusion : Based on myosin heavy chain family gene expression in Identified DEGs, the criteria for dividing the two groups were determined by the classification of slow-twitch and fast-twitch muscle according to the content of myosin heavy chain fiber. ?In addition, we confirmed the up-regulation of the genes that are characteristic of the slow-twitch muscle, and identified that the central genes that express these features play a role in maintaining cardiovascular homeostasis.

overall_design: total RNA sequencing for 18 skeletal muscles from one individual horse


title: Lonidamine enhances the oncolytic effect of M1 virus through inhibiting antiviral immune response and potentiating ER stress mediated apoptosis

status: Public on Nov 16 2020

city: Guangzhou

first: liu

last: xincheng

address: zhongshan Road 74 Street

institute: sysu

summary: Gene set enhancement analysis (GSEA) revealed that M1 treatment upregulates glycolysis and hypoxia pathway in hallmark gene sets. GSEA revealed that Lonidamine strongly inhibited the IFN-α and IFN-β response pathways after M1 virus infection. GSEA showed that gene sets in unfolded protein response, response to endoplasmic reticulum stress, intrinsic apoptotic signaling pathway were significantly upregulated by Lonidamine plus M1 treatment.

overall_design:
HCT 116 tumor cells were treated with control, M1 (MOI=1 pfu/cell), Lonidamine [cp531] (50 μM) or M1 (MOI=1 pfu/cell) plus Lonidamine (50 μM) for 24 hours. Total RNA was extracted from 1×106 cells with TRIzol Reagent (Thermo Fisher Scientific) and was sent for RNA sequencing

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first: Jing

last: Cai

first: Xincheng


title: RNA sequencing study using Prox1-eGFP mice to investigate the role of lymphatic vasculature in chronic cardiac dysfunction

first: Michael

last: Nagle

state: MA

address: 1 Portland Street

department: Internal Medicine Research Unit

institute: Pfizer

summary: The goal of the study is to examine the transcriptional changes in different cell populations isolated from heart and diaphragm in angiotensin II infusion-induced cardiac dysfunction and with a lymphangiogenic therapy (VEGFCc156s)

overall_design: Prox1-eGFP mice were treated with BSA, angiotensin II in BSA or angiotensin II and VEGFCc156s for 5-6 weeks and used for the isolation of different cell populations from heart and diaphragm. The transcriptional profile of isolated cell populations was examined using RNA-Seq.

first: LouJin

last: Song

first: Arun

last: Shipstone

middle: W


title: RNA-Seq of human fetal and adult scalp hair follicle dermal papilla (DP), dermal sheath cup (DSC), and interfollicular dermal (IFD) cells

city: Taichung

first: Yung-Chih

last: Lai

address: 7F., No. 6, Xueshi Road, North District

department: Integrative Stem Cell Center

country: Taiwan

institute: China Medical University Hospital

summary: Much is still unknown about the molecular regulatory networks which govern the dermal papilla’s (DP) ability to induce hair follicle regeneration, a capacity which gradually decreases with age.  DP and dermal sheath cup (DSC) cells from mature, anagen phase, hair follicles were manually microdissected from fresh frozen sections of 16-18 week human fetal scalp and 30-60 year old adult male scalp.  Interfollicular dermal (IFD) fibroblasts were harvested for comparison.  RNA-seq libraries from each cell population were prepared with Nugen’s Ovation RNA-Seq and Ultralow Library systems, sequenced to approximately 100 million total reads.  A set of 121 genes was identified as significantly upregulated in fetal DP cells, as compared to both fetal DSC and IFD populations.  Wnt/β-catenin, Shh, FGF, BMP, and Notch signaling pathways were significantly enriched among those genes differentially expressed between fetal and adult DP cells.  Among them, Spondin-1, a Wnt agonist, was chosen for verification and can rescue hair follicle regeneration in skin reconstitution assays using cells from adult mice.  Additionally, twenty-nine transcription factors were significantly upregulated in fetal DP compared to adult DP cells.  Of those, seven transcription factor binding motifs were significantly enriched in the candidate promoter regions of differentially expressed genes between fetal and adult DP cells, suggesting a combinatorial regulatory role in the fetal DP phenotype.  Further investigation into these regulators is warranted to determine if these proteins and/or associated pathways plays a role in the maintenance or modulation of DP cells to induce hair regeneration.

