title: RNA-seq for MDCKII 3D and 2D epithelial morphogenesis.

city: ATHENS

first: Shaying

state: GA

address: B304B Life Sciences, 120 Green Street

institute: University of Georgia

summary: We performed time-course RNA-seq experiments for MDCKII 3D cell culture, and included seeding day0 cells and over-confluent 2D cells. To study how intracellular trafficking affects transcriptome changes, we also profiled trancriptome of DENND5A and AVL9 KD MDCKII cells by RNA-seq.

overall_design: Examination of mRNA expression during epithelial morphogenesis in MDCKII cells.

first: Tianfang


title: ATAC-seq and RNA-seq for MDCKII 3D and 2D epithelial morphogenesis

status: Public on Sep 25 2020

last: Zhao

country: USA

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Characterization of universal features of partially methylated domains across tissues and species

status: Public on Sep 27 2020

city: Los Angeles

first: Benjamin

middle: E

last: Decato

state: CA

address: 1050 Childs Way

department: Molecular and Computational Biology

institute: University of Southern California

type: Methylation profiling by high throughput sequencing

summary: Partially methylated domains (PMDs) are a hallmark of epigenomes in reproducible and specific biological contexts, including cancer cells, the placenta, and cultured cell lines. Existing methods for deciding whether PMDs exist in a sample, as well as their identification, are few, often tailored to specific biological questions, and require high coverage samples for accurate identification. In this study, we outline a set of axioms that take a step towards a functional definition for PMDs, describe an improved method for comparable PMD detection across samples with substantially different sequencing depths, and refine the decision criteria for whether a sample contains PMDs using a data-driven approach. Applying our method to 267 methylomes from 7 species, we corroborated recent results regarding the general association between replication timing and PMD state, and report identification of several reproducibly “escapee” genes within late-replicating domains that escape the downregulation and hypomethylation of their immediate genomic neighborhood. We also explored the discordant PMD state of orthologous genes between human and mouse, and observed a directional association of PMD state with gene expression and local gene density. Our improved method makes low-sequencing, population-level studies of PMD variation possible and our results further refine the model of PMD formation as one where sequence context and regional epigenomic features both play a role in gradual genome-wide hypomethylation.

sample_organism:
Homo sapiens
Mus musculus musculus

platform_organism:
Homo sapiens
Mus musculus musculus

overall_design: This GEO submission contains all DNA methylation and expression data produced for the study, including human lung cancer WGBS methylomes and RNA-seq as well as mouse 4T1 breast tumor methylomes.

first: Andrew

middle: D

last: Smith

first: Elvin

last: Wagenblast

first: Simon

last: Knott


title: ATAC-seq for MDCKII 3D and 2D epithelial morphogenesis

summary: We performed ATAC-seq experiments for MDCKII 3D cells, confluent 2D cells as well as seeding day0 cells to study if transcriptome changes during epithelial morphogenesis is associated with chromatin changes.

overall_design: Examination of open chromatin during epithelial morphogenesis in MDCKII cells.

last: Wang


title: Single cell RNAseq reconstruct normal and IPF lung epithelium

status: Public on Sep 24 2020

city: los angeles

first: Changfu

last: Yao

state: Ca

address: 8700 Beverly Blvd. AHSP Room A9401

department: Lung and Regenerative Medicine Institutes

institute: cedars-sinai medical center

summary: Tissue fibrosis is a common pathological outcome of chronic disease that markedly impairs organ function leading to morbidity and mortality. In the lung, idiopathic pulmonary fibrosis (IPF) is an insidious and fatal interstitial lung disease associated with declining pulmonary function.  Single cell RNA sequencing was used to map epithelial cell types of the normal human airway and alveolaor as well as IPF explant tissue.

overall_design: Single cell RNA-seq using 10x chromium system on isolated epithelial cells (DAPI-,CD45-,CD31-,CD326+) from donor , and IPF patients lung explant tissue. Here we present data from 9 donor samples, 5 out of this 9 donors, we collect epithelial cells from tracheal, dissected proximal airway as well as distal tissue to represent all epithelial cell types of donor lung. The other 5 donor samples, we only collected distal lung tissue based on availability of tissue. For IPF explant tissue, we also present 11 ipf samples of fibrotic region of IPF lungs. Note, for dissection of airway tree, there is inevitable some distal connective tissue, that's why AT2 and AT1 cells presents in the proximal epithelial fraction.

first: Barry

middle: R

last: Stripp


title: 21-nt phasiRNAs direct target mRNA cleavage in rice male germ cells

city: Beiing

first: Yijun

last: Qi

address: NO.1 Qinghuayuan

department: School of Life Sciences

country: China

institute: Tsinghua University

type: Non-coding RNA profiling by high throughput sequencing

summary: In grasses, phased small interfering RNAs (phasiRNAs), 21- or 24-nucleotide (nt) in length, are predominantly expressed in anthers and regulate male fertility. However, their targets and mode of action on the targets remain unknown. Here we profile phasiRNA expression in premeiotic and meiotic spikelets as well as in purified male meiocytes at early prophase I, tetrads and microspores in rice. We show that 21-nt phasiRNAs are most abundant in meiocytes at early prophase I while 24-nt phasiRNAs are more abundant in tetrads and microspores. By performing highly sensitive degradome sequencing, we find that 21-nt phasiRNAs direct target mRNA cleavage in male germ cells, especially in meiocytes at early prophase I. The target genes in early prophase I meiocytes show an enrichment for carbohydrate biosynthetic and metabolic pathways. Our study provides strong evidence that 21-nt phasiRNAs act in a target-cleavage mode and may facilitate the progression of meiosis by fine-tuning carbohydrate biosynthesis and metabolism in male germ cells.

overall_design: To profile phasiRNAs and explore the potential targets of phasiRNAs in male germ cells at different stages, we collected highly pure meiocytes at early prophase I tetrads, and microspores, respectively, by micromanipulation. Pre-meiotic spikelets, in which anthers are at stage 2 to stage 3 , meiotic spikelets in which germ cells are mostly at the early prophase of meiosis I, and embryos from seeds germinated 24h at 28℃, were also collected as controls. We then using these samples performed low-input sRNA-seq, sRNA-seq and high sensitive degradome-seq in three biological replicates.

first: Pengfei

last: Jiang

first: Bi

last: Lian

first: Changzhen

last: Liu

first: Zeyu

last: Fu

first: Yi

last: Shen

first: Zhukuan

last: Cheng


title: Abeliophyllum distichum Nakai Extract exerts anti-osteoporotic effects by suppressing RANKL-induced osteoclastogenesis

status: Public on Sep 23 2020

city: Cheongju

first: Kyunghwan

last: Kim

address: Rm #202a, Bldg. S1-5, 1 chungdae-ro

country: South Korea

institute: Chungbuk National University

summary: To screen for altered gene expression during osteoclastogenesis,  BMM cells treated with RANKL or RANKL+LE were subjected to gene expression profiling.

overall_design: Transcriptome profiles of RANKL- or RANKL+LE-treated BMMswere generated by deep sequencing, in duplicate, using HiSeq 2500.


title: Expression data from primary human neutrophils incubated with complement anaphylatoxin C5a

city: Ulm

first: Markus

last: Huber-Lang

address: Helmholtzstrasse 8/1

department: Institute of Clinical and Experimental Trauma-Immunology

country: Germany

institute: University Hospital Ulm

summary:
Influence of complement anaphylatoxin C5a on neutrophil gene expression
Trauma causes an early activation of the complement system, which leads to excessive generation of the anaphylatoxin C5a. Furthermoren, alterations in neutrophil function are often associated with infectious complication after trauma. Studies have shown that C5a is a main contributor to neutrophil dysfunction. However, the pathophysiological mechanisms still remain elusive. Aim of the study was to evaluate whether C5a can induce changes in expression profiles. We identified distinct classes of up-regulated genes during this process.

overall_design: Primary polymorhoneuclear neutrophils (PMNs) were isolated from human blood drawn by peripheral venous puncture in sodium citrate monovettes. PMNs were isolated from whole blood by Ficoll-Hypaque gradient centrifugation, dextran sedimentation, followed by hypotonic lysis of residual red blood cells. CD9+ eosinophils were separated from neutrophils. Purified Neutrophils were either left untreated (n=3) or incubated with native human C5a (100ng/ml) for 60 min at 37°C on a rotating wheel (n=3).

first: Ebru

last: Karasu

first: Karlheinz

last: Holzmann

first: Rebecca

last: Halbgebauer


title: Immune signature driven by ADT-induced immune microenvironment remodeling in prostate cancer is correlated with recurrence-free survival and immune infiltration

city: Beijijng

first: Xingbo

last: Long

address: No 1, Dongdan Dahua Road, Dongcheng District

department: Urology

institute: Beijing Hospital

summary: Androgen deprivation therapy (ADT) is a cornerstone treatment for locally advanced or metastatic prostate cancer (PCa). However, its potential effects on the tumor immune microenvironment (TIM) of PCa patients and the underlying mechanism remain largely unclear.We used RNA sequencing to reveal the effects of ADT on the PCa TIM at the transcriptome level. RNA sequencing was performed on 6 paired pre-ADT biopsy and post-ADT PCa lesions and 5 paired paracancerous benign tissues from patients receiving neoadjuvant ADT with locally advanced PCa.

overall_design: RNA sequencing (RNA-seq) was performed on 6 paired pre-ADT biopsy and post-ADT PCa lesions and 5 paired paracancerous benign tissues from patients receiving neoadjuvant ADT with locally advanced Pca.

first: X

middle: B

first: Ming


city: Busan

first: Yong-Hwan

last: Moon

address: Busandaehak-ro 63Beon-gil 2, Geumjeong-gu

department: Molecular Biology

institute: Pusan National University

summary: We characterized and compared the biological and molecular functions of HRE1α and HRE1β, two alternative splicing variants of HRE1, a AP2/ERF transcription factor in Arabidopsis. To compare the downstream regulatory mechanisms of HRE1α and HRE1β, Quant-Seq analysis was carried out. The experiment was designed to identify and compare differentially expressed genes (DEGs) between WT and HRE1α-overexpressing transgneic plants (OXs) and WT and HRE1β OXs grown for 14 days under SD conditions. We analyzed the biological process gene ontology (GO) annotation categories of the DEGs in HRE1α OXs and HRE1β OXs. The genes upregulated in HRE1α OXs, but not in HRE1β OXs, were enriched in the regulation of biological processes such as flower development, shoot system development, circadian rhythms, gene expression, response to gibberellin, nitrogen compound metabolic process, and aromatic compound biosynthetic processes. However, the genes up-regulated in HRE1β OXs, but not in HRE1α OXs, were enriched in the regulation of the following processes: response to toxic substances, secondary metabolic processes, response to biotic stimulus, glutathione metabolic process, response to reactive oxygen species, cell wall organization, DNA replication, response to salicylic acid, lipid localization, response to oxidative stress, carbohydrate metabolic process, photosynthesis, mitotic cell cycle process, response to osmotic stress, and response to abscisic acid. The genes upregulated in both HRE1α OXs and HRE1β OXs were enriched in biological processes involved in response to abiotic stimulus, response to light stimulus, response to endogenous stimulus, response to oxygen-containing compound, and response to lipid. In addition, we investigated the biological function of AtRH17, a DEAD-box RNA helicase gene in Arabidopsis, in salt stress response. To investigate the downstream regulatory mechanisms of AtRH17, Quant-Seq analysis was carried out. The experiment was designed to identify DEGs between WT and AtRH17 OXs grown for 14 days under SD conditions. GO annotation enrichment and KEGG pathway analysis showed that the upregulated and downregulated genes are involved in various biological functions including secretion, signaling, detoxification, metabolic pathways, catabolic pathways, and biosynthesis of secondary metabolites as well as in stress responses. Genevestigator analysis of the upregulated genes showed that nine genes, namely, LEA4‐5, GSTF6, DIN2/BGLU30, TSPO, GSTF7, LEA18, HAI1, ABR, and LTI30, were upregulated in Arabidopsis under salt, osmotic, and drought stress conditions. In particular, the expression levels of LEA4‐5, TSPO, and ABR were higher in AtRH17 OXs than in WT under salt stress condition.

