title: Airborne particulate matter from goat farm   increases acute allergic airway responses in mice   increases acute allergic airway responses in mice

city: Leiden

first: Rob

last: Mariman

address: Zernikedreef 9

institute: TNO

summary:
Background: Inhalation exposure to biological particulate matter (BioPM) from livestock farms may provoke exacerbations in subjects suffering from allergy and asthma. The aim of this study was to use a murine model of allergic asthma to determine the effect of BioPM derived from goat farm on airway allergic responses
Methods: Fine (< 2.5 μm) BioPM was collected from an indoor goat stable. Female BALB/c mice were ovalbumin (OVA) sensitized and challenged with OVA or saline as control. The OVA and saline groups were divided in sub-groups and exposed intranasally to different concentrations (0, 0.9, 3, or 9 μg) of goat farm BioPM. Bronchoalveolar lavage fluid (BALF), blood and lung tissues were collected.
Results: In saline-challenged mice, goat farm BioPM alone induced a dose-dependent increase in neutrophils in BALF and induced production of macrophage inflammatory protein-3a). In OVA-challenged mice, BioPM significantly enhanced 1) inflammatory cells in BALF, 2) OVA-specific Immunoglobulin (Ig)G1, 3) interleukin-23 production, 4) airway mucus secretion-specific gene expression. RNAseq analysis of lungs indicates that neutrophil chemotaxis and oxidation-reduction processes were the representative genomic pathways in saline and OVA-challenged mice, respectively.
Conclusions: A single exposure to goat farm BioPM enhanced airway inflammation in both saline and OVA-challenged allergic mice, with neutrophilic response as Th17 disorder and eosinophilic response as Th2 disorder indicative of the severity of allergic responses. Identification of the mode of action by which farm PM interacts with airway allergic pathways will be useful to design potential therapeutic approaches.

overall_design: Lung mRNA profiles of C57BL/6 old wild type were generated by Next-Generation Sequencing (n=5 per experimental group) using the Illumina Nextseq

first: Mariman

last: Rob

first: Liu

last: Dingyu


title: Elevated EGFR signals in epithelial cells delay mammary gland development and skew organoids away from stem cell signatures

status: Public on Aug 01 2020

city: San Francisco

first: Jeroen

middle: P.

last: Roose

state: CA

address: 513 Parnassus Ave.

department: Anatomy

country: USA

institute: University of California, San Francisco

type: Expression profiling by high throughput sequencing

summary: During puberty, robust morphogenesis occurs in the mammary gland and mammary stem- and progenitor- cells develop into mature basal- and luminal-cells to form the ductal tree. The receptor signals that govern this process in mammary epithelial cells (MECs) are incompletely understood. Here we focused on the EGF receptor and its downstream pathway component Rasgrp1, expressed in MECs. Rasgrp1-/- or point-mutated Rasgrp1Anaef MECs demonstrated increased activation of ERK-, AKT-, and S6- kinase pathways. Rasgrp1 perturbation delayed ductal tree maturation, accompanied by aberrant MEC proliferation and AKT signals. In colony formation- and 3D Matrigel- assays, loss of Rasgrp1 function leads to elevated progenitor cell proliferation and gain-of-function branching, both in EGFR-dependent manners. Our studies revealed that unbalanced EGFR signals in Rasgrp1-/- or Rasgrp1Anaef females did not impact the intrinsic ability to form basal and luminal cells, but that a Wnt-driven stem cell gene signature disappears when EGF is added to organoid assays.

overall_design: mRNA libraries were generated from wildtype (WT) and RasGRP1-/- mouse mammary epithelial cell organoids that were grown in media containing epidermal growth factor (EGF), EGF + (next generation surrogate Wnt) NGS-Wnt + R-spondin 2 (Rspo2), or NGS-Wnt + Rspo2. Three biological replicates were performed for each condition. mRNA libraries were sequenced using HiSeq4000 (Illumina).

first: Hanna

middle: M

last: Doh

middle: P

first: Joshua

middle: D

last: Rudolph

first: Andrea

middle: J

last: Barczak

first: Walter

middle: L

last: Eckalbar


title: Characterization of a Castrate Resistant Prostate Cancer Xenograft Derived from a Patient of West African Ancestry

city: Durham

first: Jennifer

last: Freedman

address: 905 South Lasalle Street

institute: Duke Cancer Institute

summary: Here we report the establishment and characterization of a Prostate Cancer Patient Derived Explant (PCPDX) from a patient of West African ancestry with metastatic castration resistant disease. The following data represents gene expression in a series of mice carrying this PCPDX and undergoing different treatment courses.  Mice were treated for 10 weeks with either Enzalutamide, Cisplatin, or Docetaxel, or appropriate vehicle controls.

overall_design: RNA sequencing of gene expression in mice with prostate cancer after standard of care treatment

first: Brendon

last: Patierno

first: Wen-Chi

last: Foo

first: Tyler

last: Allen

first: Jason

middle: A

last: Somarelli

first: Kathryn

middle: E

last: Ware

first: Santosh

last: Gupta

first: Sandra

last: Wise

first: John

first: Xiaodi

last: Qin

first: Dadong

last: Zhang

first: Lingfan

last: Xu

first: Yanjing

last: Li

first: Xufeng

last: Chen

first: Brant

last: Inman

first: Shannon

last: McCall

first: Jiaoti

last: Huang

first: Rick

last: Kittles

first: Kouros

last: Owzar

first: Simon

last: Gregory

first: Andrew

last: Armstrong

first: Daniel

last: George

first: Steven

middle: R

first: David

middle: S

last: Hsu


title: SPIN reveals genome-wide landscape of nuclear compartmentalization

city: Pittsburgh

first: Yuchuan

last: Wang

state: PA

address: 5000 Forbes Ave

institute: Carnegie Mellon University

summary: We develop a new computational method called SPIN (Spatial Position Inference of the Nuclear genome) to identify genome-wide chromosome localization patterns relative to multiple nuclear compartments. SPIN states correlations with other features of genome structure and function, such as Hi-C subcompartments, TADs (Dixon et al., 2012; Nora et al., 2012), histone modification, and DNA replication timing.

overall_design: Multi-fraction Repli-seq on K562 cell line.

first: Takayo

last: Sasaki

last: Gilbert

first: Jian

last: Ma


title: Transcription profiling by array of embryonic chick retina treated with Hes5.3 siRNAs, Atoh7 siRNAs and non-targeting siRNAs.

city: Geneva

first: Tania

last: Rodrigues

state: Geneva

address: 30 quai Ernest-Ansermet

country: Switzerland

institute: University of Geneva

summary: The microarray analysis was designed to test the effects of Hes5.3 siRNAs, Atoh7 siRNAs and non-targeting siRNAs on gene expression at the periphery of the expanding Hes5.3 domain in embryonic chick retina. For this microarray we collected retina samples 16 hours after electroporation to complete our previous analysis performed on samples collected 36 hours after RNA interference treatment (Chiodini et al., 2013).

overall_design: HH24 chicken retinas were electroporated with either Hes5.3 siRNAs, Atoh7 siRNAs or non-targeting siRNAs and a Hes5.3-RFP reporter plasmid. Retina fragments encompassing the peripheral fluorescent domain were micro-dissected under a stereoscopic microscope 16 hours after electroporation. For each biological replicate, RNA was isolated from fragments dissected from four retinas. For each of the three experimental conditions, 4 biological replicates were tested.

first: Jean-Marc

last: Matter


title: Two novel PLS-class pentatricopeptide repeat proteins are involved in the group II intron splicing of mitochondrial transcripts in the moss Physcomitrella patens

city: Nagoya

first: Chieko

last: Sugita

state: Aichi

address: Chikusa-ku Furo-cho

department: Center for Gene Research

country: Japan

institute: Nagoya University

summary: Pentatricopeptide repeat (PPR) proteins are RNA binding proteins that function in posttranscriptional regulation as gene-specific regulators of RNA metabolism in plant organelles. Plant PPR proteins are divided into four classes: P, PLS, E and DYW. The E- and DYW-class proteins are mainly implicated in RNA editing, whereas most of the P-class proteins predominantly participate in RNA cleavage, splicing and stabilization. In contrast, the functions of PLS-class proteins still remain obscure. Here, we report the function of PLS-class PpPPR_31 and PpPPR_9 in Physcomitrella patens. The knockout (KO) mutants of PpPPR_31 and PpPPR_9 exhibited slower protonema growth compared to the wild type. The PpPPR_31 KO mutants showed a considerable reduction in the splicing of nad5 intron 3 and atp9 intron 1. The PpPPR_9 KO mutants displayed severely reduced splicing of cox1 intron 3. An RNA electrophoresis mobility shift assay showed that the recombinant PpPPR_31 protein bound to the 5' region of nad5 exon 4 and the bulged-A region in domain VI of atp9 group II intron 1 while the recombinant PpPPR_9 bound to the translated region of ORF622 in cox1 intron 3. These results suggest that PLS-class PPR proteins may influence the splicing efficiency of mitochondrial group II introns.

overall_design: To characterize the function of a mitochondria-localized P-class PPR protein PpPPR_31 in Physcomitrella patens, gene expression of organellar genome of 4 day old protonema cells of PpPPR_31 KO mutants and wild type  were measured.

first: Mizuho

last: Ichinose

first: Airi

last: Ishimaru

first: Kensaku

last: Nakajima

first: Yasuhiro

last: Kawaguchi

first: Mamoru


title: Distinct waves from the hemogenic endothelium give rise to layered Lymphoid Tissue Inducer cell ontogeny [bulk RNA-seq]

city: Marseille

first: Serge

middle: Alexander

last: van de Pavert

address: 163 Av de Luminy, case 906

department: CIML

country: France

institute: Inserm

summary: LTi cells are part of the ILC family and essential for the formation of secondary lymph nodes within the embryo. This data set contains the analysis of lymphoid tissue (LTi) cell ontogeny, studied by expression profile analysis with RNA bulk sequencing of the populations associated with LTi ontogeny isolated from fetal liver vs. embryonic periphery at embryonic stage E13.5. They indicate a proliferating precursor population mainly in the fetal liver, while the embryonic periphery harbors the definitive lineage.

overall_design: E13.5 embryos from RORγt-eGFP mice were digested for 20 min at 37C with Liberase/DNase . All subsequent procedures were at 0–4°C. Cells were enriched using anti-CD45 microbeads and an AutoMACS magnetic cell separator according to manufacturer’s instructions and stained and sorted based on the presence of surface markers CD45, IL7Rα, α4β7, RORγt, CD4. Lineage positive cells were excluded using F4/80, CD3e, CD19, CD8a, Ly6G. Cell viability was evaluated using LIVE/DEAD™ Fixable Blue Dead Cell Stain Kit (Life Technologies). LTi cells and precursors were sorted using a FACSAria III. RNA was isolated using a RNA purification kit (Norgen Biotek Corp. 51800) and the quality and concentration of the RNA was determined with the bioanalyzer using RNA 6000 pico kit (Agilent 5067-1513) and Qubit fluorometer (ThermoFisher) using the Qubit dsDNA HS Assay Kit (ThermoFisher Q32854). Only those samples with a RIN value above 8 were used for subsequent library preparation. Samples were pre-amplified with the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech).