overall_design: Dermal papilla (DP), dermal sheath cup (DSC), and interfollicular dermal (IFD) cells from mature, anagen phase, hair follicles were manually microdissected from fresh frozen sections of 16-18 week human fetal scalp and 30-60 year old adult male scalp

first: Cheng-Ming

last: Chuong

first: Erin

last: Weber


title: Next-generation sequencing analysis of circulating micro-RNA expression in response to parabolic flight as a spaceflight analogue

city: Vienna

first: Matthias

last: Hackl

state: Austria

address: Leberstrasse 20

country: Austria

institute: TAmiRNA GmbH

summary: BACKGROUND: Understanding physiologic reactions to weightlessness is an indispensable requirement for safe human space missions. While adaptations of human organ systems in response to weightlessness have been described in former studies, their molecular background needs further elucidation.  OBJECTIVE:  The study aims to analyse changes in the expression of circulating miRNAs in serum in response to gravitational changes induced by parabolic flight as a spaceflight analogue.  METHODS: Eight healthy volunteers (age: 25.4 years, male: 4, female: 4) were included. Each subject underwent 31 short-term phases of weightlessness and hypergravity induced by parabolic flight. At different time points (baseline, 1 hour after parabolic flight, and 24 hours parabolic flight), venous blood was withdrawn. Analysis of circulating miRNAs in serum was conducted by means of next generation sequencing.  RESULTS: In total, 213 miRNAs were robustly detected by small RNA sequencing in all 24 samples. 4 miRNAs (mir-941, mir-24-3p, mir-486-5p, mir-223-3p) evidenced a significant change in expression after adjusting for multiple testing. mir-941 and mir-24-3p showed a significant decrease 24 hours after parabolic flight compared to 1 hour after parabolic flight. Contrary, mir-486-5p showed a significant increase 24 hours after parabolic flight compared to 1 hour after parabolic flight. Of note, mir-223-3p showed a significant decrease 24 hours after parabolic flight compared to baseline values and values at 1 hour after parabolic flight. A target network analysis identified genes of the p53 signaling pathway and the cell cycle highly enriched among the targets of the four microRNAs.   CONCLUSIONS:  Our findings suggest cellular adaption to gravitational changes by means of weightlessness and hypergravity already at the transcriptional level. Based on our results, we suggest a change in cell cycle regulation as potential explanation for adaptational changes observed in space missions.

overall_design: 24 samples were analyzed in total. These samples were obtained from 8 subjects at three different time points.

first: Peter

last: Jirak

first: Bernhard

last: Wernly

last: Lichtenauer

first: Marcus

last: Franz

first: Thorben

last: Knost

first: Thaer

last: Abusamrah

first: Kelm

last: Malte

first: Bimpong-Buta

last: Nana-Yaw

first: Christian

last: Jung


title: YAP/TAZ in vascular smooth muscle

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

country: Germany

institute: MPI for heart and lung research

summary: Investigation of the physiogical functions of YAP/TAZ in vascular smooth muscle cells

overall_design: Total RNA was prepared using isolated mouse aortic SMC of wild-type (WT) and Sm-Yap/Taz-KO mice (KO) after 18 days tamoxifen injection

first: Lei

last: Wang


title: EOFAD-causing mutations in psen1 orchestrate dedifferentiation through remodeling of the chromatin landscape in hiPSC-derived neurons [ChIP-Seq]

status: Public on Nov 13 2020

city: La Jolla

first: Shankar

last: Subramaniam

address: 9500 Gilman Drive

department: Department of Bioengineering

country: USA

institute: University of California, San Diego

summary: In this work, we used an integrative, multi-omics approach and systems-level analysis to generate a mechanistic disease model for EOFAD in an hiPSC-derived neuron model system.

overall_design: hiPSC-derived neurons were generated from patient-specific Non-Demented Control, PSEN1M146L, PSEN1H163R, PSEN1A246E, and PSEN1A431E fibroblasts and subjected to RNA-Seq, ATAC-Seq, and histone methylation ChiP-Seq. For H3K4Me3 and H3K27Me3 ChIP-Seq experiments, NDC, PSEN1M146L, and PSEN1A246E (n = 1) hiPSC-derived neurons were processed using the Active Motif ChIP-IT High Sensitivity kit. 500 ng of purified, sonicated chromatin was incubated with 5 µL of H3K4Me3 or H3K27Me3 Rabbit polyclonal antibody overnight at 4C. After de-crosslinking, ChIP DNA was purified using the Qiagen MinElute PCR Purification Kit; libraries for H3K4Me3, H3K27Me3, and 1% Input were generated using Illumina TruSeq LT adaptors. Sequencing was performed on an Illumina HiSeq4000 generating Single-Read, 75bp reads with an average of 20 million reads per sample.

first: Andrew

middle: B

last: Caldwell

first: Qing

last: Liu

first: Gary

last: Schroth

first: Douglas

last: Galasko

first: Shauna

last: Yuan

first: Steven

last: Wagner


title: EOFAD-causing mutations in psen1 orchestrate dedifferentiation through remodeling of the chromatin landscape in hiPSC-derived neurons [RNA-Seq]

overall_design: hiPSC-derived neurons were generated from patient-specific Non-Demented Control, PSEN1M146L, PSEN1H163R, PSEN1A246E, and PSEN1A431E fibroblasts and subjected to RNA-Seq, ATAC-Seq, and histone methylation ChiP-Seq. For RNA-Seq, total RNA was extracted from NDC (n = 8), PSEN1M146L (n = 4), PSEN1H163R (n = 3), PSEN1A246E (n = 4), and PSEN1A431E (n = 3) hiPSC-derived neurons; libraries were generated using the Illumina RiboZero RNA prep and TrueSeq Stranded RNA library kits followed by sequencing on an Illumina HiSeq4000 generating Paired End, 100bp reads with an average of 25 million reads per sample.