overall_design: Differentially expressed genes between WT and HRE1α OX, WT and HRE1β OX, and WT and AtRH17 OX at 14 days after germination under SD conditions (8-h-light and 16-h-dark cycle) were explored in whole genome level.

first: Hye-Yeon

last: Seok

first: Linh

middle: V

last: Nguyen


title: Comparison of microRNA Expression Profile in Patients Newly Diagnosed with Chronic Myeloid Leukemia and Treated by Allogeneic Hematopoietic Stem Cell Transplantation

city: Botucatu

first: Juliana

middle: Ravelli Baldassarre

last: Martins

state: SP

address: Rua Mansueto Lunardi, 37

country: Brazil

institute: Faculdade de Medicina de Botucatu

summary: Expression profile of 14 newly diagnosed patients with Chronic Myeloid Leukemia and 14 Philadelphia chromosome negative patients after allo haematopoietc stem cell transplantation. We tested 754 microRNAs by reverse transcription quantitative polymerase chain reaction (RT-qPCR) array for each patient.

overall_design: Expression profile of 14 newly diagnosed patients with Chronic Myeloid Leukemia and 14 Philadelphia chromosome negative patients after allo haematopoietc stem cell tranplantation

first: Leonardo

middle: N

last: de Moraes

last: Dadalto

first: Robson

middle: F

last: Carvalho

last: Capannacci

first: Regina

middle: C

last: Nogueira

first: Newton

middle: K

last: Hokama

first: Paula

last: de Oliveira Montandon Hokama


title: Interleukin-1 promotes autoimmune neuroinflammation by suppressing endothelial heme oxygenase-1 at the blood-brain barrier

city: Mainz

first: Ari

last: Waisman

address: Obere Zahlbacher Straße 67

institute: Institute for Molecular Medicine

summary: The goal of this study is to study endothelial cell Il1r1 signaling in EAE (multiple scleroris)

overall_design: Endothelial cells from spinal cord, extracted with RiboTag (actively transcribed mRNA), either from control, or Il1r1-deficient  mice.

first: Judith

last: Hauptmann

first: Tommy

last: Regen

first: Federico

last: Marini

first: Matthias

last: Klein


title: Impact of sustained TGFβ-receptor inhibition on chromatin accessibility and gene expression in cultured endometrial MSC [RNA-Seq]

city: Clayton

first: Shanti

last: Gurung

state: Vic

address: 27-31 Wright Street

country: Australia

institute: Hudson Institute of Medical Research

summary: Endometrial mesenchymal stem cells (eMSC) drive the extraordinary regenerative capacity of the human endometrium. Clinical application of eMSC for therapeutic purposes is hampered by spontaneous differentiation and cellular senescence upon large-scale expansion in vitro. A83-01, a selective TGFbeta receptor inhibitor, promotes pharmacological expansion of eMSC in culture by blocking differentiation and senescence.  We subjected primary eMSC treated with A83-01 to RNA sequencing (RNA-seq) to map the underlying gene expression changes. RNA-seq analysis demonstrated that sustained TGFbeta-R inhibition results in differential expression of 1,463 genes.

overall_design: We subjected A83-01 treated and untreated human primary eMSC to RNA sequencing (RNA-seq) to map the underlying gene expression changes.

first: Raffaella

last: Lucciola

first: Pavle

middle: J

last: Vrljicak

first: Caitlin

last: Filby

first: Saeedeh

last: Darzi

first: Sascha

last: Ott

first: Jan

last: Brosens

first: Caroline

last: Gargett


title: Impact of sustained TGFβ-receptor inhibition on chromatin accessibility and gene expression in cultured endometrial MSC [ATAC-Seq]

summary: Endometrial mesenchymal stem cells (eMSC) drive the extraordinary regenerative capacity of the human endometrium. Clinical application of eMSC for therapeutic purposes is hampered by spontaneous differentiation and cellular senescence upon large-scale expansion in vitro. A83-01, a selective TGFbeta receptor inhibitor, promotes pharmacological expansion of eMSC in culture by blocking differentiation and senescence.  We subjected primary eMSC treated with A83-01 to Assay for Transposase Accessible Chromatin with sequencing (ATAC-seq) to map the underlying chromatin changes. A total of 185,084 open DNA loci were mapped accurately in EnSCs. ATAC-seq analysis demonstrated that sustained TGFbeta-R inhibition results in opening and closure of 3,555 and 2,412 chromatin loci, respectively. Motif analysis revealed marked enrichment of retinoic acid receptor (RAR) binding sites, which was paralleled by the induction of RARB.

overall_design: We subjected A83-01 treated and untreated human primary eMSC to Assay for Transposase Accessible Chromatin with sequencing (ATAC-seq) to map the underlying chromatin changes.


title: Impact of sustained TGFβ-receptor inhibition on chromatin accessibility and gene expression in cultured endometrial MSC


title: p63 Maintains the Proliferative Potential of Salivary Gland Stem/Progenitor Cells by Regulating Follistatin, a Key Mediator of TGF-b/Activin Signaling [scRNA-seq]

city: Buffalo

first: Jonathan

last: Bard

state: New York

address: 701 Ellicott Street

department: Genomics and Bioinformatics Core

institute: University at Buffalo

summary: Np63+ve cells are multipotent and maintain all epithelial cell lineages of the embryonic and adult salivary gland (SG). However, the molecular mechanisms by which Np63 regulates stem/progenitor (SP) cell populations in the SG remains elusive. To better understand Np63 s role in directing cell fate choices, here we have utilized Np63-null adult mice and primary salivary cell cultures to probe alterations in SP cell differentiation and function. Specifically, we have generated bulk RNA-seq and scRNA-seq data from Np63-null adult mice and p63 and H3K27Ac ChIP-seq data from primary salivary cell cultures. These genomic and epigenomic data sets were leveraged to interrogate altered SG cellular identities and differentiation states resulting from the loss of Np63. Our studies reveal that ablation of Np63 results in a loss of the SP cell population and skewed SG differentiation that is modulated by dysregulated TGF- /Activin signaling. Our findings offer new molecular revelations into the SP cell gene regulatory networks that are likely to be relevant for normal or diseased SG states.

overall_design: Single-cell RNA-seq Analysis of Mouse submandibular gland

first: Sangwon

last: Min

first: Akinsola

last: Oyelakin

first: Christian

last: Gluck

first: Christine

last: Song

first: Smalley

last: Kirsten

first: Monika

last: Che

first: Elsa

last: Flores

first: Satrajit

last: Sinha

first: Rose-Anne

last: Romano


title: p63 Maintains the Proliferative Potential of Salivary Gland Stem/Progenitor Cells by Regulating Follistatin, a Key Mediator of TGF-b/Activin Signaling


title: p63 Maintains the Proliferative Potential of Salivary Gland Stem/Progenitor Cells by Regulating Follistatin, a Key Mediator of TGF-b/Activin Signaling [RNA-seq]

overall_design: Analysis of gene expression changes in control and p63KO salivary glands using high throughput sequencing


title: p63 Maintains the Proliferative Potential of Salivary Gland Stem/Progenitor Cells by Regulating Follistatin, a Key Mediator of TGF-b/Activin Signaling [ChIP-seq]

overall_design: Analysis of p63 Binding and Histone H3K27ac modification analysis of primary mouse salivary epithelial progenitor cells using high throughput sequencing


title: Immune-Related Gene Expression and Cytokine Secretion is Reduced Among African American Colon Cancer Patients

city: New Orleans

first: Jovanny

last: Zabaleta

state: LA

address: 1700 Tulane Ave

department: Interdisciplinary Oncology

institute: LSUHSC

summary: Background: Colorectal cancer is the third most deadly cancer among African Americans (AA). When compared to Caucasian Americans (CA), AA present with more advanced disease and lower survival rates. Here, we investigated if differences in tumor immunology could contribute to the disparities observed between these populations. Methods: We examined gene expression of 20 tumor and 20 non-tumor adjacent tissues from AA and the same number from CA by whole transcriptome sequencing and generated scores for immune cell populations by NanoString. In addition, we utilized “The Cancer Genome Atlas” (TCGA) database from AA (n = 55) and CA (n = 193) as a validation cohort. Finally, we measured the secretion of cytokines characteristic of effector T helper cell (Th) subsets by ELISA using plasma from each AA and CA participant. Results: Colon tumors from AA patients showed significant fold-change increase in gene expression when compared to CA for FOXP3 (6.97 vs. 3.15), IL1B (122 vs. 14) and IL8 (262 vs. 28) (p < 0.05). In contrast, among CA we observed statistically higher gene expression of markers associated with antitumor activity such as GZMB (Granzyme B), IFNG and immunotherapy targets PDL1 (CD274) and CTLA4 (p < 0.05). TCGA data validated our observed higher expression of GZMB and PDL1 in CA patients as well as showed a 50% higher 5-year survival rate in AA patients with high expression of GZMB. Notably, our observations on immune cell populations show that AA tumors have significantly higher number of exhausted CD8+ cells (p < 0.01), mast cells (p < 0.02) and increased T regulatory cells when compared to CA.  AA colon cancer patients differed from CA in cytokine production patterns in plasma (i.e. reduced IL-12). Conclusions: Our study demonstrates significant differences of the immunological profiles of colon tumors from AA compared to CA that suggest a deficiency of appropriate immune defense mechanisms in terms of gene expression, recruitment of immune cells and systemic secretion of cytokines. As such, these immune differences could be mitigated through population-specific therapeutic approaches.

overall_design: We did RNA-seq in 80 colon cancer tissue samples from African American and Caucasian individuals (20 tumor tissues and 20 adjacent non-tumor tissues per ethnic group). RNA was extracted, qualified by Agilent 2100, quanitfied by qubit. Librarires were prepared using the Illumina's TruSeq Stranded mRNA kit and sequenced at 2 x 75bp (50M reads/sample)

first: Jenny

last: Paredes

first: Jone

last: Garai

first: Ping

last: Ji

first: Sayed

last: Imtiaz

first: Marzia

last: Spagnardi

first: Joussette

last: Alvarado

first: Li

last: Li

first: Mubarak

last: Akadri

first: Kaylene

last: Barrera

first: Maria

last: Munoz-Sagastibelza

first: Raavi

last: Gupta

first: Mohamed

last: Alshal

first: Maksim

last: Agaronov

first: Henry

last: Talus

first: Xuefeng

last: Wang

first: John

middle: M

last: Carethers

first: Jennie

middle: L

last: Williams

first: Laura

middle: A

last: Martello


title: EZH2 Reduction Is an Essential Mechanoresponse for the Maintenance of Super-enhancer Polarization

city: Beijing

first: Yu

last: Zhang

address: Xueyuan Road

institute: Peking University Health Science Center

summary: Despite the ubiquitous mechanical cues at both spatial and temporal dimensions, cell identities and functions are largely immune to the everchanging mechanical stimuli. To understand the molecular basis of this epigenetic stability, we interrogated compressive force elicited transcriptomic changes in mesenchymal stem cells purified from human periodontal ligament (PDLSCs), and identified H3K27me3 and E2F signatures populated within up- and weakly down-regulated genes respectively. Consistently, expressions of several E2F family transcription factors and EZH2, as core methyltransferase for H3K27me3, decreased in response to mechanical stress, which were attributed to force induced redistribution of RB from nucleoplasm to lamina. Importantly, although epigenomic analysis on H3K27me3 landscape only demonstrated correlating changes at one group of mechanoresponsive genes, we observed a genome-wide destabilization of super-enhancers along with aberrant EZH2 retention. These super-enhancers were tightly bounded by H3K27me3 domain on one side and exhibited attenuating H3K27ac deposition and flattening H3K27ac peaks after force exposure, analogous to increased H3K27ac entropy or decreased H3K27ac polarization. Interference of force induced EZH2 reduction could drive nuclear actin filaments dependent collision between EZH2 and super-enhancers and functionally compromise the multipotency of PDLSC following mechanical stress. These findings together unveil a specific contribution of EZH2 reduction for maintenance of super-enhancer stability and cell identity in mechanoresponse.