first: Milesa

last: Simic

first: Iris

last: Manosalva

first: Lionel

last: Spinelli


title: Discovery of small molecules that normalize the transcriptome and enhance cysteine cathepsin activity in progranulin-deficient microglia

status: Public on Aug 02 2020

city: Bar Harbor

first: Maria

last: Telpoukhovskaia

state: ME

address: 600 Main St

institute: The Jackson Laboratory

summary: Patients with frontotemporal dementia (FTD) resulting from granulin (GRN) haploinsufficiency have reduced levels of progranulin and exhibit dysregulation in inflammatory and lysosomal networks. Microglia produce high levels of progranulin, and reduction of progranulin in microglia alone is sufficient to recapitulate inflammation, lysosomal dysfunction, and hyperproliferation in a cell-autonomous manner. Therefore, targeting microglial dysfunction caused by progranulin insufficiency represents a potential therapeutic strategy to manage neurodegeneration in FTD. Limitations of current progranulin-enhancing strategies necessitate the discovery of new targets.To identify compounds that can reverse microglial defects in Grn-deficient mouse microglia, we performed a compound screen coupled with high throughput sequencing to assess key transcriptional changes in inflammatory and lysosomal pathways. Positive hits from this initial screen were then further narrowed down based on their ability to rescue cathepsin activity, a critical biochemical readout of lysosomal capacity. The screen identified nor-binaltorphimine dihydrochloride (nor-BNI) and dibutyryl-cAMP, sodium salt (DB-cAMP) as two phenotypic modulators of progranulin deficiency. In addition, nor-BNI and DB-cAMP also rescued cell cycle abnormalities in progranulin-deficient cells. These data highlight the potential of a transcription-based platform for drug screening, and advance two novel lead compounds for FTD.

overall_design: Primary mouse microglia (WT and Grn-/-) were treated with nor-BNI at 25 μM, DB-cAMP at 100 μM, or 0.1% DMSO vehicle control for 24 hours; RNA was isolated and sequenced from lysed samples.

first: Kai

last: Liu

first: Faten

last: Sayed

first: Jon

last: Iker Etchegaray

first: Min

last: Xie

first: Lihong

last: Zhan

first: Yaqiao

last: Li

first: Yungui

last: Zhou

last: Le

first: Ben

last: Bahr

first: Matthew

last: Bogyo

first: Sheng

last: Ding

first: Li

last: Gan


title: Chromatin-bound RNA in a DLBCL cell line, OCI-LY7

city: New York

first: Johannes

middle: C

last: Hellmuth

state: New York

address: 413 E 69th Street

institute: Weill Cornell Medicine

summary: We sequenced Chromatin-bound RNA (also known as ChromRNA-seq) to measure the transcriptional activity at enhancers.

overall_design: 3 biological replicates

first: Ari

last: Melnick


title: Host cell - V. vulnificus interactions

status: Public on Aug 03 2020

city: Daejeon

first: Jong Hwan

last: Kim

address: 125 Gwahak-ro, Yuseong-gu

department: Genome structure research center

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

summary: Dual transcriptome analysis of the V. vulnificus-infected human cells; To understand toxin-stimulated host-pathogen interactions, we set up dual transcriptome sequencing experiments using the human epithelial (HT-29) or immune (differentiated THP-1; dTHP-1) cells infected with the sepsis-causing pathogen Vibrio vulnificus, either in wild-type or the MARTX toxin-deficient backgrounds.

sample_organism:
Homo sapiens
Vibrio vulnificus MO6-24/O

platform_organism:
Homo sapiens
Vibrio vulnificus MO6-24/O

overall_design: HT-29 or dTHP-1 cells were infected with either wild-type or rtxA1 mutant V. vulnificus, and the total RNAs were extracted for sequencing

first: ByoungSik

first: Serry

last: Koh

first: MyungHee

first: Jong-Hwan

first: Seon-young


title: Single cell transcriptomics of index-sorted dendritic cell precursors from human peripheral blood

city: Newcastle upon Tyne

first: Anastasia

last: Resteu

address: M3.127, 3rd Floor Leech Building, Framlington Place

country: United Kingdom

institute: Newcastle University

summary: The transcriptomes of single cells from human perpheral blood were investigated at single cell level, with the aim to reconstruct the development of human dendritic cell (DC) lineages.

overall_design: 176 single cell transcriptomes were sampled from blood pre-DC populations and isolated into 96 well plates via fluorescence-activated cell sorting (FACS).

first: A

first: U

last: Cytlak

first: V

last: Bigley


title: scRNA-seq of P2 mouse cochlea

city: Baltimore

first: yang

last: song

state: MD

address: HSF-3, 3rd Floor; 670 W Baltimore St.

department: Department: Institute for Genome Sciences

institute: University of Maryland in Baltimore

summary: Age-related hearing impairment (ARHI), one of the most common medical conditions, is strongly heritable, yet its genetic causes remain largely unknown. We conducted a meta-analysis of GWAS summary statistics from multiple hearing-related traits in the UK Biobank (n = up to 323,978) and identified 31 genome-wide significant risk loci for self-reported hearing difficulty (p < 5e-8), of which 30 have not been reported previously at genome-wide significance. We interpreted these loci in the context of newly generated ATAC-seq and single-cell RNA-seq from cells in the mouse cochlea. Risk-associated genes were enriched for expression in cochlear epithelial and non-epithelial cells, as well as for genes related to sensory perception and known Mendelian deafness genes, supporting their relevance to auditory function. Regions of the human genome homologous to open chromatin in sensory epithelial cells from the mouse were strongly enriched for heritable risk for hearing difficulty, even after adjusting for baseline effects of evolutionary conservation and cell-type non-specific regulatory regions. Epigenomic and statistical fine-mapping most strongly supported 50 putative risk genes. Of these, at least 45 were expressed in mouse cochlea and 15 were enriched specifically in sensory hair cells. These results reveal new risk loci and risk genes for hearing difficulty and suggest an important role for altered gene regulation in the cochlear sensory epithelium.

overall_design: Examination of expression patterns of genes expressed in day 2 mouse cochlea.

first: Beatrice

last: Milon

first: Ronna

last: Hertzano

first: Seth

last: Ament


title: Single cell transcriptomics of index-sorted human bone marrow mature dendritic cells and precursors

summary: The transcriptomes of single cells from human bone marrow were investigated at single cell level, with the aim to reconstruct the development of human dendritic cell (DC) lineages.

overall_design: 266 single cell transcriptomes were sampled from CD34med/- pre-DC and mature DC populations of bone marrow and isolated into 96 well plates via fluorescence-activated cell sorting (FACS).


title: Extracellular vesicles from Heligmosomoides bakeri and Trichuris muris contain distinct small RNAs

city: Edinburgh

first: Amy

last: Buck

address: Ashworth Labs, Charlotte Auerbach Road

department: IIIR

institute: The University of Edinburgh

type: Non-coding RNA profiling by high throughput sequencing

summary: We report the small RNA content of extracellular vesicles (EVs) from adult parasite Trichuris muris and Heligmosomoides bakeri

sample_organism:
Trichuris muris
Heligmosomoides polygyrus bakeri

overall_design:
We purified EVs by ultracentrifugation from adult Trichuris muris and extracted RNA, treated with either Dnase and/or polyphosphatase or untreated. Small RNA libraries were prepared and sequenced also from H.bakeri EVs purified by size exclusion chromatography (Superdex 200 10/300 GL).
Third party re-analysis of GSM2885086 (miRNA T. muris exosomes rep 1, Tm_EvO_Un_1) and GSM2885087 (miRNA T. muris exosomes rep 2, Tm_EvO_Un_2).

first: Ruby

last: White

first: Sujai

last: Kumar

first: Franklin

last: Wang-Ngai Chow

first: Elaine

last: Robertson

first: Kelly

last: Hayes

first: Richard

middle: K

last: Grencis

first: María

last: Duque-Correa


title: RNA-sequencing analysis of forearm skin in diabetic patients with or without foot ulcerations

city: Boston

first: Aristidis

last: Veves

state: MA

address: 330 Brookline Ave

institute: Beth Israel Deaconess Medical Center

summary: Diabetic foot ulcers (DFUs) and associated impaired healing, represent a major problem, that significantly impairs the quality of life of diabetic patients, leading to prolonged hospitalization and resulting in more than 70,000 lower extremity amputations per year in the USA alone. In the present study, we prospectively followed a large group of DFU patients for 12 weeks and aimed to identify systemic and local factors that are associated with DFU healing.  We also studied healthy control subjects and diabetic patients without DFU and compared differences with the DFU patients. We first employed serum multiplex arrays to detect systemic cytokines, chemokines and growth factors, which correlate with DFU healing. In addition, we collected forearm biopsies for histology and bulk transcriptome analyses to establish whether DFU healing outcome was reflected at a non-ulcerative skin site. Bulk RNA-seq analysis revealed extracellular matrix (ECM) related genes up-regulated in Healers, including MMP2 as well as implication of IFNγ and IL13 as upstream regulators. According to transcriptome data analysis with a false discovery rate (FDR) <0.05 and log2 fold-change (log2FC) > 0.5, a total of 25 genes (3 up-regulated) were differentially  expressed when comparing Non-Healers and Healers, 916 (530 up-regulated) in Healers compared to DM and 160 (89 up-regulated) in Non-Healers compared to DM. Genes of interest that were increased in Healers include inflammation associated molecules lymphoid chemokine ligand 19 (CCL19), complement component 6 (C6), lipoprotein lipase (LPL) and beta-defensin 124 (DEFB124), as well as extracellular matrix linked proteins pigment-epithelium derived factor (SERPINF1), tenascin X (TNXB), biglycan (BGN) and matrix metalloproteinase-2 (MMP2). For Non-Healers, up-regulated genes were cytochrome P450 family member (CYP1A1), prostaglandin transporter (SLCO2A1) and metabolism regulator G0/G1 switch gene 2 (G0S2).

overall_design: mRNA profiles from skin isolated from the volar aspect of the forearm from 13 diabetic patients; 5 who healed their ulcers, 4 who didn't heal and 4 who had no ulcers.

first: Georgios

last: Theocharidis

first: Nikolaos

last: Patsopoulos


title: Coactivation of NF-kB and Notch signaling is sufficient to induce B cell transformation and enables B-myeloid conversion

city: Monrovia

first: Meiling

last: Jin

address: 1218 South Fifth Ave.

institute: City of Hope

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Comparison of chromatin accessibility between NF-kB and Notch coactivated marginal zone precursor (MZP) B cells and converted myeloid cells from these B cells

overall_design: NF-kB and Notch signaling were activated in CD19+ B cells by crossing ROSA26-NIKΔT3flSTOP and ROSA26-Notch2ICN mice with CD19-cre mice (TriB). MZPs from TriB mice were tranplanted into CD45.1 recipient mice. MZPs were converted into myeloid cells in some recipient mice. The MZPs and converted myeloid cells were used for chromatin accessibility (ATAC-seq) experiments.

first: Zhao

last: Chen


title: Liver cancer progression through increased miR-221 mediated tumorigenesis

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

summary: Hepatocellular carcinoma (HCC) is the third leading malignancy worldwide. MiR-221 have oncogenic functions and play a seminal role in carcinogenesis regulation including in high risk- human HCC. However, the molecular mechanism and biological functions of miR-221 has not been investigated thoroughly in HCC. In the present work, the role of miR-221 in HCC was evaluated using microarray and miR-221target genes expressions were analyzed in miR-221 inhibitor transfected HCC cell lines HepG2, Huh-7, WRL-68. Finally, we found that 89 upregulated and 52 downregulated genes by miR-221 in HCC cell lines.l

overall_design:
Agilent Human  Whole Genome 8x60k Microarray: AMADID: 072363
miR-221 inhibitor transfected HCC cell lines HepG2, Huh-7, WRL-68

first: Maheshkumar

last: Kannan

first: Sridharan

last: Jayamohan

first: Rajesh

last: Moorthy

first: Mathan

last: Ganeshan

first: Antony

last: Velanganni


title: Gene expression analysis following depletion of LOXL2 in esophgeal cancer cells

city: Shantou

first: Xiu-Hui

last: Zhan

address: 22, Xinling Road

country: China

institute: Shantou University

summary: Esophageal cancer is the sixth most common cause of cancer death globally, of which esophageal squamous cell carcinoma (ESCC) is the most common histological subtype. High level expression of LOXL2 has been shown to be associated with tumor metastasis and poor clinical outcome in ESCC. To determine whether there are genes whose expression in ESCC cells is regulated by LOXL2, next generation RNA sequencing analysis was used to compare the RNA expression profile of KYSE510 cells before and after silencing LOXL2 expression.

