title: Transimmunom whole blood RNA-seq data  from type 1 diabetic patients and healthy volunteers

city: Paris

middle: Leal

last: Valentim

state: Île-de-France

address: Bâtiment Cervi, 4ème étage, pièce 052

institute: INSERM/UPMC

summary: Patients affected by type 1 diabetes are recruited in the departments of Diabetology and Healthy Volunteers (HV) are selected based on internal records in the same hospital.  Total RNA from whole blood has been extracted following a two-step procedure. First, RNA from blood collected on PAX-Gene tubes has been extracted using Maxwell 16 LEV simplyRNA blood kit (Promega) following manufacturer recommendations and second b-globin, dominant RNA from red blood cells, has been removed using the GLOBINclear kit (Ambion) on extracted RNA. RNA sequencing has been performed from using the TruSeq Stranded mRNA preparation kit (Illumina) on 500 ng b-globin depleted RNA with a RNA Integrity Number > 8 (measured on Bioanalyzer following manufacturer recommendations), and then sequenced following a pair-end 2x75 bp protocol on NextSeq 500 or HiSeq 4000 (Illumina) at LIGAN Equipex (Lille, France).

overall_design: Starting with a protocol for recruitment of participants followed by sample acquisition (Lorenzon et al., 2018), whole blood RNA from 43 healthy donors and 39 T1D patients were sequenced and the corresponding gene expressions were estimated. Gene expression estimation was preformed by normalizing read counts using Sex and Batch as covariates.

last: Leal Valentim

first: Encarnita

last: Mariotti-Ferrandiz

first: David

last: Klatzmann

first: Adrien

last: Six

first: Oceane

last: Konza


title: Differential expression levels of mRNAs in tamoxifen-sensitive T47D versus tamoxifen-resistant T47D (T47DR) human breast cancer cells

status: Public on Jun 01 2020

city: Wuhan

first: Jun

last: Zhou

address: Jiefang Road

country: China

institute: Wuhan Union Hospital

type: Expression profiling by high throughput sequencing

summary: Tamoxifen is the most widely used antiestrogen in patients with estrogen receptor (ER) positive breast cancer . However,  less than half of patients  benefit from tamoxifen treatment and 30-50% acquire resistance and the disease progresses. Resistance to tamoxifen  is a serious  problem in breast cancer therapy and major efforts are underway to find out underlying mechanisms. To find out the differential expression levels of mRNAs in tamoxifen-sensitive T47D versus tamoxifen-resistant T47D (T47DR) human breast cancer cells,  T47DR (tamoxifen-resistant) cell line was established from T47D cells after the following continuous exposure to 1 μmol/L 4-Hydroxytamoxifen (H7904, Sigma, USA) for more than 6 months.Thousands of significantly different mRNA expression levels were found and analysed. Our study provides a reference data for the study of tamoxifen resistance .

overall_design: A high throughput sequencing about mRNAs was perfomed  in T47D and T47DR cells, and both cell lines were cultured in tamoxifen-free medium for more than 7 days before high throughput sequencing.

first: Shengnan

last: Ruan

first: Kehao

last: Le

first: Ming

last: Xu

first: Tao

last: Huang


title: Transcriptional profile of stemness in the ovarian surface epithelium

city: Ottawa

last: Cook

state: ON

address: 501 Smyth Rd

department: Cancer Therapeutics Program

country: Canada

institute: Ottawa Hospital Research Institute

summary: We leverage RNA sequencing to identify the transcriptional changes assocaited with several experimental conditions that induce a stemness phenotype in the ovarian surface epithelium, including spheroid culture, Snail overexpression, and BRCA1 deletion

overall_design: RNA sequencing of mOSE cultured as monolayers or spheroids (+/- TGFB1), and monolayer cells overexpressing Snail, or following deletion of BRCA1 (n=3 for each experiment)

first: Lauren

middle: E

last: Carter

first: Barbara

middle: C

last: Vanderhyden


title: Understanding microRNAs regulation in heat shock response in the sea cucumber Apostichopus japonicus

city: Qingdao

first: Dongxue

address: Changcheng road No.700

institute: Qingdao Agricultural University

type: Non-coding RNA profiling by high throughput sequencing

summary: In this study, we sought to determine the expression profiles of miRNAs under HS in A. japonicus by using HiSeq techinique.  Nine miRNA libraries of sea cucumbers (Control: C1, C2, C3; HS 6h: 6h1, 6h2, 6h3; HS 48h: 48h1, 48h2, 48h3 ) were sequenced respectively. We highlighted differentially expressed miRNAs among HS groups, many of which were invovled of immunity process and disease regulation.


title: Genome-wide expression of mRNAs and microRNAs in response to ERI2 knockdown

city: Houston

first: Yuanxin

last: Xi

state: TX

address: 1400 Pressler St

department: Bioinformatics and Computational Biology

country: USA

institute: The University of Texas MD Anderson Cancer Center

summary: Here we describe the biological properties of new member of the Enhancer of RNAi (ERI) subfamily of DEDDh nucleases in humans, called ERI-2 that is important for miRNA processing and decay for a large subset of eukaryotic miRNA transcripts.  hERI-2 is a potent Mg2+ dependent 3’-5’ exoribonuclease that also regulates the cell cycle and is a negative regulator of RISC.

overall_design: miRNA-seq and RNA-seq in ERI2 KD and control samples


title: miRNA expression profile and function analysis in psoriasis lesional skin and normal control of human

city: Jinan

first: Q

last: Sun

state: Shandong

address: Medical College of Shandong University 44 Wenhua West Road, Lixia District,

department: Dermatology

institute: Shandong University; Qilu hospital

summary: miRNAs have received much attention in the past several years. They have been proven  to play important role in the biology of autoimmune and immune-related disorders (AID). To identify miRNAs  specifically expressed in psoriasis, the expression of lncRNAs in biopsies obtained from patients with psoriasis  were compared with biopsies obtained from healthy volunteers using a microarray.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: In this study, eight samples from patients with psoriasis and  healthy volunteers were used to acquire the miRNA expression profiling and the function of the abudant miRNAs in the skin were analyzed by bioinformatic methods,finally, miR-145-5p and miR-320b were experimentally validated to play important roles in psoriasis.

first: Qing


title: Early defects of airway mucin sialylation and of mucociliary clearance at the onset of lung pathogenesis in a pig model of cystic fibrosis

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

summary: Chronic infection of the lungs by bacteria such as Pseudomonas aeruginosa plays an important role in the natural history of Cystic Fibrosis (CF). Altered mucin secretions and glycosylations are hallmarks of bacterial infections but their exact contributions to the development of chronic infection and/or inflammation remain to be established. We studied the lung environment in newborn CFTR-/- pigs, which closely mirrors the human CF phenotype at the levels of mucin glycosylation, mucociliary transport (MCT) and immune response to P. aeruginosa infections. We show an increased sialylation of mucins from the tracheal mucosa of CFTR-/- pigs, which is also associated to increased Pseudomonas aeruginosa adherence. RNA-seq analysis did not show any altered expression of inflammatory genes, nor of sialylation enzymes. CFTR-/- piglets were unable to clear P. aeruginosa from the airways, leading to increased bacteria time of residence in the airways. We propose that alterations in mucin sialylation and MCT directly contribute to the early development of a favorable environment for bacterial colonization of the CF airways in the absence of an intrinsic inflammation.

overall_design: Four experimental groups were analyzed, including 9 CFTR+/+ and 10 CFTR-/- piglets.  Half of the animals from each group were inoculated with Pseudomonas aeruginosa.

first: Pascal

last: Barbry

first: Agnes

last: Paquet

first: Nicolas

last: Pons

first: Ignacio

last: Caballero


title: Small RNA sequencing of murine pancreatic tumors driven by polyoma middle-T antigen with wild-type or single-copy loss of Dicer

city: Worcester

first: Brian

last: Quattochi

state: MA

address: 364 Plantation Street

department: MCCB

institute: UMass Medical School

summary: We report the small RNA sequencing results of mouse pancreatic tumor cell lines driven by polyoma middle-T antigen, which have additionally been engineered to have either wild-type (herein "PDwt") or single-copy loss (herein "PDhet") of the Dicer gene. As expected, PDhet cell lines exhibit lower miRNA levels compared to PDwt cell lines. Principle component analysis, detailed in the published manuscript, reveals PDwt cell lines to be more widely varying in miRNA signature compared to PDhet cell lines. Grouping miRNAs by family reveals several families to be significantly downregulated in PDhet cells lines below 50% of PDwt levels, including miR-10, -148, -17, -28, -299, -30, -34, and -379.

overall_design: 50-cycle single-end reads using the Illumina platform were performed on small RNAs isolated from low-passage tumor cell lines derived from Elastase-tva, Trp53(fl/fl), Dicer(wt/wt), p48-Cre or Elastase-tva, Trp53(fl/fl), Dicer(fl/wt), p48-Cre mice which had been infected with RCAS-Polyoma middle-T virus at postnatal day 3.

middle: J

last: Quattrochi

last: Lewis


title: Low-nitrogen stress reduces cell flux and cell elongation rate in maize leaf via reducing GA synthesis

city: zheng zhou

first: xiaohuan

last: mu

address: zhengzhou long zi hu

institute: Henan Agricultural University

summary: Using an integrated approach including kinematic growth analysis, tissue-specific RNA-seq dissection and hormone determination to investigated cell division and elongation in maize leaf growth in response to LN stress. Two biological replicates were generated for each tissue.

overall_design: RNA-seq of maize B73 sixth leaf from plants subjected to low nitrogen stress or control nitrogen levels.

first: Xiaohuan

last: Mu

first: Qinwu

last: Chen

first: Xiangyu

last: Wu

first: Fanjun

first: Lixing

last: Yuan

first: Guohua

last: Mi


title: Organoids derived from pancreatic adenocarcinoma patients share morphological and genetic features with the primary tumor

city: New York

first: Miguel

last: Brown

state: New York

address: 1230 York Ave Box 186

institute: The Rockefeller University

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

overall_design: Refer to individual Series


title: Gene Expression Profiles of Human Granulosa Cells Treated With Bioequivalent Doses of Corifollitrophin Alfa or Recombinant Human Follicle-Stimulating Hormone

city: Modena

first: Antonio

last: La Marca

state: Modena

address: Via del pozzo, 71

department: Mother-Infant Department, Institute of Obstetrics and Gynecology

country: Italy

institute: University of Modena and Reggio

summary:
Using recombinant DNA technologies, a new chimeric gene containing the coding sequences of the follicle stimulating hormone (FSH) β-subunit and the C-terminal peptide of the human chorionic gonadotrophin (hCG) β-subunit have been designed to generate a new gonadotrophin named corifollitrophin alfa. Corifollitrophin alfa has longer elimination half-life and a slower rate of absorption compared with FSH, which makes corifollitrophin alfa a long-acting hormone employed as a substitute of the recombinant FSH (recFSH) in the controlled ovarian stimulation (COS).
The purpose of this study is to compare the gene expression profiles elicited by bioequivalent doses of corifollitrophin alfa or recFSH in primary cultures of human granulosa cells (hGCs). Both gonadotrophins exert their functions by binding FSH receptors (FSHRs), activating signaling pathways that increase the cyclic adenosine monophosphate (cAMP) intracellular content. Bioequivalence has been defined as the dose/duration of gonadotrophin treatment able to promote the same amount of intracellular cAMP. Primary cultured hGCs were treated with different doses of either gonadotrophin and the cAMP was measured after different incubation times to establish the bioequivalence. Results obtained by comparing the bioequivalent treatments, showed that corifollitrophin alfa is more effective than recFSH in inducing aromatase gene expression after 6 and 24 hours from the initial stimulation in agreement with its long-acting characteristic’s.