overall_design: PDLSC mRNA profiling.


overall_design: Refer to individual Series


overall_design: ChIP-seq analysis in PDLSC


title: Binding of the Treslin-MTBP Complex to Specific Regions of the Human Genome Promotes the Initiation of DNA Replication

status: Public on Sep 22 2020

city: Pasadena

first: Akiko

last: Kumagai

state: California

address: 1200 E. California Blvd

department: Division of Biology and Biological Engineering

institute: California Institute of Technology

summary:
In this study, we have mapped the binding sites for the MTBP subunit of the Treslin-MTBP complex throughout the human genome by using the CUT&RUN method.  Our results have indicated that MTBP associates reproducibly with several tens of thousands of sites in the genome.  Many binding sites contain either G4 DNA or an AP-1 motif in a nucleosome-free region at transcription start sites (TSSs) or enhancers, respectively.  In addition, this nucleosome-free region is adjacent to a nucleosome containing certain histone marks characteristic of open chromatin that have also been implicated in initiation.
We also mapped early initiation zones with EdU-labeling (EdU-seq) and found that these initiation domains contain a large number of MTBP binding sites.  Taken together, these findings indicate that Treslin-MTBP associates with multiple genomic signals to promote initiation of replication.

overall_design: Binding sites of endogenously FLAG-tagged versions of wild-type and C-terminally truncated MTBP were probed with CUT&RUN in triplicate experiments. G1-arrested cells were released into S-phase and early initiation domains were labeled with EdU in the presence of HU and aphidicolin.  EdU-labeled DNA was sequenced in triplicate experiments.

first: William

middle: G

last: Dunphy


title: Adaptation of pathogenic Leptospira to oxidative stress

city: Paris

first: Rachel

last: Legendre

address: 28, rue du docteur Roux

department: Research and Resource Center for Scientific Informatics

country: France

institute: Institut Pasteur

summary: Pathogenic Leptospira spp. are the causative agents of the zoonotic disease leptospirosis. During infection, Leptospira are confronted with deadly reactive oxygen species (ROS). Withstanding ROS produced by the host innate immunity is an important strategy evolved by pathogenic Leptospira for persisting in and colonizing hosts. The peroxide stress regulator, PerR, represses genes involved in ROS defenses in L. interrogans. We have performed RNA sequencing in WT and perR mutant strains to characterize the L. interrogans adaptive response to hydrogen peroxide. We showed that Leptospira solicit three main peroxidase machineries (catalase, cytochrome C peroxidase and peroxiredoxin) and heme to adapt to peroxide stress as well as canonical chaperones of the heat shock response, and DNA repair. Determining the PerR regulon allowed to identify the PerR-dependent mechanisms of the peroxide adaptive response and has revealed a regulatory network involving other transcriptional regulators, two-component systems and sigma factors as well as non-coding RNAs that putatively orchestrate, in concert with PerR, this adaptive response. Our findings provide comprehensive insight into the mechanisms required by pathogenic Leptospira to overcome infection-related oxidants. This will participate in framing future hypothesis-driven studies to identify and decipher novel virulence mechanisms.

overall_design: RNA sequencing performed on L. interrogans WT strain cultivated in the absence or presence of 10 micromolar or 1 mM of hydrogen peroxide and on L. interrogans perR mutant strain cultivated in the absence or presence of 10 micromolar of hydrogen peroxide.

first: Crispin

last: Zavala-Alvarado

first: Odile

last: Sismeiro

first: Hugo

last: Varet

first: Giovanni

last: Bussotti

first: Jan

last: Bayram

first: Samuel

last: Garcia Huete

first: Guillaume

last: Rey

first: Jean-Yves

last: Coppée

first: Mathieu

last: Picardeau

first: Nadia

last: Benaroudj


title: Global transcriptomic analyses of pluripotent stem cell-derived type II alveolar epithelial-like cells at 1 and 4 days after infection with SARS-CoV-2

status: Public on Sep 21 2020

city: Boston

first: Carlos

last: Villacorta-Martin

state: MA

address: 670 Albany St

institute: Center for Regenerative Medicine at Boston University

summary: We performed transcriptomic profiling of cells derived from human pluripotent stem cells (PSCs) using our previously described distal lung directed differentiation protocol to generate alveolar type II epithelial-like cells (iAT2s). We used the SPC2 human iPSC line containing a SFTPC-tdTomato knock-in reporter.  SFTPC-tdTomato+ iAT2s were sorted on day 41 and again on day 69 of differentiation. iAT2s were single-cell passaged in self-renewing 3D alveolosphere culture approximately every 2 weeks through day 194 of differentiation. On day 208, iAT2s were single-cell passaged onto Transwell inserts. Apical media was removed on day 210 to initiate air-liquid interface culture. On day 218, 6 replicate wells of iAT2s were exposed to SARS-CoV-2 in an apical inoculum and 3 replicate wells were exposed to mock. On day 219, three mock and three post-infection samples (1 dpi) were collected. Three additional post-infection samples (4 dpi) were collected on day 222. We find that SARS-CoV-2 infected iAT2s express a rapid global transcriptomic change characterized by a shift to an inflammatory phenotype, time-dependent epithelial interferon responses, and rapid loss of the mature lung alveolar epithelial program.

overall_design: Global transcriptomic analysis of hiPSC-derived iAT2s cultured at ALI comparing mock (mock), 1 day post infection with SARS-CoV-2 (1dpi), and 4 days post infection with SARS-CoV-2 (4dpi) in triplicate (n=3 Transwells per condition).

first: Jessie

last: Huang

first: Kristine

last: Abo

first: Rhiannon

last: Werder

first: Adam

last: Hume

first: Konstantinos

last: Alysandratos

first: Mohsan

last: Saeed

first: Finn

last: Hawkins

first: Elke

last: Muhlberger

first: Andrew

last: Wilson

first: Darrell

last: Kotton


title: Genome wide analysis points towards subtype specific diseases in different genetic forms of Amyotrophic Lateral Sclerosis

city: Rostock

first: Andreas

last: Hermann

state: Mecklenburg-Western Pomerania

address: Gehlsheimer Str.20

department: Neurology

institute: University Medical Center Rostock

summary:
We established iPSCs from healthy donors, FUS-ALS and SOD1-ALS patients. Using our differentiation protocol originally developed by Reinhardt et al.,2013, we diferentiated these iPSCs toward spinal motor neurons (MNs) and reproduce ALS pathology in a dish. To extend our understanding of finding different molecular mechanisms and pathways related to FUS- and SOD mutations in ALS disease, we have performed a comprehensive gene expression profiling study using microarray hybridization of the iPSC-derived MN models from control individuals and carefully compared with those from FUS-ALS and SOD1-ALS patients.
In addition, we further analyzed previously published independent datasets containing the genome-wide RNA profiling of iPSC-derived MN samples from patients with FUS and SOD1 mutations and controls. This microaray dataset GSE10638 (Fujimori et al., 2018) was retrieved from GEO database and was screened to identifiy potential drug candidates which suppressed the detected ALS-related phenotypes of these ALS models. Finally, we made a systematic comparison with our results to the ones independently obtained previously.Here through this study, we create a gene profile of ALS by analyzing the differentially expressed genes (DEGs), the kyoto  encyclopedia of Genes and Genomes (KEGG) pathways, the interactome as well as transcription factor profiles (TF) that would identify altered functional/molecular signatures and their interactions at both transcriptional (mRNAs) and translational levels (hub proteins and TFs) which stands validation across the different datasets (including different differentiation protocols etc.). By doing so we provide condensed pathophysiological pathways of FUS-ALS and SOD1-ALSto better understand the biological mechanisms underlying motor neuron disease.

overall_design: We isolated total RNA from iPSC-derived MNs (healthy donor: 4 samples, FUS-ALS: 4 samples, SOD1-ALS: 3 samples. Total 11 samples) for the gene expression microarray analysis. All of the iPSC lines we used were low passage number (less than 20) and analysis were performed at DIV 30-45.

first: A

first: B

middle: P

last: Dash


title: NFIA differentially controls adipogenic and myogenic gene program through distinct pathways to ensure adipocyte differentiation

city: Tokyo

first: Hironori

last: Waki

address: Hongo 7-3-1, Bunkyo-ku

country: Japan

institute: The University of Tokyo

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


title: CRISPR screening of porcine sgRNA library identifies host factors associated with Japanese encephalitis virus replication

city: Wuhan

first: Shengsong

last: Xie

state: Hubei

address: 1st Shizishan Street, Hongshan

institute: Huazhong Agricultural University

summary: We design a porcine genome-scale CRISPR/Cas9 knockout (PigGeCKO) library containing 85,674 single guide RNAs targeting 17,743 protein-coding genes, 11,053 long ncRNAs, and 551 microRNAs. Subsequently, we use the PigGeCKO library to identify key host factors facilitating JEV infection in porcine cells.

overall_design: We initially used CRISPR-offinder (v1.2, BiooTools.com) to design 85,674 specific and predicted high-efficiency single guide RNAs (sgRNAs), that collectively targeted 17,743 protein-coding genes, 11,053 long ncRNAs (lncRNAs), and 551 microRNAs (miRNAs) in the porcine genome, as well as 1,000 negative control sgRNA constructs predicted not to target any porcine genome loci. These designed sgRNA constructs were synthesized as an oligo array, which was employed as the template for PCR amplification of the sgRNA oligos that were subsequently cloned into lentiviral vectors using Gibson assembly. We then developed a screening strategy to identify host genes required for successful JEV infection.

first: Shuhong

last: Zhao

first: Changzhi

first: Hailong

last: Liu


title: Role of CITED2 in shaping macrophage inflammatory response

city: Cleveland

first: Ernest

last: Chan

state: OH

address: 10900 Euclid Ave, Robbins E211

department: PQHS

institute: CWRU

summary: CBP/p300-interacting transactivator with glutamic acid/aspartic acid-rich carboxyl-terminal domain 2 (CITED2) is a member of the CITED family of proteins that play very critical roles in cellular development and differentiation. Several independent studies have revealed that mutation in the CITED2 gene is associated with human congenital heart defects. Concordant with these observations, experimental murine studies affirmed that mutation or loss of Cited2 resulted in congenital heart defects, as well as perturbation in the left-right patterning of the body axis. Furthermore, deficiency of Cited2 significantly impaired the development of lung, liver, placenta, and adrenal tissue at the embryonic stage (PMCID: PMC5809687).