overall_design: RNA-sequencing of LOXL2 silencing and control ESCC KYSE510 cells was performed in triplicate using the BGISEQ-500 platform.

first: Ji-Wei

last: Jiao

first: En-Min

last: Li


title: Single cell transcriptomics of index-sorted human bone marrow CD34+ progenitors

first: Anastasia

last: Resteu

summary: The transcriptomes of single cells from human bone marrow were investigated at single cell level, with the aim to reconstruct the development of human dendritic cell lineages.

overall_design: 399 human bone marrow mononuclear cells were isolated into 96 well plates via fluorescence-activated cell sorting (FACS). CD34+ cells from the following phenotypic spaces were sequnced at single cell level: CD38-CD45RA-hematopoietic stem cells (HSC) and multipotent progenitors (MPP),   CD38+CD45RA- common myeloid progenitors (CMP), CD38-CD45RA+ lymphoid-primed multipotent progenitors (LMPP) and CD38+CD45RA+ granulocyte-macrophage progenitors (GMP).

first: A

first: U

last: Cytlak

first: V

last: Bigley


title: RNA-seq of goat mammary gland cells samples from different treatment groups

city: Qingdao

first: Yong

last: Zhao

state: Shandong

address: 700 Changcheng Road

department: College of Life Sciences

institute: Qingdao Agricultural University

summary: The goal of this project is to explore lncRNA55666 regulation goat mammary gland lipid metabolism. We tried to search the mechanism of lncRNA55666 regulation lipid metabolism. RNA-seq of goat mamamary gland cells samples from different groups: 5NC,  lncRNA55666 overexpression, 3NC, lncRNA55666 knockdown. The goat mammary gland cells were cultured in 3D condition. The cell were transfected with virus with lncRNA55666 gene (overexpression), or inhibition of lncRNA expression (lncRNA gene knockdown).

overall_design: RNA-seq of goat mammary gland cells samples from different groups: 5NC,  lncRNA55666 overexpression, 3NC, lncRNA55666 knockdown. The goat mammary gland cells were cultured in 3D condition. The cell were transfected with virus with lncRNA55666 gene (overexpression), or inhibition of lncRNA expression (lncRNA gene knockdown).

first: Dongxue

last: Ma

first: Lingjiang

last: Min


title: Genome-wide CRISPR knockout screen using GeCKO v2 to identify synthetic lethal interactions with the PARP inhibitor Olaparib

city: Munich

first: Tamas

last: Schauer

address: Feodor-Lynen-Straße 21

department: Institute of Epigenetics and Stem Cells

country: Germany

institute: Helmholtz Zentrum München

summary: In this study, a population of knockout cells was generated using the GeCKO v2 sgRNA library. The population of knockout cells was treated with the PARP inhibitor olaparib for 14 days. Over this time, knockout cells that were sensitive to olaparib treatment would die and a population of knockout cells that was resistant to olaparib treatment remained. Cells from olaparib and DMSO conditions and the sgRNA cassette in the knockout cells was amplified and sequenced to identify synthetic lethal or suppressor interactions with olaparib treatment.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: CRISPR screen using Human GeCKOv2 Library A or B comparing Olaparib and DMSO (control) treated Hela cells in 2 biological replicates.

first: Rebecca

last: Smith

first: Gyula

last: Timinszky


title: RiboTag analysis of Gfi1Cre/Cre and Gfi1Cre/+ cochlear and vestibular hair cells

first: yang

last: song

summary: In order to identify the transcriptional cascade downstream of the GFI1 repressor in inner ear hair cells, we performed a RiboTag-based expression analysis of Gfi1cre/cre mutant hair cells compared to their heterozygous controls. Through this analysis, we identified a significant downregulation of genes involved in normal hair cell development and function within the mutant hair cells, suggesting that in the absence of GFI1, the hair cells undergo a maturation arrest. Furthermore, the Gfi1 deficient hair cells displayed a significant upregulation of genes involved in neurodifferentiation and neuronal function.

overall_design: Comparison of the P0-P1 hair cell translatome of Gfi1 mutants and heterozygous controls by HA-tagged ribosome immunoprecipitation and RNA-seq. Cochlear and vestibular immunoprecipitated samples were compared in independent biological triplicates.

first: Maggie

last: Matern

first: Beatrice

last: Milon

first: Ran

last: Elkon

first: Yang

last: Song

first: Ronna

last: Hertzano


title: miRNA expression in CTRL1790 cells transfected with miR mimics

city: Rockville

first: Jeffrey

last: Robinson

state: United States

address: 9630 Gudelsky Dr

department: Translational Life Sciences Technology

institute: UMBC

summary: 800-plex Nanostring miRNA experession from CRL1790 cells transfected with miR mimics or no-transfection control.

overall_design: CRL1790 cells were grown to confluency on Millipore 1uM permeable membrane insert, transfected with miRNA mimics for c.elegans miR67, human miR142-3p, human miR155, human miR18b, and human miR890.  Specified samples below use the same extracted total RNA corresponding with the 250-plex expression panel “Sebelius2” reported in GEO series GSE132501, Corresponding raw data and sample identifiers are reported in fields below.

first: Sarah

last: Abey

first: Natnael

last: Kenea

first: Greg

last: Gonye

first: Wendy

last: Henderson


title: Activation of the Mitochondrial Stress Response in Clear Cell Renal Cell Carcinoma

first: Johannes

middle: C.

last: van der Mijn

state: NY

address: 1300 York Ave

department: Pharmacology

summary: Kidneys from our transgenic mouse model of early stage cancer of the kidney (TRACK) exhibit a mitochondrial stress response (MSR) signature, as indicated by increased mRNA for Atf4, a key transcription factor activated in the MSR, and increased transcripts of Atf4 targets, including Asns, Mthfd2, Trib3, Ddit3(Chop;Gadd153), Atf3, Ppp1r15a(Gadd34), Aldh1l2, Fgf21, and Slc20a1. By performing transcriptomics analyses from TRACK versus wild type (WT) kidneys after dietary vitamin A deprivation, we show that both vitamin A deficiency (VAD) and expression of constitutively active HIF1α intensify the MSR, redirect amino acids to one carbon metabolism, and facilitate the biosynthesis of reduced glutathione.

overall_design: We performed RNAseq on kidney cortex samples from transgenic mice with constitutive activation of HIF1A and wild type mice fed on a regular chow and vitamin A deficient diet

first: Lorraine

last: Gudas


title: SEAweb: The small RNA Expression Atlas on web

city: Hamburg

first: Maksims

last: Fiosins

address: Falkenried 94

department: Center for Molecular Neurobiology

institute: University Medical Center Hamburg-Eppendorf

summary: We determine Parkinson’s disease-specific blood biomarker signature using novel data.

overall_design: Peripheral blood samples were collected into PAXgene Blood RNA tube (PreAnalytiX) from consenting patients and healthy controls

first: Raza-Ur

last: Rahman

first: Ashish

last: Rajput

first: Claudia

last: Trenkwalder

first: Brit

last: Mollenhauer


title: Transcriptomic analysis of HOK following interaction with diploid and haploid Candida albicans strains

city: Singapore

first: Jaya

last: Seneviratne

address: 20 College Road

country: Singapore

institute: National Dental Centre

summary: A comprehensive RNASeq analysis was performed on Primary Human Oral Keratinocytes following their interaction with the haploid WT strain GZY903 and the diploid strain SC5314. Results imply the differential response of host to both strain types.

overall_design: Primary Human Oral Keratinocytes (HOK) were co-cultured with Haploid Wild type strain GZY903 and diploid wild type strain SC5314 at an MOI of 1 for 6 hours. Uninfected HOK were processed in parallel as controls. RNA was extracted from infected and uninfeted cultures for RNA Seq analysis.

first: Nityasri

last: Venkiteswaran

first: Chaminda


title: Effect of 6-azasteroids on Mycobacterium tuberculosis wild type and 6-azasteroid resistant mutants

city: Stony Brook

first: Xinxin

last: Yang

address: 100 Nicolls Road

department: Chemistry

institute: Stony Brook University

summary: Transcriptional profiling of Mycobacterium tuberculosis CDC1551 and 6-azasteroid resistant mutants ASR1 and ASR2 with treatment of 6-azasteroids, 4a and 6a, for 6 hours.

overall_design: Three different strains, wild type CDC1551 and two clones resistant to compound 6a, ASR1 and ASR2, were grown to OD~0.6 and treated with 30 μM of 4a or 6a or vehicle control for 6h. Total RNA was extracted and processed for RNAseq.

first: Nicole

last: Sampson


title: RNA-seq gene expression profiles of primary murine peritoneal mesothelial cells.

city: Cleveland

first: Thaddeus

last: Stappnbeck

state: OH

address: 9500 Euclid Ave

department: Inflammation and Immunity

institute: Cleveland Clinic, Lerner Research Institute

summary: Local factors produced in the tissue microenvironment play essential roles in promoting the ontogeny and phenotype of tissue resident macrophages (TRM). In the peritoneal cavity, large peritoneal macrophages (LPM) are the dominant TRMs that functionally mediate type 2 immunity, facilitate tissue repair of the mesothelium, and protect against peritoneal fibrosis.  It is established that retinoic acid derived from the omentum induces transcription factor Gata6 expression in LPMs, which in turn regulates gene expression of factors that define peritoneal macrophages. It is still unclear whether retinoic acid is the sole local factor that regulates Gata6 expression in LPMs.  Mesothelial cells line the entire peritoneal cavity and produce a protective, non-adhesive barrier against injury, at least in part by recruiting immune cells with secreted cytokines, such as M-CSF. We hypothesized that secreted factors from peritoneal mesothelial cells are also responsible for regulating LPM development including both ontogeny and function. Due to their immediate proximity to the peritoneal cavity, we propose that mesothelial cells can produce and secrete proteins into the peritoneum to maintain Gata6 expression by LPMs. To identify secreted factors that are highly and specifically expressed in mesothelial cells, we harvested primary mesothelial cells from 10-week-old C57BL/6 mice using FACS selection (CD45- PDPN+ GPM6a+).  Total RNA was isolated from these cells and subjected to RNA-seq analysis after depletion of ribosomal RNA.

overall_design: To measure mesothelial gene expression at homeostasis, 10-week-old C57BL/6 mice were sacrificed (n=4 animals).  Total peritoneal cells were isolated by trypsin digestion of the peritoneal cavity.  Primary mesothelial cells were sorted from the cell suspension on a FACS Aria II Flow cytometer, using CD45- Pdpn+ GPM6a+ gating.  Cells were sorted into DMEM + 10% FBS and stored on ice. Total RNA was extracted from the sorted mesothelial cells using the NucleoSpin RNA kit (Macherey-Nagel).  rRNA was depleted using Ribo-Zero kit. RNA libraries were prepared for sequencing using standard Illumina protocols at the Washington University Genome Technology Access Center (GTAC).