middle: R


title: RNAseq to profile transcriptomes in adipose tissue macrophages (ATMs) from TKO(mir-106a~363-/- mir-106b~25-/- mir-17~92flox/flox Lyz2-Cre) and WT(Lyz2-Cre) mice fed with regular chow diet or high fat diet.

status: Public on Nov 15 2020

city: Beijing

first: Xiang

last: Zhang

address: Tsinghuayuan Street

country: China

institute: Tsinghua University

summary: We performed the transcriptomic analysis of RNA-seq of ATMs generated from WT and TKO mice fed with regular chow diet or high fat diet.

overall_design: ATMs from WT and TKO mice were fluorescence-activated cell sorting (FACS) sorted and then were lysed. RNA was extracted, polyA enriched and prepared for sequencing libraries.


title: EOFAD-causing mutations in psen1 orchestrate dedifferentiation through remodeling of the chromatin landscape in hiPSC-derived neurons


title: Effect of BET Inhibitors on Rheumatoid Synovial Fibroblast Cells [ChIP-seq]

status: Public on Nov 12 2020

city: Spring House

first: Vinod

last: Krishna

state: Pennsylvania

address: 1400 McKean Road

institute: Janssen R&D LLC

summary: We demonstrate that JQ1 inhibits IL1B based RA Synovial Fibroblast activation and proliferation, by inhibiting key BRD2/4 superenhancer genes.

overall_design: FLS cells pre and post JQ1 treatment; associated ChIP-Seq of POL2, BRD2, and BRD4.

first: Sunil

last: Nagpal


title: Temporal and Spatial Heterogeneity of Host Response to SARS-CoV-2 Pulmonary Infection [gene expression]

status: Public on Nov 14 2020

city: Seattle

first: Jason

last: Reeves

state: WA

address: 530 Fairview Blvd

department: R&D

institute: Nanostring

summary:
The relationship of SARS-CoV-2 lung infection and severity of pulmonary disease is not fully understood. We analyzed specimens from 24 autopsies from patients who succumbed to SARS-CoV-2 infection using a combination of different RNA and protein analytical platforms to characterize inter- and intra- patient heterogeneity of pulmonary virus infection.  There was a spectrum of high and low virus cases that was associated with duration of disease and activation of interferon pathway genes.  Using a digital spatial profiling platform, the intra-pulmonary spatial heterogeneity of the virus corresponded to focal expression of interferon response genes and association with immune checkpoint genes
In this dataset, we capture the GeoMx DSP RNA profiling work done in conjunction with this study. The files here represent SARS-CoV-2 infected rapid autopsy patients (n = 6) which were profiled with the NanoString GeoMx COVID19 Atlas RNA panel v1.0. This panel was then read out using Illumina sequencing following standard library preparation according to manufacturer protocols. Attached below are low-resolution images of each slide with placement of all ROIs, as well as individual images of each ROI, segments, and UV illuminated IF channels. For access to high resolution (single channel, composite, or ROI) images please contact GeoMxSupport@nanostring.com or the corresponding author of the study. RNA sequencing data and results for bulk RNA profiling can be accessed in study GSE150316.

sample_organism: Severe acute respiratory syndrome coronavirus 2

overall_design: This dataset contains expression from localized sampling within 6 SARS-CoV-2 infected patient FFPE samples collected during rapid autopsy, with 3 non-infected control samples. Up to 48 segments were collected within each patient sample. RNA Scope on serial sections was used to guide ROI selection, and ROI ISH staining by RNA Scope is noted in the sample annotations.

first: Niyati

last: Desai

first: Azfar

last: Neyaz

first: Annamaria

last: Szabolcs

first: Angela

last: Shih

first: Jonathan

last: Chen

first: Vishal

last: Thapar

first: Linda

last: Nieman

first: Alexander

last: Solovyov

first: Arnav

last: Mehta

first: David

last: Lieb

first: Anupriya

last: Kulkarni

first: Christopher

last: Jaicks

last: Pinto

first: Dejan

last: Juric

first: Ivan

last: Chebib

first: Robert

last: Colvin

first: Arthur

middle: Y

last: Kim

last: Monroe

first: Sarah

middle: E

last: Warren

first: Patrick

last: Danaher

first: Jingjing

last: Gong

first: Erroll

last: Rueckert

first: Benjamin

middle: D

last: Greenbaum

first: Nir

last: Hacohen

first: Stephen

last: Lagana

first: Miguel

last: Rivera

first: Lynette

last: Sholl

first: James

last: Stone

last: Ting

first: Vikram

last: Deshpande


title: Effect of BET Inhibitors on Rheumatoid Synovial Fibroblast Cells [RNA-seq]

first: Vinod

last: Krishna

overall_design: RNASeq of FLS cells pre and post JQ1 and IL1B treatments.