overall_design: Here we isolated bone marrow of 3 mice per group (Lyz2cre and Lyz2cre:CITED2Fl/Fl) and differentiated into macrophages by culturing them in M-CSF containing media. These cells were stimulated with 100ng/ml LPS for 4hours, 10ng/ml IFNg for 6 hours or 20ng/ml IL4 for 18 hours. Total RNA was isolated and subjected to RNAseq analyses.

first: Ganapati

middle: H

last: Mahabeleshwar

first: E


title: Differential H3K27ac ChIP-seq Analysis of HCT116 Cells In Response To Interferon Beta

city: La Jolla

first: Nathaniel

last: Delos Santos

address: 9500 Gilman Drive MC 0640

institute: University of California San Diego

summary: To show the utility of our method, MEIRLOP, we performed a differential motif enrichment analysis of regulatory elements modulated by interferon beta (IFN-β) treatment in HCT116 cells as measured by H3K27ac ChIP-seq.

overall_design:
Cell culture and treatment: HCT116 CMV-osTIR1 RAD21-mAC cells were obtained from Masato T. Kanemaki and cultured in McCoy’s 5A medium supplemented with 10% FBS. Cells were grown in a 37˚C incubator with 5% CO2. Cells were treated with 0.1% final DMSO for 6 hours and then treated with either IFN-β (1000 unit/ml) (n=2) for one hour or not further treated (n=2).
ChIP-seq and Crosslinking: Crosslinking and ChIP-seq were performed as described in Heinz et al., 2018 with few adjustments. Briefly, cells were fixed directly by adding formaldehyde into media to a final concentration of 1% formaldehyde for 10min at room temperature and quenched with 125mM Glycine. Cells were then pelleted at 300g for 5min at 4˚C, washed twice with cold PBS (with 0.5% BSA), snap frozen in liquid nitrogen and stored at -80˚C. ChIP-seq was performed on 500,000 cells as described in Heinz et al., 2018. H3K27ac antibodies were obtained from Active Motif (cat#:39133). Libraries were single-end sequenced for 84bp to a depth of 5.5 - 8.6 reads on an Illumina NextSeq500 instrument.
Differential ChIP-seq analysis: After sequencing and adapter trimming with FastP, 5.5M - 8.6M reads per library were aligned to the GRCh38 reference genome using bowtie2 at overall alignment rates of 98.5% - 99.5%. For each stimulation (n = 2) and control sample (n = 2), MACS2 was used to call peaks of median length 1kbp relative to a background input sample (of 16M reads). DiffBind was used to call differentially acetylated peaks between stimulated and unstimulated conditions.

first: Lorane

last: Texari

first: Christopher

last: Benner


title: Modulation of immune system mediated by ibrutinib in chronic lymphocytic leukemia

status: Public on Sep 18 2020

city: Modena

first: Rossana

last: Maffei

state: Modena

address: Via del Pozzo 71

department: Dept of Hematology and Oncology

country: Italy

institute: University of Modena and Reggio Emilia

summary: Our project is based on the hypothesis that ibrutinib could interfere with chronic lymphocytic leukemia (CLL) microenvironment, modulating the immune response.  The aim of the project is to understand if and how ibrutinib modifies the tumor microenvironment accessory cells in CLL, specifically nurse like cells (NLC).

overall_design: Large-scale gene expression profiling (GEP) was performed on total RNA extracted from NLC treated or not (control sample) over-night with 0.5µM Ibrutinib  (RNeasy Mini kit Plus, QIAGEN, Valencia, CA, USA)  from 10 individual CLL patients by hybridization on 4X44K Whole Human Genome Microarray (Agilent Technologies, Palo alto, CA). Fluorescence data were analysed with Feature Extraction Software v.10.5 (Agilent Technologies) an QC Chart tool v.1.3.

first: Roberto

last: Marasca


title: Giant island mice exhibit widespread gene regulatory evolution in key metabolic organs

city: Madison

first: Colin

last: Dewey

address: 425 Henry Mall, 5420 Genetics/Biotechnology Center

institute: University of Wisconsin-Madison

summary:
Background: Island populations repeatedly evolve extreme body sizes, but the genomic basis of this morphological pattern remains largely unknown. To understand how organisms on islands evolve gigantism, we compared genome-wide patterns of gene expression in Gough Island mice, the largest wild house mice in the world, and mice from the WSB/EiJ wild-derived inbred strain. In a highly replicated experiment, we used RNASeq to quantify differences in gene expression in three key metabolic organs:  gonadal adipose depot, hypothalamus, and liver.
Results: We discovered pervasive evidence of transcriptional evolution, with 20% or more of differentially regulated transcripts in each organ exhibiting expression fold changes of at least 2X. By considering differential expression jointly with the genomic positions of quantitative trait loci for body size and single nucleotide differences located within established tissue-specific regulatory elements, we nominated 66 candidate genes for extreme size evolution, including Irs1 and Lrp1. Patterns of differential expression across three developmental time points in the liver revealed that Arid5b potentially regulates tens of co-regulated gene groups. Functional enrichment analyses on thousands of differentially expressed genes pointed to cell cycling, mitochondrial function, signaling pathways, immune reactivity, and nutrient metabolism as potential causes of weight accumulation in Gough Island mice.
Conclusion: Collectively, our results suggest that extensive regulatory evolution in metabolic organs contributed to the rapid evolution of gigantism during the short time house mice have inhabited Gough Island.

overall_design: mRNA profiles were generated for 5 females and 5 males for two mouse strains in each of 5 conditions: 28-day-old gonadal adipose depot, 28-day-old hypothalamus, Theiler stage 24-25 (E16.5) liver, 14-day-old liver, and 28-day-old liver.

first: Bret

last: Payseur

first: Mark

last: Nolte


title: Inhibition of the autophagic protein ULK1 attenuates axonal degeneration in vitro and in vivo and modulates differential splicing

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

summary: Several traumatic and neurodegenerative disorders of the CNS show axonal degeneration as a key and early pathological feature. Following a focal axonal lesion, an extended axonal disintegration by acute axonal degeneration (AAD) occurs within several hours. During AAD, activation of autophagic proteins including Unc-51 like autophagy activating kinase 1 (ULK1) has been demonstrated, but its role is incompletely understood. Here, we overexpressed a dominant negative of ULK1 (ULK1.DN) in primary rat cortical neurons in vitro and in the spinal cord (SC) and optic nerve (ON) in vivo. We found a significant inhibitory effect on autophagy in vitro and in vivo. While no effect on cell survival could be observed, ULK1.DN attenuated AAD after axotomy in microfluidic chambers in vitro. Models of SC injury and ON crush in vivo confirmed an attenuation of axonal degeneration by ULK1.DN. In a translational approach, we employed the selective ULK1 inhibitor SBI-0206965 (SBI) and found an attenuation of AAD after ON crush in vivo mediated by a reduction of autophagy by SBI. Quantitative proteomic profiling after ULK1.DN overexpression in vitro revealed a regulation of proteins associated with translation and splicing. A differential exon expression analysis identified the genes kinesin family member 1B (Kif1b), DNA damage inducible transcript 3 (Ddit3) and WD repeat domain 6 (Wdr6) as targets of ULK1.DN and potential mediators of its degeneration-attenuating effect. These findings reveal ULK1 as an important mediator of axonal degeneration and elucidate its function in splicing, defining it as a putative therapeutic target.

overall_design: Analysis of differential exon and gene expression in primary E18 rat cortical neurons (DIV 8) after transduction with AAV.ULK1.DN and AAV.mCherry (control, Genbank ID: KT345943), from 3 independent cultures.

first: Björn

last: Vahsen

first: Lucas

last: Caldi Gomes

last: Salinas-Riester

first: Orr

last: Shomroni

first: Paul

last: Lingor


title: Dissection of FUS domains involved in regulation of SnRNP70 gene expression

status: Public on Sep 17 2020

city: Okawa

first: Tadashi

last: Nakaya

state: Fukuoka

address: 137-1 Enokizu

department: School of Pharmacy at Fukuoka

institute: International University of Health and Welfare

summary: To identify FUS regulated genes and its dependency of snRNP70, the gene expression profiles in neurons expressing the Gly-rich domain deleted FUS mutant coupled with Snrnp70 gene knock down were analyzed.

overall_design: Mouse ES cell derived neurons were infected with lentivirus encoding FLAG-tagged Gly-rich domain deleted FUS, shRNA for Snrnp70 gene or both, and analysed the gene expression by RNA-seq.


title: ABCF1 regulates dsDNA-induced immune responses in human airway epithelial cells

status: Public on Sep 16 2020

city: Waterloo

first: Jennifer

middle: A.

last: Aguiar

state: ON

address: 200 University Avenue East

department: Biology

country: Canada

institute: University of Waterloo

summary: The airway epithelium represents a critical component of the human lung that helps orchestrate defences against respiratory tract viral infections, which are responsible for more than 2.5 million deaths/year globally. Innate immune activities of the airway epithelium rely Toll-like receptors (TLRs), nucleotide binding and leucine-rich-repeat pyrin domain containing (NLRP) receptors, and cytosolic nucleic acid sensors. ATP Binding Cassette (ABC) transporters are ubiquitous across all three domains of life – Archaea, Bacteria, and Eukarya – and expressed in the human airway epithelium. ABCF1, a unique ABC family member that lacks a transmembrane domain, has been defined as a cytosolic nucleic acid sensor that regulates CXCL10, interferon-b expression, and downstream type I interferon responses. We tested the hypothesis that ABCF1 functions as a dsDNA nucleic acid sensor in human airway epithelial cells important in regulating antiviral responses.

overall_design: Human airway epithelial cell line HBEC-6KT submerged monolayer cultures (n=24) were exposed to basal and VACV-70 viral stimulation conditions, with and without ABCF1 knock-down via siRNA. Basal conditions were as follows: media only (n=3), transfection agent only (n=3), transfection agent + control siRNA (n=3), and transfection agent + ABCF1 siRNA (n=3). Stimulation conditions were as follows: control siRNA + control VACV-70 (n=3), control siRNA + VACV-70 (n=3), ABCF1 siRNA + control VACV-70 (n=3), and ABCF1 siRNA + VACV-70 (n=3). After knock-down via 24 hour transfection with ABCF1 or control siRNA, cells were transfected with an immunostimulatroy ligand for 24 hours followed by gene expression outcome measurement via Affymetrix Clariom S Human microarray analysis.

first: Q

middle: T

last: Cao

first: J

first: B

last: Tremblay

first: N

last: Abbas

last: Tiessen

first: S

last: Revill

last: Makhdami

first: G

last: Cox

first: K

last: Ask

first: A

last: Doxey

last: Hirota


title: Deregulated immune signature orchestrated by FOXM1 impairs human diabetic wound healing

city: Bethesda

first: Stephen

middle: R

last: Brooks

state: MD

address: 50 SOUTH DR, RM 1140

department: Biodata Mining and Discovery Section

institute: NIAMS/NIH

summary: We performed RNA-seq on tissue biopsies derived from patients with DFUs and compared it to human oral and skin wounds to identify the molecular mechanisms and transcriptional networks that are deregulated in DFUs. Our results identified a unique inflammatory transcriptional signature unique to oral and skin wounds involved in promoting cell proliferation and cell survival of immune cells that are deficient in DFUs. In addition, we identified a signature immune-cell profile in which activation and proliferation of macrophages and neutrophils were absent in DFUs. These results suggest that a deregulated immune response in which impaired activation, proliferation and survival of immune cells contribute to pathogenesis of DFUs and provides novel avenues for development of therapies aimed at reprogramming DFUs into healing-competent wounds.