first: Lai

last: Chin-Wen

first: Brian

last: Muegge

last: Stappenbeck


title: Eomes broadens the scope of CD8 T cell memory by inhibiting apoptosis in low-affinity cells

city: Rijeka

first: Felix

middle: M.

last: Wensveen

address: Braće Branchetta 20

department: Histology & Embryology

country: Croatia

institute: University of Rijeka

summary: The memory CD8 T cell pool must select for high-affinity clones to efficiently counter re-infection yet must retain a level of clonal diversity to allow recognition of pathogens with mutated immuno-dominant epitopes. How this is mediated is unclear, especially in the context of a selective drive for antigen-affinity. We find that low-affinity memory exclusively depends on the transcription factor Eomes in the first days after antigen encounter. Eomes is induced at low activating signal strength and directly drives transcription of the pro-survival protein Bcl-2. At higher signal intensity T-bet is induced which suppresses Bcl-2, generating a survival advantage for low-affinity cells. High-affinity cells form memory independent of Eomes and have a proliferative advantage over low-affinity cells, which compensates for their survival deficit. Thus, we demonstrate on a molecular level how sufficient diversity of the memory pool is established in an environment of affinity-based selection.

overall_design: Examination of 2 different independent samples for 2 cell types.

first: Inga

last: Kavazović

first: Hongya

last: Han

first: Giulia

last: Balzaretti

first: Erik

last: Slinger

first: Niels

last: Lemmermann

first: Anja

last: ten Brinke

first: Doron

last: Merkler

first: Jan

last: Koster

first: Yenan

middle: T

last: Bryceson

first: Niek

last: de Vries

first: Stipan

last: Jonjić

first: Paul

last: Klarenbeek

first: Bojan

last: Polić

first: Eric

last: Eldering


title: mRNA expression analysis of bovine endometrial side and main population cells by using next generation sequencer

status: Public on Jul 31 2020

city: Nagoya

first: Ryoki

last: Tatebayashi

address: Furo-cho, Chikusa

department: Graduate school of Bioagricultual Sciences

institute: Nagoya University

summary: We report mRNA expression of side and main population cells derived from bovine endometrium during luteal phase. We aimed to identify mRNA expression differences between side and main population cells and provide the results that side population cells show stem cells like mRNA expression profiles.

overall_design: mRNA profiles of side and main population cells derived from bovine endometrial cells

first: Shuichi

last: Matsuyama


title: Integrin alpha-V drives pancreatic adenocarcinoma progression due to activation of TGF-β

city: Moscow

first: Sergey

last: Nikulin

address: 7, Vavilova st.

department: Faculty of Biology and Biotechnology

country: Russia

institute: HSE University

summary: In a previous study by our group, it could be shown that peritoneal selectins mediate the peritoneal spread of pancreatic ductal adenocarcinoma (PDA). In the absence of selectins, Integrin alpha-V (ITGAV) is upregulated in the remaining tumor spots. To study the relevance of ITGAV for PDA’s progression, a knockdown of ITGAV was generated using a shRNA-mediated approach in two PDA cell lines.

overall_design: Human PDA cells (cell lines BxPC3 and PaCa 5061) with (ITGAV) and without (LUC) shRNA mediated ITGAV knockdown were transplanted subcutaneously into mice. Total RNA was prepared from subcutaneous tumors.

first: Marius

last: Kemper

first: Alina

last: Schiecke

first: Hanna

last: Maar

first: Andrey

last: Poloznikov

first: Evgeny

last: Knyazev

first: Christoph

last: Krisp

first: Michael

last: Tachezy

first: Florian

last: Gebauer

first: Tobias

last: Lange

first: Kristoffer

last: Riecken

first: Alexander

last: Tonevitsky

first: Achim

last: Aigner

first: Guido

last: Sauter

first: Jakob

last: Izbicki

first: Udo

last: Schumacher

first: Daniel

last: Wicklein


title: Expression data from 16H and 24H post-stratification seeds from Arapidopsis thaliana pme36-1 and Col0 lines

city: AMIENS

first: Laurent

last: Gutierrez

address: 33 rue Saint Leu

institute: CRRBM-UPJV

summary: Pectins localize in the primary cell wall and consist of multiblock co?polymers among which homogalacturonan (HG) is the simplest and most abundant form. Methylesterification pattern of HG is tuned by pectin methylesterases (PMEs), which activity is itself controlled by specific inhibitors or PMEIs. PME?mediated regulation of HG methylesterification plays a major role in controlling several developmental processes, including seed germination and dark grown hypocotyl elongation. Arabidopsis PME36 is preferentially expressed during the late stages of silique development and, using the knock?out mutant pme36-1, we showed that PME36 is required to implement the characteristic pattern of demethylesterified pectins in mature seed. However, although this pattern was strongly impaired in pme36-1 mature seed, no phenotypical change was observed in the mutant during seed germination and seedling dark growth, suggesting the existence of a compensatory mechanism overcoming the defect in pectin demethylesterification. To get insight into this mechanism, a transcriptomic analysis by microarrays was performed on pme36-1 and Col0 wild-type, in seed at two early stages of germination, preceding tegument rupture: 16 hours and 24 hours after transfer from cold room (stratification) to dark growth condition.

overall_design: Affymetrix four-arrays strips (Arabidopsis Gene 1,1 ST Array strip) were used to analyse four replicates of 16H and 24H post-stratification seeds.

first: Gaëlle

last: Mongelard

first: Hervé

last: Demailly

first: Stéphanie

last: Guénin


title: Paracrine Ras/ERK signalling drives gene expression plasticity in a model of basal-like breast cancer

city: Davis

first: Celina

last: Juliano

state: California

address: 149 Briggs Hall

department: MCB

institute: University of California Davis

summary: The EGFR/Ras/ERK signalling pathway is a primary driver of cancer cell proliferation and metastasis in tumours that exhibit high cell-to-cell heterogeneity. While the signalling activity of this pathway is frequently amplified in tumours, it is not understood how the kinetic aspects of its activation in tumours differ from normal cellular signalling. We explored these single-cell kinetic differences using live-cell reporters of ERK signalling in the breast cancer progression series HMT-3522 and found that ERK activity in invasive cells is similar in amplitude to non-malignant cells but is highly dynamic and more disordered, leading to more heterogeneous expression of ERK target genes. We traced this variability to a high degree of amphiregulin-mediated autocrine signalling by invasive cells. Dynamic ERK activity could be transferred from invasive to pre-malignant cells through paracrine signalling in co-culture, and could drive temporal variation in the expression of genes including Fra-1, c-Myc, and Egr1 at the single-cell level. Our findings establish a mechanism for the generation of tumour cell plasticity, in which paracrine signalling in the microenvironment is translated into continually shifting diversity in gene expression profiles, helping drive the phenotypic heterogeneity of tumour cells.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Drop-seq analysis of HMT-3522 cell culture lines S1, T4 (10,212 cells, 5 samples total including 1 species mixing experiment)

first: Stefan

last: Siebert

last: Davies


title: DNA Methylation Profile in Human Cord Blood Mononuclear Leukocytes from Term Neonates: Effects of Histological Chorioamnionitis

city: Philadelphia

first: Zubair

middle: H

last: Aghai

address: 833 Chestnut Street, Suite 1201

department: Pediatrics/ Neonatology

institute: Thomas Jefferson University/ Nemours

type: Methylation profiling by genome tiling array

summary: Genome wide DNA methylation profiling of human cord blood mononuclear leokocytes (CBML) from neonates exposed to histological chorioamnionitis (HCA) compared to healthy neonates. The Infinium HumanMethylationEPIC BeadChip array was used to obtain DNA methylation profiles across 866,836 CpGs in five HCA and five control samples.

overall_design: Bisulphite converted DNA from the 10 samples (5 HCA + 5 healthy control) were hybridised to the Illumina Infinium HumanMethylationEPIC BeadChip

first: Gina

last: Fong

first: Suhita

last: Gayen nee’ Betal

first: Swati

last: Murthy

last: Favara

first: Joanna

last: Chan

first: Sankar

last: Addya

first: Thomas

last: Shaffer

first: Jay

last: Greenspan

first: Vineet

last: Bhandari

first: Dongmei

last: Li

first: Irfan

last: Rahman


title: The expression profiles of lncRNAs in hippocampus from mice with prenatal glyphosate exposure

city: HangZhou City

first: Hua

last: Ji

state: Zhejiang

address: No.481 Bingwen road

department: Department of Basic Medicine

institute: Hangzhou medical college

summary:
In this study, the lncRNAs expression pattern in hippocampus of postnatal day (PND) 28 mice offsprings which were exposured by glyphosate-based herbicide (GBH) during pregnancy and lactation was investigated.
LncRNA microarray had detected 840 upregulated and 919 downregulated lncRNAs in the PND28 mice offsprings' hippocampus

overall_design: In this study, the isolated total RNA taken from two pooled samples of two groups, was used to acquire expression profiles, and the result shows 1759 differentially-expressed lncRNAs, some of them are known to be involved in brain development or the pathogenesis of neurodevelopmental disorders, indicate that dysregulated expression of lncRNAs may be involved in the mechanism of glyphosate-induced neurotoxicity.

first: Xinli

last: Fan

first: Dawei

last: Wang


title: Blockade of MYCN-dependent transcription using orally-bioavailable CDK9 inhibitors

city: Belmont

first: Evon

last: Poon

state: Surrey

address: 15, Cotswold Road, Godstone Road

department: Clinical Studies

institute: Institute of Cancer Research

summary: Neuroblastoma is a common solid tumor that accounts for 15% of cancer deaths in children and amplification of the MYCN oncogene is the most common genomic alteration in aggressive tumors.  Although MYCN is expressed as a tumor-specific oncoprotein in poor-outcome neuroblastoma, making it a therapeutic target of great potential importance, no drugs with significant activity against MYCN or MYC are available for clinical use.  The aim of this study was to explore the sensitivity of neuroblastoma cells in vitro and in vivo to the tri-substituted purine CDK inhibitors, CYC065, chemical analogues of seliciclib, (Cyclacel Ltd).

overall_design:
Kelly, SKNAS, BE(2)C, and SH-SY-5Y neuroblastoma cell lines were analyzed in this study. Kelly, SKNAS cells, BE(2)C, and SH-SY-5Y (3 biological replicates) treated with CYC065 and compared with cells treated with the equivalent of DMSO (3 biological replicates). Total RNA was isolated from cells and tumor tissue using the RNAeasy plus minikit (Qiagen), labelled and hybridized to Gene Chip® human  transcriptome expression array (Affymetrix).
10 mice were analyzed in this study. 4 TH-MYCN tumors treated with CYC065 were compared with 6 untreated TH-MYCN tumors. Total RNA was isolated from cells and tumor tissue using the RNAeasy plus minikit (Qiagen), labelled and hybridized to Gene Chip® mouse transcriptome expression array (Affymetrix).

first: Louis

last: Chesler


title: Paternal nicotine exposure promotes hepatic fibrosis in offspring

city: Shanghai

first: Dong

last: Zhang

address: dongchuan road

institute: shanghaijiaotong university

summary: Paternal nicotine exposure can alter phenotypes in future generations. To explore whether paternal nicotine exposure affects the hepatic repair to chronic injury which would lead to hepatic fibrosis in offspring, we establish a paternal effect model based on nicotine exposure in mice.

overall_design: RNA profiles of the liver of 8-weeks old  F1-C(whose father were treated with saline) and F1-N(whose father were treated with nicotine) mice were generated by RNA sequencing.