overall_design: Primary cultures of human granulosa cells from five different patients were treated with bioequivalent doses of corifollitrophin alfa or rhFSH then washed to remove the unbuond hormone. Controls and gonadotrophin-stimulated samples were processed for total RNA extraction and hybridization on Affymetrix microarrays after 24 hours of incubation.

first: Sandro

last: Sacchi

first: Elena

last: Tenedini

first: Debora

last: Tondelli

first: Sandra

last: Parenti

first: Daniela

last: Tagliasacchi

first: Susanna

last: Xella

first: Tiziana

last: Marsella

first: Enrico

last: Tagliafico


title: Resident macrophages promote homeostasis of hyaluronan-associated extracellular matrix in the mammary gland stroma

status: Public on May 31 2020

city: Minneapolis

first: Rebecca

last: LaRue

state: MN

address: 117 Pleasant St SE

department: Department of Lab medicine and Pathology

institute: University of Minnesota

summary: Tissue resident macrophages in the mammary gland are found in close association with epithelial structures and within the adipose stroma, and are important for mammary gland development and tissue homeostasis. While epithelial-associated macrophages have been linked to ductal development, the contributions of stromal macrophages to mammary gland homeostasis remain unknown. Using transcriptional profiling, we identify a distinct resident stromal macrophage subpopulation that is characterized by expression of Lyve-1, a receptor for the extracellular matrix component hyaluronan. This subpopulation is enriched in genes associated with extracellular matrix remodeling and is found to be specifically associated with hyaluronan-rich regions within the mammary stroma. Furthermore, macrophage depletion leads to increased accumulation of hyaluronan-associated extracellular matrix in the mammary stroma. These results demonstrate the presence of a distinct subpopulation of macrophages and provide insights into the functional contributions of these macrophages to stromal homeostasis in the mammary gland.

overall_design: Macrophages were sorted from mammary glands based on their expression of the cell surface marker Lyve-1 and subjected to bulk RNA-seq analysis.

first: Ying

last: Wang

first: Thomas

last: Chaffee

first: Danielle

last: Huggins

first: Patrice

last: Witschen

first: Ayman

last: Ibrahim

first: Andrew

last: Nelson

first: Heather

last: Machado

first: Kathryn

last: Schwertfeger


title: Interferon-regulated lncRNA analysis identifies IRF1-AS as a tumor suppressor in esophageal squamous cell carcinoma (ESCC)

city: Beijing

first: Jianbing

last: Huang

state: State...

address: No. 17 Pan-jia-yuan South Lane, Chaoyang District, 100021 Beijing, China

institute: Cancer Institute and Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences

summary: Interferons and its downstream pathway play pleiotropic roles in antitumor reaction. However, targeting IFN pathway is unsatisfied due to unpredictable effects. Exploiting players other than known proteins involved in IFN pathway is pivotal for targeting this pathway. In our study, we comprehensively analyzed IFN-regulated lncRNAs and identified the top-ranking candidate IRF1-AS which functions as a positive regulator of IFN response and a tumor suppressor in ESCC. We also identified a positive feedback loop between IRF1-AS and IRF1, which was supposed to maintain the positive feedback loop between IFN signaling and IRF1-AS.

overall_design: IFN-β treated (1000 IU/ml; 72 h) and control KYSE30, KYSE180 and KYSE450 cells, and IRF1-AS knockdown and control KYSE30 and KYSE180 cells were used to perform RNA sequencing (RNA-seq).

first: Jie

last: He


title: Gene expression profiling of MDA-MB-231 cells transfected with hsa-miR-205-5p and hsa-miR-214-3p compared to scrambled miRNA precursors

city: Riyadh

first: Nehad

middle: M

last: Alajez

address: 1st floor College of Medicne

department: Anatomy

country: Saudi Arabia

institute: King Saud University College of Medicine

summary: We have employed whole genome microarray to identify changes in gene expression in MDA-MB-231 cells transfected with hsa-miR-205-5p and hsa-miR-214-3p compared to scrambled miRNA precursors at 72 hours after transfection.


title: microRNA expression profiling of paired primary and lymph node metastatic breast cancer patients

summary: Extracted total RNA from FFPE tissue were used for RNA labeling and hybridization on to the Agilent Human SurePrint 8 × 60k v16 miRNA microarray chip according to the manufacturer's protocol.

overall_design: Total RNA was extracted from FFPE tissue using the recover all total nucleic acid isolation kit (Ambion Inc., Life Technologies, USA) according to the manufacturer’s protocol. RNA was then subjected to labeling and hybridization on to the Agilent Human SurePrint 8×60k v16 miRNA microarray chip according to the manufacturer's protocol.


title: Global gene expression profiling of tissue engineered neofascia of hernia patients with good and bad healing characterisitics.

city: Würzburg

first: Claus

middle: Juergen

last: Scholz

address: Josef-Schneider-Str. 2

department: Core Unit SysMed

country: Germany

institute: University Hospital Würzburg

summary:
The prevalence of hernia after laparatomy has been estimated at 2-15%. Apart from male gender, smoking and obesity (BMI>25), increased age (>45 years) were identified as potential risk factors. To support the wound healing process, synthetic mesh is now routinely used in laparatomy.
A patient's risk for hernia formation and relapse can be estimated by his/her collagen type I / collagen type III ratio using sirius red stains.

overall_design: We generated global mRNA expression profiles from 4 good and 2 bad healers obtained from native tissue and bioreactor cultures in the presence of commercially available meshs.

first: Christian

middle: A

last: Schulz

first: David

last: Niehaus

first: Ulrich

last: Dietz


title: Investigating the role and mechanism of stress induced protein Sesn2 in aged-related adaptive response to cardiac ischemia reperfusion injury

city: Jackson

first: Ji

last: Li

state: MS

address: 2500 N. State st.

department: Physiology and Biophysics

institute: University of Mississippi Medical Center

summary:
Purpose: to reveal the myocardium transcriptomic profile shift pattern before/after Ischemia Reperfusion stress in young, aged, and Sesn2-knockout mice. The goals of this study are to compare the transcriptomic shift pattern among young, aged, and Sesn2-knockout to explore the caridoprotective mechanism of Sesn2 in Ischemia Reperfusion stress and the critical roles of Sesn2 in age-related adapting response to Ischemia Reperfusion stress.
Methods: Myocardium transcriptome profiles of young (3-4 months) wild-type, aged (24-26 months) wild-type, and Sesn2-knockout (3-4 months) mice in normal physiological and Ischemia Reperfusion stressed conditions.
Results: Sesn2 is critical to repress inflammation and maintain metabolic and mitochondria homeostasis in hearts under Ischemia Reperfusion stress, especially to aged hearts.

first: Di

last: Ren


title: Pre-transplantational control of the post-transplantational fate of human pluripotent stem cell-derived cartilage

first: Jia

state: Texas

address: 2121 W HOLCOMBE BLVD

department: CEDP

institute: Guangzhou Medical University

summary: Cartilage pellets generated from ectomesenchymal progeny of human pluripotent stem cells (hPSCs) in vitro eventually show signs of commitment of chondrocytes to hypertrophic differentiation. When transplanted subcutaneously, most of the surviving pellets were fully mineralized by 8 weeks. In contrast, treatment with the adenylyl cyclase activator, forskolin, in vitro resulted in slightly enlarged cartilage pellets containing an increased proportion of proliferating immature chondrocytes that expressed very low levels of hypertrophic/terminally matured chondrocyte-specific genes. Forskolin treatment also enhanced hyaline cartilage formation by reducing type I collagen gene expression and increasing sulfated glycosaminoglycan accumulation in the developed cartilage. Furthermore, forskolin treatment in vitro increased the frequency at which the cartilage pellets maintained unmineralized chondrocytes after subcutaneous transplantation. To elucidate the type of cartilage that forskolin preferentially promotes and potential molecular mechanisms involved in the forskolin-suppression of chondrocyte hypertrophic differentiation in vitro, we performed genome-wide, comparative transcriptomic analyses on the cartilage pellets formed from 3 to 4 independent pellet cultures of ectomesenchymal cells with or without forskolin treatment. RNAs were isolated on day 26-28 and mRNA-sequencing (RNA-seq) analyses were performed.

overall_design: Three independent sets of PTB (PDGF+TGFβ3+BMP4) cartilage pellets, and four independent sets of PTBFk (PTB+30 uM forskolin) pellets were prepared from passage 5-8 ectomesenchymal cells (i.e., FSb[FGF2+SB431542]-expanded CD271hiCD73- neural crest-like progeny of H9 hESCs). On day 26-28 of pellet culture, 5 to 6 cartilage pellets were harvested, combined and total RNA was extracted with an RNeasy mini kit (Qiagen). Poly (A)-tailed messenger RNA was enriched using Poly(A)Purist Kit (Ambion, Foster City, CA) before the preparation of the RNA-seq library using an Ultra directional RNA library prep kit for Illumina (New England Biolabs, Ipswich, MA) per manufacturer’s instructions. RNA-seq was performed using the Illumina Nextseq500 with the 150 bp pair-ended running mode. Sequencing reads were aligned against the GRCh37/hg19 reference genome using bowtie2 (Langmead and Salzberg, 2012) with default parameter. Only uniquely mapped reads were used for downstream analysis. HTseq was used to count the read numbers mapped to each gene. DESeq2 (Love et al., 2014) was used to call the significantly differentially expressed genes (fold change ≥2; false discovery rate ≤0.05) between two conditions. The normalized gene counts from DESeq2 was used to do the normalization.

first: Minjung

last: Lee

first: Azim

last: Pothiawala

first: Bryan

middle: K

last: Ang

first: John

middle: Y

first: Deqiang

last: Sun

first: Yun

first: Naoki

last: Nakayama


title: microRNA expression profiling of paired primary and lymph node metastatic breast cancer patients, and gene expression profiling of MDA-MB-231 cells transfected with hsa-miR-205-5p and hsa-miR-214-3p compared to scrambled miRNA precursors

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


title: Innate immune stimulation of whole blood reveals IFN-1 hyper-responsiveness in type 1 diabetes

city: Bethesda

first: Kristin

middle: V

last: Tarbell

state: MD

address: 10 Center Dr, Bldg 10 5-5832

department: Diabetes, Endocrinology, and Obesity Branch

institute: NIH/NIDDK

summary: TruCulture human whole blood ex vivo stimulation was performed on 17 healthy individuals and 17 post-onset type 1 diabetics, then gene expression was analyzed using Nanostring to characterize stimulated innate immune responses. Ex vivo whole blood stimulation revealed higher induced IFN-1 responses in type 1 diabetes as compared to healthy controls.

overall_design: Samples from 17 type 1 diabetes subjects and 17 age-matched healthy controls were collected concurrently over six months, usually as age-matched pairs collected within one week of each other. type 1 diabetes subjects had history of clinical type 1 diabetes diagnosis and presence of type 1 diabetes-associated autoantibodies, were diagnosed between 3 months and 8 years prior to draw, and had history of good glucose control as represented by typical Hemoglobin A1c (HbA1c) < 8%, though HbA1c at draw was not an exclusion criterion. Healthy controls had no first-degree relatives with type 1 diabetes. While the groups were not sex-matched, gene expression changes were not associated with patient sex either within disease groups or across all subjects. All subjects were enrolled in the Benaroya Research Institute Immune Mediated Disease Registry. All subjects fasted overnight prior to the blood draw. HbA1c was measured under CLIA-approved protocols at the University of Washington’s Northwest Lipid Metabolism and Diabetes Research Laboratories (Seattle, WA, USA). Data paired with luminex protein measurements from the Truculture tube supernatant.