overall_design: Transcriptome profiles from patients with diabetic foot ulcers generated by deep sequencing using Illumina NextSeq500.

first: Maria

last: Morasso

first: Marjana

last: Tomic-Canic


title: CRISPR-Cas protein Cas3 controls virulence in the oral pathogen Porphyromonas gingivalis.

city: Gainesville

first: Jose

last: Solbiati

state: Florida

address: 1395 Center Drive

department: Oral biology

institute: University of Florida

summary: Our results show that compared to wild type, a deletion mutant of the cas3 gene, an essential nuclease part of the class 1 type I CRISPR-Cas system, increases the virulence of P gingivalis.

sample_organism:
Porphyromonas gingivalis
Galleria mellonella

overall_design: we performed targeted deletion of cas3 to understand type I CRISPR-Cas systems and because it was among the most up-regulated CRISPR-Cas genes in our metatranscriptomic study (30). Using dual transcriptomic evaluations, coupled with cell and infection assays, this study demonstrates that Cas3 controls P. gingivalis virulence upon intracellular infection, but seems to have no role in virulence when growing in the planktonic phase

first: Ana

last: Duran-Pinedo

first: Fernanda

last: Rocha

first: Frank

last: Gibson

first: Jorge

last: Frias-Lopez


title: Use of the Illumina EPIC methylation array for epigenomic research in the crab-eating macaque (Macaca fascicularis)

status: Public on Sep 15 2020

city: Kumamoto

first: Kazuya

last: Iwamoto

address: 1-1-1 Honjo, Chuo-ku

department: Faculty of Life Sciences

institute: Kumamoto University

summary: Among the 865,918 probes in the Illumina DNA methylation arrays MethylationEPIC BeadChip, a total of 183,509 probes (21.2%) were selected as high-confidence array probes in the crab-eating macaque. Subsequent comparisons revealed that the data from these probes showed good concordance with other DNA methylation datasets of the crab-eating macaque. The selected high-confidence array probes would be useful for high-throughput DNA methylation assays of the crab-eating macaque.

overall_design: Through bioinformatic analyses involving cross-species comparison and consideration of probe performance, we selected array probes that can be reliably used for the crab-eating macaque genome. A DNA methylation assay using an EPIC array was performed on genomic DNA extracted from the brains of five crab-eating macaques. The obtained DNA methylation data were compared with a publicly available dataset.

first: Yutaka

last: Nakachi

first: Kazuhiro

last: Ishii

first: Miki

last: Bundo

first: Tomoyuki

last: Masuda


title: Transcriptome analysis of metabolic tissues in young and aged mice

city: Lausanne

first: Xu

last: Wang

address: EPFL SV IBI-SV NCEM AI 1148 (Bâtiment AI) Station 15

department: School of Life Sciences

country: Switzerland

institute: École polytechnique fédérale de Lausanne

summary:
Studies on aging have largely included one or two OMICS layers, which may not necessarily reflect the signatures of other layers. Moreover, most aging studies have often compared very young (4-5 wks) mice with old (24 months) mice which does not reflect the aging transition after the attainment of adulthood. Therefore, we aimed to study and compared muti-OMICS aging signatures across key metabolic tissues of mature adults (6 months) and old (24 months) C57BL/6J mice (the most commonly used mouse strain).
We compared the differentially regulated genes and enriched pathways for transcriptome, proteome and epigenome (H3K27ac, H3K4me3, H3K27me3, DNA methylation) across different tissues. Here are transcriptome data from Affymatrix microarrays.

overall_design: The goal of this study is to establish the global gene expression profiles of metabolic tissues from young and aged mice.

first: Pooja

last: Jha

first: Johan

last: Auwerx


title: H3K36me3 ChIP-seq in non-treated and raltitrexed-treated UGI-expressing HCT116 cells

status: Public on Sep 20 2020

city: Budapest

first: Angela

last: Bekesi

address: Műegyetem rakpart 3.

department: Department of Applied Biotechnology and Food Science

country: Hungary

institute: Budapest University of Technology and Economics, Faculty of Chemical Technology and Biotechnology

summary: We report ChIP-seq for H3K36me3 that were performed as supplementary experiments to the U-DNA-Seq study (GSE126822). H3K36me3 ChIP-seq was conducted in raltitrexed (RTX) treated or non-treated (NT) HCT116 cells expressing the UNG inhibitor (UGI). We found that the applied RTX treatment did not result in major differences in the genome-wide distribution of the H3K36me3 histone marker. For wider context of the study, see the related publication.

overall_design: For the H3K36me3 ChIP-seq experiments, cross-linked chromatin was isolated from non-treated and RTX treated HCT116 cells expressing UGI, and fragmented to approximately 100-500 bp fragments by sonication. Anti-H3K36me3 antibody (Cat. No. 4909T, Cell Signaling Technologies) was used for the IP, and samples were sequenced by PE 150 bp in a Novaseq 6000 platform. Reads were filtered and aligned to the reference human genome (GRCh38.d1.vd1, (https://gdc.cancer.gov/about-data/data-harmonization-and-generation/gdc-reference-file)) using BWA. Genome scaled coverage tracks and fold change over control tracks were calculated using deepTools package (bamCoverage and bigwigCompare tools, respectively). Genomic background data from the ENCODE (ENCFF489VMD) was used as control. Broad peaks were also called using MACS2. For details see the Supplementary file 3 of the related publication.

first: Hajnalka

last: Pálinkás

first: Angéla

last: Békési

first: Beáta

last: Vértessy


title: KRAS K104 modification affects KRASG12D-GEF interaction and mediated cell growth and motility

status: Public on Sep 19 2020

city: Kaohsiung City

first: Tsung-Hua

last: Hsieh

address: 6 Yi-Da Rd., Yan-Chau District

country: Taiwan

institute: E-Da Hospital

summary: Mutant RAS genes play an important role in regulating tumors through lysine residue 104 to impair GEF-induced nucleotide exchange, but the regulatory role of KRAS K104 modification on the KRASG12D mutant is not yet clear.  We found that KRASG12D/K104Q decreased the bind to RBD of Raf1 and also decreased cell growth, invasion and migration as well as whole-genome cDNA microarray found that KRASG12D/K104Q decrease the expression of NPIPA2, DUSP1 and IL6 in lung and ovarian cancer cells. This study clear implicates computational and experimental studies involving Lys104 of KRASG12D and GEF and provides a target for the analysis of future treatments.

overall_design: Examination of 4 different KRASG12D mutation in  H1299 and MCAS

first: Chih-Chieh

last: Chen

first: Chia-Yi

last: Hsu

first: Hsiao-Yun

last: Lin

first: Hong-Qi

last: Zeng

first: Kuang-Hung

last: Cheng

first: Chia-Wei

last: Wu

first: Eing-Mei

last: Tsai


title: Expression data of murine liver sinusoidal endothelial cells

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

overall_design: Refer to individual Series


title: Comparative analysis of gene expression in TGF-ß3 mutant mice with cleft palate

city: Lincoln

first: Sree

middle: Krishna

last: Chanumolu

state: NE

department: Department of Electrical & Computer Engineering

institute: University of Nebraska Lincoln

summary: Comparison of global palatal transcriptomes between wild‐type (WT) and TGF‐β3 ‐/‐ homozygous (HM) mouse embryos at crucial palatogenesis stages, E14.5 when initial contact is reached between palatal shelves and E16.5 when palatal fusion in completed in mice using RNA sequencing technology (RNA-Seq). Our RNA-Seq data revealed that 4115 and 5304 genes were statistically deferentially (p < 0.05) expressed at E14.5 vs E16.5 in WT palates and HM palates, respectively.  We then applied a 2.0-fold change cut-off to emphasize on significantly deferentially expressed genes. Genes that were uniquely up/down–regulated in either WT or HM at E16.5 vs E14.5 were identified and considered CP-related genes.

overall_design: Palatal mRNA profiles of wild type (WT)  and TGFβ3-/- mice at E14.5 and E16.5 were generated by deep sequencing, in triplicate, using Illumina HiSeq2000

first: J

last: Liu

first: S

first: K

last: White

first: M

last: Albahrani

first: H

last: Otu

first: A

last: Nawshad


title: Accurate ethnicity prediction from placental DNA methylation data

status: Public on Oct 14 2020

city: Vancouver

first: Wendy

last: Robinson

state: BC

address: 950 W 28th Ave

department: Medical Genetics

institute: University of British Columbia

type: Methylation profiling by genome tiling array

summary: The influence of genetics on DNA methylation (DNAme) variation is well documented, yet confounding from population stratification is often unaccounted for in DNAme association studies. Existing approaches have been developed to address confounding by population stratification by directly using DNAme data, but have not been validated in additional human populations or tissues, such as the placenta.  Results: To aid future placental DNAme studies in assessing population stratification, we developed an ethnicity classifier, PLANET (placental elastic net DNAme ethnicity classifier), on combined Infinium Human Methylation 450k BeadChip array (HM450k) data from placental samples. We used data from five North American cohorts from private and public repositories (n = 509) and show that PLANET can not only accurately predict (accuracy = 0.9379, kappa = 0.8227) major classes of self-reported ethnicity/race (African: n = 58, Asian: n = 53, Caucasian: n = 389), but can also produce probabilities that are highly correlated with genetic ancestry inferred from genome-wide SNP (>2.5 million SNP) and ancestry informative markers (n=50) data. We found that PLANET’s ethnicity classification relies on 1860 DNAme microarray sites, and over half of these were also linked to nearby genetic polymorphisms (n=955). Lastly, we found our placental-optimized method outperforms existing approaches in assessing population stratification in our placental samples from individuals of Asian, African, and Caucasian ethnicities.  Conclusion: PLANET outperforms existing methods and heavily relies on the genetic signal present in DNAme microarray data. PLANET can be used to address population stratification in future placental DNAme association studies, and will be especially useful when ethnicity information is missing and genotyping markers are unavailable.

overall_design: 508 samples were used to develop and validate PLANET, our placental ethnicity classifier. These samples are mixed in phenotype (healthy, preeclamptic, IUGR, a range of gestational ages across the third trimester and birthweights), as they come from multiple studies. For ethnicity and sex, these samples mainly consist of Caucasian, Asian, and African samples and are matched for sex (259 males and 249 females). This repository contains processed DNAm data for all 508 samples in the form of a beta value matrix, with a corresponding detection p value matrix, and sample-specific metadata information (e.g. ethnicity, sex). The majority of the 508 samples were collected from other GEO repositories; therefore only raw idat files for never-published-before samples were included in this repository. This amounts to 6 samples (12 idat files). Please see the samples metadata .xls file for a list of these samples.

first: Victor

middle: W

last: Yuan


title: Yes-Associated Protein (YAP) Induces a Secretome Phenotype and Transcriptionally Regulates Plasminogen Activator Inhibitor-1 (PAI-1) Expression in Hepatocarcinogenesis

summary: To investigate how tumour cell-derived YAP is changing the paracrine communication network between tumour cells and non-tumorous cells in hepatocarcinogenesis, the expression and secretion of cytokines, growth factors and chemokines were analysed in transgenic mice with liver-specific and inducible expression of constitutively active human YAP (YAPS127A). Transcriptome analysis of primary isolated hepatocytes  revealed that YAP overexpression induced the expression and secretion of many paracrine-acting factors with potential impact on other tumorous or non-tumorous cells (e.g. plasminogen activator inhibitor-1 (PAI-1), C-X-C motif chemokine ligand 13 (CXCL13), CXCL16).