first: Zhongdong

last: Qiao


title: Blood espression in Frailty and Robust patients

city: San Sebastián

first: David

last: Otaegui

state: Guipuzcoa

address: Paseo Dr begiristain s/n

department: Neurosciences

country: Spain

institute: Biodonostia Research institute

summary: Frailty is a geriatric syndrome that represents a state of vulnerability with increased risk of negative health outcomes. In the last years, independent studies attempted to identify biomarkers of frailty at biological level, but no consensus has been reached to date. In this work, we performed a transcriptomic analysis of 25 robust and frail community-dwelling individuals based on Timed Up and Go, Gait Speed and Tilburg Frailty Indicator scales. The comparison between individuals classified as frail or robust by the three tools revealed the expression of 35 transcripts associated with frailty status. These include genes linked to inflammation- and hypoxia-related pathways, immune response or microRNAs. Among them, additional analyses showed that the expression of a 3-gene pattern, increased EGR1 and reduced DDX11L1 and miR454, was able to identify frail individuals with an area under the curve (AUC) of 0.86

overall_design: 25 blood samples: NO replicates

first: A

last: Alberro

first: D

last: Matheu


title: Single cell transcriptomics and chromatin  accessibility in human fetal microglia

city: Groningen

first: Bart

last: Eggen

state: Groningen

address: Antonius Deusinglaan 1

department: Department of Biomedical Sciences

country: Netherlands

institute: UMCG Groningen

summary: Microglia, the myeloid cells of the central nervous system (CNS), are heterogeneous and exhibit distinct stages during mouse development; however, human microglia development is not elucidated. Here, single cell gene expression profiles of 15,782 human microglia and bulk chromatin profiles were assessed in 23 fetuses during development from gestational week (GW) 9 to 18. Microglia are highly heterogeneous at all developmental stages and exhibit transcriptional profiles similar to a phagocytic microglia phenotype associated with disease. Microglia start to mature during this developmental period and increasingly express homeostatic and sensome markers at later gestational stages. Concomitantly, chromatin accessibility increases in microglia from older fetuses with underlying transcriptional networks reminiscent of adult microglia. In conclusion, this work demonstrates that microglia already progress to a more mature, immune-sensing competent phenotype during early human fetal development, which might render microglia vulnerable towards environmental or inflammatory perturbations during early pregnancy.

overall_design: Single cell RNA sequencing was performed to obtain single cell transcriptomes of microglia from 20 fetal CNS samples derived during GW9-18 (GW9 n=4, GW10 n=3, GW11 n=3, GW12 n=3, GW13 n=1, GW15 n=3, GW16 n=1, GW17 n=1, GW18 n=1). Assay for transposase accessibility sequencing (ATACseq) was performed to obtain chromatin accessibility profiles of bulk microglia from 8 fetal CNS samples derived during GW9-18 (GW9 n=1, GW10 n=1, GW11 n=1, GW12 n=1, GW15 n=2, GW16 n=1, GW17 n=1).

first: Laura

last: Kracht

first: Malte

last: Borggrewe

first: Sharon

last: Eskandar

first: Nieske

last: Brouwer

first: Susana

last: Chuva de Sousa Lopes

first: Jon

last: Laman

first: Sicco

last: Scherjon

first: Jelmer

last: Prins

first: Susanne

last: Kooistra


title: Observation of the Changes in Chemokine-related Gene Expression of Endometriotic Cyst Stromal Cells by Three-dimensional Collagen Gel Culture

city: yufu

first: Ruofei

last: Zhu

institute: Oita University

summary: Endometriotic cyst stromal cells (ECSCs) were isolated from ovarian endometriotic cyst and cultured for 48 hours in the floating three-dimensional collagen gel culture or in the conventional two-dimensional culture. Total mRNAs were extracted and subjected to gene expression microarray.

overall_design: ECSCs were isolated from ovarian endometriotic cyst and cultured for 48 hours in the floating three-dimensional collagen gel culture or in the conventional two-dimensional culture. Total mRNAs were extracted with an RNeasy Mini kit (Qiagen, Valencia, CA, USA). Then, the samples were subjected to a gene expression microarray analysis with a commercially available human mRNA microarray (SurePrint G3 Human GE Microarray Kit 8x60K v2).


title: RNA sequencing of visceral fat tissue and E0771 tumor tissue harvested from WT and fat specific PD-L1 KO host

city: Washington

first: Rong

last: Li

state: DC

address: 2300 I Street

department: Biochemistry and Molecular Medicine

institute: The George Washington University

summary: To study the transcriptome differences of tumor transplanted into WT and KO host, E0771 tumors harvested from WT and KO host were extracted for total RNA and mRNA sequencing was performed. To study the transcriptome differences of WT and KO fat tissue, visceral fat tissue were harvested from obese WT and KO mice and total RNA was extracted and sequenced.

overall_design: Tumor and visceral fat tissue were harvested and snap frozen for total RNA extraction. mRNA library construction and seuqencing were performed.

first: Bogang

last: Wu

first: Huai-Chin

last: Chiang


title: Epigenetic and Expression Profiling of Tissue Selective Estrogen Compounds in Breast Epithelial Cell Lines (RNA-seq)

city: Burlington

first: Jonathan

middle: AR

last: Gordon

state: VT

address: 89 Beaumont Ave Given E209

department: Biochemistry

institute: University of Vermont

summary: Current approaches to menopausal hormone therapy consist of compounds which provide tissue specific beneficial effects while working to minimize any increase in cancer risk associated with replacement therapy.  In this study, an examination of the genomic distribution of histone modification and expression changes in two breast epithelial cell lines, the normal MCF10A cell line and the MCF-7 breast cancer cell line, upon treatment with several of the current therapies used for treating post-menopausal symptoms is presented. Analysis of the observed changes upon treatment with either 17-estradiol (E2), a combined treatment with the top 10 most abundant Premarin chemical equivalents (EC10), the non-steroidal SERM, Bazadoxifene (BZA) and the TSEC; BZA combined with EC10 (Duavee) or BZA combined with E2 provides evidence of expression changes in genes involved in DNA replication, nucleosome assembly, RNA-splicing and processing, biological regulation and cell signaling, and many of the known steroid response genes.  There were distinct global changes in chromatin states observed that were specific to each of the breast epithelial cell type normal, basal MCF10A and ESR/PGR positive luminal breast cancer MCF7 cell lines and selective changes observed upon treatment with each of the treatment groups.  Specifically, we observed a global loss of H3K4ac upon treatment with BZA.  These changes were observed in both ESR1 bound and non-bound regions suggesting modifications in both promoters and enhancer regions.  The levels of H3K4ac upon treatment of BZA showed a decrease below basal non-treated H3K4ac levels in MCF7.  There was an increase observed with E2 and EC10 treatment in MCF7 that was mitigated by the addition of BZA to either steroid as a combined treatment.  This study provides a better understanding of the role of epigenetic modifications in endocrine responsiveness and provides evidence of an improved therapeutic profile for combined TSEC compounds for treating and managing the overall physiological effects of declining estrogen.

overall_design: 6 drug treatments in 2 cell lines with 3 biological replicates

first: Terri

last: Messier

first: Joseph

last: Boyd

first: Gary

last: Stein


title: The nucleosome remodeling and deacetylase (NuRD) complex mediates the mitochondrial unfolded protein response and longevity in C. elegans

city: Beijing

first: Ye

last: Tian

address: No.1 West Beichen Road,Chaoyang District

institute: Institute of genetics and developmental biology

summary: Mitochondrial stress during development causes widespread changes in chromatin structure to promote mitochondrial unfolded protein response (UPRmt), perpetuating an early response across a lifetime results in lifespan extension. We found that the nucleosome remodeling and deacetylase (NuRD) complex interact with the transcription factor DVE-1 to initiate the global chromatin condensation and induce the UPRmt in animals experienced with mild mitochondrial dysfunction. The condensed chromatin structure can be well maintained into later life that is beneficial for lifespan extension. Moreover, overexpression of the core component of the NuRD complex is sufficient to induce the UPRmt response and longevity in C. elegans. Thus, a transient mitochondrial stress response during early development is established and propagated into later life through the NuRD-dependent chromatin remodeling pathway to extend lifespan.

overall_design: Comparison of gene expression changes in response to cco-1 RNAi treatment in N2 and lin-40(yth27) populations of C. elegans L4 animals

first: Di

first: Xueying


title: Ependymoma subpopulation lineages underlie clinical classification and outcome

city: Aurora

first: Andrew

middle: M

last: Donson

state: CO

department: Pediatrics

institute: CU Anschutz Medical Campus

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

overall_design: Refer to individual Series


title: Robust Hi-C maps of enhancer-promoter interactions reveal the function of non-coding genome in neural development and diseases

city: Cleveland

first: Xiaoxiao

last: Liu

state: Ohio

address: 10900 Euclid Ave

department: Genetics and Genomes Sciences

institute: Case Western Reserve University

summary: Genome-wide mapping of chromatin interactions at high resolution remains experimentally and computationally challenging. Here we used a low-input “easy Hi-C” protocol to map the 3D genome architecture in human neurogenesis and brain tissues and also demonstrated that a rigorous Hi-C bias-correction pipeline (HiCorr) can significantly improve the sensitivity and robustness of Hi-C loop identification at sub-TAD level, especially the enhancer-promoter (E-P) interactions. We used HiCorr to compare the high-resolution maps of chromatin interactions from 10 tissue or cell types with a focus on neurogenesis and brain tissues. We found that dynamic chromatin loops are better hallmarks for cellular differentiation than compartment switching. HiCorr allowed direct observation of cell-type- and differentiation-specific E-P aggregates spanning large neighborhoods, suggesting a mechanism that stabilizes enhancer contacts during development. Interestingly, we concluded that Hi-C loop outperforms eQTL in explaining neurological GWAS results, revealing a unique value of high-resolution 3D genome maps in elucidating the disease etiology.

overall_design: 3D genome structure mapping in human brain tissues using a newly designed easy Hi-C method

first: Paola

last: Giusti

first: Leina

last: Lu

first: Fulai

last: Jin

first: Patrick

last: Sullivan


title: Expression data from whole human skin samples

city: LYON

first: Jerome

last: Lamartine

address: 7 passage du Vercors

institute: Université Lyon I

summary:
Comparison of skin samples (neck skin, non photoexposed) from aged women with various perceived age
We used microarray to identify molecular markers of the perceived age

overall_design: 12 samples of skin from 12 women aged between 56 and 71 years old: 6 women with perceived aged higher than their real age (group 1, samples 1 to 6) and 6 women with a perceived age lower than their real age (group2, samples 7 to 12).


title: The effect of hydrostatic pressure in C. elegans

city: Tsukuba

first: Akira

last: Higashibata

state: Ibaraki

department: Department of Space Biology and Microgravity Sciences

institute: Japan Aerospace Exploration Agency

summary: We examined whether hydrostatic-pressure induced nuclear DAF-16 functions as a transcription factor. The expression changes were monitored by using DNA microarray analyses, after the WT adult hermaphrodites were exposed to a pressure of ≥30 MPa for 5 minutes. The results showed significant and reproducible increase of 31 genes after 30 minutes

overall_design: The hydrostatic pressure induced gene expression in  C. elegans was measured at 30 miniutes. after exposure to doses of  40 MPa 5 miniutes.

first: Atsushi

last: Higashitani

first: Naoshi

last: Watanabe


title: RNA-seq analysis of the DTA-injured retina

city: Minato-ku

first: Hideto

last: Koso

state: Tokyo

address: 4-6-1 Shirokanedai

institute: Institute of Medical Science, The University of Tokyo

summary:
The goal of this study is to identify genes upregulated in the DTA-injured retina.