first: Sunil

last: Nagpal


title: Single-cell RNAseq analysis of murine salivary gland development

status: Public on Nov 11 2020

city: Bethesda

first: Daniel

last: Martin

state: Maryland

address: 30 Convent Dr Bldg 30 Room 320A-3

department: OSD

institute: NIDCR

summary: Development of branching organs involves a series of events regulated by proliferation, differentiation, and intricate cell-cell communication networks. Understanding the molecular drivers for these developmental stages is instrumental to device effective regenerative therapies. Here, we use single cell RNAseq of murine submandibular gland (SMG) from developmental stages corresponding to end bud initiation (E12), branching morphogenesis (E14), cytodifferentiation (E16) and postnatal development (P1, P30, and adult) to generate an atlas of SMG development. The generated resource highlights the heterogeneity in the salivary gland epithelium throughout development and allowed us to identify putative transcription factors involved in secretory acinar cell specification that occurs around E16, including Ybx1, Eno1, Atf3, and Atf4. Clustering and trajectory inference (pseudotime) analyses of this atlas illustrate and suggest that end bud and acinar populations represent the most differentiated state relative to other populations from the same developmental stage, which was associated with a global decrease in expression of numerous transcription factors. Lastly, we identified and characterized two subsets of intercalated duct cells, a Kit+ population defined by Gfra3, and a subset characterized by Gstt1 with sexually dimorphic Smgc co-expression in females and high Serpinb11 co-expression in males. Our analysis indicates that the Gstt1+ population originates from proacinar precursors suggesting plasticity in this population. This atlas can be combined with other available resources to learn about specific cell functions and to predict mechanisms involved in development of branching organs.

overall_design: Examination of epithelial and mesenchymal cells in mouse SMG at five developmental stages

first: Belinda

last: Hauser

first: Marit

last: Aure

first: Michael

last: Kelly

first: Erich

last: Boger

first: Matthew

last: Hoffman

first: Alejandro

last: Chibly


title: Effect of BET Inhibitors on Rheumatoid Synovial Fibroblast Cells

overall_design: Refer to individual Series


title: Effect of BET Inhibitors on Rheumatoid Synovial Fibroblast Cells [ATAC-seq]

overall_design: FLS cells pre and post JQ1 and IL1B treatments; associated ATAC-Seq to assess changes in chromatin accessibility.


title: Total RNA-Seq of KHSRP knockdown (KD) and control samples in HepG2 and K562

city: Århus N

first: Trine Line

middle: Hauge

last: Okholm

address: Palle Juul-Jensens Boulevard 99

department: Department of Molecular Medicine (MOMA)

institute: Aarhus University Hospital

summary: We profile the expression of circular RNAs (circRNAs) upon KHSRP KD in HepG2 and K562 cells

overall_design: KHSRP KD and control samples were originally generated for the ENCODE project by Brenton Graveley’s Lab, UConn. We sequenced total RNA to evaluate the expression of circRNAs

first: Trine

first: Archana

last: Shankar

first: Mark

last: Perellis

first: Shashank

last: Sathe

first: Stefan

last: Aigner

first: Søren

last: Vang

first: Gene

last: Yeo

first: Jakob

last: Pedersen


title: EOFAD-causing mutations in psen1 orchestrate dedifferentiation through remodeling of the chromatin landscape in hiPSC-derived neurons [ATAC-Seq]

first: Shankar

last: Subramaniam

overall_design: hiPSC-derived neurons were generated from patient-specific Non-Demented Control, PSEN1M146L, PSEN1H163R, PSEN1A246E, and PSEN1A431E fibroblasts and subjected to RNA-Seq, ATAC-Seq, and histone methylation ChiP-Seq. For ATAC-Seq, transposition experiments were performed as previously reported on 50,000 NDC (n = 5), PSEN1M146L (n = 2), PSEN1H163R (n = 3), PSEN1A246E (n = 2), and PSEN1A431E (n = 3) hiPSC-derived neuron cells using the Illumina Nextera DNA Sample Preperation kit and Qiagen MinElute PCR Purification kit. ATAC-Seq libraries were generated from transposed DNA using the Kapa Biosystems Real-Time Library Amplification kit and further purified using the Qiagen MinElute PCR Purification kit; sequencing was performed an Illumina HiSeq4000 platform generating Paired-End, 50bp reads with an average of 25 million reads per sample.