overall_design: 6 samples were analyzed, Three samples derived from wt livers, three samples derived from enlarged livers (YapS127A)

first: Stefan

last: Thomann

first: Kai

last: Breuhahn


title: Single Cell RNA Sequencing of Mouse Mammary Epithelial Cells

status: Public on Sep 14 2020

city: Irvine

last: Kessenbrock

state: CA

address: 839 Health Sciences Road

department: Biological Chemistry

institute: UC Irvine

summary: The mammary epithelial cell (MEC) system is a bi-layered ductal epithelial network consisting of luminal and basal cells, maintained by a lineage of stem and progenitor cell populations. Here, we used integrated single-cell transcriptomics and chromatin accessibility analysis to reconstruct the cell types of the mouse MEC system and their underlying gene regulatory features in an unbiased manner. We define differentiation states within the secretory type of luminal cells, which can be defined as a continuous spectrum of progenitor and mature secretory cells. By integrating single-cell transcriptomics and chromatin accessibility landscapes, we identified cis- and trans-regulatory elements that are differentially activated in the specific epithelial cell types and our newly defined luminal differentiation states. Our work provides an unprecedented resource to reveal cis/trans regulatory elements associated with MEC identity and differentiation that will serve as a valuable reference to determine how the chromatin accessibility landscape changes during breast cancer.

overall_design: Library generation for three 10x Genomics v2 chemistry was performed following the Chromium Single Cell 3’ Reagents Kits v2 User Guide: CG00052 Rev B. Libraries were sequenced on the Illumina HiSeq4000 platform targeting approximately 50,000 reads per cells.

first: Nicholas

last: Pervolarakis

first: Quy

last: Nguyen


title: scATAC-seq and scRNA-seq of Mouse Mammary Epithelial Cells

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


title: RNA sequencing analyses of grl/hey2-overexpressing hearts and control hearts, as well as grl/hey2-deficient hearts and wild-type hearts following ventricular resection at 7 dpa

city: Shanghai

first: Peilu

last: She

address: 500 Dongchuan Road

institute: East China Normal University

summary: As Grl/Hey2 directly binds DNA through E box motifs and mediates transcription repression, we aim to gain insights into potential target genes of Grl/Hey2 during heart regeneration. We performed RNA-seq analyses using total RNAs collected from 4-HT-treated Tg(cmlc2:creER;cmlc2:nRSGG) hearts and Tg(cmlc2:nRSGG) control hearts, as well as grl5nt-/- mutant hearts and wild-type hearts following ventricular resection at 7 dpa. Using RNA profile analyses, we have identified some potential genes act downstream of Grl/Hey2-dependent transcriptional repression during heart regeneration.

overall_design: Transcriptome profiles of 4-HT-treated Tg(cmlc2:creER;cmlc2:nRSGG) hearts and Tg(cmlc2:nRSGG) control hearts, as well as grl5nt-/- mutant and wild-type hearts following ventricular resection at 7 dpa were generated by next generation sequencing using the Illumina HiSeq 2500. Six hearts were pooled per biological replicate. Each group had three biological replicates.

first: Tao

last: Zhong


title: CtIP-mediated DNA resection is dispensable for IgH class switch recombination by alternative end-joining

city: New York

first: Xiaobin

middle: Summer

last: Wang

state: NEW YORK

address: 1130 Siant Nicholas Ave, Room 501

department: Institute for Cancer Genetics

institute: Columbia University Medical Center

summary: To generate antibodies with different effector functions, B cells undergo Immunoglobulin class switch recombination (CSR). The ligation step of CSR is usually mediated by the classical non-homologous end-joining (cNHEJ) pathway. In cNHEJ-deficient cells, a remarkable ~25% CSR can be achieved by the alternative end-joining (A-EJ) pathway that preferentially uses microhomology (MH) at the junctions. While A-EJ mediated repair of endonuclease generated breaks requires DNA end-resection, we show that CtIP-mediated DNA end-resection is dispensable for A-EJ-mediated CSR using cNHEJ-deficient B cells. High-throughput sequencing analyses revealed that loss of ATM/ATR phosphorylation of CtIP at T855 or ATM kinase inhibition suppress resection without altering the MH-pattern of the A-EJ-mediated switch junctions. Moreover, we found that ATM kinase promotes Alt-EJ mediated CSR by suppressing inter-chromosomal translocations independent of end-resection. Finally, temperol analyses reveal that MHs are enriched in early internal deletions even in cNHEJ-proficient B cells. Thus, we propose that repetitive IgH switch regions represent favoriate substrates for MH-mediated end-joining contributing to the robustness and resection-indepndence of A-EJ-mediated CSR.

overall_design: Studies of A-EJ-mediated CSR are complicated by the fact that junctional MHs, a characteristic feature of A-EJ, can also be generated by cNHEJ. Although the MHs of cNHEJ junctions are thought to be shorter than those generated by A-EJ, the cutoff is not absolute and junctions with short MHs (1-3nt) cannot be definitively attributed to either DSB repair pathway. To circumvent this ambiguity, we examined CSR in B cells that are genetically deficient for cNHEJ owing to loss of the core cNHEJ factor XRCC4, an obligatory partner of LIG4. The role of CtIP in A-EJ-mediated CSR in Xrcc4-/- murine B cells was then evaluated by either conditional inactivation of CtIP or non-phosphorylatable CtIP mutation (T855A). Unexpectedly, we found that isotype switching in Xrcc4-/- B cells was unaffected by either deletion or mutation (T855A) of CtIP.  Moreover, despite a significant reduction in end-resection, the CSR junctions recovered from Xrcc4-deficient alone and Xrcc4-deficient & CtIP-T855A mutant cells displayed similar MH usage, suggesting that MH-mediated end-ligation can occur without extensive end-resection during CSR. Similarly, ATM kinase inhibitor (ATMi) also attenuated end-resection without affecting MH-usage during A-EJ-mediated CSR. The analysis of ATMi-treated Xrcc4-/- cells also identified an end-resection independent role for ATM in regulating the orientation of CSR by both cNHEJ and A-EJ. Finally, when CSR junctions were analyzed by cell division, MHs (4-15 bps) are significantly enriched in early internal deletion junctions even in cNHEJ-proficient B cells. Taken together, our findings showed that A-EJ-mediated CSR can occur independent of CtIP-mediated end-resection, suggesting that the repetitive IgH switch regions are uniquely prone to MH-mediated repair.

middle: S

first: Junfei

last: Zhao

first: Zhengping

last: Shao

first: Shan

last: Zha


title: Pancreatic cancer cells require the transcription factor MYRF (Myelin Regulatory Factor) to maintain ER homeostasis

city: Milan

first: Chiara

last: Balestrieri

address: Via Olgettina 58

department: Center for Omics Sciences

institute: IRCCS San Raffaele Scientific Institute


title: Expression data of primary murine liver sinusoidal endothelial cells after 10 weeks of CDAA diet

first: Carsten

last: Sticht

summary:
Liver sinusoidal endothelial cells (LSEC) constitute discontinuous, permeable microvessels, with a characteristic program of gene expression that differs significantly from continuous microvascular endothelial cells e.g. in the lung. LSEC play a pivotal role in liver fibrogenesis in the CDAA dietary model of non-alcoholic steatohepatitis (NASH).
We used microarrays to analyse the program of gene expression in murine liver endothelial cells after 10 weeks of CDAA diet.

overall_design: Murine liver sinusoidal endothelial cells (mLSEC) of Gata4 endothelial cell-subtype specific knockout (Gata4-LSEC-KO) and sibling control mice were isolated for RNA extraction and hybridization on Affymetrix microarrays.

first: Manuel

last: Winkler


title: Effect specific ablation of the NCoR corepressor delta and omega splice-variants on liver gene expression

status: Public on Sep 11 2020

city: Davis

first: Michael

last: Goodson

address: One Shields Ave

institute: University of California Davis

summary: Knockin mice were created that contained a point mutation that elminated the requisite GT in the 5' donor site of each of the NCoRω or NCoRδ splice variants, thus preventing splicing at that site and forcing splicing of the reciprocal splice variant.

overall_design: Adult C57BL/6N (WΤ) mice and  NCoRω-/- (OKO) or NCoRδ-/- (DKO) mice were fed a 60% kcal fat (HFD, Research Diets #D12492 )or 10% kal fat (LFD, Research Diets #D12450B) diet for 17 weeks. Liver samples were collected and analyzed for gene expression.

first: Martin

last: Privalsky

first: Trina

last: Knotts


title: Emergence of neuronal diversity during vertebrate brain development

city: Philadelphia

first: Bushra

last: Raj

state: PA

address: 421 Curie Boulevard

institute: University of Pennsylvania

summary: Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated, but the landscape of transcriptional changes underlying brain development are poorly characterized. Here, we describe a developmental single-cell RNA-seq catalog of ~220,000 zebrafish brain cells encompassing 12 stages from 12 hours post-fertilization to 15 days post-fertilization. We characterize known and novel gene markers for ~800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9-edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post-embryonic stages. Reconstruction of cell specification trajectories reveals that late-stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis.

overall_design: 10X Genomics v2 scRNA-seq libraries and scGESTALT


title: IRF2 maintains the stemness of colonic stem cells by limiting physiological stress from interferon

city: Bunkyo-ku

first: Kana

last: MINAMIDE

state: Tokyo

department: Medical Research Institute

institute: Tokyo Medical and Dental University

summary: The physiological stresses that diminish tissue stem-cell characteristics remain largely unknown. We previously reported that type I interferon (IFN), which is essential for host antiviral responses, is a physiological stressor for hematopoietic stem cells (HSCs) and that interferon regulatory factor-2 (IRF2), which attenuates IFN signaling, maintains the stemness of HSCs. Here, we explore the role of IRF2 in maintaining colonic epithelial stem cells (CoSCs). In mice with a conditional Irf2 deletion in the intestinal epithelium (hereafter Irf2ΔIEC mice), both the number and the organoid-forming potential of CoSCs was markedly reduced. Consistent with this finding, the ability of Irf2ΔIEC mice to regenerate colon epithelium after injury by dextran sodium sulfate (DSS) was severely impaired, independently of microbial dysbiosis. Mechanistically, CoSCs differentiated prematurely into transit-amplifying (TA) cells in Irf2ΔIEC mice, which might explain their low CoSC counts. A similar phenotype was induced in wild-type mice by repeated injections of low doses of poly(I:C), which induces type I IFN. Collectively, we demonstrated that chronic IFN signaling physiologically stresses CoSCs. This study provides new insight into the molecular mechanisms that maintain functional CoSCs throughout life.

overall_design: To identify the differentially regulated biological process that accounts for the reduction of CoSCs in Irf2ΔIEC mice, we performed microarray of sorted colonic crypt epithelial cells from naïve Irf2ΔIEC and Irf2fl/fl control mice.

last: Minamide

first: Taku

last: Sato

first: Yusuke

last: Nakanishi

first: Jumpei

last: Asano

first: Hiroshi

last: Ohno

first: Tamotsu

last: Kato

first: Toshiaki

last: Ohteki


title: Digital Gene Expression profiles analysis of patients with HCV-related hepatic fibrosis

status: Public on Sep 10 2020

city: Shijiazhuang

last: Fu

state: Hebei

address: No. 139 ziqiang road

department: Hepatology

institute: The Third Hospital of Hebei Medical University

summary: Hepatitis C virus (HCV) infection is an important etiology of chronic liver disease. Multiple possible molecular mechanisms were involved in the progression of liver fibrosis in chronically HCV-infected patients. Therefore, the further revealing novel genes for regulating liver fibrosis might provide evidence for gene diagnosis and molecular-targeted therapy. In this study, we examined the differentially expressed mRNA in plasma samples from the healthy control and patients with HCV-related liver fibrosis, in order to explore the potential predicted and therapeutic target for the development of HCV-related liver fibrosis.