Methods: Retinal mRNA profiles of control (DTAwt) and DTA (DTAmut) mice at day 1 and 5 post-injry were generated by deep-sequencing with Illumina sequencer.

Results: RNA-seq tags were mapped to the mouse mm9 reference genome assembly using Tophat2 ver. 2.0.8b, with FPKM values caluculated with Cufflinks ver. 2.1.1 with the default option.Comparison of the genes upregulated in the DTA-injured retina at day 1 and 5 revealed commonly upregulated genes as well as the genes specific to day 1 and 5.

Conclusions: Our study provides the detailed analysis of retinal transcriptomes in the DTA-injured retina.

overall_design: Retinal mRNA profiles of retina harvested from 8-week-old control (DTAwt) or DTA (DTAmut) mice at day 1 or 5 post-injury were generated by deep-sequencing with Illumina Sequencer.

first: Sumiko


title: Angiotensin IV mitigates diabetic cardiomyopathy via downregulating FoxO1-mediated autophagy

status: Public on Jul 30 2020

city: jinan

first: meng

last: zhang

address: Jinan 250012, Shandong, China

institute: Shandong University

summary:
Activation of the systemic and myocardial rennin-angiotensin-aldosterone system (RAAS) by hyperglycemia plays a critical role in the development of diabetic cardiomyopathy. To test the hypothesis that AngIV protects against diabetic cardiomyopathy via stimulation of AT4R and inhibition of overactive autophagy, diabetic mice were treated with low-, medium- and high-dose AngIV, AT4R antagonist divalinal, forkhead box protein O1 (FoxO1) inhibitor AS1842856 (AS) or their combinations. In vitro, cardiomyocytes were treated with different concentrations of glucose, low-, medium- and high-dose AngIV, divalinal, FoxO1-overexpression plasmid (FoxO1-OE), AS or their combinations.
The results showed that AngIV treatment dose-dependently attenuated left ventricular dysfunction, remodeling, fibrosis, and myocyte apoptosis in diabetic mice. Besides, autophagy and FoxO1 protein expression enhanced by diabetes were dose-dependently suppressed by AngIV treatment. However, these cardioprotective effects of AngIV were completely abolished by divalinal administration. Bioinformatic analyses revealed that the differentially expressed genes were enriched in autophagy, apoptosis, and FoxO signaling pathways among control, diabetes, and diabetes+high-dose AngIV groups. Similar to AngIV, AS treatment ameliorated diabetic cardiomyopathy in mice. In vitro, AngIV inhibited collagen expression, apoptosis, overactive autophagy flux, and FoxO1 nuclear translocation induced by high glucose in cardiomyocytes. However, these protective effects of AngIV were completely blocked by the use of divalinal or FoxO1-OE, and these detrimental effects were reversed by the additional administration of AS. In summary, AngIV treatment dose-dependently attenuated left ventricular dysfunction and remodeling in a mouse model of diabetic cardiomyopathy, and the mechanism involved stimulation of AT4R, suppression of FoxO1 nuclear translocation and inhibition of FoxO1-mediated overactive autophagy.

overall_design: Myocardial tissues were isolated from mice of negative control, diabetes mellitus, and diabetes mellitus+high-dose angiotensin IV groups;  four mice in each group

first: Meng

last: Zhang

first: Panpan

last: Hao


title: Transcriptomic and epigenomic dynamics associated with development of human iPSC-derived GABAergic interneurons

city: Atlanta

last: Escayg

state: GA

address: 615 Michael Street

department: Human Genetics

institute: Emory University

summary: GABAergic interneurons (GINs) are a heterogeneous class of inhibitory neurons that collectively maintain normal neuronal excitability and network activity. Identification of the genetic regulatory elements and transcription factors that contribute toward GIN function may provide new insight into the pathways underlying proper GIN activity, while also indicating potential therapeutic targets for GIN-associated disorders, such as epilepsy and schizophrenia. In this study, we examined temporal changes in gene expression and chromatin accessibility by collecting human iPSC-derived GINs at three time points for transcriptomic and epigenomic analysis: neural progenitor cells at 22 days post-differentiation (D22), then GINs at D50 and D78. Collectively, these data provide a resource for examining the molecular networks regulating normal GIN functionality.

overall_design: iPSCs independently derived from two healthy male controls (HC1 and HC2) were differentiated into GABAergic interneurons with 81-85% efficiency, and samples were collected at three points for RNA-seq and ATAC-seq: 22 days post-differentiation (D22), D50, and D78.

first: George Andrew

last: Inglis

first: Ying

last: Zhou

first: Dillon

middle: G

last: Patterson

first: Yanfei

last: Han

first: Christopher

last: Scharer

first: Jeremy

last: Boss

first: Zhexing

last: Wen


title: Pregnancy Downregulates Plasmablast Metabolic Gene Expression Following Influenza without Altering Long-Term Antibody Function

first: Lisa

last: Mills

address: 1600 Clifton Road

institute: CDC

summary: The normal response to influenza A infection is to remain asymptomatic; indeed, a study of volunteers who tested positive for antibodies against 2009 H1N1 revealed that a majority did not experience symptoms. However, studies of influenza pandemics since the 20th century, and to a lesser degree seasonal flu, suggest that pregnancy increases influenza-associated morbidity and mortality. The confounding effect of pregnancy has been well established to adversely alter the clinical course of influenza, with short term complications to mother and baby apparent, and long-term consequences to the fetus hypothesized. However, how the condition of pregnancy impacts long-term maternal anti-influenza immunity remains contentious; while vaccination studies suggest humoral responses sufficient for protection, published research on adaptive immune responses against influenza formed during pregnancy is limited. This study expands upon published work from our lab and others by comprehensively examining compartmental and systemic changes following pandemic A/California/07/2009 influenza infection. Previously, we linked seasonal influenza infection to clinical observations of adverse outcomes in pregnancy, enhanced lung and placental histopathology, and reduced control of viral replication in lungs of infected pregnant mothers. Here, we observe that the results of a lower infectious dose of pandemic influenza are similar to that of seasonal influenza. Importantly, we expand upon work which suggests infection during pregnancy may also affect humoral immunity. Our observations of reduced early antibody hemagglutinin inhibition and virus neutralization which resolved within 8 weeks of delivery demonstrate that influenza infection impacts antibody maturation mechanisms  without alterations to B cell frequency or antibody secretion. This hypothesis is further supported by plasmablast transcriptional data, which demonstrates downregulated B cell metabolism and post-translational modification systems only among pregnant animals. These findings corroborate a link between adverse pregnancy outcomes and severe pathology observed during influenza infection, and propose resolving humoral deficiencies following influenza infection confounded by pregnancy. Additional studies are required to specify the involvement of plasmablast metabolism with early humoral immunity abnormalities to best guide vaccination strategies and improve our understanding of the immunological consequences of pregnancy.

overall_design: On day 12 of pregnancy (determined by 20% weight gain and/or presence of a copulation plug), pregnant and non-pregnant BALB/c mice were lightly anesthetized with isoflurane and infected intranasally with 30 µl 0.5xLD50 of mouse adapted A/California/07/2009, approximately 30 plaque forming units (p.f.u.). 10,000 plasmablasts (CD138+B220int) were sorted from the spleens of pregnant and non-pregnant influenza virus infected mice at 10 days post infection. Single-end RNA sequencing was performed on samples in duplicate to increase sequencing depth (101 base pair reads). Sequencing was checked for quality using FastQC (Barbaham Institute, United Kingdom). Processing of single end reads was performed within the R programming language. The Rsubread package align function (Liao et al., 2019) was used to align single end reads to the Mus musculus genome (GRCm38.93). BAM files of duplicate samples were merged prior to the counting of reads for each gene using the featureCounts function of the Rsubread package. Differential gene expression analysis was performed in R using the DESeq2 package (Love et al., 2014). Gene set enrichment analysis (Subramanian et al., 2005) was performed as previously described in pre-ranked mode with the clusterProfiler package (Yu et al., 2012). RNA sequencing was performed by the Yerkes National Primate Research Center, Non-human Primate Genomics Core.

first: Dominika

last: Swieboda

first: Elizabeth

middle: Q

last: Littauer

first: Jacob

last: Beaver

first: Kattherine

last: Bricker

first: E

last: Esser

first: Olivia

last: Antao

first: Dahnide

last: Williams

first: Ioanna

last: Skountzou


title: The hepatocyte clock and feeding control chronophysiology of multiple liver cell types

city: Houston

first: Dongyin

last: Guan

state: TX

address: 1 Baylor Plaza, ABBR

institute: Baylor College of Medicine


title: RNAseq analysis of a genome-wide loss-of-function CRISPR/Cas9 library in haploid human embryonic stem cells (hESCs) differentiated into three germ layers

city: Jerusalem

first: Carmel

last: Braverman-Gross

address: The Edmond J. Safra Campus

country: Israel

institute: Hebrew University of Jerusalem

summary: Pluripotent stem cells can differentiate into all embryonic germ layers, a process that is orchestrated by the dissolution of pluripotency network and activation of pro-differentiation pathways. Yet, the genes essential for these cell fate transitions in human are still elusive. Here, we  used a genome-wide loss-of-function library established in haploid hPSCs  and differentiated  these cells into  into the three germ layers. We analyzed the transcriptome of the differentiated mutant library cells to assess their differentiation status, as well as to determine lineage-specific expression of essential genes for the differentiation of hESCs into each germ layer.

overall_design: hESCs were differentiated towards definitive endoderm, early mesoderm and neuroectoderm. For each germ layer, three biological replicates of differentiated and undifferentiated cells were analyzed.

first: Atilgan

last: Yilmaz

first: Nissim

last: Benvenisty


title: Transcriptome analysis of differentiated human embryonic stem cells (hESCs) upon CRISPR/Cas9-mediated mutagenesis of lineage-specific and common essential genes

summary: Pluripotent stem cells can differentiate into all embryonic germ layers, a process that is orchestrated by the dissolution of pluripotency network and activation of pro-differentiation pathways. We established a genome-wide loss-of-function library in haploid hPSCs and differentiated  these cells into the three germ layers.  The analyses of our high-throughput genetic screening revealed  germ layer-specific essential transcription factors, as well as common essential genes for the transition from pluripotency into the three embryonic germ layer fates. Here, we have generated individual knockouts of seven lineage-specific and four common essential genes in human embryonic stem cells by CRISPR/Cas9 mutagenesis and analyzed the transcriptomes of the mutants upon either directed or spontaneous differentiation.

overall_design: mutant and control hESCs were either specifically differentiated towards definitive endoderm, early mesoderm or neuroectoderm, or were allowed to undergo spontanaeos differentiation as embryoid bodies (EBs). Two or three biological replicates were analyzed for the differentiated and undifferentiated cells of each transcription factor mutant. EBs were harvested at two time points (after 5 and 10 days of differentiation), and one sample was analyzed for each time point for each common essential gene mutant.


title: ATAC-seq of wild type and Stat3-deficient or Rorgt-deficient Th17 cells

first: Chen

last: Dong

address: Haidian District

department: Institute for Immunology and School of Medicine

institute: Tsinghua University

summary: STAT3 has a more profound effect on chromatin accessibility regulation than RORgt during Th17 cell differentiation.

overall_design: Examination of chromatin accessibility changes in Stat3- or Rorgt-deficient Th17 cells cultured in vitro.