first: Kameron

middle: B

last: Rodrigues

first: Matthew

last: Dufort

first: Alba

last: Llibre

first: Vincent

last: Bondet

first: Cate

last: Speake

first: Darragh

last: Duffy


title: Organoids derived from pancreatic adenocarcinoma patients share morphological and genetic features with the primary tumor [RNA-seq]

first: Miguel

last: Brown

summary: RNA sequencing demonstrates molecular profiles common to primary tumor, PDX and organoid models

overall_design: RNAseq of 7 patient tumors and their models, consisting of 7 tumors, 4 PDX, 5 cell line, 4 organoid, and 6 normal for a total of 25 samples.

first: Isabel

middle: R

last: Calvo

first: Kori

last: Kirby

first: Samantha

last: Sparrow


title: Expression data from human BPH1 and WPMY-1 cells treated with PAO.

city: nanjing

first: jiakuan

last: liu

address: 12 xuefu road, pukou district

institute: nanjing university

summary:
Pao extract is an herbal preparation of the bark of an amazonian rain forest tree,Pao Pereira (Geissospermum vellosii),which could inhibit Benign prostatic hyperplasia (BPH).Characterizing the molecular alterations of BPH1 and WPMY-1 cells treated with PAO is important for understanding the molecular mechanisms of PAO inhibiting BPH.
We used microarrays to detail the RNA expression.

overall_design: 8 samples were analyzed, 2 replicates. BPH1 and WPMY-1 cells were treated with vehicle or PAO (250μg/ml). These cells were used for RNA extraction and hybridization on Affymetrix microarrays.

first: Jiakuan

last: Liu

first: Jun

last: Yan


title: DNA structure-specific endonuclease FEN1 as a novel drug target in tamoxifen resistant breast cancer.

city: Amsterdam

first: Koen

last: Flach

address: Plesmanlaan 121

country: Netherlands

institute: NKI

type: Genome binding/occupancy profiling by high throughput sequencing

type: Methylation profiling by high throughput sequencing

summary: Estrogen receptor α (ERα) is a key transcriptional regulator in the majority of breast cancers. ERα-positive patients are frequently treated with tamoxifen, but resistance is common. In this study, we refined a previously identified 111-gene outcome prediction-classifier, revealing FEN1 as the strongest determining factor in ERα-positive patient prognostication. FEN1 levels were predictive of outcome in tamoxifen-treated patients, and FEN1 played a causal role in ERα-driven cell growth. FEN1 impacted the transcriptional-activity of ERα by facilitating coactivator recruitment to the ERα transcriptional complex. FEN1 blockade induced proteasome-mediated degradation of activated ERα, resulting in loss of ERα-driven gene expression and eradicated tumor cell proliferation. Finally, a high-throughput 465,195 compound screen identified a novel FEN1 inhibitor, which effectively blocked ERα-function and inhibited proliferation of tamoxifen-resistant cell lines as well as ex-vivo cultured ERα-positive breast tumors. Collectively, these results provide therapeutic proof-of-principle for FEN1 blockade in tamoxifen-resistant breast cancer.

overall_design:
RNA-seq and Chip-seq of ERα, FOXA1, XRCC1, PCNA, POLII, PARP1, XRCC1, BRG1 and FAIRE-seq in MCF-7 cells treated with siRNAs or FEN1 inhibitor
RRBS of MCF-7 cells treated -+ 45 min E2 -+ FEN1 inhibitor

middle: D

first: Wilbert

last: Zwart


title: Organoids derived from pancreatic adenocarcinoma patients share morphological and genetic features with the primary tumor [Drop-seq]

summary: In this study, we applied Drop-seq, a high throughput single cell RNA-seq platform, to characterize the different cell types present in pancreatic cancer organoids. We sequenced the transcriptomes of 7675 single cells from organoids derived from a patient undergoing a Whipple procedure for pancreatic ductal adenocarcinoma (PDAC). We then developed a novel clustering approach based on a class of probabilistic generative models called topic models, leading to the identification of subpopulations of cells.

overall_design: Dropseq of organoids derived from patient 1. Mature organoids were pooled, made into single cell suspension and 17 single cell RNAseq libraries were generated starting from 15 separate dropseq runs.

first: Mohana

last: Ray

first: Rajib

last: Nandi

last: Romero-Calvo


title: Gene regulation by restoration of KMT2C in human colorectal cancer cells HCT116 and RKO

city: Uppsala

first: L.

last: He

address: Dag Hammarskjölds Väg 20

country: Sweden

institute: Uppsala University

summary: The histone 3 lysine 4 (H3K4) monomethylase KMT2C is mutated across several cancer types, however the effects of mutations on epigenome organization, gene expression and cell growth are not clear. To study effects of KMT2C expression in CRC cells we restored one allele to wild type KMT2C in the two CRC cell lines RKO and HCT116, which both are homozygous KMT2C c.8390delA mutant, by gene editing. RNA sequencing was performed to profile gene expression when KMT2C was restored in RKO and HCT116 cells.

overall_design: Three independently isolated RNA samples each were sequenced from parental cell lines HCT116 and RKO. Single samples were sequenced for KMT2C knock-in clones, except RKO KMT2C KI2 where duplicate samples were sequenced. Gene expression levels in KMT2C knock-in clones were compared to those in the respective parental cells.

first: Chatarina

last: Larsson

first: Tobias

last: Sjöblom


title: Wnt signaling inhibition in human colon cancer cell lines (SW480 and SW620) drives changes in gene programs for cell adhesion, mobility, and cell junction

city: Irvine

first: Marian

last: Waterman

state: CA

address: 224 Sprague Hall

institute: University of California Irvine

summary:
Overactive Wnt signaling has been found to be a significant driver in colon cancer carcinogenesis targeting many cellular processes such as cel proliferation, migration, and metabolism. The purpose of this study was to use high throughput transcriptional profiling (RNA-seq) to identify Wnt signaling gene targets in human colon cancer cells.
Transcriptional profiles of human colon cancer cell lines (SW480 and SW620) with overactive Wnt signaling were compared to their matching Wnt low genetically modified stable cell (SW480-dnLEF1 and SW620-dnLEF1) through high throughput RNA-seq with four biological replicates. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat2 followed by HTseq and DESEQ2.
Using an optimized data analysis workflow, we mapped about 30-40 million sequence reads per sample to the human genome (build hg38). RNAseq analysis of dnLEF1 expression in SW480 and SW620 cells cultured in vitro showed changes in gene programs for cell adhesion, mobility, cell junction, and extracellular matrix.

overall_design:
Experiment 1: SW480 GFP (mock/control) vs SW480 dnLEF1 (Wnt inhibited/experimental)
Experiment 2: SW620 GFP (mock/control) vs SW620 dnLEF1 (Wnt inhibited/experimental)

first: Lyou

last: Yung

first: Waterman

last: Marian


title: Transcriptional profile of Th17 cells: The role of glycolysis

city: Pasadena

first: Boyoung

last: Shin

state: California

address: 1200 E. California Blvd

institute: Californial Institute of Technology

summary: The aim of this study is to investigate a role of glycolysis in transcriptional programing of Th17 cells during differentiation.  Naïve CD4 T cells were differentiated towards Th17 cells with or without a mild inhibition of glycolysis, and transcriptome signature was analyzed.  We found about 200 transcripts were differentially regulated.  Further pathway analysis suggested that glycolysis controls genes associated with IL-2/STAT5 signaling during Th17 differentiation.  Inhibition of glycolysis resulted in enrichment of genes associated with translational processes and Th17 signature genes.

overall_design: Naïve CD4 T cells were differentiated into Th17 cells in the presence of vehicle or 2DG (glycolysis inhibitor) for 48 hours.  Total mRNA profiles were generated by deep sequencing in triplicate using Illumina HiSeq 2500.

first: Gloria

last: Benavides

first: Victor

last: Darley-Usmar

first: Laurie

last: Harrington


title: Transcriptomic analysis of mouse brain microglia on aging-associated changes in response to cerebral ischemia

city: Pittsburgh

first: Yejie

last: Shi

state: PA

address: S-510 Biomedical Science Tower, 3500 Terrace Street

department: Neurology

institute: University of Pittsburgh

summary: Senescence-associated alterations in microglia may have profound impact on cerebral homeostasis and stroke outcomes. However, the lack of a transcriptome-wide comparison between young and aged microglia in the context of ischemia limits our understanding of aging-related mechanisms. Herein, we performed bulk RNA sequencing analysis of microglia purified from cerebral hemispheres of young adult (10-week-old) and aged (18-month-old) mice 5 days after distal middle cerebral artery occlusion or sham operation. Considerable transcriptional differences were observed between young and aged microglia in healthy brains, indicating heightened chronic inflammation in aged microglia. Following stroke, the overall transcriptional activation was more robust in young microglia than in aged microglia. Gene clusters with functional implications in immune inflammatory responses, immune cell chemotaxis, tissue remodeling, and cell-cell interactions were markedly activated in microglia of young but not aged stroke mice. These alterations in microglial gene response may contribute to aging-driven vulnerability and poorer recovery after ischemic stroke.

overall_design: Young adult (10 weeks old) and aged (18 months old) male C57BL/6 mice were subjected to focal cerebral ischemia induced by permanent occlusion of the left distal middle cerebral artery and left common carotid artery (abbreviated as "dMCAO"). The CD11b+CD45low cell population was collected by fluorescence-activated cell sorting from the brain after sham operation, or 5 days after brain ischemia. There were 4 groups: young sham, young dMCAO 5d, aged sham, and aged dMCAO 5d. In each group there were 2 biological replicates. Each replicate was pooled from 5 mouse brains. The sorted cells were subjected to mRNA sequencing.

last: Chen


title: Molecular mechanisms underlying heat stress effects on Mytilus edulis and galloprovincialis hybrids at early larval stages

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

institute: University of Padova

summary: The present work sought first to identify the impacts of increasing water temperatures on M. galloprovincialis and M. edulis pure larvae and their hybrids on embryo larval development. Second, based on a recently developed targeted Mussel’s microarray, we investigated the transcriptional response to elucidate possible differences in heat stress-induced gene expression between these species.

sample_organism: Mytilus edulis x Mytilus galloprovincialis

platform_organism:
Mytilus californianus
Mytilus edulis
Mytilus galloprovincialis
Magallana gigas

overall_design: Total RNA was prepared from a group of 200.000 larvae from each experimental condition . Dual color competitive hybridizations (18°C vs 22°C) was performed using the STREM platform . Each experimental condition was calculated as 9 different values (3 biological replicates  and 3 technical).

first: PACCHIONI

last: Beniamina

first: MILLINO

last: Caterina

first: BANNI

last: Mohamed

first: OLIVERI

first: VIARENGO

last: Aldo


title: Gene expression in xenograft tumors derived from HCT116 and its oxaliplatin resistant clones

city: Nishinomiya

first: Tomoki

last: Yamano

state: Hyogo

address: 1-1 Mukogawa-cho

department: Department of Surgery

country: Japan

institute: Hyogo College of Medicine

summary: To explore the mechanisms associated with oxaliplatin resistance, we compared gene expression in xenograft tumors derived from human colorectal cancer tumor cells HCT116 and its oxaliplatin resistant clones (HCT/OHP1 and HCT/OHP5).

overall_design: Messenger RNA was extracted from xenograft tumors derived from HCT116 and its oxaliplatin resistant clones (HCT/OHP1 and HCT/OHP5). Then gene expression was compared between HCT116 and oxaliplatin resistant clones (HCT/OHP1 and HCT/OHP5).


title: Carbonic anhydrase 13 decreases bone metastasis of iCSCL-10A breast cancer stem cells

city: Minato-ku

first: Satomi

last: Yogosawa

state: Tokyo

address: 3-25-8, Nishi-shinbasi

department: Department of Biochemistry

institute: Jikei University School of Medicine

summary: iRFP713-lebeled iCSCL-10A cells were injected into immunodeficient mice. 5 weeks later, bone metastasized iCSCL-10A cells were extracted from bone marrow was compared with injected cell in vitro culture by microarray and pathway analysis.