overall_design: Plasma samples from HCV patients with moderate to severe liver fibrosis (F3-4) and healthy control subjects (each group included 3 cases) were used for whole transcript digital gene expression (DGE) profiling sequencing.

first: Yuemin


title: Expression data of Gata4 endothelial cell-subtype specific knockout primary murine liver sinusoidal endothelial cells

summary:
Liver sinusoidal endothelial cells (LSEC) constitute discontinuous, permeable microvessels, with a characteristic program of gene expression that differs significantly from continuous microvascular endothelial cells e.g. in the lung. Gata4 is described as master regulator of LSEC specification during liver development. Here, we sought to analyze the role of endothelial Gata4 in the adult liver.
We used microarrays to analyse the program of gene expression in murine liver endothelial cells with Gata4 deficiency.


title: Experimental Autoimmune Encephalomyelitis is Associated with Changes of the Microbiota Composition in the Gastrointestinal Tract

city: Charlottesville

first: David

middle: Michael

last: Johanson

state: VA

address: 200 Jeanette Lancaster Way

department: Department of Neuroscience

institute: UVa School of Medicine

summary: The gut microbiome is known to be sensitive to changes in the immune system, especially during autoimmune diseases such as Multiple Sclerosis (MS). Our study examines the changes to the gut microbiome that occur during Experimental Autoimmune Encephalomyelitis (EAE), an animal model for MS. We collected fecal samples at key stages of EAE progression and quantified microbial abundances with 16S V4 amplicon sequencing. Our analysis of the data suggests that commensal Lactobacillaceae fall in abundance during EAE while other commensal populations belonging to the Clostridiaceae, Ruminococcaceae, and Peptostreptococcaceae families expand. Community analysis with microbial co-occurrence networks points to these three taxa as mediators of gut microbiome dysbiosis. We also employed PICRUSt2 to impute MetaCyc Enzyme Consortium (EC) pathway abundances from the original microbial abundance data. From this analysis, we found that a number of imputed EC pathways responsible for the production of compounds with indole groups are enriched in mice undergoing EAE. Our analysis and interpretation of results provides a detailed picture of the changes to the gut microbiome that are occurring throughout the course of EAE disease progression.

sample_organism:
Mus musculus
blank sample

platform_organism:
Mus musculus
blank sample

overall_design:
Three-group experimental autoimmune encephalomyelitis (EAE) study in which one group was left naïve, one was immnuized with Complete Freund's Adjuvant (CFA), and one was immunized with an emulsion of MOG (myelin oligodendrocyte protein) and CFA to induce EAE. Fecal samples were taken at 2 days before immunizations and at 8, 14, 19, and 29 days afterwards during the progression of EAE. Fecal samples were processed for 16S amplicon sequencing to identify and quantify microbes and their abundances over time and accross immunization treatments.

Sequencing performed at UVa Genome Analysis & Technology Core,
Office of Research Core Administration.
University of Virginia Health System,
P.O. Box 800741,
Charlottesville, VA 22908-0741

last: Johanson II

first: Alban

last: Gaultier

first: Ioana

last: Marin

first: Jennifer

last: Goertz


title: Expression data of Gata4 endothelial cell-subtype specific knockout whole liver lysates

first: Carsten

last: Sticht

summary:
Liver sinusoidal endothelial cells (LSEC) constitute discontinuous, permeable microvessels, with a characteristic program of gene expression that differs significantly from continuous microvascular endothelial cells e.g. in the lung. Gata4 is described as master regulator of LSEC specification during liver development. Here, we sought to analyze the role of endothelial Gata4 in the adult liver.
We used microarrays to analyse the program of gene expression in murine whole liver lysates with LSEC-specifig Gata4 deficiency.

overall_design: Murine whole liver lysates of Gata4 endothelial cell-subtype specific knockout (Gata4-LSEC-KO) and sibling control mice were isolated for RNA extraction and hybridization on Affymetrix microarrays.

first: Manuel

last: Winkler


title: Reduced representation bisulfite sequencing (RRBS) of xenografts of mouse breast cancer cell line treated with C29, 5-aza-2'-deoxycytidine or a combination of both

city: Montréal

first: Mathieu

last: Vernier

state: Quebec

address: 2900 Edouard Montpetit

department: Biochemistry

institute: Université de Montréal

summary: Inhibition of estrogen related receptor alpha (ERRa) with C29 decreases global levels of DNA methylation and sensitizes breast cancer cells to the cytostatic effect of the DNMT inhibitor 5-aza-2'-deoxycytidine. We performed RRBS to understand the mechanisms behind the tumor suppression effect observed upon cotreatment with C29 and 5-azadC . We observed distinct patterns of differentially methylated regions in promoters for each condition and discovered that IRF4 was hypomethylated specifically in the condition with drug combination. Further analysis revealed that IRF4 was re-expressed in this context and was invovled in the tumor suppression response.

overall_design: NIC5231 mouse breast cancer cell lines were injected in mammary fat pad of NSG mice. Then,  primary tumors were treated with either C29 (10 mg/kg) and/or 5-azadC (1 mg/kg), or vehicle control (5 mice per group). When the largest tumor had reached the maximum tumor size limit (1.5 mm3), DNA was extracted and sent to Diagenode for RRBS analysis (2 replicates consisting of a pool of DNA from 2 mice per condition).

first: Shawn

last: McGuirk

first: Catherine

last: Dufour

first: Sydney

last: Wan

first: Etienne

last: Audet-Walsh

first: Julie

last: St-Pierre

first: Vincent

last: Giguère


title: Swimming under elevated hydrostatic pressure increases glycolytic activity in gas gland cells of the European eel

city: Innsbruck

first: Gabriel

last: Schneebauer

address: Technikerstrasse 25

country: Austria

institute: University of Innsbruck

summary: In spite of many decades of research, the spawning migration of the European eel Anguilla anguilla from the European coast to the Sargasso Sea remains a mystery. In particular, the role of the swimbladder as a buoyancy regulating structure is not yet understood. In this study, we exercised silver eels in a swim tunnel under elevated hydrostatic pressure. The transcriptome of gas gland tissue of these exercised eels was then compared to the known transcriptome of not exercised (control) silver eel gas gland cells. Due to the high infection rate of the eel population with the swimbladder parasite Anguillicola crassus, the comparison also included an exercised group of silver eels with a heavily damaged swimbladder, and we compared the previously published transcriptome of not exercised silver eels with a highly damaged swimbladder with the exercised group of silver eels with a heavily damaged swimbladder. The comparisons of unexercised (control) silver eels with exercised silver eels with functional swimbladder (EF), as well as with exercised silver eels with damaged swimbladder(ED), both showed a significant elevation in transcripts related to glycolytic enzymes. This could also be observed within the comparison of unexercised silver eels with a highly infected swimbladder with exercised eels with a damaged swimbladder (DED). In contrast to EF, in ED a significant elevation in transcript numbers of mitochondrial NADH dehydrogenase was observed. While in EF the transcriptional changes suggested that acid production and secretion was enhanced, in ED these changes appeared to be related to thickened tissue and thus elevated diffusion distances. The remarkable number of differentially expressed transcripts coding for proteins connected to cAMP-dependent signaling pathways indicated that metabolic control in gas gland cells includes cAMP-dependent pathways. In contrast to ED, in EF significant transcriptional changes could be related to the reconstruction of the extracellular matrix, while in ED tissue repair and inflammation was more pronounced. Surprisingly, in exercised eels hypoxia inducible transcription factor expression was elevated. In EF, a large number of genes related to the circadian clock were transcriptionally modified, which may be connected to the circadian vertical migrations observed during the spawning migration.

overall_design:
Using Illumina Sequencing to obtain RNA-Seq data and statistical Deseq analysis, the transcriptomes of European eel gas gland tissues of animals with different previous swimming exercise and with different gas gland tissue health status were compared.

Please note that the control samples in GSE102221 were re-analyzed in the current study and the duplicated sample records were included for the convenient retrieval of the complete raw data from SRA (as indicated in the sample description field).

first: Constantin

last: Lindemann

first: Victoria

last: Drechsel

first: Lasse

last: Marohn

first: Klaus

last: Wysujack

first: Elena

last: Santidrian

first: Ron

last: Dirks

first: Reinhold

last: Hanel

first: Bernd

last: Pelster


title: Single Cell ATAC Sequencing of Mouse Mammary Epithelial Cells

first: Kai

last: Kessenbrock

overall_design: Library generation for single cell ATACseq were performed following the Chromium Single Cell ATAC Reagent Kits User Guide: CG000168 Rev B. Libraries were sequenced on the Illumina HiSeq4000 platform targeting approximately 50,000 reads per cells.

first: Nicholas

last: Pervolarakis

first: Quy

last: Nguyen


title: Chidamide used in MM cell line [ChIP-seq]

status: Public on Sep 09 2020

first: Yifeng

last: Sun

institute: Zhongshan Hospital, Fudan University

summary: Most patients with multiple myeloma (MM) will eventually relapse and current treatments have limited effect. Herein, we demonstrate that succinate dehydrogenase subunitA (SDHA) was low expressed in MM patients, and patients with SDHA relatively high expression had long overall survival and progression-free survival. Furthermore, SDHA high expression inhibited proliferation and invasion in multiple myeloma (MM) cell lines and enhanced the anti-tumor and synergistic effect of chemotherapeutics. To investgate regulation of SDHA on epigenetic level,  we conducted ChIP-seq experiments to compare the H3K27ac signal between H929 cells treated with DMSO and H929 cells treated with chidamide.

overall_design: ChIP-Seq profiles for H929 cells treated with DMSO. ChIP-Seq profiles for  H929 cells treated with chidamide.

first: Zhao

last: Xu

first: Tianhong

first: Jiadai

first: Peng

last: Liu


title: Chidamide effect on MM

overall_design: Refer to individual Series


title: Hypoxia Triggers the Intravasation of Clustered Circulating Tumor Cells

status: Public on Sep 08 2020

city: Zurich

first: Francesc

last: Castro-Giner

address: Otto-Stern-Weg 7

institute: ETH Zurich

summary: Circulating tumor cells (CTCs) are shed from solid cancers in the form of single or clustered cells, with the latter displaying an extraordinary ability to initiate metastasis. Yet, the biological phenomena that trigger the intravasation of CTC clusters are largely unknown. Here, we compare gene expression of hypoxic and normoxic CTC clusters to identify genes that are not only upregulated as a consequence to hypoxia, but that may also play a pivotal role in promoting CTC clusters generation and metastasis.

overall_design: We isolated a total of 31 live CTCs from a breast cancer patient (BR61) and two breast cancer xenografts (BR16 and LM2) and labeled them with HypoxiaRed, a cell-permeable dye that tags hypoxic cells based on their nitroreductase activity, allowing to compare the gene expression profile of hypoxic versus normoxic CTC clusters. Following previously published protocol for parallel DNA and RNA sequencing from individual cells, transcriptomes of lysed cells were separated and amplified according to the Smart-Seq2. Subsequently, libraries were prepared with Nextera XT (Illumina) and sequenced on NextSeq75, single read for RNA. Final hypoxic condition was defined as HypoxiaRed-positivity as well as expression of HIF1α and VEGFA.