first: Dehui

last: Chang

first: Xiaohong

last: Zhao


title: DNAseq analysis of a genome-wide loss-of-function CRISPR/Cas9 library in haploid human embryonic stem cells (hESCs) differentiated into three germ layers

summary: Pluripotent stem cells can differentiate into all embryonic germ layers, a process that is orchestrated by the dissolution of pluripotency network and activation of pro-differentiation pathways. Yet, the genes essential for these cell fate transitions in human are still elusive. Here, we  used a genome-wide loss-of-function library established in haploid hPSCs  and differentiated  these cells into  into the three germ layers. We performed a genetic screening of the differentited library and identified genes that are essential for the differentiation of human pluripotent stem cells (hPSCs) towards ectoderm, mesoderm and endoderm.

overall_design: hESCs were differentiated towards definitive endoderm, early mesoderm and neuroectoderm. For each of the germ layers three biological replicates of differentiated cells and three biological controls of undifferentiated cells were analyzed.


title: RNA-seq analysis comparing transcriptome of wild type and transgenic sunlight-exposed hybrid poplar

status: Public on Jul 29 2020

city: Victoria

first: C. Peter

last: Constabel

state: British Columbia

address: 3800 Finnerty Rd

department: Biology

country: Canada

institute: University of Victoria

summary: We compared the transcriptome of MYB134 RNAi and wild-type hybrid poplars in order to identify differentially expressed genes in the RNAi plants.

overall_design: Three wildtype and three MYB134 RNAi transgenic poplar saplings were grown in the greenhouse (University of Victoria) for two months in 2017. For sunlight treatment, three wild type and three MYB134 RNAi transgenic poplars were moved outdoors and exposed to natural sunlight for two weeks in August 2017.

first: Dawei

last: Ma

first: Geraldine

last: Gourlay

first: C

middle: P


title: Transcriptomic profiles of whole blood from SARS-CoV-2 rhesus macaques

city: New York

first: Adam

last: Price

address: 722 West 168th St.

department: Center for Infection and Immunity

institute: Columbia University

summary: Total RNAseq profiling of whole blood collected longitudinally from 8 macaques infected with SARS-CoV-2

overall_design: Longitudinal host response profiling was performed to assess host responses associated with moderate COVID-19 pneumonia in a rhesus macaque model.

first: Angela

middle: L

last: Rasmussen


title: Amelioration of autism-like social deficits by targeting histone  methyltransferases EHMT1/2 in Shank3-deficient mice

city: Buffalo

first: Fengwei

last: Yang

address: 955 Main St

institute: University at Buffalo

summary: Many of the genes disrupted in autism are identified as histone-modifying enzymes and chromatin remodelers, most prominently those that mediate histone methylation/demethylation. However, the role of histone methylation enzymes in the pathophysiology and treatment of autism remains unknown. To address this, we used mouse models of haploinsufficiency of the Shank3 gene (a highly penetrant monogenic autism risk factor), which exhibits prominent autism-like social deficits. We found that histone methyltransferases EHMT1 and EHMT2, as well as histone lysine 9 dimethylation (specifically catalyzed by EHMT1/2), were selectively increased in the prefrontal cortex (PFC) of Shank3-deficient mice and autistic human postmortem brains. Treatment with the EHMT1/2 inhibitor UNC0642 or knockdown of EHMT1/2 in PFC induced a robust rescue of autism-like social deficits in Shank3-deficient mice, and restored NMDAR-mediated synaptic function. Activityregulated cytoskeleton-associated protein (Arc) was identified as one of the causal factors underlying the rescuing effects of UNC0642 on NMDAR function and social behaviors in Shank3-deficient mice. UNC0642 treatment also restored a large set of genes involved in neural signaling in PFC of Shank3-deficient mice. These results suggest that targeting histone methylation enzymes to adjust gene expression and ameliorate synaptic defects could be a potential therapeutic strategy for autism.

overall_design: Examination of 2 different histone modifications in Neural progenitor cells. histone methyltransferases in Shank3-deficient mice

first: Zi-Jun

last: Wang

first: Ping

last: Zhong

first: Kaijie

first: Ji-Seon

last: Seo

first: Zihua

last: Hu

first: Freddy

last: Zhang

first: Lin

last: Lin

first: Jie

first: Tao

last: Liu

first: Emmanuel

last: Matas

first: Paul

last: Greengard

first: Zhen

last: Yan


title: Custom DNA microarrays reveal the selective recognition of BMVC to MYC promoter G-quadruplex: a large-scale assessment of ligand binding selectivity

status: Public on Jul 28 2020

city: Bethesda

first: Desiree

last: Tillo

state: MD

address: 41 Center Dr, Room D310

institute: NIH/NCI

summary: G-quadruplexes (G4) are considered new drug targets for human diseases such as cancer. More than 10,000 G4s have been discovered in human chromatin, posing challenges for assessing the selectivity of a G4-interactive ligand. 3,6-bis(1-Methyl-4-vinylpyridinium) carbazole diiodide (BMVC) is the first fluorescent small molecule for G4 detection in vivo. Our previous structural study shows that BMVC binds to the MYC promoter G4 (MycG4) with high specificity. Here, we utilize high-throughput, large-scale custom DNA G4 microarrays to analyze the G4-binding selectivity of BMVC. BMVC preferentially binds to the parallel MycG4 and selectively recognizes flanking sequences of parallel G4s, especially the 3′-flanking thymine. Importantly, the microarray results are confirmed by orthogonal NMR and fluorescence binding analyses. Our study demonstrates the potential of custom G4 microarrays as a platform to broadly and unbiasedly assess the binding selectivity of G4-interactive ligands, and to help understand the properties that govern molecular recognition.

overall_design: Binding microarray experiments were performed for G-quadruplex (G4) DNA interacting small molecules pyridostatin (PDS), BMVC.  Briefly, the binding experiments involved incubating Cy5-conjugated PDS with unlabeled molecules (PDS and BMVC) to 180K feature Agilent microarrays pre-incubated with 100mM potassium chloride (KCl) in order to determine the binding preferences of the unlabelled molecules to G4-forming sequences.


title: Knockout LYCAT modulates altered gene expression profile in H2122 cells

city: Chicago

first: Mark

last: Maienschein-Cline

state: IL

address: 900 S Ashland Ave, Rm 1058, M/C 937

department: Research Resources Center

institute: University of Illinois at Chicago

summary:
We present the set of gene expression in in H2122 cells with transfection of control shRNA vs H2122 cells with transfection of LYCAT shRNA.
Methods: Cell mRNA profiles of H2122 control cells and H2122 LYCAT KO cells were generated by deep sequencing, in triplicate, using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two way ANOVA (ANOVA).

overall_design: H2122 with transfection of control shRN or LYCAT shRNA for 48 hours, the total cell mRNA from these cells were isolated and applied to array.

first: Longshuang

last: Huang

first: Rama

last: Kamesh

first: Viswanathan

last: Natarajan


title: Heterogeneous Origins and Functions of Mouse Skeletal Muscle Resident Macrophages

first: Gregory

middle: Robert

last: Smith

state: NY

address: 1 Gustave L. Levy Pl

department: Neurology

institute: Mount Sinai Hospital

summary: Tissue resident macrophages can arise from either embryonic or adult hematopoiesis and play important roles in a wide range of biological processes, such as tissue remodeling during organogenesis, tissue homeostasis in the steady state, tissue repair following injury, and immune response to pathogens. Although the origins and tissue-specific functions of resident macrophages have been extensively studied in many other tissues, they are not well characterized in skeletal muscle. In the present study, we have characterized for the first time the ontogeny of skeletal muscle resident macrophages, showing evidence that they arise from both embryonic hematopoietic progenitors, including yolk sac primitive macrophages and fetal liver monocytes, and adult bone marrow hematopoietic stem cells. Single cell-based transcriptome analysis revealed that skeletal muscle resident macrophages were highly distinctive from resident macrophages in other tissues, expressing a specific set of transcription factors and containing functionally diverse subsets correlating to their origins. They appear more active in maintaining tissue homeostasis and promoting muscle growth and regeneration.

overall_design: Skeletal muscle resident macrophages from quadriceps and diaphragm, as well as peritoneal macrophages and lung alveolar macrophages, of 8 weeks old C57 BL/6J mice were sorted by flow cytometry and were then subjected to single cell-based RNA sequencing.

first: Xingyu

first: Adwait

middle: A

last: Sathe

first: Frederique

last: Ruf-Zamojski

first: Venugopalan

last: Nair

first: Kory

middle: J

last: Lavine

first: Xing

last: Chao

first: Stuart

last: Sealfon

first: Lan

last: Zhou


title: High expressed genes enriched with H3K27me3 in maize genome [ChIP-seq]

city: Nanjing

first: tao

middle: shen

last: tong

address: Weigang street 1st

institute: Nanjing Agricultural University

summary: H3K27me3 usually enriched with low or no expressed genes in animal or plant genomes. However, some researches indicate that H3K27me3 can be enriched with high expressed genes in human genome. It's still unknown that whether this kind of gene is appeared in plant genomes and the mechanisms are also unclear. In this study，we used ChIP-seq to develop high resolution profiles of H3K27me3 distributions in several tissues or cell-types of maize to better understand the role of this mark in an important crop. The integration of ChIP-seq H3K27me3 profiles with RNA-seq and WGBS-seq data sets suggested that H3K27me3 may play diverse roles in regulation chromatin structure and function. We found that subsets of highly expressed genes are significantly enriched with H3K27me3 in maize. The profiles of several maize mutants reveal functional divergence for the control of H3K27me3 among maize genes. The analysis of existing rice and Arabidopsis data finds that a subset of highly expressed genes in these species are also associated with high levels of H3K27me3. Collectively, our analyses demonstrate that H3K27me3 alone or cooperating with DNA methylation and other chromatin features actively regulates subsets of gene expression, thereby providing new insights in diverse functions of H3K27me3 in plants.

overall_design: BS and M cell were used to exclude false positive genes. High expressed genes enriched with H3K27me3 and mez mutants were used to study correlation between H3K27me3 and gene expression levels. Root were used to identify tissue-specific enriched genes.

first: Wenli

last: Zhang

first: Shentong

last: Tao

first: Lifen

last: chen


title: A genome-wide CRISPR/Cas phenotypic screen for modulators of DUX4 cytotoxicity reveals screen complications

city: Utrecht

first: Niels

last: Geijsen

state: Utrecht

address: Uppsalalaan, 8

institute: Hubrecht institute

summary: In pursuit of unraveling the underlying mechanism of FSHD we performed a genome-wide CRISPR/Cas9 phenotypic rescue screen in an inducible DUX4 transgenic cell line (DIE) to identify modulators of DUX4-induced apoptosis.

overall_design: Inducible DUX4 cells were spin transfected with viral Brunello particles containing a construct with both a spCas9 and a sgRNA. Cells were than maintained and passaged for 6 days, before treating a portion of cells with doxycycline. The remaining untreated cells were harvested. After the 24h doxycyline treatment and a recovery period, surviving cells were harvested, genomic DNA extracted, and samples processed for seuqencing.

first: Ator

last: Ashoti

first: Francesco

last: Limone

first: Kevin

last: Eggan

first: Federica

last: Piccioni

first: Melissa

last: van Kranenburg

first: Anna

last: Arias


title: Transposase assisted tagmentation of RNA/DNA hybrid duplexes

city: Beijing

first: Chengqi

last: Yi

address: No.5 YiHeYuan Road

institute: Peking University

summary: Tn5-mediated transposition of double-strand DNA has been widely utilized in various high-throughput sequencing applications. Here, we report that the Tn5 transposase is also capable of direct tagmentation of RNA/DNA hybrids in vitro. As a proof-of-concept application, we utilized this activity to replace the traditional library construction procedure of RNA sequencing, which contains many laborious and time-consuming processes. Results of Transposase assisted RNA/DNA hybrids Co-tagmEntation (termed “TRACE-seq”) are comparable to traditional RNA-seq methods in terms of detected gene number, gene body coverage, gene expression measurement, library complexity, and differential expression analysis; at the meantime, TRACE-seq enables a one-tube library construction protocol and hence is more rapid (within 6h) and convenient. We expect this tagmentation activity on RNA/DNA hybrids to have broad potentials on RNA biology and chromatin research.