first: Andrew

last: Caldwell

first: Qing

last: Liu

first: Gary

middle: P

last: Schroth

first: Douglas

last: Galasko

first: Shauna

middle: H

last: Yuan

first: Steven

last: Wagner


title: Comparison of gene expression profiles in paired synovial biopsies from rheumatoid arthritis (RA) patients

city: Brussels

first: Bernard

middle: Robert

last: Lauwerys

address: Avenue Hippocrate 10

department: Institut de Recherches Expérimentales et Cliniques

country: Belgium

institute: Université catholique de Louvain

summary:
We explored transcriptomic profiles of paired synovial biopsies from RA patients, in order to assess heterogeneity in synovial tissue at the individual level.
Pairwise comparison of transcriptomic profiles showed similar expression of RA-related molecular pathways (TCR signaling, T cell co-stimulation and response to TNF⍺), thereby showing that global molecular alterations in RA synovitis are similar between small and large joints from the same patient.

overall_design: 20 paired biopsies (3 to 5 fragments pooled per biopsy) from 10 RA patients with active disease were analyzed. Synovial biopsies were performed simultaneously in one small and one large joint per patient using needle-arthroscopy for the knee and ultrasound-guided biopsy for the hand or wrist. Synovium from individuals with osteoarthritis was used as controls. Total RNA was hybridized on HGU133 Plus 2.0 arrays.

first: Clément

last: Triaille

first: Louise

last: Vansteenkiste

first: Patrick

last: Durez


title: RNA-seq for UBR5-regulated genes in tumor associated macrophages

status: Public on Nov 10 2020

city: New York

first: Xiaojing

last: Ma

address: 1300 York Ave.

institute: Weill Cornell Medicine

summary: RNA-seq analysis of peritoneal macrophages derived from non-tumor bearing, WT ID8 tumor-bearing, and Ubr5 KO ID8 tumor bearing C57BL/6 mice.

overall_design: Xiaojing,Ma

first: Mei

last: Song

first: Tuo

last: Zhang


title: Baricitinib treatment resolves lower airway inflammation and neutrophil recruitment in SARS-CoV-2-infected rhesus macaques [scRNA-Seq]

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

summary: SARS-CoV-2 induced hypercytokinemia and inflammation are critically associated with COVID-19 disease severity. Baricitinib, a clinically approved JAK1/2 inhibitor, is currently being investigated in COVID-19 clinical trials. Here, we investigated the immunologic and virologic efficacy of baricitinib in a rhesus macaque model of SARS-CoV-2 infection. Viral shedding measured from nasal and throat swabs, bronchoalveolar lavages and tissues was not reduced with baricitinib. Type-I IFN antiviral responses and SARS-CoV-2-specific T-cell responses remained similar between the two groups. Importantly, animals treated with baricitinib showed reduced inflammation, decreased lung infiltration of neutrophils, reduced NETosis activity, and more limited lung pathology. Moreover, baricitinib treated animals had a rapid and remarkably potent suppression of lung macrophages production of cytokines and chemokines responsible for inflammation and neutrophil recruitment. These data support a beneficial role for, and elucidate the immunological mechanisms underlying, the use of baricitinib as a frontline treatment for severe inflammation induced by SARS-CoV-2 infection.

overall_design: Five rhesus macaques (Macaca mulatta) were infected with SARS-CoV-2. Two RMs were administered 4 mg Baricitinib starting at day 2 post-infection (DPI) for 8-9 consecutive days. scRNA-Seq profiling of cells isolated from BAL (bronchoalveolar lavages) prior to SARS-CoV-2 inoculation (-5 DPI; Baseline); and 4 days after infection, and 48 hours after beginning baricitinib (4 DPI).

first: Timothy

middle: N

last: Hoang

first: Maria

last: Pino

first: Arun

last: Boddapati

first: Elise

middle: G

last: Viox

first: Carly

last: Starke

first: Amit

last: Upadhyay

first: Sanjeev

last: Gumber

first: Michael

last: Nekorchuk

first: Kathleen

last: Busman-Sahay

first: Zachary

last: Strongin

first: Justin

middle: L

last: Harper

first: Kathryn

last: Pellegrini

first: Shannon

last: Kirejczyk

first: Keivan

last: Zandi

first: Sijia

last: Tao

first: Tristan

last: Horton

first: Elizabeth

last: Beagle

first: Ernestine

last: Mahar

first: Michelle

last: Lee

first: Joyce

last: Cohen

first: Sherrie

last: Jean

first: Jennifer

last: Wood

first: Fawn

last: Connor-Stroud

first: Rachelle

last: Stammen

first: Olivia

last: Delmas

first: Shelly

last: Wang

first: Kimberly

last: Cooney

last: Sayegh

first: Lanfang

first: Daniela

last: Weiskopf

first: Peter

last: Filev

first: Jesse

last: Waggoner

first: Anne

last: Piantadosi

first: Sudhir

last: Kasturi

first: Hilmi


title: RNA-Seq of circCDYL knockdown (KD) samples in HepG2, J82, and UMUC3 cells and of GRWD1, IGF2BP1, and IGF2BP2 knockdown (KD) samples in J82 and UMUC3 cells