overall_design: mRNA expression of iCSCL-10A cells extracted from bone marrow was compared with injected cell in vitro culture.

first: Kiyotsugu

last: Yoshida


title: Difference of gene expression among DLD1, oxaliplatin resistant clones derived from DLD1, HCT116, and oxaliplatin resistant clones derived from HCT116

summary:
Gene expression between DLD1 and DLD1 derived oxaliplatin resistant clones (DLD/OHP1, DLD/OHP4, and DLD/OHP5) was assessed
Gene expression between HCT116 and HCT116 derived oxaliplatin resistant clones (HCT/OHP1, HCT/OHP3, and HCT/OHP5) was assessed

overall_design: Oxaliplatin resistant clones were established and analyzed. Cells were harvested for RNA extraction without drug.


title: The Atlantic salmon gill transcriptome response in a natural outbreak of salmon gill pox virus infection reveals new biomarkers of gill pathology and suppression of mucosal defense

status: Public on May 30 2020

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

country: Norway

institute: Nofima AS

summary: The salmon gill poxvirus (SGPV) is a large DNA virus that infects gill epithelial cells in Atlantic salmon and is associated with acute high mortality disease outbreaks in aquaculture. The pathological effects of SGPV infection include gill epithelial apoptosis in the acute phase of the disease and hyperplasia of gill epithelial cells in surviving fish, causing damage to the gill respiratory surface.  Transcriptome responses to virus were assessed in gills at different stages of disease

overall_design: Gills were sampled from Atlantic salmon presmolts during a natural outbreak of SGPV disease. Samples covered the early phase of infection, the acute mortality phase, the resolving phase of the disease and control fish from the same group and facility.

first: Krasnov

last: Aleksei

first: Dahle

last: Maria K.

first: Gjessing

last: Mona


title: Differential gene expression of Salmonella Typhimurium after exposure to chlorine

city: Dallas

first: Palmy

last: Jesudhasan

department: Microbiology

institute: University of Texas Southwestern Medical Center

summary: The oxidative stress response to chlorine was analysed by the global gene expression profile for Salmonella Typhimurium

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium

overall_design:
0 min_OC: The genomic response of cells in log phase (fresh culture) and stataionary phase (overnight culture) of growth of S. Typhimurium after exposing the cells to chlorine at a concentration of 10 ppm for 0.5 min were compared with cells that were not treated with chlorine. Transcriptomic analysis was also done on cells after resuscitation in growth medium (TSB) for 30 min.
30 min_OC: The genomic response of cells in log phase (fresh culture) and stataionary phase (overnight culture) of growth of S. Typhimurium after exposing the cells to chlorine at a concentration of 10 ppm for 0.5 min were compared with cells that were not treated with chlorine. Transcriptomic analysis was also done on cells after resuscitation in growth medium (TSB) for 30 min.
0 min_FC: The genomic response of cells in log phase (fresh culture) and stataionary phase (overnight culture) of growth of S. Typhimurium after exposing the cells to chlorine at a concentration of 10 ppm for 0.5 min were compared with cells that were not treated with chlorine. Transcriptomic analysis was also done on cells after resuscitation in growth medium (TSB) for 30 min.
30 min_FC: The genomic response of cells in log phase (fresh culture) and stataionary phase (overnight culture) of growth of S. Typhimurium after exposing the cells to chlorine at a concentration of 10 ppm for 0.5 min were compared with cells that were not treated with chlorine. Transcriptomic analysis was also done on cells after resuscitation in growth medium (TSB) for 30 min.

first: Grihalakshmi

last: Kakani

first: Suresh

last: Pillai


title: Genetic Adaptation of a Mevalonate Pathway Deficient Mutant in Staphylococcus aureus

city: Geneva

first: FRANCOIS

last: Patrice

state: Ge 4

address: Rue Gabrielle-Perret-Gentil, 4

department: Service of Infectious Diseases

country: Switzerland

institute: Genomic Research Laboratory

summary: In this study we addressed the question how a mevalonate (MVA)-auxotrophic Staphylococcus aureus ΔmvaS mutant can revert to prototrophy.

overall_design: Microarray was used to evaluate alteration in the transcriptome between wild type strain HG001 and its mvaS deleted mutant

first: Sebastian

last: Reichert

first: Patrick

last: Ebner

first: Eve-Julie

last: Bonetti

first: Arif

last: Luqman

first: Mulugeta

last: Nega

first: Jacques

last: Schrenzel

first: Cathrin

last: Spröer

first: Boyke

last: Bunk

first: Jörg

last: Overmann

first: Peter

last: Sass

first: Patrice

last: François

first: Friedrich

last: Götz


title: Effect of short-term prescription opioids on DNA methylation of the OPRM1 promoter

city: Memphis

first: Jose Vladimir

last: Sandoval Sierra

state: TN

address: 66 North Pauline street

department: Preventive Medicine

institute: UTHSC

type: Methylation profiling by genome tiling array

summary: Evaluate the effect of short-term use of precribed  opioids on DNA methylation

overall_design: Genome-wide DNA methylation was assayed in a cohort of opioid-naïve participants who underwent standard dental surgery followed by opioid self-administration. Saliva samples were collected longitudinally before surgery (visit 1), and at two postsurgery visits at 2.7 ± 1.5 days (visit 2), and 39 ± 10 days (visit 3) after the discontinuation of opioid analgesics.

first: Khyobeni

last: Mozhui

first: Jose

last: Sandoval-Sierra


title: RNA exosome mutations in pontocerebellar hypoplasia alter ribosome biogenesis and p53 levels

city: Newcatle Upon Tyne

first: Helen

last: Griffin

address: William Leech Building, Floor 3, Medical School

country: United Kingdom

institute: Newcastle University

summary: The eukaryotic RNA exosome is a ubiquitously expressed complex of nine core proteins (EXOSC1-9) and associated nucleases responsible for RNA processing and degradation. Autosomal recessive mutations in EXOSC3, EXOSC8, EXOSC9 and the exosome cofactor RBM7 cause pontocerebellar hypoplasia and motor neuronopathy. To understand the importance of the exosome in neurodegeneration, we investigated the consequences of exosome mutations on RNA metabolism and cellular survival in zebrafish and human cell models. We observed that levels of mRNAs encoding p53 and ribosome biogenesis factors are upregulated in zebrafish lines with homozygous mutations of exosc8 or exosc9, respectively. In addition, exosome deficiency leads to increased levels of multiple non-coding RNAs (e.g. tRNAs, snoRNAs, scaRNAs). Consistent with higher p53 levels, mutant zebrafish have a reduced head size, smaller brain and cerebellum caused by an increased number of apoptotic cells during development. Downregulation of EXOSC9 in human cells leads to p53 protein stabilisation and G2/M cell cycle arrest. The work provides explanation for the pathogenesis of exosome-related disorders and highlights the link between exosome function, ribosome biogenesis and p53-dependent signalling.

sample_organism:
Danio rerio
Homo sapiens

platform_organism:
Danio rerio
Homo sapiens

overall_design: RNAseq case - control analysis of Human induced Neuronal Progenitor Cells (iNPCs) and CRISPR/cas9 Zebrafish embryos. Human fibroblasts with recessive mutations in EXOSC3, EXOSC8 or EXOSC9 and three different healthy contols were reprogrammed to iNPCs and sequenced with total RNAseq. Zebrafish embryos homozygous for CRISPR/cas9 induced mutations in exosc8 or exosc9 underwent total RNA sequencing along with three sets of non-mutant embyo controls. Sequencng was performed on three biological replicates of all samples across four lanes of an Illumina HiSeq 2500 platform.

first: Juliane

middle: S

last: Mueller

first: David

middle: T

last: Burns

first: Graeme

last: Wells

first: Benjamin

last: Munro

first: Claudia

last: Schneider

first: Rita

last: Horvath


title: Lack of Rybp in Mouse Embryonic Stem Cells Impairs Cardiac Differentiation

status: Public on May 29 2020

city: Munich

first: Alexander

last: Graf

address: Feodor-Lynen-Str. 25

department: Gene Center Munich

institute: Ludwig-Maximilians-Universität München

summary: Ring1 and Yy1 binding protein (Rybp) has been implicated in transcriptional regulation, apoptotic signaling and as a member of the polycomb repressive complex 1, it has an important function in regulating pluripotency and differentiation of embryonic stem cells (ESCs). Earlier, we had proved that Rybp plays an essential role in mouse embryonic and central nervous system development. This work identifies Rybp, as a critical regulator of heart development. Rybp is readily detectable in the developing mouse heart from day 8.5 of embryonic development. Prominent Rybp expression persists during all embryonic stages, and Rybp marks differentiated cell types of the heart. By utilizing rybp null ESCs in an in vitro cardiac differentiation assay, we found that rybp null ESCs do not form rhythmically beating cardiomyocytes (CMCs). Gene expression profiles revealed a downregulation of cardiac terminal and upregulation of germline-specific markers in the rybp null CMCs. Furthermore, transcriptome analysis uncovered a number of novel candidate target genes regulated by Rybp. Among these are several that are important in cardiac development and contractility such as Plagl1, Isl1, and Tnnt2. Importantly, forced expression of rybp in rybp-deficient ESCs by a lentiviral vector was able to rescue the mutant phenotype. Our data provide evidence for a previously unrecognized function of Rybp in heart development and point out the importance of germ cell lineage gene silencing during somatic differentiation.

overall_design: Examination of the transcriptomic profile of wild type and Rybp null mutant ES cells and derived CMCs during in vitro cardiac differentiation.

first: Stefan

last: Krebs

first: Melinda

last: Pirity


title: Microarray analysis of c-Jun/JunB knockout mice treated with dithranol

status: Public on May 28 2020

city: Graz

first: Karin

last: Wagner

state: Styria

address: Stiftingtalstrasse 24

department: Molecular Biology

country: Austria

institute: Medical University Graz

summary: Ears of c-Jun/JunB knockout mice were topically treated with dithranol

overall_design: Mice carrying floxed alleles for the JunB and c-Jun locus and expressing the K5-CreERT transgene received consecutive i.p. injections of tamoxifen for a period of 5 days, leading to deletion of both genes in the epidermis by inducible Cre-recombinase activity. One week after the last injection, psoriasis-like lesions on the ears were treated daily with vehicle (Vaseline) or dithranol in series of increasing concentrations.

first: Theresa

last: Benezeder

last: Wolf


title: Compared gene expression profile of Lgr5-expressing and deficient stem cells in the intestine

city: Brussels

first: Frederick

last: Libert

address: 808 route de Lennik

department: IRIBHM

country: Belgium

institute: ULB

summary: The Lgr5 receptor is a marker of intestinal stem cells (ISCs) that regulates Wnt/b-catenin signaling. In this study, phenotype analysis of knockin/knockout Lgr5-eGFP-IRES-Cre and Lgr5-DTReGFP embryos revealed that Lgr5 deficiency during Wnt-mediated cytodifferentiation results in amplification of ISCs and early differentiation into Paneth cells, which can be counteracted by in utero treatment with the Wnt inhibitor LGK974. Conditional ablation of Lgr5 postnatally, but not in adults, altered stem cell fate towards the Paneth lineage. Together, these in vivo studies suggest that Lgr5 is part of a feedback loop to adjust the Wnt tone in ISCs. Moreover, transcriptome analyses revealed that Lgr5 controls fetal ISC maturation associated with acquisition of a definitive stable epithelial phenotype, that depends on the capacity of ISCs to generate their own extracellular matrix. Finally, using the ex vivo culture system, evidences are provided that Lgr5/Rspondin 2 interaction negatively regulates the pool of ISCs in organoids, revealing a sophisticated regulatory process for Wnt signaling in ISC.