first: Cinzia

last: Donato

first: Leo

last: Kunz

first: Aino

last: Paasinen-Sohns

first: Barbara

last: Szczerba

first: Ilona

last: Krol

first: Ramona

last: Scherrer

first: Nunzia

last: Di Maggio

first: Wolf

last: Heusermann

first: Oliver

last: Biehlmaier

first: Christian

last: Beisel

first: Marcus

last: Vetter

first: Christoph

last: Rochlitz

first: Walter

last: Weber

first: Andrea

last: Banfi

first: Tim

last: Schroeder

first: Nicola

last: Aceto


title: RNA-seq of GR WT and GR DIM ileum/IEC with DEX, Zn and untreated controls

status: Public on Sep 07 2020

city: Gent

first: Steven

last: Timmermans

address: Technologiepark 71

country: Belgium

institute: VIB-UGent

summary: The cytokine TNF drives inflammatory diseases, e.g. Crohn disease. In a mouse model of TNF-induced systemic inflammatory response syndrome (SIRS), severe impact on intestinal epithelial cells (IECs) is observed. Zinc confers complete protection in this model. We found that zinc no longer protects in animals which lack glucocorticoids (GCs), or express mutant versions of their receptor GR in IECs, nor in mice which lack gut microbiota. RNA-seq studies in IECs showed that zinc caused reduction of expression of constitutive (STAT1-induced) interferon-stimulated response (ISRE) genes and Interferon Regulatory Factor (IRF) genes. Since some of these genes are involved in TNF-induced cell death in intestinal crypt Paneth cells, and since zinc has direct effects on the composition of the gut microbiota (such as several Staphylococcus species) and on TNF-induced Paneth cell death, we postulate a new zinc-related anti-inflammatory mechanism. Zinc modulates the gut microbiota, causing less induction of ISRE/IRF genes in crypt cells, less TNF-induced necroptosis in Paneth cells and less fatal evasion of gut bacteria into the system.

overall_design: Examination of changes in gene expresion in ileum/IEC of mice after treatment with DEX, Zinc or DEX+Zinc and a control group in the GR WT genotype and Grdim genotype  a total of 22 samples was sequenced (in 2 sets) in 4 conditions

first: Jolien

last: Souffriau

first: Tineke

last: Vanderhaeghen

first: Charlotte

last: Wallaeys

first: Kelly

last: Van Looveren

first: Lindsy

last: Aelbrecht

first: Sylviane

last: Dewaele

last: Vandewalle

first: Evy

last: Goossens

first: Serge

last: Verbanck

first: Filip

last: Boyen

first: Melanie

last: Eggermont

first: Lindsey

last: De Commer

first: Riet

last: De Rycke

first: Michiel

last: De Bruyne

first: Raul

last: Tito

first: Marlies

last: Ballegeer

first: Sofie

last: Vandevyver

first: Tiago

last: Velho

first: Luis

middle: F

last: Moita

first: Tino

last: Hochepied

first: Karolien

last: De Bosscher

first: Jeroen

last: Raes

last: Van Immerseel

first: Rudi

last: Beyaert

first: Claude

last: Libert


title: INO80C chromatin remodeler prevents promiscuous transcription at replication origins

city: Worcester

first: Salih

last: Topal

state: MA

address: 373 Plantation Street

institute: UMass Medical School

summary: INO80C chromatin remodeler colocalizes to yeast replication origins together with the transcription factors Mot1 and NC2. INO80C maintains genome stability by preventing noncoding transcription around origins both in yeast and mammals.

overall_design: Native elongating transcript sequencing (NET-seq) in WT-AA, INO80-AA, Mot1-AA, INO80-AA Mot1-AA; Break-seq in WT-AA, INO80-AA, Mot1-AA, INO80-AA Mot1-AA, ChIP-seq for Orc5-AA and Arp5-AA

first: Craig

last: Peterson


title: Next Generation Sequencing Facilities Quantitative Analysis of Wild type CD8+ T cells with 0.3T static magnetic field or not

city: shanghai

first: liu

last: yan

address: yueyang road 320

institute: shanghai institute of biochemistry and cell biology

summary:
Purpose:Next Generation Sequencing applying for compare the CD8+ T cells with 0.3T static magnetic field (SMF) or not transcriptome, included pathway-enrichment analysis and genes expression of interests
Methods:CD8+ T cells were isolated from splenocytes in 8 week old wild type mice through STEMCELL Technologies negative selection kit. FACS sort CD8+ T cells after 3 days with CD3/CD28 costimulation at 0.3T static magnetic field or not. RNA was extracted, purified and checked for integrity using an Agilent Bioanalyzer 2100. Libraries were generated for sequencing using the SMARTer Stranded Total RNA-Seq Kit - Pico Input Mammalian. Libraries were sequenced using an Illumina HiSeq X Ten sequencer.
Resluts: Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to further analyse
Conclusions:Our study represents the detailed analysis of CD8+ T cells with 0.3T static magnetic field or not transcriptomes

overall_design:
CD8+ T cells with 0.3T static magnetic field or not mRNA profiles of 8 week old wild type mice were generated by deep sequencing

Samples were replaced on October 5th, 2020.

first: X

last: Zhu

first: Y

last: Liu


title: m6A RNA methyltransferases Mettl3/14 regulate immune responses to anti-PD-1 therapy

city: San Diego

first: Lingling

last: Wang

state: California

address: 9500 Gilman Dr

institute: University of California San Diego

summary: We analyzed the RNA-seq and MeRIP-seq data from Mettl3/14 CRISPR knock-out and control CT26 colon cancer's mouse model.

overall_design: Differentially expressed genes in Mettl3/14 depleted tumors compared to control tumors under anti-PD-1 therapy were determined by RNA-seq. Change of RNA methylation states was detected by MeRIP-seq, downstream genes of Mettl3/14 were identified from the comparison of results in RNA-seq and MeRIP-seq

first: Tariq

last: Rana


title: Maternal Influenza A Virus Infection Restricts Fetal and Placental Growth and Adversely Affects the Fetal Thymic Transcriptome

city: Fort Collins

first: Thomas

last: Hansen

state: CO

address: 3107 Rampart Rd

department: Biomedical Sciences

institute: Colorado State University

summary: Maternal influenza A viral infections in humans are associated with low birth weight, increased risk of pre-term birth, stillbirth and congenital defects. To examine the effect of maternal influenza virus infection on placental and fetal growth, pregnant C57BL/6 mice were inoculated intranasally with influenza A virus A/CA/07/2009 pandemic H1N1 or PBS at E3.5, E7.5 or E12.5, and the placentae and fetuses collecgted and weighed at E18.5. Fetal thymuses were pooled from each litter. Placentae were examined histologically, stained by IHC for CD34 and vascular channels quantified. RNA from E7.5 and E12.5 placentae and E7.5 fetal thymuses was subjected to RNA sequencing and pathway analysis. Placental weights were decreased in litters inoculated with influenza at E3.5 and E7.5. Placentae from E7.5 and E12.5 inoculated litters exhibited decreased labyrinth development and transmembrane protein 150A gene was upregulated in E7.5 placentae.  Fetal weights were decreased in litters inoculated at E7.5 and E12.5 compared to controls. RNA sequencing of E7.5 thymuses indicated that 957 genes were downregulated 2-fold including Mal, which is associated with Toll-like receptor signaling and T cell differentiation. There were 28 upregulated genes.  It is concluded that maternal influenza A virus infection impairs fetal thymic gene expression as well as restricting placental and fetal growth.

overall_design: RNA was extracted from individual E18.5 mouse placenta and fetal thymus pools following either control or influenza (H1N1) infection on E.7.5 and E12.5 or E7.5 of pregnancy; respectively and analyzed for RNA sequence (RNA-Seq).

first: Hana

last: Van Campen


title: Effects of long-term and brain-wide colonization of peripheral bone marrow-derived myeloid cells in the CNS

city: Irvine

first: Kim

last: Green

address: 3208 Biological Sciences 3

department: Neurobiology and Behavior

institute: University of California, Irvine

summary: This dataset allows for the exploration of irradiation and long-term monocyte engraftment on gene expression in wild-type (C57/BL6) mice, across multiple brain regions.

overall_design: C57BL/6 mice received a bone marrow transplant from CAG-EGFP mice following whole body irradiation (1000 cGy) and following 3.5 mo treated with PLX3397 at a dose of 600 ppm for 14d. After this mice were returned to control chow diet, and allowed to recover for 6 mo. Brains were collected and micro-dissected for specific brain regions: hippocampus, cortex, and thalamus. n=3-4/group

middle: N

first: Lindsay

last: Hohsfield

first: Neelakshi

last: Soni


title: Vascular smooth muscle cell derived from iPS cell of Moyamoya disease - Comparative characterization with endothelial cell transcriptome

city: Sapporo

first: Masaki

last: Ito

address: North 15 West 7

department: Neurosurgery

institute: Hokkaido University

summary:
Transcriptome analysis of vascular smooth muscle cells differentiated from iPS-derived neural crest stem cells in Moyamoya disease
Moyamoya disease (MMD) is a rare cerebrovascular disorder characterized by steno-occlusive changes in the cerebral arteries at the base of the brain with unknown etiology, although histopathological features have demonstrated as fibrocellular thickening of the intima and medial thinning on the steno-occlusive arteries. However, the pathophysiology of proliferating cells in the thickened intima is still obscure. Furthermore, biological features of the vascular smooth muscle cells are unclear in MMD. Here, we aimed to analyze whole genome gene expression profile in VSMC using induced pluripotent stem (iPS) cell line. We generated iPS cell line from the blood of MMD with RNF213 R4810K risk allele (rs112735431) or healthy control without the risk allele. VSMCs were differentiated from iPS-derived neural crest stem cells. As a result, we successfully established cranio-cervical region specific VSMC confirmed by immunocytochemistry. Biological cellular features, including cellular proliferation, migration, and contraction ability were similar in VSMCs between MMD and control. Genome-wide gene expression analysis showed similar transcriptome profile in the VSMCs between MMD and control. Differential gene expression analysis in MMD-VSMC revealed 6 differentially expressed genes (4 upregulated, 2 down regulated in MMD), including decorin (DCN, upregulated in MMD), playing an inhibitory role in angiogenesis. In conclusion, VSMCs are not impaired in cellular function with similar transcriptome profile in MMD compared to healthy control. Since many previous studies have shown impaired EC features in MMD, our study suggests EC may play more role in the vascular pathogenesis in MMD rather than VSMC.

overall_design: We analyzed vascular smooth muscle cells (VSMC) in three patients with Moyamoya disease and three healthy control volunteers using the Affymetrix GeneChip HG-U133 Plus 2 platform. Array data was processed by Affymetrix Exon Array Computational Tool. VSMCs were differentiated from iPS-derived neural crest stem cells derived from peripheral blood mononuclear cells. No technical replicates were performed.

first: Kikutaro

last: Tokairin

first: Shuji

last: Hamauchi

first: Kiyohiro

last: Houkin


title: RNA-seq of human RUES2 and iPSC derived CMs at day 15 of differentiation

city: Rozzano

first: Simone

last: Serio

state: Milano

address: Via Alessandro Manzoni, 56

department: Cardiovascular Medicine

institute: Humanitas Research Hospital

summary: The definition of lncRNAs conservation remain a crucial challenge. In order to identify more promising relevant cardiac ncRNAs, we selected transcripts also present in human cardiac cells. We performed total RNA-seq  in human RUES2 and iPSC derived cardiomyocyte at day 15  of differentiation, first for human transcripts identification and secondly for the orthologous selection.

overall_design: Profiling of human RUES2 and iPSC derived CMs at day 15 of differentiation

first: Irene

last: Salamon

first: Condorelli

last: Gianluigi