first: Trine Line

last: Okholm

summary: We profile gene expression upon circCDYL KD in HepG2 cells and in two bladder cancer cell lines J82 and UMUC3 as well as upon knockdown of the RNA binding proteins (RBP) GRWD1, IGF2BP1, and IGF2BP2 in J82 and UMUC3

overall_design: Cells were treated with a control scramble (scr) siRNA or an siRNA that specifically knock down the expression of circCDYL or the RBP of interest. mRNA profiling upon treatment were generated using QuantSeq

first: Trine

first: Andreas

last: Kamstrup

first: Hanne

last: Steen

first: Søren

last: Vang

first: Christian

last: Damgaard

first: Jakob

middle: S

last: Pedersen


title: Baricitinib treatment resolves lower airway inflammation and neutrophil recruitment in SARS-CoV-2-infected rhesus macaques

first: Gregory

last: Tharp

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


title: Genome-wide occupancy of AIPP3 in Arabidopsis

status: Public on Nov 08 2020

city: shanghai

first: Yizhe

last: Zhang

address: No.300 Fenglin Road

institute: Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences

summary: ChIP-seq was performed to detect genome-wide binding sites of AIPP3

overall_design: Arabidopsis wild-type Col-0 and AIPP3-4Myc plants were subject to ChIP-seq analysis using the Myc antibody.

first: Yi-Zhe

first: Li

last: Peng

first: Cheng-Guo

last: Duan


title: PerSorted dim and lit cells of MSM-mEos2

status: Public on Nov 09 2020

first: Vivek

last: Srinivas

address: 401 Terry Ave N

institute: ISB

summary: Mycobacterium tuberculosis (MTB) generates phenotypic diversity to persist and survive the harsh conditions encountered during infection. MTB avoids immune effectors and antibacterial killing by entering into distinct physiological states. The surviving cells, persisters, are a major barrier to the timely and relapse-free treatment of tuberculosis (TB). We present for the first time, PerSort, a method to isolate and characterize persisters in the absence of antibiotic, or other pressure. We demonstrate the value of PerSort to isolate translationally dormant cells that pre-exist in small numbers within Mycobacterium spp. cultures growing under optimal conditions, but which dramatically increased in proportion under stress conditions. The translationally dormant subpopulation exhibited multidrug tolerance and regrowth properties consistent with persister cells. Furthermore, PerSort enabled single-cell transcriptional profiling that provided evidence that the translationally dormant persisters were generated through a variety of mechanisms, including vapC30, mazF, and relA/spoT overexpression. Finally, we demonstrate that notwithstanding the varied mechanisms by which the persister cells were generated, they converge on a similar low oxygen metabolic state that was reversed through activation of respiration to rapidly eliminate persisters fostered under host-relevant stress conditions. We conclude that PerSort provides a new tool to study MTB persisters, enabling targeted strategies to improve and shorten the treatment of TB.

overall_design: Dim and lit cells (n= 300,000) were PerSorted into 1 mL TriZol having ~ 1000 bone marrow derived macrophage cells. RNA was extracted with phenol chloroform method described previously (PMID:30833303), rRNA was depleted with Illumina rRNA depletion kit, and mycobacterium RNA was enriched with Path-seq methodology described previously (PMID:30833303). A total of 100,240 probes were designed to cover M. smegmatis mc2155 (Agilent probe library ELID number S3206492).

first: Eliza

middle: J

last: Peterson

first: Amardeep

last: Kaur

first: Nitin

last: Baliga


title: Craniofacial periosteum-derived cells as source for bone tissue engineering

status: Public on Nov 07 2020

city: Rotterdam

first: Eskeatnaf

last: Mulugeta

address: Wytemaweg 80

department: Cell Biology

country: Netherlands

institute: Erasmus University Medical Center Rotterdam (Erasmus MC)

summary: The development of alternatives for autologous bone grafts is a major focus of bone tissue engineering. To produce living implants, the use of skeletal stem and progenitor cells (SSPCs) are envisioned as key ingredients. SSPCs can be obtained from bone marrow, adipogenic tissue, dental pulp and periosteum. Human periosteum-derived cells (hPDCs) exhibit a number of progenitor characteristics and have well-documented in vivo bone formation capacity. Here, we have characterized and compared hPDCs derived from tibia with new sources of hPDCs, i.e. from maxilla and mandible (craniofacial hPDCs, as a potential source for tissue engineered implants for craniofacial applications.

overall_design: 18 RNA samples were sequenced in with technical duplicates (A and B). Periosteal samples were obtained from the posterior areas of the maxilla and mandible of 16 to 30-year old healthy patients who underwent bimaxillary orthognathic surgery, after informed consent was obtained (Belgian registration number B322201731127). The tibial samples were harvested by orthopedic surgeons as described previously (Eyckmans and Luyten, 2006). RNA-seq samples were obtained from maxillary, mandibular and tibial samples obtained from donors.