overall_design: mRNA profiles of knockin/knockout Lgr5-eGFP-IRES-Cre and Lgr5-DTReGFP embryos versus heterozygous ISC at embryonic and adult stage.

first: Valeria

last: Fernandez Vallone

first: Morgane

last: Leprovots

first: Didac

last: Ribatallada-Soriano

first: Romain

last: Gerbier

first: Anne

last: Lefort

first: Frédérick

first: Gilbert

last: Vassart

first: Marie-Isabelle

last: Garcia


title: Regulation of RNA localization by FMR1

city: Aurora

first: Matthew

last: Taliaferro

state: CO

address: 12801 E 17th Ave, RC1 South Room 10403D

department: Biology

institute: University of Colorado Anschutz Medical Campus

summary: We use subcellular fractionation to probe the regulation of RNA localization by FMR1 in neuronal cells.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Examination of RNA abundances in soma and neurite compartments of wildtype and FMR1 null neuronal cells


title: A Multiplexed Barcodelet Single-Cell RNA-Seq Approach Elucidates Combinatorial Signaling Pathways that Drive ESC Differentiation

status: Public on May 26 2020

city: Boston

first: Richard

middle: I

last: Sherwood

state: MA

address: 77 Avenue Louis Pasteur

department: Division of Genetics, Department of Medicine

institute: Brighan and Women's Hospital and Harvard Medical School

summary:
Empirical optimization of stem cell differentiation protocols is time consuming, is labor intensive, and typi- cally does not comprehensively interrogate all relevant signaling pathways. Here we describe barcodelet sin- gle-cell RNA sequencing (barRNA-seq), which enables systematic exploration of cellular perturbations by tagging individual cells with RNA ‘‘barcodelets’’ to identify them on the basis of the treatments they receive. We apply barRNA-seq to simultaneously manipulate up to seven developmental pathways and study effects on embryonic stem cell (ESC) germ layer specification and mesodermal specification, uncovering combina- torial effects of signaling pathway activation on gene expression. We further develop a data-driven frame- work for identifying combinatorial signaling perturbations that drive cells toward specific fates, including several annotated in an existing scRNA-seq gastrulation atlas, and use this approach to guide ESC differen- tiation into a notochord-like population. We expect that barRNA-seq will have broad utility for investigating
Q2 and understanding how cooperative signaling pathways drive cell fate acquisition.

overall_design: Multiplexed transcriptome profiling of 32-384 distinct populations per experiment at single-cell resolution

first: Grace

middle: H

last: Yeo

first: Lin

last: Lin

first: Celine

last: Qi

first: Minsun

last: Cha

first: David

last: Gifford


title: RNA polymerase II elongation rate controls gene expression by alternative polyadenylation

city: Namur

first: Carlo

last: Yague-Sanz

address: 61 rue de Bruxelles

department: Medecine

institute: Namur University

summary:
To study the impact of the RNA polymerase II (Pol II) elongation rate on gene expression, we used CRISPR-Cas9 genome editing in S. pombe to generate a "slow" Pol II mutant with decreased elongation rate. Although the mutation is well tolerated as far as cell growth is concerned, transcriptomic analyses revealed that the slow mutant tends to terminate transcription prematurely. We distinguished two mechanisms by which premature termination affects gene expression in the slow mutant: It either (1) shortens 3'UTR, or (2) derepresses protein coding genes by prematurely terminating upstream interfering RNAs.
Strikingly, the genes affected by these mechanisms are enriched for genes involved in phosphate uptake and purine synthesis, two processes essential for the maintenance of the nucleotide pool of the cell. Together with evidences that nucleotides are conditional for Pol II processive elongation, our results suggest that Pol II elongation rate acts as both sensor and effector in response to nucleotide depletion.

overall_design: RNA-seq of Rpb1 N494D S. pombe mutant (2 independent clones) vs wild-type (parental strain)

first: Yann

last: Vanrobeays

first: Pierre-Étienne

last: Jacques

first: François

last: Bachand


title: IL-12 signaling contributes to the reprogramming of neonatal CD8+ T cells

status: Public on May 25 2020

city: Cuernavaca

first: Darely

middle: Yarazeth

last: Gutiérrez Reyna

state: Morelos

address: Av. Universidad 1001, Col. Chamilpa

department: Centro de Investigación en Dinámica Celular

country: Mexico

institute: Universidad Autónoma del Estado de Morelos

summary: Neonates are highly susceptible to intracellular pathogens, leading to high morbidity and mortality rates.  CD8+ T lymphocytes are responsible for the elimination of infected cells. Understanding the response of these cells to normal and high stimulatory conditions is important to propose better treatments for neonates. We have previously shown that human neonatal CD8+ T cells overexpress innate inflammatory genes and have a low expression of cytotoxic and cell signaling genes. To investigate the activation potential of these cells, we evaluated the transcriptome of human neonatal and adult naïve CD8+  T cells after TCR/CD28 signals +/- IL-12. We found that in neonatal cells, IL-12 signals contribute to the adult-like expression of genes associated with cell-signaling, T-cell cytokines, metabolism and cell division.  Additionally, IL-12 signals contributed to the downregulation of the neutrophil signature transcription factor CEBPE and other immaturity related genes. To validate the transcriptome results, we evaluated the expression of a series of genes by RT-qPCR and the promoter methylation status on independent samples.  We found that, in agreement with the transcriptome, IL-12 signals induced both the chromatin closure of neutrophil-like genes and the opening of cytotoxicity genes, suggesting that IL-12 signals contribute to the epigenetic reprogramming of neonatal lymphocytes. Furthermore, a high expression of some inflammatory genes was observed in naive and stimulated neonatal cells, in agreement with the high inflammatory profile of neonates to infections.  Altogether our results point to an important contribution of IL-12 signals to the reprogramming of the neonatal CD8+ T cells.

overall_design: Analysis of 3 biological replicates of RNA-seq data from naive human CD8+ T cells from neonate and adult donors,  in basal conditions and  stimulated for 36 hr with CD3/CD28 or CD3/CD28/IL-12.

last: Gutiérrez-Reyna

first: Alejandra

last: Cedillo-Baños

first: Linda

last: Kempis-Calanis

first: Oscar

last: Ramirez-Pliego

first: Denis

last: Puthier

last: Thieffry

first: Thomas-Chollier

last: Chollier

last: Medina-Rivera

first: Salvatore

last: Spicuglia

first: Angelica

last: Santana


first: Karin

last: Wagner

summary: Microarray analysis of dithranol-treated psoriasis lesions before, during and after therapy

overall_design: Psoriasis patients were daily topically treated with dithranol for 2-3 weeks; Clinical Trials.gov no. NCT02752672

first: Theresa

last: Benezeder

first: Peter

last: Wolf


title: Human-iPSC-Derived Cardiac Stromal Cells Enhance Maturation in 3D Cardiac Microtissues and Reveal Non-cardiomyocyte Contributions to Heart Disease

city: Leiden

first: Valeria

last: Orlova

address: Einthovenweg 20

institute: Leiden University Medical Center

summary: Cardiomyocytes (CMs) from human induced pluripotent stem cells (hiPSCs) are functionally immature, but this is improved by incorporation into engineered tissues or forced contraction. Here, we showed that tri-cellular combinations of hiPSC-derived CMs, cardiac fibroblasts (CFs), and cardiac endothelial cells also enhance maturation in easily constructed, scaffold-free, three-dimensional microtissues (MTs). hiPSC-CMs in MTs with CFs showed improved sarcomeric structures with T-tubules, enhanced contractility, and mitochondrial respiration and were electrophysiologically more mature than MTs without CFs. Interactions mediating maturation included coupling between hiPSC-CMs and CFs through connexin 43 (CX43) gap junctions and increased intracellular cyclic AMP (cAMP). Scaled production of thousands of hiPSC-MTs was highly reproducible across lines and differentiated cell batches. MTs containing healthy-control hiPSC-CMs but hiPSC-CFs from patients with arrhythmogenic cardiomyopathy strikingly recapitulated features of the disease. Our MT model is thus a simple and versatile platform for modeling multicellular cardiac diseases that will facilitate industry and academic engagement in high-throughput molecular screening.

overall_design: 101bp Paired-End sequencing, Hiseq4000 platform

first: Elisa

last: Giacomelli

first: Viviana

last: Meraviglia

first: Giulia

last: Campostrini

first: Amy

last: Cochrane

first: Xu

last: Cao

first: Ruben

last: van Helden

first: Ana

last: Krotenberg Garcia

first: Maria

last: Mircea

first: Sarantos

last: Kostidis

first: Richard

middle: P

last: Davis

first: Berend

last: van Meer

first: Carolina

last: Jost

first: Abraham

last: Koster

first: Hailiang

last: Mei

middle: G

last: Míguez

first: Aat

last: Mulder

first: Mario

last: Ledesma-Terrón

first: Giulio

last: Pompilio

first: Luca

last: Sala

first: Daniela

last: Salvatori

first: Roderick

last: Slieker

first: Elena

last: Sommariva

first: Antoine

last: de Vries

first: Martin

last: Giera

first: Stefan

last: Semrau

first: Leon

last: Tertoolen

first: Milena

last: Bellin

first: Christine

middle: L

last: Mummery


title: RNA-seq from human hepatic stellate cells treated with TGF-β

city: Rochester

first: Aditya

last: Bhagwate

address: 200 1st Street SW

institute: Mayo Clinic

summary:
Background and Aims: Transforming growth factor (TGF-β) induced activation of quiescent hepatic stellate cells (HSC) and their transformation to myofibroblasts is a key event in liver fibrosis and portal hypertension. GIPC (also referred to as synectin) is a downstream signal activation molecule of TGF-β and other receptors. In this study, we sought to identify novel genes targeted by TGF-β and GIPC and elucidate if and how they may contribute to liver fibrosis.
Methods and Results: We performed sequential mRNA sequencing analysis on TGF-β stimulated HSC and then on TGF-β-stimulated HSC in presence and absence of GIPC knockdown. IGFBP-3, an insulin growth factor transport protein, emerged as a top activation target of both TGF-β and GIPC, which was confirmed by qPCR, ELISA and Western blot (WB) analysis.  Targeted chromatin immunoprecipitation (ChIP) revealed that GIPC increases the histone 3 lysine 27 (H3K27) acetylation activating mark and concurrently decreases the H3K27 inhibitory trimethylation (H3K27m3) mark providing an epigenetic correlate to the gene regulation changes. In vivo, global knockout of IGFBP-3 mice resulted in attenuation of HSC activation markers and attenuation of portal pressure in response to chronic liver injury models.  Analysis of serum levels from cirrhotic patients also showed IGFBP-3 increase of more than 2-fold compared to healthy controls. Finally, in vitro mechanism studies revealed that IGFBP-3 promotes HSC migration through integrin dependent phosphorylation of AKT.
Conclusion: TGF-β upregulates IGFBP-3 through GIPC leading to increased HSC migration in vitro and promotes portal hypertension in vivo.  These studies support the role of IGFBP-3 as a potential pathophysiologic target or biomarker in chronic liver disease.

overall_design: next generation RNAseq data from human hepatic stellate cells treated with TGFb compared to non-treated hepatic stellate cells reveals IGFBP3 as one of the top target genes downstream of TGFb

first: Vijay

last: Shah

first: Usmann

last: Yaqoob


title: RNA-seq from human hepatic stellate cells treated with GIPC shRNA reveals contribution of GIPC to hepatic fibrosis

overall_design: next generation RNAseq data from human hepatic stellate cells with GIPC knockdown (GIPC shRNA) compared to controls shows that HSC activation/fibrosis pathway is differentially regulated by GIPC.