overall_design: mRNA profiles of HEK293T cells were generated by TRACE-seq with different RT primers (random primer, in duplicates; oligodT primer, in duplicates) and by NEBNext Ultra II RNA kit in duplicates with 10ng mRNA as input. In addition, mRNA profiles of HEK293T cells were generated by TRACE-seq with different amounts of total RNA as input (200ng total RNA, in triplicates; 20ng total RNA, in duplicates; 2ng total RNA, in duplicates) and by Smart-seq2 with 20ng and 2ng total RNA as input in duplicates respectively. What's more, differential gene expression analysis between differential and undifferential mESC cells was performed by TRACE-seq and NEBNext Ultra II RNA kit in triplicates respectively.

first: Bo

last: Lu

first: Liting

last: Dong

first: Danyang

first: Meiling


title: H3K79me2 and H3K4me3 in CD8 T cell subsets

city: Amsterdam

first: Fred

last: van Leeuwen

address: Plesmanlaan 121

department: Gene Regulation

institute: Netherlands Cancer Institute

summary: We studied the role of the histone methyltransferase DOT1L in T cell development and differentiation. H3K79me2 and H3K4me3 ChIP-sequencing data was generated from sorted CD8 single positive thymocytes, naïve CD8 splenocytes and memory CD8 splenocytes. This was compared to RNA-sequencing data from WT and Dot1L KO mice in order to study the link between H3K79me2 and transcription.

overall_design: Examination of H3K4me3 and H3K79me2 in sorted CD8 T cell populations.

first: Teun

last: van den Brand

first: Tibor

last: van Welsem

first: Eliza

last: Kwesi-Maliepaard


title: Common bean resistance to Xanthomonas is associated with upregulation of the salicylic acid pathway and downregulation of photosynthesis.

status: Public on Jul 27 2020

city: Beaucouze

first: Nicolas

last: Chen

address: 42 rue Georges Morel

institute: IRHS

summary:
Background: Common bacterial blight (CBB) caused by Xanthomonas phaseoli pv. phaseoli and Xanthomonas citri pv. fuscans is one of the major threats to common bean crops (Phaseolus vulgaris L.). Resistance to CBB is particularly complex as 26 quantitative resistance loci to CBB have been described so far. To date, transcriptomic studies after CBB infection have been very scarce and the molecular mechanisms underlying susceptibility or resistance are largely unknown.
Results: We sequenced and annotated the genomes of two common bean genotypes being either resistant (BAT93) or susceptible (JaloEEP558) to CBB. Reciprocal BLASTp analysis led to a list of 20,787 homologs between these genotypes and the common bean reference genome (G19833), which provides a solid dataset for further comparative analyses. RNA-Seq after inoculation with X. phaseoli pv. phaseoli showed that the susceptible genotype initiated a more intense and diverse biological response than the resistant genotype. Resistance was linked to upregulation of the salicylic acid pathway and downregulation of photosynthesis and sugar metabolism, while susceptibility was linked to downregulation of resistance genes and upregulation of the ethylene pathway and of genes involved in cell wall modification.
Conclusions: This study helps better understanding the mechanisms occurring during the early colonization phase of common bean by Xanthomonas and unveils new actors potentially important for resistance and susceptibility to CBB. We discuss the potential link between the pathways induced during bean colonization and genes induced by transcription activator-like effectors (TALEs), as illustrated in other Xanthomonas pathovars.

overall_design: mRNA from two common bean genotypes vacuum-infiltrated with Xanthomonas bacterial strain CFBP6546R or water as control. Done in triplicates

first: Mylene

last: Ruh

first: Justine

last: Foucher

first: Anne

last: Preveaux


title: An open-label, phase II basket study of an oral hypomethylating agent CC-486 and durvalumab in advanced solid tumors

status: Public on Jul 26 2020

city: Toronto

first: Ankur

last: Chakravarthy

state: Ontario

address: 101 College Street

institute: Princess Margaret Cancer Center

summary: Purpose: To evaluate whether administration of the oral DNA hypomethylating agent (HMA) CC-486 enhances the poor response rate of immunologically ‘cold’ solid tumors to immune checkpoint inhibitor durvalumab.

overall_design: PD-L1/PD-1 inhibitor naïve patients with advanced microsatellite stable colorectal cancer; platinum resistant ovarian cancer; and estrogen receptor positive, HER2 negative breast cancer were enrolled in this single-institution, investigator-initiated trial. Two 28-day regimens, regimen A (CC-486 300mg QD Days 1-14 (cycles 1-3 only) in combination with durvalumab 1500mg IV Day 15) and regimen B (CC-486 100 mg QD Days 1-21 (cycles 1-3 only), vitamin C 500mg QD continuously and durvalumab 1500mg IV Day 15) were investigated. Patients underwent paired tumor biopsies and serial peripheral blood mononuclear cells (PBMCs) collection for immune-profiling, transcriptomic, and epigenomic analysis.  Transcriptomic data presented here.

first: Helen

last: Yau

first: Daniel

middle: D

last: De Carvalho

first: Lillian

last: Siu


title: Downstream targets of ATR in CIN612 HPV-positive cells

first: Yan

last: Li

address: 900 East 57th St.

department: Center for Research Informatics

institute: The University of Chicago

summary: High-risk human papillomaviruses (HPVs) constitutively activate the ataxia telangiectasia and Rad3-related (ATR) DNA damage response pathway for their replication. Although ATR has many reported functions, knowledge of how it regulates viral replication is limited. Most studies regarding ATR function focus on its roles in cell survival and initiation of DNA damage response. In this study, we examined whether the transcriptional regulatory properties directed by ATR are critical for HPV pathogenesis, and if so which downstream targets are important. Using RNA-seq approaches, we observed that ATR knockdown increases expression of many inflammatory genes. This mechanism is dependent on the p62/GATA4 signaling pathway.

overall_design: CIN612 cells were transduced with ATR shRNAs and selected for the stable lines, before the analysis

first: Shiyuan

last: Hong


title: DNA polymerase stalling at structured DNA predicts the stability of short tandem repeats

city: Cambridge UK

first: Julian

middle: E

last: Sale

address: Cambridge Biomedical Campus, Francis Crick Ave

department: PNAC

institute: MRC Laboratory of Molecular Biology

summary: Short tandem repeats (STRs) significantly contribute to de novo mutagenesis, driving phenotypic diversity and genetic disease. Although highly diverse, their low complexity and repetitive nature induces DNA polymerase slippage and stalling, leading to length variation and base substitutions. However, the characterisation of DNA synthesis through STR loci has been restricted to a handful of selected sequences, limiting our broader understanding of their evolutionary behaviour. In order to understand the interplay between the ability of a given STR to impair DNA synthesis and its genomic stability, we developed a high-throughput polymerase extension assay that allows monitoring the kinetics of DNA synthesis at all STR permutations in different lengths in parallel. We have used the assay to map at single-nucleotide resolution the movement of a prototypical A-family replicative DNA polymerase (T7 DNA polymerase) through the repeats over time. From this data we can infer the secondary structure adopted by a given STR from the precise manner in which it stalls polymerase and link this to slippage and point mutation during DNA synthesis.

overall_design: Deep sequencing of the replication intermediates observed during primer extension reactions using a library of repeated sequences.

first: Pierre

last: Murat

first: Guillaume

last: Guilbaud


title: The LIM protein Ajuba promotes a metastatic phenotype in colon cancer cells

status: Public on Jul 25 2020

city: Bern

last: Sanchez-Taltavull

address: Murtenstrasse 35

department: Department of BioMedical Research

institute: University of Bern

summary: RNA-seq of Colon cancer cell line Sw480 with Ajuba OE and KD.Colon cancer, along with its potential for recurrence and metastasis is a major health problem. Understanding the proteins and pathways that regulate cell growth and metastasis may provide new targets for patient care. Ajuba is a LIM domain protein often found overexpressed in cancers, however the exact function role of Ajuba in colon cancer is not known.  Our data demonstrates that Ajuba is highly expressed in colon cancer cell lines and tumour tissue compared to adjacent non-tumour tissue. Using publicly available data from The Cancer Genome Atlas, we correlated poor colon cancer patient survival with high Ajuba expression. To investigate the function of Ajuba in colon cancer metastasis we transduced cells with lentiviral constructs to knock down and overexpress Ajuba protein and performed an RNA-seq transcriptomic analysis on each modified line. Analysing the pathways enriched in the differentially expressed genes, we found Ajuba to be involved in cell proliferation, migration and differentiation. We confirmed our findings in biological assays, cells depleted of Ajuba were less proliferative, more sensitive to irradiation, migrated less and were less efficient in colony formation. Our data indicates that increased Ajuba expression observed in colon cancer supports proliferation, epithelial-to-mesenchymal transition and metastasis.

overall_design: 6 different cell lines in triplicates with Parental, ShScrambled, shAjuba 1, shAjuba2, Control and AjubaOE

first: Noëlle

last: Dommann

first: Linda

last: Eggs

first: Fabienne

last: Birrer

first: Tess

last: Brodie

first: Michaela

last: Medova

first: Magali

last: Humbert

first: Mario

last: Tschan

first: Guido

last: Beldi

last: Candinas

first: Deborah

last: Stroka


title: Streamlined low-input transcriptomics through EASY-RNAseq

city: chongqing

first: peng

last: zhou

address: 重庆市大渡口区天安数码城5栋10层

institute: First Affiliated Hospital of Army Medical University

summary: we describe a streamlined RNAseq protocol (EASY RNAseq) for sensitive transcriptome assessment starting from low amount of input materials. EASY RNAseq is technically robust enough for sequencing small pools of homogenous and heterogeneous cells, recovering higher numbers of genes and with a more even expression distribution pattern than other commonly used methods.

overall_design: To evaluate the capbility of EASY-RNASeq respect to the amount of input materials, different amount of input materials extracted from mice spleen(0.1ng, 0.5ng, 1.0ng, 5.0ng) were used for constructing EASY-RNASeq libraries. And for cells sample, different number of input cells obtained from murine CD3+ T cells(1e2, 5e2, 1e3, 1e4) were used to do EASY-RNASeq library construction. All libraries were sequenced by Illumina platform.

first: Yiwen

last: Zhou

first: Hao

last: Xu


title: Comprehensive analyses of B cell compartments across the human body reveal novel subsets and a gut resident memory phenotype

city: Pittsburgh

first: Mark

middle: Jay

last: Shlomchik

state: PA

address: W1052 Biomedical Science Tower 200 Lothrop St

department: Department of Immunology

institute: University of Pittsburgh

summary: A comprehensive analysis of B lineage cells in various tissues of multiple healthy organ donors reveals tissue-specific differences and lack of correspondence between blood and tissues. New, functionally distinct memory B cell subsets were discovered, including one subset specific to the gut that has unique surface markers and a unique gene expression signature.

overall_design: RNA profiling of memory B cell subsets defined by CD45RB and CD69 expression in spleen and gut, spleen has 4 biological replicates, gut has 3 replicates

first: Nadine

last: Weisel