first: Lisanne

last: Groeneveldt

first: Danny

last: Huylebroeck


title: Baricitinib treatment resolves lower airway inflammation and neutrophil recruitment in SARS-CoV-2-infected rhesus macaques [RNA-Seq]

overall_design: Eight rhesus macaques (Macaca mulatta) were infected with SARS-CoV-2. Four RMs were administered 4 mg Baricitinib starting at day 2 post-infection (DPI) for 8-9 consecutive days. RNA-Seq profiling of cells isolated from BAL (bronchoalveolar lavages) prior to SARS-CoV-2 inoculation (-5 DPI; Baseline); 2 days after virus inoculation, prior to baricitinib treatment (2 DPI); and 4 days after infection, and 48 hours after beginning baricitinib (4 DPI).

first: Timothy

last: Hoang

first: Maria

last: Pino

first: Arun

last: Boddapati

first: Elise

last: Viox

first: Carly

last: Starke

first: Amit

middle: A

last: Upadhyay

first: Sanjeev

last: Gumber

first: Michael

last: Nekorchuk

first: Kathleen

last: Busman-Sahay

first: Zachary

last: Strongin

first: Justin

last: Harper

first: Kathryn

last: Pellegrini

first: Shannon

last: Kirejczyk

first: Keivan

last: Zandi

first: Sijia

last: Tao

first: Tristan

last: Horton

first: Elizabeth

last: Beagle

first: Ernestine

last: Mahar

first: Michelle

last: Lee

first: Joyce

last: Cohen

first: Sherrie

middle: M

last: Jean

first: Jennifer

last: Wood

first: Fawn

last: Connor-Stroud

first: Rachelle

last: Stammen

first: Olivia

last: Delmas

first: Shelly

last: Wang

first: Kimberly

last: Cooney

last: Sayegh

first: Lanfang

first: Daniela

last: Weiskopf

first: Peter

last: Filev

first: Jesse

last: Waggoner

first: Anne

last: Piantadosi

first: Sudhir

last: Kasturi

first: Hilmi


title: Single-cell RNA transcriptomics of thymic iNKT cells from C57BL/6 and Hivep3-/- mice

status: Public on Nov 06 2020

city: Aurora

first: Laurent

last: Gapin

state: CO

department: Immunology and Microbiology

institute: University of Colorado Anschutz Medical campus

summary: Single-cell RNA-seq analysis of murine thymic iNKT cells from two independent C57BL/6 mice and two independent Hivep3-deficient mice

overall_design: Processed thymocytes were enriched for PBS57-CD1d reactive cells by incubating thymocyte cell suspensions with PE or APC conjugated PBS57-CD1d tetramers for 45 minutes at 4C, then incubated with anti-PE or anti-APC magnetic microbeads (Miltenyi Biotec) for 15 minutes at 4C, followed by separation by using an autoMACS Pro Separator (Miltenyi Biotec) according to manufacturer’s instructions. A 50:50 mix of CD44low and CD44high PBS57-CD1d tetramer+ cells were sorted using a BD Facs Aria. Single-cell RNA-seq was performed using 10X Genomics Chromium isingle-cell controller and 5' gene expression kit.


title: RNA-seq analysis of WT, aipp3, aipp2, paipp2, aipp2/paipp2, cpl2, lhp1, and clf in Arabidopsis

first: Yizhe

last: Zhang

summary: RNA-seq was performed to detect transcripts level of WT and mutants.

overall_design: Total RNAs were extracted from 12-day-old seedlings grown during long days using a RNeasy Plant Mini kit (Qiagen).

first: Yi

middle: Z

first: Li

last: Peng

first: Cheng

last: Duan


title: Genomic and transcriptomic alterations associated with drug vulnerabilities and prognosis in adenocarcinoma at the gastroesophageal junction

first: Chen

last: Wu

address: 17 Panjiayuan Nanli, Chaoyang District

institute: Cancer Hospital, Chinese Academy of Medical Sciences

summary: Adenocarcinoma at the gastroesophageal junction (ACGEJ) has dismal clinical outcomes and there are currently few specific effective therapies because of limited knowledge on its genomic and transcriptomic alterations. The present study investigates genomic and transcriptomic changes in ACGEJ from Chinese patients and analyzes their drug vulnerabilities and associations with the survival time. Here we show that the major genomic changes of Chinese ACGEJ patients are chromosome instability promoted tumorigenic focal copy-number variations and COSMIC Signature 17-featured single nucleotide variations. We provide a comprehensive profile of genetic changes that are potentially vulnerable to existing therapeutic agents and identify Signature 17-correlated IFN-α response pathway as a prognostic marker that might have practical value for clinical prognosis of ACGEJ. These findings further our understanding on the molecular biology of ACGEJ and may help develop more effective therapeutic strategies.

overall_design:
We performed bulk RNA-seq on 123 pairs of tumor and adjacent normal tissue samples obtained from 123 individuals on Illumina HiSeq X Ten platform.