title: JAK2 inhibition in Philadelphia chromosome like acute lymphoblastic leukemia

city: Loma Linda`

first: Christian

last: Hurtz

address: 11085 Campus Street

department: Basic Science

institute: Loma Linda University

summary: CRLF2 rearranged Ph-like ALL cells are driven by oncogenic cytokine receptor signaling mediated by CRLF2 and JAK2. MHH-cALL4 cells were treated with ruxolotinib (JAK2 inhibitor) to provide insight into mechanisms of drug resistance.

overall_design: MHH-cALL4 cells were cultured in vitro in RPMI 20%FBS 1%Pen/Strep and treated either with DMSO or 1uM ruxolitinib for 12h.

last: Carroll

first: Sarah

last: Tasian


title: Gene expression profiles of human retinal microvascular pericytes (HRMVPC) and human lipoaspirate derived mesenchymal stromal cells (adipose stromal cells, ASC)

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

summary:
Comparative gene expression profiles of human retinal pericytes (HRMPC) and lipoaspirate derived mesenchymal stromal cells (adipose stromal cells, ASC) cultivated either in normal (1g/l) or high (4.5g/l) glucose medium to identify similarities and discrepancies and elucidate high glucose effects considering cell-based therapies in diabetic retinopathy. A hallmark of diabetic retinopathy is pericyte- dropout increased vascular permeability and progressive vascular occlusion.
ASC and HRMVPC were cultured in NG or HG for 7 days. Then cells were trypsinized, washed and RNA isolated using Qiagen RNeasy mini Kit (Qiagen, Hilden, Germany). RNA quality was tested by capillary electrophoresis on an Agilent 2100 Bioanalyzer (Agilent) and high quality (RNA integrity values ≥ 9) was confirmed.

overall_design: 3 biological replicates for each cell type.

first: Julia

last: Gebauer

first: Karen

last: Bieback


title: PLCG2 Regulates Divergent Microglial Functions via TREM2-Dependent and -Independent Signaling

status: Public on May 24 2020

city: South San Francisco

first: Thomas

last: Sandmann

email: genomics@dnli.com, sandmann@dnli.com

address: 161 Oyster Point Blvd

institute: Denali Therapeutics

summary: We use genetically engineered human iPSC-derived microglia-like cells (iMG) to show that TREM2 signals through PLCγ2 to mediate cell survival, phagocytosis, and lipid metabolism following myelin challenge. Loss of TREM2 or PLCγ2 signaling leads to a shared signature of transcriptional dysregulation that underlies these phenotypes. However, PLCγ2 also signals downstream of Toll-like receptors to mediate inflammatory responses in a TREM2-independent manner. Therefore, PLCγ2 activity regulates divergent microglial functions via distinct TREM2-dependent and -independent signaling and may be involved in the transition to a microglial state associated with neurodegenerative disease.

overall_design: Comparison of microglia differentiated from induced pluripotent stem cells (iPSCs) carrying homozyous deletions in theTREM2 or PLCG2 loci or the parental control line. A subset of samples were challenged with Zymosan particles.

first: Benjamin

middle: J

last: Andreone

first: Laralynne

last: Przybyla

first: Ceyda

last: Llapashtica

first: Anil

last: Rana

first: Sonnet

last: Davis

first: Bettina

last: van Lengerich

first: Karin

last: Lin

first: Ju

last: Shi

last: Mei

first: Giuseppe

last: Astarita

first: Gilbert

last: Di Paolo

first: Kathryn

middle: M

last: Monroe

first: Joseph

middle: W

last: Lewcock


title: Modelling rostro-caudal neural tube regionalization from human embryonic stem cells with a  microfluidic morphogenic gradient

city: Copenhagen

first: Gaurav

middle: Singh

last: Rathore

address: Department of Neuroscience Faculty of Health and Medical Sciences Blegdamsvej 3B, Building 7, 4th floor

department: Department of Neuroscience

country: Denmark

institute: University of Copenhagen

summary: Studies in animal models have been fundamental for understanding brain development but only a fraction of these findings have been validated in a human context. Here, we tissue-engineered a model (MiSTR) of human neural tube regionalization based on human embryonic stem cells (hESCs) and microfluidic cell culturing. By exposing differentiating hESCs to a WNT signalling gradient we mimicked early rostro-caudal neural patterning, and with >80% reproducibility generated a coherent tissue with progressive caudalization from forebrain over midbrain to hindbrain, including formation of isthmic organiser characteristics. Single-cell transcriptomics revealed that rostro-caudal organization was established already at 24 hours of differentiation, before expression of neural markers. Moreover, the transcriptomic hallmarks of rostro-caudal MiSTR organization accurately recapitulated gene expression patterns of the early rostro-caudal neural plate in mouse embryos. MiSTR thereby represents a novel in vitro model of human neurodevelopment to deconstruct and systematically analyze factors responsible for rostro-caudal neural tube patterning.

overall_design: Single-cell transcriptomics of an in vitro model of early human neural patterning, at various time points and dorsal and ventral locations.

first: Pedro

last: Rifes

first: Marc

last: Isaksson

first: Patrick

middle: A

last: kirk

first: Oliver

middle: K

last: Møller

first: Guido

last: Barzaghi

first: Julie

last: Lee

first: Kristoffer

last: Egerod

first: Dylan

last: Rausch

first: Malin

last: Parmar

first: Tune

last: Pers

last: Laurell

first: Agnete

last: Kirkeby


first: Valeria

last: Orlova

overall_design: 10X-based scRNA-seq data human induced pluripotent stem cell derived cardiomyocytes and 3D cardac microtissues. Two batches of cardiomyocytes (CM) and two batches of  3D cardiac microtissues (MT) differentiated from hiPSCs.

first: Elisa

last: Giacomelli

first: Viviana

last: Meraviglia

first: Giulia

last: Campostrini

first: Amy

last: Cochrane

first: Xu

last: Cao

first: Ruben

last: van Helden

first: Ana

last: Krotenberg Garcia

first: Maria

last: Mircea

first: Sarantos

last: Kostidis

first: Richard

last: Davis

first: Berend

last: van Meer

first: Carolina

last: Jost

first: Abraham

last: Koster

first: Hailiang

last: Mei

first: David

last: Míguez

first: Aat

last: Mulder

first: Mario

last: Ledesma-Terrón

first: Giulio

last: Pompilio

first: Luca

last: Sala

first: Daniela

last: Salvatori

first: Roderick

last: Slieker

first: Elena

last: Sommariva

first: Antoine

last: de Vries

first: Martin

last: Giera

first: Stefan

last: Semrau

first: Leon

last: Tertoolen

middle: V

first: Milena

last: Bellin

first: Christine

last: Mummery


title: The regulation and pharmacological modulation of immune complex induced type III IFN production by plasmacytoid dendritic cells

status: Public on May 23 2020

city: Uppsala

first: Pascal

last: Pucholt

address: Dag Hammarskjölds väg 20

department: Medical Science

institute: Uppsala University

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

overall_design: Refer to individual Series


title: Gene expression profiling of Splenic Marginal Zone Lymphoma

city: Omaha

first: Javeed

last: Iqbal

state: NE

address: 40th St

institute: University of Nebraska Medical Center

summary: Splenic marginal zone lymphoma (SMZL) is a rare, indolent non-Hodgkin’s lymphoma that affects 0.13 per 100,000 persons annually. Overall survival of SMZL is estimated to reach 8 to 11 years in most cases, but up to 30% of SMZL cases develop aggressive presentations resulting in greatly diminished time of survival. SMZL presents with a very heterogeneous molecular profile, making diagnosis problematic and accurate prognosis even less likely. The study herein has utilized this data to assist in identifying a potential diagnostic gene expression signature with highly specific predictive utility for further evaluation among control and SMZL patient samples. Delineation of a unique SMZL signature that could provide diagnostic utility for a malignancy that has historically been difficult to identify. These results should be further investigated and validated in subsequent molecular investigations of SMZL so it may be potentially incorporated into standard oncology practice for improving the understanding and outlook for SMZL patients.

overall_design: Affymetrix U133 plus 2.0 array profiling was performed according to the manufacturer's directions on RNA extracted from cryopreserved lymphoma tumor specimens


title: FoxO targets in Tsc1-deficient cells under normal food and nutrient restriction food

city: Zurich

first: Avantika

last: Gupta

state: Zurich

address: Otto-Stern-Weg 3

department: Institute of Molecular Systems Biology

institute: ETH Zurich

summary: Exploring downstream regulation by the transcription factor FoxO is necessary to understand its function as a tumor suppressor or promoter in different biological contexts. Here, we employed RNA-seq profiling on single clones isolated using laser capture microdissection from Drosophila larval eye imaginal discs to identify FoxO targets that restrict the proliferation of Tsc1-deficient cells under nutrient restriction (NR).

overall_design: Four single clones each were microdissected for isogenic control and Tsc1 mutant cells, with or without foxo knockdown, from larvae raised on normal food and NR. 31 cDNA libraries with sufficient material were sequenced. Differential gene expression analysis was performed on 29 samples that passed quality control.

first: Hugo

last: Stocker


title: Contrasting inflammatory signatures in peripheral blood and bronchoalveolar cells reveal compartment-specific effects of HIV infection

city: Durban

first: Daniel

last: Muema

address: 719 Umbilo Road

country: South Africa

institute: Africa Health Research Institute

summary: The mechanisms by which HIV increases susceptibility to tuberculosis and other respiratory infections are incompletely understood. We used transcriptomics of paired whole bronchoalveolar lavage (BAL) fluid and peripheral blood mononuclear cells to compare the effect of HIV at the lung mucosal surface and in the peripheral blood. The large majority of HIV-induced differentially expressed genes (DEGs) were specific to either the peripheral or lung mucosa compartments (1,307/1,404, 93%). Type I interferon signaling was the dominant signature of DEGs in HIV-positive blood with a less dominant and qualitatively distinct type I interferon gene set expression pattern in HIV-positive BAL. DEGs in the HIV-positive BAL were significantly enriched for infiltration with cytotoxic CD8+ T cells. Higher expression of representative transcripts and proteins in BAL CD8+ T cells during HIV infection, including IFNG (IFN-), GZMB (Granzyme B) and PDCD1 (PD-1), was confirmed by cell-subset specific transcriptional analysis and flow cytometry. Thus, we report that a whole transcriptomic approach revealed qualitatively distinct effects of HIV in blood and bronchoalveolar compartments. Further work exploring the impact of distinct type I interferon programs and CD8+ T cells infiltration of the lung mucosa during HIV infection may provide novel insights into HIV-induced susceptibility to respiratory pathogens.

overall_design: Transcriptional profilling of paired BAL and PBMCs samples from HIV negative and HIV positive individuals

first: Maphe

last: Mthembu

first: Thumbi

last: Ndung’u

first: Emily

middle: B

last: Wong


title: The regulation and pharmacological modulation of immune complex induced type III IFN production by plasmacytoid dendritic cells  [microarray]

summary: Objective: Patients with Systemic Lupus Erythematosus (SLE) have an ongoing interferon (IFN) production due to an activation of plasmacytoid dendritic cells (pDCs), which can be triggered to type I IFN synthesis by RNA containing immune complexes (RNA-IC). Considering emerging data suggesting a role of type III interferon (IFN) in the SLE disease process, we asked if RNA-IC can induce type III IFN production in pDC, and how this production can be regulated.  Methods:  Peripheral blood mononuclear cells (PBMCs) or immune cell subsets were isolated from healthy blood donors or SLE patients and stimulated with IC containing U1 snRNP and SLE-IgG (RNA-IC). Hydroxychloroquine (HCQ) and an interleukin receptor 1 associated kinase 4 inhibitor (IRAK4i) were added to cell cultures. Cytokine mRNA levels were determined with a microarray and protein levels with immunoassays. Single-cell RNA-sequencing of pDCs using ddSEQ technology was performed.   Results: Type III IFN mRNA and protein was induced in RNA-IC stimulated pDC-NK and pDC-B cell co-cultures. A subset of activated pDCs (3%) expressed both type III and type I IFN mRNA. IFN-λ2, IFN-α2b, interleukin (IL)-3, IL-6 or granulocyte-macrophage colony stimulating factor (GM-CSF) enhanced IFN-λ1/3 production 2-5-fold. HCQ and an IRAK4i blocked the RNA-IC-triggered IFN-λ1/3 production (p<0.01). IFN-α2b and GM-CSF increased the proportion of SLE patients producing IFN-λ1/3 in response to RNA-IC from 11 to 33%.   Conclusions: Type III IFN production is triggered by RNA-IC in pDCs in a TLR-MyD88-dependent manner, enhanced by NK and B cells as well as several pro-inflammatory cytokines. These results support a contributing role for both type I and type III IFNs in SLE, which needs to be considered when targeting the IFN system in this disease.

overall_design: RNA was isolated after 6 hours treatment of cells from two healthy individuals with RNA-IC or medium (mock).

first: Karin

last: Hjorton

first: Niklas

last: Hagberg

first: Maija-Leena

last: Eloranta

first: Lars

last: Rönnblom


title: The regulation and pharmacological modulation of immune complex induced type III IFN production by plasmacytoid dendritic cells [RNA-seq]

overall_design:
PDCs from two healthy blood donors (50 x 103cells/well) were stimulated with RNA-IC together with IFN-α2b (500 IU/ml) and IL-3 (1 ng/ml).