**Submitter declares that the raw data have been deposited in the Genome Sequence Archive (GSA) in BIG Data Center, Beijing Institute of Genomics (BIG), Chinese Academy of Sciences (https://bigd.big.ac.cn/gsa-human) under accession number HRA000025.**

first: Yuan

last: Lin

first: Yingying

last: Luo

first: Wenjia

last: Guo

first: Yanxia

last: Sun

first: Yiyi

last: Xi

first: Yuling

last: Ma

first: Mingming

last: Shao

first: Wen

last: Tan

first: Ge

last: Gao

first: Dongxin


title: TINC - a method to dissect transcriptional complexes at single locus resolution - reveals novel Nanog regulators in mouse embryonic stem cells

status: Public on Nov 05 2020

city: Clayton

first: Monika

last: Mohenska

state: VIC

address: 15 Innovation Walk

country: Australia

institute: Monash University

summary: We developed a novel epigenetic method termed TINC: TALE-mediated Isolation of Nuclear Chromatin. Using TINC we interrogated the protein complex formed at the Nanog promoter in embryonic stem cells (ESCs) and identified many known interactors as well as numerous previously unknown complex members, including RCOR2. Further interrogation of the role of RCOR2 in the ESC network revealed its involvement in the repression of lineage genes and the fine-tuning of pluripotency genes. Consequently, using the Nanog promoter as a paradigm, we demonstrated the power of TINC to provide important insights into the molecular makeup of transcriptional complexes at individual REs as well as into control of cellular identity in general.

overall_design: Single locus interrogation of the protein complex formed at the Nanog promoter using TINC, the RCOR2 binding profile in ESCs, and mRNA profiles in Rcor2 KO and WT ESCs.

first: Jose

last: Polo

first: Anja

last: Knaupp

first: Michael

middle: R

last: Larcombe


title: MeRIP sequencing

first: Yanan

last: Wang

state: China

address: No. 1 Shuai Fu Yuan Street

institute: Peking Union Medical College Hospital

summary: MeRIP sequencing for 12 samples

overall_design: To establishe a transcriptome-wide m6A methylome profile of psoriasis vulgaris and healthy skin

first: Ya-Nan

first: Hong-Zhong

last: Jin


title: Primary Meningioma WHO grade III

city: Heidelberg

first: Christel

last: Herold-Mende

department: Department of Neurosurgery

institute: University Hospital Heidelberg

summary: Comparative transcriptomic analysis of n=10 primary Meningioma WHO grade III

first: Rolf

last: Warta


title: Sequencing in L02 cells

status: Public on Nov 04 2020

city: WUHAN

first: heng

middle: zhi

last: du

address: 1095 Jiefang Dadao, Wuhan City, Hubei Province, China

institute: Wuhan Tongji Hospital

overall_design: Refer to individual Series


title: mRNA sequencing in L02 cells

summary: mRNA was performed in L02 cells

overall_design: We report the application of sequencing technology for high-throughput profiling of mRNA expressions in L02 cells. In this project, rRNA was removed from the total RNA by ribosomal RNA removal kit, and the way of ion breaking were used to break the RNA into 200-300bp fragments. By using RNA as template, the first strand of cDNA was synthesized with 6 base random primers and reverse transcriptase. The first strand cDNA was used as the template to synthesize the second strand cDNA. When the second strand cDNA is synthesized, the base T is replaced by U to achieve the goal of a chain specific library. All of our RNA-seq projects used strand specific kits to construct the libraries. Finally, we show that  mRNA different expression in  L02 cells. This study provides abundance of mRNA that may predict liver diseases.

first: yinzhong

last: wei

first: zhaoyan

last: ru

first: duheng

last: zhi


title: RIP sequencing in L02 cells

summary: RIP-SEQ was performed in L02 cells

overall_design: We report the application of sequencing technology for high-throughput profiling of mRNA expressions in L02 cells.L02 cells were lysed and then incubated with anti-Ago2 antibody (Abnova Corporation, Taiwan, China) after transfected with miR-320a mimics or miR-con for 24 h. After incubating at 4 °C overnight, protein A/G magnetic beads (Thermo Scientific, Shanghai, China) were added into the solution and incubated for another 2 h at 4 °C. Then, the beads were washed five times with PBST and the remaining products were extracted with TRIzol agent. In this project, rRNA was removed from the total RNA by ribosomal RNA removal kit, and the way of ion breaking were used to break the RNA into 200-300bp fragments. By using RNA as template, the first strand of cDNA was synthesized with 6 base random primers and reverse transcriptase. The first strand cDNA was used as the template to synthesize the second strand cDNA. When the second strand cDNA is synthesized, the base T is replaced by U to achieve the goal of a chain specific library. All of our RNA-seq projects used strand specific kits to construct the libraries. Finally, we show that  mRNA different expression in  L02 cells. This study provides abundance of mRNA that may predict liver diseases.