**Raw data not provided due to privacy concerns**


title: Characterization of radioresistant epithelial stem cell heterogeneity in the damaged mouse intestine

status: Public on May 22 2020

city: Tokyo

first: Taku

last: Sato

address: 1-5-45 Yushima Bunkyo-ku

department: Department of Biodefense Research

institute: Medical Research Institute, Tokyo Medical and Dental University (TMDU)

summary: The small intestine has a robust regenerative capacity, and various cell types serve as “cells-of-origin” in the epithelial regeneration process after injury. However, how much each population contributes to regeneration remains unclear. Using lineage tracing, we found that Lgr5-expressing cells’ derivatives contained radioresistant ISCs crucial for epithelial regeneration in the damaged intestine after radiation. Single-cell RNA sequencing analysis of Lgr5-derivatives identified primary source of epithelial regeneration in the irradiation damaged intetsine.

overall_design: Lgr5-EGFP-Ires-CreERT2: Rosa-lsl-tdTomato mice were injected with tamoxifen at 24 hrs before 10 Gy total body irradiation (TBI). Mice were sacrificed and prepared crypt epithelial cells 48 hrs after TBI. FCM sorted tdTomato+ Sca1- crypt epithelial cells were applied to single cell RNA-seq.

first: Miwako

last: Sase

first: Toshiaki

last: Ohteki


title: Transcriptomic comparison between LGR5 and POLI double tumor cell populations in CRC

city: Sabadell

first: Antoni

last: Berenguer-LLergo

state: Barcelona

address: Parc del Taulí, 1

department: A8G2 Group - Rheumatology Service

country: Spain

institute: Parc Taulí Research and Innovation Institute (I3PT)

summary: A transcriptomic comparative analysis was performed to explore and characterize in terms of gene expression and biological pathways the different LGR5 and POLI population from colorectal tumor xenografts.

overall_design: Colorectal cancer tumor organoids were knocked-in with fluorescent reporters to label LGR5 and POLR1A  populations. These modified organoids were injected and grown as subcutaneous tumor xenografts. Derived tumor were processed and the double LGR5 and POLI tumor cells populations (LGR5+/POL1high, LGR5+POL1low/LGR5-POL1high/LGR5-POL1low) were isolated and processed for transcirptomic analyses.

first: C

last: Morral

first: E

last: Batlle


title: Dek Modulates Global Intron Retention to Control Quiescence Exit in Muscle Stem Cells

city: Hong Kong

first: Tom

last: Cheung

address: Clear Water Bay, Kowloon

department: Division of Life Science

country: Hong Kong

institute: Hong Kong University of Science and Technology

summary: To identify Dek-associated RNA in muscle stem cells during quiescence to activation transition, we used Dek antibody to immunoprecipitated Dek-associated RNA from fresh-isolated quiescent muscle stem cell and profiled pull down by RNA-Seq.

overall_design: The input or DEK-immunoprecipitated RNA was sequencing using an BGISEQ-500RS (2 x 100).

first: Lu

last: Yue


title: A single-cell view on alga-virus interactions reveals sequential transcriptional programs and infection states

city: Taipei

first: Chuan

last: Ku

address: 128 Academia Road, Section 2, Nankang

department: Institute of Plant and Microbial Biology

country: Taiwan

institute: Academia Sinica

summary: We performed single-cell transcriptome analysis (using MARS-seq) for the worldwide-distributed microalga Emiliania huxleyi during infection by its specific coccolithovirus. Our results provide insights into the expression programs and infection strategies of the large virus, and highlight the potential of single-cell RNA-sequencing for microbial eukaryotes in the lab and in the field.

sample_organism:
Emiliania huxleyi
Coccolithovirus

platform_organism:
Emiliania huxleyi
Coccolithovirus

overall_design: Cells were sorted into 384-well plates at different hours post infection (hpi) for single-cell RNA-seq, including 2 plates for control culture, 10 plates for infected culture (0-24 hpi), 1 plate for infected culture pretreated with translation-inhibitor cycloheximide (6 hpi), and 2 plates for culture mock-infected with UV-deactivated virus.

first: Uri

last: Sheyn

first: Arnau

last: Sebé-Pedrós

first: Amos

last: Tanay

first: Shilo

last: Rosenwasser

first: Assaf

last: Vardi


title: Effect of adat2 silencing in Neurospora crassa on translation kinetics and transcriptome

city: Dallas

first: xueliang

last: lyu

address: 6001 Forest Park Road

department: Physiology

country: USA

institute: UT Southwestern Medical Center

summary: The silencing of tRNA-specific adenosine deaminase adat2 in Neurospora crassa abolished most of the I34 modification, resulting in major tRNA profile changes. The adat2 silencing caused genome-wide codon usage-biased ribosome pausing on mRNAs corresponding to changes in the tRNA profile, which reprograms translation elongation kinetics on ADAT-related codons. The ribosome profiling in this study was used to measure the effect of defective I34 modification of the eight tRNAs on translation kinetics during elongation stage. The accompanying mRNA-seq was used to normalize the ribosome profiling data using the same library construction protocol (reference to ARTseq™ Ribosome Profiling Kit (Catalog Number: RPYSC12116)) under the same growth condition. The independent mRNA-seq was used to measure the effect of I34 abolishment on transcriptome change using standard Illumina protocols. Meanwhile, to isolate the role of codon usage in translation elongation and protein level changes when adat2 is silenced, the independent mRNA-seq was also used to exclude the effect of mRNA level changes.

overall_design: The transcription profile and ribosome protected fragment (RPF) profiles of wild-type strain and adat2-silenced mutant of Neurospora crassa were generated by deep sequencing using Illumina sequencing platform.

first: Xueliang

last: Lyu

first: Yi

last: Liu


title: Transcriptome profiling of Dek over-expressed quiescent muscle stem cells in vivo

summary: To understand the molecular signatures of Dek over-expressed quiescent muscle stem cells in vivo, we isolated quiescent muscle stem cells by fixation using perfusion technique and profiled the transcriptome by RNA-Seq.

overall_design: The polyA+ RNA from satellite cells were sequenced using Illumina NextSeq 500 (2 x 75).

first: Raymond

last: Wan


title: iPS derived microglia like cells cultured with human neurons and astrocytes

city: Clayton

first: Jan

last: Schroeder

state: VIC

address: Building 75 Innovation Walk

department: Anatomy & Developmental Biology

country: Australia

institute: Monash University

summary: In this article, Jose Polo and colleagues molecularly compare existing microglia differentiation methods from stem cells, generate a new dual fluorescent and enzymatic reporter tool to study microglia in vitro and in vivo and show that human astrocyte/neuron co-culture pushes the regulatory landscape of in vitro microglia-like cells to more closely resemble bona fide microglia.

overall_design: RNA-seq experiment examination of iPS-derived microglia like cells cultured in presence (or not) of human astrocytes/neurons, or cholesterol

first: Jose

last: Polo

first: Alexandra

last: Grubman

first: Teresa

last: Vandekolk

last: Schröder

first: Guizhi

last: Sun

first: Cameron

last: Hunt

first: John

last: Haynes

first: Colin

last: Pouton


title: Nucleoporin 153 links nuclear pore complex to chromatin architecture by mediating CTCF and cohesin binding [RNA-Seq]

status: Public on May 21 2020

city: Durham

first: Eda

last: Yildirim

state: NC

address: DUMC Box 3709

department: Cell Biology

institute: Duke University School of Medicine

summary: Establishment of cell lineage specification, maintenance of cellular states and cellular responses to developmental cues rely on gene regulation and spatial genome organization during early development. Emerging data point to highly coordinated activity between epigenetic mechanisms that involve nuclear architecture, chromatin structure and chromatin organization. We show that the nuclear pore complex (NPC) basket protein, Nucleoporin 153 (NUP153) interacts with the nuclear architectural proteins, CTCF and cohesin, and mediates their binding across cis-regulatory elements in pluripotent mouse embryonic stem (ES) cells. NUP153 depletion results in altered occupancy of architectural proteins coupled with differential changes in transcription. This affect is most prevalent at the bivalent genes. To provide molecular insights onto NUP153-mediated gene regulation, we utilized Epidermal Growth Factor (EGF)-inducible immediate early gene (IEG) loci, which we identified as NUP153 targets. IEG transcription is regulated through a POL II pause-release mechanism. We provide evidence that NUP153 is critical for CTCF and cohesin occupancy and subsequent POL II recruitment to the IEG proximal-promoter sites during the paused state. In particular, establishment of a poised IEG chromatin environment relies on co-regulatory function of NUP153 and CTCF, which underlies efficient and timely IEG transcription at the NPC. Our results uncover a key role for the mammalian NPC in distribution of chromatin architectural proteins and demonstrate that NUP153 acts as a cis-acting factor that causally links the NPC to chromatin organization during transcription regulation.

overall_design: Examination of mouse ES mRNA profiles of WT and NUP153 KD cells.

first: Shinichi

last: Kadota

first: Jianhong

last: Ou

first: Yuming

last: Shi

first: Jiayu


title: Transcriptome high-throughput sequencing of ESRP1-overexpressing cells ESRP1-SKOV3

city: Changsha

first: Guanming

last: Deng

state: Hunan

address: 283 Tongzipo Road, Yuelu District

department: Gynecologic Oncology

country: China

institute: Hunan Cancer Hospital/the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University

summary: ESRP1 is an epithelial-specific splicing factor. It mainly regulates expressions of genes related to intercellular adhesion, actin cytoskeleton, cell polarity and cell migration at the post-transcriptional level by alternative splicing. It also plays an important role in the development and progression of cancers. This study analyzed the transcriptome changes of ESRP1 stably overexpression SKOV3 cells by high-throughput sequencing, discovered and validated the functional effects of ESRP1 on ovarian cancer cells

overall_design: We constructed ESRP1 stably overexpression cell line ESRP1-SKOV3 and control group EV-SKOV3 using lentivirus.Total RNA was extracted from ESRP1-SKOV3 and EV-SKOV3 after routine cell culture, three copies per group. After high-throughput sequencing of RNA from both groups, differentially expressed genes and alternative splicing differential genes were obtained.

first: Jie

last: Tang


title: Nucleoporin 153 links nuclear pore complex to chromatin architecture by mediating CTCF and cohesin binding (ChIP-Seq)

overall_design: DamID-Seq of NUP153 and ChIP-Seq of CTCF, SMC3 in undifferentiated mouse embryonic stem (ES) cells.

first: Jeannie T.

last: Lee


title: Nucleoporin 153 links nuclear pore complex to chromatin architecture by mediating CTCF and cohesin binding


title: RNAseq for CDK7 brown adipose tissue specific knockout mice under room temperature and 6 hrs cold exposure.

status: Public on May 20 2020

city: Lausanne

first: Rene

last: Dreos

state: VD

address: Ecublens

department: CIG

institute: UNIL

summary:
Purpose:  The goal of this study are to compare global gene expression profile in brown adipose tissue in Cdk7 bKO and WT control mice at both RT and after 6 hours cold exposure
Methods: Interscapular BAT pads were taken from 12-week-old CDK7 bKO and control littermates either at room temperature or after 6 hours of cold exposure with food. Mice were sacrificed at zeitgeber time 9. Total RNA was extracted with TRI Reagent (Sigma). Two RNA samples from two mice with same genotype and condition were pool together (each 250 ng) to constitute 500 ng of total RNA from biological triplicates (three WT-RT, three CDK7 bKO-RT, three WT-cold, and three CDK7 bKO-cold) for sequencing.
Results: Reads were also aligned to the Mus musculus.GRCm38.86 transcriptome using STAR (v. 2.5.2b, Dobin et al. 2013) and the estimation of the isoforms abundance was computed using RSEM (v. 1.2.31, Li and Dewey 2011).
Conclusions: Differentially expressed genes (DEGs) were identified between genotype and treatment.

first: Honglei

last: Ji

first: Lluis

last: Fajas


title: CDK7 adipose tissue specific knockout mice


title: RNAseq for perigonadal WAT of adipose tissue specific CDK7 knockout mice under CL or saline treatment for 7 days.

summary:
Purpose:  The goal of this study are to compare global gene expression profile in pgWAT in Cdk7 aKO and WT control mice after CL or saline treatment for 7 days.
Methods: pgWAT pads were taken from 9-week-old CDK7 aKO and control littermates either treated with CL or saline control for 7 days. Mice were sacrificed at zeitgeber time 9. Total RNA was extracted with TRI Reagent (Sigma). Two RNA samples from two mice with same genotype and condition were pool together (each 250 ng) to constitute 500 ng of total RNA from biological triplicates for sequencing.
Results: Reads were also aligned to the Mus musculus.GRCm38.86 transcriptome using STAR (v. 2.5.2b, Dobin et al. 2013) and the estimation of the isoforms abundance was computed using RSEM (v. 1.2.31, Li and Dewey 2011).
Conclusions: Differentially expressed genes (DEGs) were identified between genotype and treatment.

overall_design: pgWAT were taken from 9-week-old CDK7 aKO and control littermates either after CL or saline treatment for 7 days. Mice were sacrificed at zeitgeber time 9. Total RNA was extracted with TRI Reagent (Sigma). Two RNA samples from two mice with same genotype and condition were pool together (each 250 ng) to constitute 500 ng of total RNA from biological triplicates for sequencing.

first: Yizhe

last: Chen


title: Transcriptome of murine lumbar spinal cord at E12.5 in control and DOT1L cKO through Wnt1cre2 (B6.Cg-E2f1Tg(Wnt1-cre)2Sor/J, Jackson Laboratory #022501)

city: Freiburg im Breisgau

first: Angelica

last: Gray de Cristoforis

address: Albertstr. 19

department: Department of Molecular Embryology

country: Germany

institute: Albert-Ludwigs University Freiburg, Institute of Anatomy and Cell Biology

summary: DOT1L has a proven function in the cortical and cerebellar development of the mouse model, but has never been studied in the developing spinal cord. Here, we created a transgenic mouse line for Dot1l conditional knock-out in the  spinal cord over neurogenesis. We investigated the changes in the trascriptome by performing bulk RNAseq of lumbar spinal cords in controls and Dot1l-cKO. The DEG analysis of cKO littermates revealed a higher degree of differentiation profile as opposed to the controls, concurrent with decreased cell proliferation and altered axonal projection and interneuron migration, supporting the importance of DOT1L activity in the developing spinal cord.

overall_design: 10 mouse embryos (5 controls and 5 Dot1l-cKOs) from 2 litters at E12.5 (3 n per condition from the first, 2 n per condition from the second). Lumbar spinal cord isolation is followed by RNA extraction of single samples, library preparation and sequencing.

first: Francesco

last: Ferrari

first: Henriette

last: Franz

first: Frédéric

last: Clotman

first: Tanja

last: Vogel


title: Genome wide transcript analysis in Mouse embryonic fibroblasts where endogenous BRD4 is deleted

city: Bethesda

first: Dinah

middle: S.

last: Singer

state: MD

address: Building 10, Room 4B-17

department: Division of Cancer Biology

institute: National Cancer Institute

summary: The goal of this experiment was to find global transcriptional changes upon BRD4 deletion. We report significant changes in transcript profiles upon loss of BRD4.

overall_design: mRNA transcript profiles of  MEF cells with endogenous BRD4 (control) or BRD4 deleted (Cre)were generated using Illumina HiSeq in triplicate

first: Ballachanda

last: Devaiah


title: Synergism between IL7R and CXCR4 drives BCR-ABL induced transformation in Philadelphia chromosome-positive acute lymphoblastic leukemia

status: Public on May 19 2020

city: Ulm

first: Marc

last: Young

state: Baden-Württemberg

address: Albert-Einstein-Allee 11

department: Institute für Immunologie

institute: Universitätsklinikum Ulm

summary: Ph+ acute lymphoblastic leukemia (ALL) is characterized by the expression of an oncogenic fusion kinase termed BCR-ABL1. Here, we show that interleukin 7 receptor (IL7R) interacts with the chemokine receptor CXCR4 to recruit BCR-ABL1 and JAK kinases in close proximity. Treatment with BCR-ABL1 kinase inhibitors result in elevated expression of IL7R which enable the survival of transformed cells when IL7 was added together with the kinase inhibitors. Importantly, treatment with anti-IL7R antibodies prevents leukemia development in xenotransplantation models using patient-derived Ph+ ALL cells. Our results suggest that the association between IL7R and CXCR4 serves as molecular platform for BCR-ABL1 induced transformation and development of Ph+ ALL. Targeting this platform with anti-IL7R antibody eliminates Ph+ ALL cells including those with resistance to commonly used ABL1 kinase inhibitors. Thus, anti-IL7R antibodies may provide alternative treatment options for ALL in general and may suppress incurable drug-resistant leukemia forms.

overall_design: 6 individually generated control WT pre-B cell lines and 6 BCR-ABL-transformed pre-B cell counterparts were analyzed.

first: Hend

last: Abdelrasoul

first: Anila

last: Vadakumchery

first: Markus

last: Werner

first: Lennart

last: Lenk

first: Ahmad

last: Khadour

first: Omar

last: El Ayoubi

first: Fotini

last: Vogiatzi

last: Krämer

first: Vera

last: Schmid

first: Zhengshan

first: Yasar

last: Yousafzai

first: Gunnar

last: Cario

first: Martin

last: Schrappe

last: Müschen

first: Christina

last: Halsey

first: Medhanie

last: Mulaw

first: Denis

last: Schewe

first: Elias

last: Hobeika

first: Ameera

last: Alsadeq

first: Hassan

last: Jumaa


title: Skeletal muscle transcriptome profile in LLC mice model of cancer cachexia [miRNA-seq]

city: Botucatu

first: Geysson Javier

middle: Fernandez

last: Garcia

state: Sao Paulo

address: Departamento morfologia IBB UNESPRubiao Junior

country: Brazil

institute: UNESP

summary: Cancer cachexia is a metabolic syndrome with alterations in gene expression profile that consequently lead to skeletal muscle wasting. Here, we used RNA sequencing to analyze the microRNA expression profile in the tibialis anterior muscles of the Lewis lung carcinoma (LLC) model of cancer cachexia.

overall_design: Eight-week-old healthy C57BL/10 male mice were inoculated subcutaneously with a total of 1.5 x106 LLC cells (7.5 x 105 cells in 0.1 mL PBS, in each flank). Ten mice (control group) were injected with equal volumes of 1X PBS. LCC and control mice were studied after 22 days after LLC cells inoculation when the LLC group had developed overt cachexia.

first: Fernandez

last: Geysson

first: Carvalho

last: Robson


title: Skeletal muscle transcriptome profile in LLC mice model of cancer cachexia.

summary: Cancer cachexia is a metabolic syndrome with alterations in gene expression profile that consequently lead to skeletal muscle wasting. Here, we used RNA sequencing to analyze the mRNA expression profile in the tibialis anterior muscles of the Lewis lung carcinoma (LLC) model of cancer cachexia.

first: Robson

last: Carvalho

first: Geysson

last: Fernandez


title: Next Generation Sequencing of syncytializing first trimester human cytotrophoblasts.

city: Vienna

last: Knöfler

address: Währinger Gürtel 18-20, 5Q,

department: Department of Obstetrics and Gynaecology, Reproductive Biology Unit

institute: Medical University of Vienna

summary: Aim of this study was to monitor differentially expressed gene signatures of human first trimester villous cytotrophoblasts (vCTBs) undergoing spontaneous differentiation into syncytiotrophoblasts (STB).

overall_design: Villous cytotrophoblasts (vCTB) were isolated from of first trimester human pooled placentas (6-7th weeks of gestation), seeded onto fibronectin-coated cell culture dishes and analyzed after 20 and 72 hours. Examination of gene expression signatures of fusing cytorophoblasts was performed by Next Generation sequencing, the analyses contain in total 6 samples, 3 replicates of 3 individual cell preparations.

first: Gudrun

last: Meinhardt

first: Szabolcs

last: Hetey

first: Andras

last: Szilagyi


title: Comparison of CRISPR-Cas9 genome-edited JEG-3 YAP knockout  and wild type choriocarcinoma cells.

summary: The Hippo signalling-dependent co-activator YAP controls organ size by regulating cell proliferation, apoptosis, stem cell renewal and is involved in cell contact inhibition. Aim of this study was to identify human trophoblast-specific YAP regulated gene signatures by comparing YAP wilde type and YAP knock out JEG-3 coriocarcinoma cell lines. YAP knockout cell lines were established by CRISPR-Cas9 technology.

overall_design: To investigate gene expression signatures of CRISPR-Cas9 genome-edited YAP  knock out JEG-3 choriocarcinoma cell lines Next Generation Sequencing was performed. In total 12 samples, 2 JEG-3 YAP wilde type and 4 JEG-3 YAP knock out cell lines were analyzed in duplicates.


title: Next Generation Sequencing of first trimester human cytotrophoblasts expressing a constitutively active mutant (5SA) of the transcriptional co-activator YAP.

summary: Aim of the study was to elucidate YAP-regulated trophoblast-specific genes by analyzing differentially-expressed gene signatures between first trimester human cytotrophoblasts (vCTBs) transfected with a YAP-5SA mutant or a control plasmid.

overall_design: To examine gene expression patterns of human trophoblasts expressing constitutively active YAP 5SA Next Generation Sequencing was performed. vCTBs, isolated from pooled placentas from 6-8th weeks of gestation, were transfected with pCMV-flag YAP2 -5SA or as control with pcDNA 3.1(-)plasmid DNA using electroporation following 24h cultivation on fibronectin-coated cell culture dishes. The analyses comprise in total 6 samples, 3 replicates of 3 individual trophoblast cell preparations.